Daily Papers

Melanoma is a dangerous form of skin cancer caused by the abnormal growth of skin cells. Fully Convolutional Network (FCN) approaches, including the U-Net architecture, can automatically segment skin lesions to aid diagnosis. The symmetrical U-Net model has shown outstanding results, but its use of a convolutional operation limits its ability to capture long-range dependencies, which are essential for accurate medical image segmentation. In addition, the U-shaped structure suffers from the semantic gaps between the encoder and decoder. In this study, we developed and evaluated a U-shaped hierarchical Transformer-based structure for skin lesion segmentation while we proposed an Inter-scale Context Fusion (ISCF) to utilize the attention correlations in each stage of the encoder to adaptively combine the contexts coming from each stage to hinder the semantic gaps. The preliminary results of the skin lesion segmentation benchmark endorse the applicability and efficacy of the ISCF module.

In this paper, we introduce a set of simple yet effective TOken REduction (TORE) strategies for Transformer-based Human Mesh Recovery from monocular images. Current SOTA performance is achieved by Transformer-based structures. However, they suffer from high model complexity and computation cost caused by redundant tokens. We propose token reduction strategies based on two important aspects, i.e., the 3D geometry structure and 2D image feature, where we hierarchically recover the mesh geometry with priors from body structure and conduct token clustering to pass fewer but more discriminative image feature tokens to the Transformer. Our method massively reduces the number of tokens involved in high-complexity interactions in the Transformer. This leads to a significantly reduced computational cost while still achieving competitive or even higher accuracy in shape recovery. Extensive experiments across a wide range of benchmarks validate the superior effectiveness of the proposed method. We further demonstrate the generalizability of our method on hand mesh recovery. Visit our project page at https://frank-zy-dou.github.io/projects/Tore/index.html.

Propelled by the rapid advancement of deep learning technologies, the YOLO series has set a new benchmark for real-time object detectors. Researchers have continuously explored innovative applications of reparameterization, efficient layer aggregation networks, and anchor-free techniques on the foundation of YOLO. To further enhance detection performance, Transformer-based structures have been introduced, significantly expanding the model's receptive field and achieving notable performance gains. However, such improvements come at a cost, as the quadratic complexity of the self-attention mechanism increases the computational burden of the model. Fortunately, the emergence of State Space Models (SSM) as an innovative technology has effectively mitigated the issues caused by quadratic complexity. In light of these advancements, we introduce Mamba-YOLO a novel object detection model based on SSM. Mamba-YOLO not only optimizes the SSM foundation but also adapts specifically for object detection tasks. Given the potential limitations of SSM in sequence modeling, such as insufficient receptive field and weak image locality, we have designed the LSBlock and RGBlock. These modules enable more precise capture of local image dependencies and significantly enhance the robustness of the model. Extensive experimental results on the publicly available benchmark datasets COCO and VOC demonstrate that Mamba-YOLO surpasses the existing YOLO series models in both performance and competitiveness, showcasing its substantial potential and competitive edge.The PyTorch code is available at:https://github.com/HZAI-ZJNU/Mamba-YOLO

The past several years have witnessed Variational Auto-Encoder's superiority in various text generation tasks. However, due to the sequential nature of the text, auto-regressive decoders tend to ignore latent variables and then reduce to simple language models, known as the KL vanishing problem, which would further deteriorate when VAE is combined with Transformer-based structures. To ameliorate this problem, we propose DELLA, a novel variational Transformer framework. DELLA learns a series of layer-wise latent variables with each inferred from those of lower layers and tightly coupled with the hidden states by low-rank tensor product. In this way, DELLA forces these posterior latent variables to be fused deeply with the whole computation path and hence incorporate more information. We theoretically demonstrate that our method can be regarded as entangling latent variables to avoid posterior information decrease through layers, enabling DELLA to get higher non-zero KL values even without any annealing or thresholding tricks. Experiments on four unconditional and three conditional generation tasks show that DELLA could better alleviate KL vanishing and improve both quality and diversity compared to several strong baselines.

The diffusion model has long been plagued by scalability and quadratic complexity issues, especially within transformer-based structures. In this study, we aim to leverage the long sequence modeling capability of a State-Space Model called Mamba to extend its applicability to visual data generation. Firstly, we identify a critical oversight in most current Mamba-based vision methods, namely the lack of consideration for spatial continuity in the scan scheme of Mamba. Secondly, building upon this insight, we introduce a simple, plug-and-play, zero-parameter method named Zigzag Mamba, which outperforms Mamba-based baselines and demonstrates improved speed and memory utilization compared to transformer-based baselines. Lastly, we integrate Zigzag Mamba with the Stochastic Interpolant framework to investigate the scalability of the model on large-resolution visual datasets, such as FacesHQ 1024times 1024 and UCF101, MultiModal-CelebA-HQ, and MS COCO 256times 256. Code will be released at https://taohu.me/zigma/

Quantum algorithms, represented as quantum circuits, can be used as benchmarks for assessing the performance of quantum systems. Existing datasets, widely utilized in the field, suffer from limitations in size and versatility, leading researchers to employ randomly generated circuits. Random circuits are, however, not representative benchmarks as they lack the inherent properties of real quantum algorithms for which the quantum systems are manufactured. This shortage of `useful' quantum benchmarks poses a challenge to advancing the development and comparison of quantum compilers and hardware. This research aims to enhance the existing quantum circuit datasets by generating what we refer to as `realistic-looking' circuits by employing the Transformer machine learning architecture. For this purpose, we introduce KetGPT, a tool that generates synthetic circuits in OpenQASM language, whose structure is based on quantum circuits derived from existing quantum algorithms and follows the typical patterns of human-written algorithm-based code (e.g., order of gates and qubits). Our three-fold verification process, involving manual inspection and Qiskit framework execution, transformer-based classification, and structural analysis, demonstrates the efficacy of KetGPT in producing large amounts of additional circuits that closely align with algorithm-based structures. Beyond benchmarking, we envision KetGPT contributing substantially to AI-driven quantum compilers and systems.

Chemical similarity searches are widely used in-silico methods for identifying new drug-like molecules. These methods have historically relied on structure-based comparisons to compute molecular similarity. Here, we use a chemical language model to create a vector-based chemical search. We extend implementations by creating a prompt engineering strategy that utilizes two different chemical string representation algorithms: one for the query and the other for the database. We explore this method by reviewing the search results from five drug-like query molecules (penicillin G, nirmatrelvir, zidovudine, lysergic acid diethylamide, and fentanyl) and three dye-like query molecules (acid blue 25, avobenzone, and 2-diphenylaminocarbazole). We find that this novel method identifies molecules that are functionally similar to the query, indicated by the associated patent literature, and that many of these molecules are structurally distinct from the query, making them unlikely to be found with traditional chemical similarity search methods. This method may aid in the discovery of novel structural classes of molecules that achieve target functionality.

Neural image compression, necessary in various machine-to-machine communication scenarios, suffers from its heavy encode-decode structures and inflexibility in switching between different compression levels. Consequently, it raises significant challenges in applying the neural image compression to edge devices that are developed for powerful servers with high computational and storage capacities. We take a step to solve the challenges by proposing a new transformer-based edge-compute-free image coding framework called Easz. Easz shifts the computational overhead to the server, and hence avoids the heavy encoding and model switching overhead on the edge. Easz utilizes a patch-erase algorithm to selectively remove image contents using a conditional uniform-based sampler. The erased pixels are reconstructed on the receiver side through a transformer-based framework. To further reduce the computational overhead on the receiver, we then introduce a lightweight transformer-based reconstruction structure to reduce the reconstruction load on the receiver side. Extensive evaluations conducted on a real-world testbed demonstrate multiple advantages of Easz over existing compression approaches, in terms of adaptability to different compression levels, computational efficiency, and image reconstruction quality.

3D shape generation aims to produce innovative 3D content adhering to specific conditions and constraints. Existing methods often decompose 3D shapes into a sequence of localized components, treating each element in isolation without considering spatial consistency. As a result, these approaches exhibit limited versatility in 3D data representation and shape generation, hindering their ability to generate highly diverse 3D shapes that comply with the specified constraints. In this paper, we introduce a novel spatial-aware 3D shape generation framework that leverages 2D plane representations for enhanced 3D shape modeling. To ensure spatial coherence and reduce memory usage, we incorporate a hybrid shape representation technique that directly learns a continuous signed distance field representation of the 3D shape using orthogonal 2D planes. Additionally, we meticulously enforce spatial correspondences across distinct planes using a transformer-based autoencoder structure, promoting the preservation of spatial relationships in the generated 3D shapes. This yields an algorithm that consistently outperforms state-of-the-art 3D shape generation methods on various tasks, including unconditional shape generation, multi-modal shape completion, single-view reconstruction, and text-to-shape synthesis.

Knowledge graph (KG) link prediction aims to infer new facts based on existing facts in the KG. Recent studies have shown that using the graph neighborhood of a node via graph neural networks (GNNs) provides more useful information compared to just using the query information. Conventional GNNs for KG link prediction follow the standard message-passing paradigm on the entire KG, which leads to superfluous computation, over-smoothing of node representations, and also limits their expressive power. On a large scale, it becomes computationally expensive to aggregate useful information from the entire KG for inference. To address the limitations of existing KG link prediction frameworks, we propose a novel retrieve-and-read framework, which first retrieves a relevant subgraph context for the query and then jointly reasons over the context and the query with a high-capacity reader. As part of our exemplar instantiation for the new framework, we propose a novel Transformer-based GNN as the reader, which incorporates graph-based attention structure and cross-attention between query and context for deep fusion. This simple yet effective design enables the model to focus on salient context information relevant to the query. Empirical results on two standard KG link prediction datasets demonstrate the competitive performance of the proposed method. Furthermore, our analysis yields valuable insights for designing improved retrievers within the framework.

Despite the significant advancements in pre-training methods for point cloud understanding, directly capturing intricate shape information from irregular point clouds without reliance on external data remains a formidable challenge. To address this problem, we propose GPSFormer, an innovative Global Perception and Local Structure Fitting-based Transformer, which learns detailed shape information from point clouds with remarkable precision. The core of GPSFormer is the Global Perception Module (GPM) and the Local Structure Fitting Convolution (LSFConv). Specifically, GPM utilizes Adaptive Deformable Graph Convolution (ADGConv) to identify short-range dependencies among similar features in the feature space and employs Multi-Head Attention (MHA) to learn long-range dependencies across all positions within the feature space, ultimately enabling flexible learning of contextual representations. Inspired by Taylor series, we design LSFConv, which learns both low-order fundamental and high-order refinement information from explicitly encoded local geometric structures. Integrating the GPM and LSFConv as fundamental components, we construct GPSFormer, a cutting-edge Transformer that effectively captures global and local structures of point clouds. Extensive experiments validate GPSFormer's effectiveness in three point cloud tasks: shape classification, part segmentation, and few-shot learning. The code of GPSFormer is available at https://github.com/changshuowang/GPSFormer.

Since radiology reports needed for clinical practice and research are written and stored in free-text narrations, extraction of relative information for further analysis is difficult. In these circumstances, natural language processing (NLP) techniques can facilitate automatic information extraction and transformation of free-text formats to structured data. In recent years, deep learning (DL)-based models have been adapted for NLP experiments with promising results. Despite the significant potential of DL models based on artificial neural networks (ANN) and convolutional neural networks (CNN), the models face some limitations to implement in clinical practice. Transformers, another new DL architecture, have been increasingly applied to improve the process. Therefore, in this study, we propose a transformer-based fine-grained named entity recognition (NER) architecture for clinical information extraction. We collected 88 abdominopelvic sonography reports in free-text formats and annotated them based on our developed information schema. The text-to-text transfer transformer model (T5) and Scifive, a pre-trained domain-specific adaptation of the T5 model, were applied for fine-tuning to extract entities and relations and transform the input into a structured format. Our transformer-based model in this study outperformed previously applied approaches such as ANN and CNN models based on ROUGE-1, ROUGE-2, ROUGE-L, and BLEU scores of 0.816, 0.668, 0.528, and 0.743, respectively, while providing an interpretable structured report.

Graph-structured scene descriptions can be efficiently used in generative models to control the composition of the generated image. Previous approaches are based on the combination of graph convolutional networks and adversarial methods for layout prediction and image generation, respectively. In this work, we show how employing multi-head attention to encode the graph information, as well as using a transformer-based model in the latent space for image generation can improve the quality of the sampled data, without the need to employ adversarial models with the subsequent advantage in terms of training stability. The proposed approach, specifically, is entirely based on transformer architectures both for encoding scene graphs into intermediate object layouts and for decoding these layouts into images, passing through a lower dimensional space learned by a vector-quantized variational autoencoder. Our approach shows an improved image quality with respect to state-of-the-art methods as well as a higher degree of diversity among multiple generations from the same scene graph. We evaluate our approach on three public datasets: Visual Genome, COCO, and CLEVR. We achieve an Inception Score of 13.7 and 12.8, and an FID of 52.3 and 60.3, on COCO and Visual Genome, respectively. We perform ablation studies on our contributions to assess the impact of each component. Code is available at https://github.com/perceivelab/trf-sg2im

We propose a way to use a transformer-based language model in conversational speech recognition. Specifically, we focus on decoding efficiently in a weighted finite-state transducer framework. We showcase an approach to lattice re-scoring that allows for longer range history captured by a transfomer-based language model and takes advantage of a transformer's ability to avoid computing sequentially.

Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in generating 3D molecules conditioned on the protein pocket. However, most existing methods consider molecular generation for protein pockets independently while neglecting the underlying connections such as subpocket-level similarities. Subpockets are the local protein environments of ligand fragments and pockets with similar subpockets may bind the same molecular fragment (motif) even though their overall structures are different. Therefore, the trained models can hardly generalize to unseen protein pockets in real-world applications. In this paper, we propose a novel method DrugGPS for generalizable structure-based drug design. With the biochemical priors, we propose to learn subpocket prototypes and construct a global interaction graph to model the interactions between subpocket prototypes and molecular motifs. Moreover, a hierarchical graph transformer encoder and motif-based 3D molecule generation scheme are used to improve the model's performance. The experimental results show that our model consistently outperforms baselines in generating realistic drug candidates with high affinities in challenging out-of-distribution settings.

Despite the tantalizing success in a broad of vision tasks, transformers have not yet demonstrated on-par ability as ConvNets in high-resolution image generative modeling. In this paper, we seek to explore using pure transformers to build a generative adversarial network for high-resolution image synthesis. To this end, we believe that local attention is crucial to strike the balance between computational efficiency and modeling capacity. Hence, the proposed generator adopts Swin transformer in a style-based architecture. To achieve a larger receptive field, we propose double attention which simultaneously leverages the context of the local and the shifted windows, leading to improved generation quality. Moreover, we show that offering the knowledge of the absolute position that has been lost in window-based transformers greatly benefits the generation quality. The proposed StyleSwin is scalable to high resolutions, with both the coarse geometry and fine structures benefit from the strong expressivity of transformers. However, blocking artifacts occur during high-resolution synthesis because performing the local attention in a block-wise manner may break the spatial coherency. To solve this, we empirically investigate various solutions, among which we find that employing a wavelet discriminator to examine the spectral discrepancy effectively suppresses the artifacts. Extensive experiments show the superiority over prior transformer-based GANs, especially on high resolutions, e.g., 1024x1024. The StyleSwin, without complex training strategies, excels over StyleGAN on CelebA-HQ 1024, and achieves on-par performance on FFHQ-1024, proving the promise of using transformers for high-resolution image generation. The code and models will be available at https://github.com/microsoft/StyleSwin.

Image restoration in adverse weather conditions is a difficult task in computer vision. In this paper, we propose a novel transformer-based framework called GridFormer which serves as a backbone for image restoration under adverse weather conditions. GridFormer is designed in a grid structure using a residual dense transformer block, and it introduces two core designs. First, it uses an enhanced attention mechanism in the transformer layer. The mechanism includes stages of the sampler and compact self-attention to improve efficiency, and a local enhancement stage to strengthen local information. Second, we introduce a residual dense transformer block (RDTB) as the final GridFormer layer. This design further improves the network's ability to learn effective features from both preceding and current local features. The GridFormer framework achieves state-of-the-art results on five diverse image restoration tasks in adverse weather conditions, including image deraining, dehazing, deraining & dehazing, desnowing, and multi-weather restoration. The source code and pre-trained models will be released.

The Transformer architecture model, based on self-attention and multi-head attention, has achieved remarkable success in offline end-to-end Automatic Speech Recognition (ASR). However, self-attention and multi-head attention cannot be easily applied for streaming or online ASR. For self-attention in Transformer ASR, the softmax normalization function-based attention mechanism makes it impossible to highlight important speech information. For multi-head attention in Transformer ASR, it is not easy to model monotonic alignments in different heads. To overcome these two limits, we integrate sparse attention and monotonic attention into Transformer-based ASR. The sparse mechanism introduces a learned sparsity scheme to enable each self-attention structure to fit the corresponding head better. The monotonic attention deploys regularization to prune redundant heads for the multi-head attention structure. The experiments show that our method can effectively improve the attention mechanism on widely used benchmarks of speech recognition.

Discovering novel drug candidate molecules is one of the most fundamental and critical steps in drug development. Generative deep learning models, which create synthetic data given a probability distribution, have been developed with the purpose of picking completely new samples from a partially known space. Generative models offer high potential for designing de novo molecules; however, in order for them to be useful in real-life drug development pipelines, these models should be able to design target-specific molecules, which is the next step in this field. In this study, we propose DrugGEN, for the de novo design of drug candidate molecules that interact with selected target proteins. The proposed system represents compounds and protein structures as graphs and processes them via serially connected two generative adversarial networks comprising graph transformers. DrugGEN is trained using a large dataset of compounds from ChEMBL and target-specific bioactive molecules, to design effective and specific inhibitory molecules against the AKT1 protein, which has critical importance for developing treatments against various types of cancer. On fundamental benchmarks, DrugGEN models have either competitive or better performance against other methods. To assess the target-specific generation performance, we conducted further in silico analysis with molecular docking and deep learning-based bioactivity prediction. Results indicate that de novo molecules have high potential for interacting with the AKT1 protein structure in the level of its native ligand. DrugGEN can be used to design completely novel and effective target-specific drug candidate molecules for any druggable protein, given target features and a dataset of experimental bioactivities. Code base, datasets, results and trained models of DrugGEN are available at https://github.com/HUBioDataLab/DrugGEN

In the past, normalizing generative flows have emerged as a promising class of generative models for natural images. This type of model has many modeling advantages: the ability to efficiently compute log-likelihood of the input data, fast generation and simple overall structure. Normalizing flows remained a topic of active research but later fell out of favor, as visual quality of the samples was not competitive with other model classes, such as GANs, VQ-VAE-based approaches or diffusion models. In this paper we revisit the design of the coupling-based normalizing flow models by carefully ablating prior design choices and using computational blocks based on the Vision Transformer architecture, not convolutional neural networks. As a result, we achieve state-of-the-art quantitative and qualitative performance with a much simpler architecture. While the overall visual quality is still behind the current state-of-the-art models, we argue that strong normalizing flow models can help advancing research frontier by serving as building components of more powerful generative models.

In recent years, Transformer-based language models have become the standard approach for natural language processing tasks. However, stringent throughput and latency requirements in industrial applications are limiting their adoption. To mitigate the gap, model compression techniques such as structured pruning are being used to improve inference efficiency. However, most existing neural network inference runtimes lack adequate support for structured sparsity. In this paper, we propose an efficient sparse deep learning inference software stack for Transformer-based language models where the weights are pruned with constant block size. Our sparse software accelerator leverages Intel Deep Learning Boost to maximize the performance of sparse matrix - dense matrix multiplication (commonly abbreviated as SpMM) on CPUs. Our SpMM kernel outperforms the existing sparse libraries (oneMKL, TVM, and LIBXSMM) by an order of magnitude on a wide range of GEMM shapes under 5 representative sparsity ratios (70%, 75%, 80%, 85%, 90%). Moreover, our SpMM kernel shows up to 5x speedup over dense GEMM kernel of oneDNN, a well-optimized dense library widely used in industry. We apply our sparse accelerator on widely-used Transformer-based language models including Bert-Mini, DistilBERT, Bert-Base, and BERT-Large. Our sparse inference software shows up to 1.5x speedup over Neural Magic's Deepsparse under same configurations on Xeon on Amazon Web Services under proxy production latency constraints. We also compare our solution with two framework-based inference solutions, ONNX Runtime and PyTorch, and demonstrate up to 37x speedup over ONNX Runtime and 345x over PyTorch on Xeon under the latency constraints. All the source code is publicly available on Github: https://github.com/intel/intel-extension-for-transformers.

Document AI aims to automatically analyze documents by leveraging natural language processing and computer vision techniques. One of the major tasks of Document AI is document layout analysis, which structures document pages by interpreting the content and spatial relationships of layout, image, and text. This task can be image-centric, wherein the aim is to identify and label various regions such as authors and paragraphs, or text-centric, where the focus is on classifying individual words in a document. Although there are increasingly sophisticated methods for improving layout analysis, doubts remain about the extent to which their findings can be generalized to a broader context. Specifically, prior work developed systems based on very different architectures, such as transformer-based, graph-based, and CNNs. However, no work has mentioned the effectiveness of these models in a comparative analysis. Moreover, while language-independent Document AI models capable of knowledge transfer have been developed, it remains to be investigated to what degree they can effectively transfer knowledge. In this study, we aim to fill these gaps by conducting a comparative evaluation of state-of-the-art models in document layout analysis and investigating the potential of cross-lingual layout analysis by utilizing machine translation techniques.

Autonomous vehicles operating in complex real-world environments require accurate predictions of interactive behaviors between traffic participants. This paper tackles the interaction prediction problem by formulating it with hierarchical game theory and proposing the GameFormer model for its implementation. The model incorporates a Transformer encoder, which effectively models the relationships between scene elements, alongside a novel hierarchical Transformer decoder structure. At each decoding level, the decoder utilizes the prediction outcomes from the previous level, in addition to the shared environmental context, to iteratively refine the interaction process. Moreover, we propose a learning process that regulates an agent's behavior at the current level to respond to other agents' behaviors from the preceding level. Through comprehensive experiments on large-scale real-world driving datasets, we demonstrate the state-of-the-art accuracy of our model on the Waymo interaction prediction task. Additionally, we validate the model's capacity to jointly reason about the motion plan of the ego agent and the behaviors of multiple agents in both open-loop and closed-loop planning tests, outperforming various baseline methods. Furthermore, we evaluate the efficacy of our model on the nuPlan planning benchmark, where it achieves leading performance.

Layout generation is the foundation task of intelligent design, which requires the integration of visual aesthetics and harmonious expression of content delivery. However, existing methods still face challenges in generating precise and visually appealing layouts, including blocking, overlap, or spatial misalignment between layouts, which are closely related to the spatial structure of graphic layouts. We find that these methods overly focus on content information and lack constraints on layout spatial structure, resulting in an imbalance of learning content-aware and graphic-aware features. To tackle this issue, we propose Content and Graphic Balance Layout Generation with Transformer-based Diffusion Model (CGB-DM). Specifically, we first design a regulator that balances the predicted content and graphic weight, overcoming the tendency of paying more attention to the content on canvas. Secondly, we introduce a graphic constraint of saliency bounding box to further enhance the alignment of geometric features between layout representations and images. In addition, we adapt a transformer-based diffusion model as the backbone, whose powerful generation capability ensures the quality in layout generation. Extensive experimental results indicate that our method has achieved state-of-the-art performance in both quantitative and qualitative evaluations. Our model framework can also be expanded to other graphic design fields.

We study the computational limits of Low-Rank Adaptation (LoRA) update for finetuning transformer-based models using fine-grained complexity theory. Our key observation is that the existence of low-rank decompositions within the gradient computation of LoRA adaptation leads to possible algorithmic speedup. This allows us to (i) identify a phase transition behavior and (ii) prove the existence of nearly linear algorithms by controlling the LoRA update computation term by term, assuming the Strong Exponential Time Hypothesis (SETH). For the former, we identify a sharp transition in the efficiency of all possible rank-r LoRA update algorithms for transformers, based on specific norms resulting from the multiplications of the input sequence X, pretrained weights W^star, and adapter matrices alpha B A / r. Specifically, we derive a shared upper bound threshold for such norms and show that efficient (sub-quadratic) approximation algorithms of LoRA exist only below this threshold. For the latter, we prove the existence of nearly linear approximation algorithms for LoRA adaptation by utilizing the hierarchical low-rank structures of LoRA gradients and approximating the gradients with a series of chained low-rank approximations. To showcase our theory, we consider two practical scenarios: partial (e.g., only W_V and W_Q) and full adaptations (e.g., W_Q, W_V, and W_K) of weights in attention heads.

Inverse design of solid-state materials with desired properties represents a formidable challenge in materials science. Although recent generative models have demonstrated potential, their adoption has been hindered by limitations such as inefficiency, architectural constraints and restricted open-source availability. The representation of crystal structures using the SLICES (Simplified Line-Input Crystal-Encoding System) notation as a string of characters enables the use of state-of-the-art natural language processing models, such as Transformers, for crystal design. Drawing inspiration from the success of GPT models in generating coherent text, we trained a generative Transformer on the next-token prediction task to generate solid-state materials with targeted properties. We demonstrate MatterGPT's capability to generate de novo crystal structures with targeted single properties, including both lattice-insensitive (formation energy) and lattice-sensitive (band gap) properties. Furthermore, we extend MatterGPT to simultaneously target multiple properties, addressing the complex challenge of multi-objective inverse design of crystals. Our approach showcases high validity, uniqueness, and novelty in generated structures, as well as the ability to generate materials with properties beyond the training data distribution. This work represents a significant step forward in computational materials discovery, offering a powerful and open tool for designing materials with tailored properties for various applications in energy, electronics, and beyond.

Current Structure-from-Motion (SfM) methods typically follow a two-stage pipeline, combining learned or geometric pairwise reasoning with a subsequent global optimization step. In contrast, we propose a data-driven multi-view reasoning approach that directly infers 3D scene geometry and camera poses from multi-view images. Our framework, DiffusionSfM, parameterizes scene geometry and cameras as pixel-wise ray origins and endpoints in a global frame and employs a transformer-based denoising diffusion model to predict them from multi-view inputs. To address practical challenges in training diffusion models with missing data and unbounded scene coordinates, we introduce specialized mechanisms that ensure robust learning. We empirically validate DiffusionSfM on both synthetic and real datasets, demonstrating that it outperforms classical and learning-based approaches while naturally modeling uncertainty.

We propose Samba ASR, the first state-of-the-art Automatic Speech Recognition (ASR) model leveraging the novel Mamba architecture as both encoder and decoder, built on the foundation of state-space models (SSMs). Unlike transformer-based ASR models, which rely on self-attention mechanisms to capture dependencies, Samba ASR effectively models both local and global temporal dependencies using efficient state-space dynamics, achieving remarkable performance gains. By addressing the limitations of transformers, such as quadratic scaling with input length and difficulty in handling long-range dependencies, Samba ASR achieves superior accuracy and efficiency. Experimental results demonstrate that Samba ASR surpasses existing open-source transformer-based ASR models across various standard benchmarks, establishing it as the new state of the art in ASR. Extensive evaluations on benchmark datasets show significant improvements in Word Error Rate (WER), with competitive performance even in low-resource scenarios. Furthermore, the computational efficiency and parameter optimization of the Mamba architecture make Samba ASR a scalable and robust solution for diverse ASR tasks. Our contributions include: A new Samba ASR architecture demonstrating the superiority of SSMs over transformer-based models for speech sequence processing. A comprehensive evaluation on public benchmarks showcasing state-of-the-art performance. An analysis of computational efficiency, robustness to noise, and sequence generalization. This work highlights the viability of Mamba SSMs as a transformer-free alternative for efficient and accurate ASR. By leveraging state-space modeling advancements, Samba ASR sets a new benchmark for ASR performance and future research.

Articulated 3D object generation is fundamental for creating realistic, functional, and interactable virtual assets which are not simply static. We introduce MeshArt, a hierarchical transformer-based approach to generate articulated 3D meshes with clean, compact geometry, reminiscent of human-crafted 3D models. We approach articulated mesh generation in a part-by-part fashion across two stages. First, we generate a high-level articulation-aware object structure; then, based on this structural information, we synthesize each part's mesh faces. Key to our approach is modeling both articulation structures and part meshes as sequences of quantized triangle embeddings, leading to a unified hierarchical framework with transformers for autoregressive generation. Object part structures are first generated as their bounding primitives and articulation modes; a second transformer, guided by these articulation structures, then generates each part's mesh triangles. To ensure coherency among generated parts, we introduce structure-guided conditioning that also incorporates local part mesh connectivity. MeshArt shows significant improvements over state of the art, with 57.1% improvement in structure coverage and a 209-point improvement in mesh generation FID.

Predicting physical properties of materials from their crystal structures is a fundamental problem in materials science. In peripheral areas such as the prediction of molecular properties, fully connected attention networks have been shown to be successful. However, unlike these finite atom arrangements, crystal structures are infinitely repeating, periodic arrangements of atoms, whose fully connected attention results in infinitely connected attention. In this work, we show that this infinitely connected attention can lead to a computationally tractable formulation, interpreted as neural potential summation, that performs infinite interatomic potential summations in a deeply learned feature space. We then propose a simple yet effective Transformer-based encoder architecture for crystal structures called Crystalformer. Compared to an existing Transformer-based model, the proposed model requires only 29.4% of the number of parameters, with minimal modifications to the original Transformer architecture. Despite the architectural simplicity, the proposed method outperforms state-of-the-art methods for various property regression tasks on the Materials Project and JARVIS-DFT datasets.

Multi-person motion prediction is a challenging problem due to the dependency of motion on both individual past movements and interactions with other people. Transformer-based methods have shown promising results on this task, but they miss the explicit relation representation between joints, such as skeleton structure and pairwise distance, which is crucial for accurate interaction modeling. In this paper, we propose the Joint-Relation Transformer, which utilizes relation information to enhance interaction modeling and improve future motion prediction. Our relation information contains the relative distance and the intra-/inter-person physical constraints. To fuse relation and joint information, we design a novel joint-relation fusion layer with relation-aware attention to update both features. Additionally, we supervise the relation information by forecasting future distance. Experiments show that our method achieves a 13.4% improvement of 900ms VIM on 3DPW-SoMoF/RC and 17.8%/12.0% improvement of 3s MPJPE on CMU-Mpcap/MuPoTS-3D dataset.

To remove redundant components of large language models (LLMs) without incurring significant computational costs, this work focuses on single-shot pruning without a retraining phase. We simplify the pruning process for Transformer-based LLMs by identifying a depth-2 pruning structure that functions independently. Additionally, we propose two inference-aware pruning criteria derived from the optimization perspective of output approximation, which outperforms traditional training-aware metrics such as gradient and Hessian. We also introduce a two-step reconstruction technique to mitigate pruning errors without model retraining. Experimental results demonstrate that our approach significantly reduces computational costs and hardware requirements while maintaining superior performance across various datasets and models.

In this paper, we describe our submission to the BabyLM Challenge 2023 shared task on data-efficient language model (LM) pretraining (Warstadt et al., 2023). We train transformer-based masked language models that incorporate unsupervised predictions about hierarchical sentence structure into the model architecture. Concretely, we use the Structformer architecture (Shen et al., 2021) and variants thereof. StructFormer models have been shown to perform well on unsupervised syntactic induction based on limited pretraining data, and to yield performance improvements over a vanilla transformer architecture (Shen et al., 2021). Evaluation of our models on 39 tasks provided by the BabyLM challenge shows promising improvements of models that integrate a hierarchical bias into the architecture at some particular tasks, even though they fail to consistently outperform the RoBERTa baseline model provided by the shared task organizers on all tasks.

Even with strong sequence models like Transformers, generating expressive piano performances with long-range musical structures remains challenging. Meanwhile, methods to compose well-structured melodies or lead sheets (melody + chords), i.e., simpler forms of music, gained more success. Observing the above, we devise a two-stage Transformer-based framework that Composes a lead sheet first, and then Embellishes it with accompaniment and expressive touches. Such a factorization also enables pretraining on non-piano data. Our objective and subjective experiments show that Compose & Embellish shrinks the gap in structureness between a current state of the art and real performances by half, and improves other musical aspects such as richness and coherence as well.

The Mixture-of-Experts (MoE) structure scales the Transformer-based large language models (LLMs) and improves their performance with only the sub-linear increase in computation resources. Recently, a fine-grained DeepSeekMoE structure is proposed, which can further improve the computing efficiency of MoE without performance degradation. However, the All-to-All communication introduced by MoE has become a bottleneck, especially for the fine-grained structure, which typically involves and activates more experts, hence contributing to heavier communication overhead. In this paper, we propose a novel MoE structure named BigMac, which is also fine-grained but with high communication efficiency. The innovation of BigMac is mainly due to that we abandon the communicate-descend-ascend-communicate (CDAC) manner used by fine-grained MoE, which leads to the All-to-All communication always taking place at the highest dimension. Instead, BigMac designs an efficient descend-communicate-communicate-ascend (DCCA) manner. Specifically, we add a descending and ascending projection at the entrance and exit of the expert, respectively, which enables the communication to perform at a very low dimension. Furthermore, to adapt to DCCA, we re-design the structure of small experts, ensuring that the expert in BigMac has enough complexity to address tokens. Experimental results show that BigMac achieves comparable or even better model quality than fine-grained MoEs with the same number of experts and a similar number of total parameters. Equally importantly, BigMac reduces the end-to-end latency by up to 3.09times for training and increases the throughput by up to 3.11times for inference on state-of-the-art AI computing frameworks including Megatron, Tutel, and DeepSpeed-Inference.

For text summarization, the role of discourse structure is pivotal in discerning the core content of a text. Regrettably, prior studies on incorporating Rhetorical Structure Theory (RST) into transformer-based summarization models only consider the nuclearity annotation, thereby overlooking the variety of discourse relation types. This paper introduces the 'RSTformer', a novel summarization model that comprehensively incorporates both the types and uncertainty of rhetorical relations. Our RST-attention mechanism, rooted in document-level rhetorical structure, is an extension of the recently devised Longformer framework. Through rigorous evaluation, the model proposed herein exhibits significant superiority over state-of-the-art models, as evidenced by its notable performance on several automatic metrics and human evaluation.

Extracting tables from documents is a crucial task in any document conversion pipeline. Recently, transformer-based models have demonstrated that table-structure can be recognized with impressive accuracy using Image-to-Markup-Sequence (Im2Seq) approaches. Taking only the image of a table, such models predict a sequence of tokens (e.g. in HTML, LaTeX) which represent the structure of the table. Since the token representation of the table structure has a significant impact on the accuracy and run-time performance of any Im2Seq model, we investigate in this paper how table-structure representation can be optimised. We propose a new, optimised table-structure language (OTSL) with a minimized vocabulary and specific rules. The benefits of OTSL are that it reduces the number of tokens to 5 (HTML needs 28+) and shortens the sequence length to half of HTML on average. Consequently, model accuracy improves significantly, inference time is halved compared to HTML-based models, and the predicted table structures are always syntactically correct. This in turn eliminates most post-processing needs.

Tables organize valuable content in a concise and compact representation. This content is extremely valuable for systems such as search engines, Knowledge Graph's, etc, since they enhance their predictive capabilities. Unfortunately, tables come in a large variety of shapes and sizes. Furthermore, they can have complex column/row-header configurations, multiline rows, different variety of separation lines, missing entries, etc. As such, the correct identification of the table-structure from an image is a non-trivial task. In this paper, we present a new table-structure identification model. The latter improves the latest end-to-end deep learning model (i.e. encoder-dual-decoder from PubTabNet) in two significant ways. First, we introduce a new object detection decoder for table-cells. In this way, we can obtain the content of the table-cells from programmatic PDF's directly from the PDF source and avoid the training of the custom OCR decoders. This architectural change leads to more accurate table-content extraction and allows us to tackle non-english tables. Second, we replace the LSTM decoders with transformer based decoders. This upgrade improves significantly the previous state-of-the-art tree-editing-distance-score (TEDS) from 91% to 98.5% on simple tables and from 88.7% to 95% on complex tables.

Self-attention-based vision transformers (ViTs) have emerged as a highly competitive architecture in computer vision. Unlike convolutional neural networks (CNNs), ViTs are capable of global information sharing. With the development of various structures of ViTs, ViTs are increasingly advantageous for many vision tasks. However, the quadratic complexity of self-attention renders ViTs computationally intensive, and their lack of inductive biases of locality and translation equivariance demands larger model sizes compared to CNNs to effectively learn visual features. In this paper, we propose a light-weight and efficient vision transformer model called DualToken-ViT that leverages the advantages of CNNs and ViTs. DualToken-ViT effectively fuses the token with local information obtained by convolution-based structure and the token with global information obtained by self-attention-based structure to achieve an efficient attention structure. In addition, we use position-aware global tokens throughout all stages to enrich the global information, which further strengthening the effect of DualToken-ViT. Position-aware global tokens also contain the position information of the image, which makes our model better for vision tasks. We conducted extensive experiments on image classification, object detection and semantic segmentation tasks to demonstrate the effectiveness of DualToken-ViT. On the ImageNet-1K dataset, our models of different scales achieve accuracies of 75.4% and 79.4% with only 0.5G and 1.0G FLOPs, respectively, and our model with 1.0G FLOPs outperforms LightViT-T using global tokens by 0.7%.

Linear sequences of words are implicitly represented in our brains by hierarchical structures that organize the composition of words in sentences. Linguists formalize different frameworks to model this hierarchy; two of the most common syntactic frameworks are Constituency and Dependency. Constituency represents sentences as nested groups of phrases, while dependency represents a sentence by assigning relations between its words. Recently, the pursuit of intelligent machines has produced Language Models (LMs) capable of solving many language tasks with a human-level performance. Many studies now question whether LMs implicitly represent syntactic hierarchies. This thesis focuses on producing constituency and dependency structures from LMs in an unsupervised setting. I review the critical methods in this field and highlight a line of work that utilizes a numerical representation for binary constituency trees (Syntactic Distance). I present a detailed study on StructFormer (SF) (Shen et al., 2021), which retrofits a transformer encoder architecture with a parser network to produce constituency and dependency structures. I present six experiments to analyze and address this field's challenges; experiments include investigating the effect of repositioning the parser network within the SF architecture, evaluating subword-based induced trees, and benchmarking the models developed in the thesis experiments on linguistic tasks. Models benchmarking is performed by participating in the BabyLM challenge, published at CoNLL 2023 (Momen et al., 2023). The results of this thesis encourage further development in the direction of retrofitting transformer-based models to induce syntactic structures, supported by the acceptable performance of SF in different experimental settings and the observed limitations that require innovative solutions to advance the state of syntactic structure induction.

Temporal Graph Neural Networks have garnered substantial attention for their capacity to model evolving structural and temporal patterns while exhibiting impressive performance. However, it is known that these architectures are encumbered by issues that constrain their performance, such as over-squashing and over-smoothing. Meanwhile, Transformers have demonstrated exceptional computational capacity to effectively address challenges related to long-range dependencies. Consequently, we introduce Todyformer-a novel Transformer-based neural network tailored for dynamic graphs. It unifies the local encoding capacity of Message-Passing Neural Networks (MPNNs) with the global encoding of Transformers through i) a novel patchifying paradigm for dynamic graphs to improve over-squashing, ii) a structure-aware parametric tokenization strategy leveraging MPNNs, iii) a Transformer with temporal positional-encoding to capture long-range dependencies, and iv) an encoding architecture that alternates between local and global contextualization, mitigating over-smoothing in MPNNs. Experimental evaluations on public benchmark datasets demonstrate that Todyformer consistently outperforms the state-of-the-art methods for downstream tasks. Furthermore, we illustrate the underlying aspects of the proposed model in effectively capturing extensive temporal dependencies in dynamic graphs.

Models based on machine learning can enable accurate and fast molecular property predictions, which is of interest in drug discovery and material design. Various supervised machine learning models have demonstrated promising performance, but the vast chemical space and the limited availability of property labels make supervised learning challenging. Recently, unsupervised transformer-based language models pretrained on a large unlabelled corpus have produced state-of-the-art results in many downstream natural language processing tasks. Inspired by this development, we present molecular embeddings obtained by training an efficient transformer encoder model, MoLFormer, which uses rotary positional embeddings. This model employs a linear attention mechanism, coupled with highly distributed training, on SMILES sequences of 1.1 billion unlabelled molecules from the PubChem and ZINC datasets. We show that the learned molecular representation outperforms existing baselines, including supervised and self-supervised graph neural networks and language models, on several downstream tasks from ten benchmark datasets. They perform competitively on two others. Further analyses, specifically through the lens of attention, demonstrate that MoLFormer trained on chemical SMILES indeed learns the spatial relationships between atoms within a molecule. These results provide encouraging evidence that large-scale molecular language models can capture sufficient chemical and structural information to predict various distinct molecular properties, including quantum-chemical properties.

BACKGROUND: Radiology reports are typically written in a free-text format, making clinical information difficult to extract and use. Recently the adoption of structured reporting (SR) has been recommended by various medical societies thanks to the advantages it offers, e.g. standardization, completeness and information retrieval. We propose a pipeline to extract information from free-text radiology reports, that fits with the items of the reference SR registry proposed by a national society of interventional and medical radiology, focusing on CT staging of patients with lymphoma. METHODS: Our work aims to leverage the potential of Natural Language Processing (NLP) and Transformer-based models to deal with automatic SR registry filling. With the availability of 174 radiology reports, we investigate a rule-free generative Question Answering approach based on a domain-specific version of T5 (IT5). Two strategies (batch-truncation and ex-post combination) are implemented to comply with the model's context length limitations. Performance is evaluated in terms of strict accuracy, F1, and format accuracy, and compared with the widely used GPT-3.5 Large Language Model. A 5-point Likert scale questionnaire is used to collect human-expert feedback on the similarity between medical annotations and generated answers. RESULTS: The combination of fine-tuning and batch splitting allows IT5 to achieve notable results; it performs on par with GPT-3.5 albeit its size being a thousand times smaller in terms of parameters. Human-based assessment scores show a high correlation (Spearman's correlation coefficients>0.88, p-values<0.001) with AI performance metrics (F1) and confirm the superior ability of LLMs (i.e., GPT-3.5, 175B of parameters) in generating plausible human-like statements.

Existing full text datasets of U.S. public domain newspapers do not recognize the often complex layouts of newspaper scans, and as a result the digitized content scrambles texts from articles, headlines, captions, advertisements, and other layout regions. OCR quality can also be low. This study develops a novel, deep learning pipeline for extracting full article texts from newspaper images and applies it to the nearly 20 million scans in Library of Congress's public domain Chronicling America collection. The pipeline includes layout detection, legibility classification, custom OCR, and association of article texts spanning multiple bounding boxes. To achieve high scalability, it is built with efficient architectures designed for mobile phones. The resulting American Stories dataset provides high quality data that could be used for pre-training a large language model to achieve better understanding of historical English and historical world knowledge. The dataset could also be added to the external database of a retrieval-augmented language model to make historical information - ranging from interpretations of political events to minutiae about the lives of people's ancestors - more widely accessible. Furthermore, structured article texts facilitate using transformer-based methods for popular social science applications like topic classification, detection of reproduced content, and news story clustering. Finally, American Stories provides a massive silver quality dataset for innovating multimodal layout analysis models and other multimodal applications.

Modern methods for vision-centric autonomous driving perception widely adopt the bird's-eye-view (BEV) representation to describe a 3D scene. Despite its better efficiency than voxel representation, it has difficulty describing the fine-grained 3D structure of a scene with a single plane. To address this, we propose a tri-perspective view (TPV) representation which accompanies BEV with two additional perpendicular planes. We model each point in the 3D space by summing its projected features on the three planes. To lift image features to the 3D TPV space, we further propose a transformer-based TPV encoder (TPVFormer) to obtain the TPV features effectively. We employ the attention mechanism to aggregate the image features corresponding to each query in each TPV plane. Experiments show that our model trained with sparse supervision effectively predicts the semantic occupancy for all voxels. We demonstrate for the first time that using only camera inputs can achieve comparable performance with LiDAR-based methods on the LiDAR segmentation task on nuScenes. Code: https://github.com/wzzheng/TPVFormer.

A central goal of machine learning is the development of systems that can solve many problems in as many data domains as possible. Current architectures, however, cannot be applied beyond a small set of stereotyped settings, as they bake in domain & task assumptions or scale poorly to large inputs or outputs. In this work, we propose Perceiver IO, a general-purpose architecture that handles data from arbitrary settings while scaling linearly with the size of inputs and outputs. Our model augments the Perceiver with a flexible querying mechanism that enables outputs of various sizes and semantics, doing away with the need for task-specific architecture engineering. The same architecture achieves strong results on tasks spanning natural language and visual understanding, multi-task and multi-modal reasoning, and StarCraft II. As highlights, Perceiver IO outperforms a Transformer-based BERT baseline on the GLUE language benchmark despite removing input tokenization and achieves state-of-the-art performance on Sintel optical flow estimation with no explicit mechanisms for multiscale correspondence.

We introduce Structured 3D Features, a model based on a novel implicit 3D representation that pools pixel-aligned image features onto dense 3D points sampled from a parametric, statistical human mesh surface. The 3D points have associated semantics and can move freely in 3D space. This allows for optimal coverage of the person of interest, beyond just the body shape, which in turn, additionally helps modeling accessories, hair, and loose clothing. Owing to this, we present a complete 3D transformer-based attention framework which, given a single image of a person in an unconstrained pose, generates an animatable 3D reconstruction with albedo and illumination decomposition, as a result of a single end-to-end model, trained semi-supervised, and with no additional postprocessing. We show that our S3F model surpasses the previous state-of-the-art on various tasks, including monocular 3D reconstruction, as well as albedo and shading estimation. Moreover, we show that the proposed methodology allows novel view synthesis, relighting, and re-posing the reconstruction, and can naturally be extended to handle multiple input images (e.g. different views of a person, or the same view, in different poses, in video). Finally, we demonstrate the editing capabilities of our model for 3D virtual try-on applications.

Background: Electronic Health Records hold detailed longitudinal information about each patient's health status and general clinical history, a large portion of which is stored within the unstructured text. Existing approaches focus mostly on structured data and a subset of single-domain outcomes. We explore how temporal modelling of patients from free text and structured data, using deep generative transformers can be used to forecast a wide range of future disorders, substances, procedures or findings. Methods: We present Foresight, a novel transformer-based pipeline that uses named entity recognition and linking tools to convert document text into structured, coded concepts, followed by providing probabilistic forecasts for future medical events such as disorders, substances, procedures and findings. We processed the entire free-text portion from three different hospital datasets totalling 811336 patients covering both physical and mental health. Findings: On tests in two UK hospitals (King's College Hospital, South London and Maudsley) and the US MIMIC-III dataset precision@10 0.68, 0.76 and 0.88 was achieved for forecasting the next disorder in a patient timeline, while precision@10 of 0.80, 0.81 and 0.91 was achieved for forecasting the next biomedical concept. Foresight was also validated on 34 synthetic patient timelines by five clinicians and achieved relevancy of 97% for the top forecasted candidate disorder. As a generative model, it can forecast follow-on biomedical concepts for as many steps as required. Interpretation: Foresight is a general-purpose model for biomedical concept modelling that can be used for real-world risk forecasting, virtual trials and clinical research to study the progression of disorders, simulate interventions and counterfactuals, and educational purposes.

Structured illumination microscopy (SIM) is an optical super-resolution technique that enables live-cell imaging beyond the diffraction limit. Reconstruction of SIM data is prone to artefacts, which becomes problematic when imaging highly dynamic samples because previous methods rely on the assumption that samples are static. We propose a new transformer-based reconstruction method, VSR-SIM, that uses shifted 3-dimensional window multi-head attention in addition to channel attention mechanism to tackle the problem of video super-resolution (VSR) in SIM. The attention mechanisms are found to capture motion in sequences without the need for common motion estimation techniques such as optical flow. We take an approach to training the network that relies solely on simulated data using videos of natural scenery with a model for SIM image formation. We demonstrate a use case enabled by VSR-SIM referred to as rolling SIM imaging, which increases temporal resolution in SIM by a factor of 9. Our method can be applied to any SIM setup enabling precise recordings of dynamic processes in biomedical research with high temporal resolution.

Large language models (LLMs) such as generative pretrained transformers (GPTs) have shown potential for various commercial applications, but their applicability for materials design remains underexplored. In this article, we introduce AtomGPT, a model specifically developed for materials design based on transformer architectures, to demonstrate the capability for both atomistic property prediction and structure generation. We show that a combination of chemical and structural text descriptions can efficiently predict material properties with accuracy comparable to graph neural network models, including formation energies, electronic bandgaps from two different methods and superconducting transition temperatures. Furthermore, we demonstrate that AtomGPT can generate atomic structures for tasks such as designing new superconductors, with the predictions validated through density functional theory calculations. This work paves the way for leveraging LLMs in forward and inverse materials design, offering an efficient approach to the discovery and optimization of materials.

Large Language Models (LLMs) for code are a family of high-parameter, transformer-based neural networks pre-trained on massive datasets of both natural and programming languages. These models are rapidly being employed in commercial AI-based developer tools, such as GitHub CoPilot. However, measuring and explaining their effectiveness on programming tasks is a challenging proposition, given their size and complexity. The methods for evaluating and explaining LLMs for code are inextricably linked. That is, in order to explain a model's predictions, they must be reliably mapped to fine-grained, understandable concepts. Once this mapping is achieved, new methods for detailed model evaluations are possible. However, most current explainability techniques and evaluation benchmarks focus on model robustness or individual task performance, as opposed to interpreting model predictions. To this end, this paper introduces ASTxplainer, an explainability method specific to LLMs for code that enables both new methods for LLM evaluation and visualizations of LLM predictions that aid end-users in understanding model predictions. At its core, ASTxplainer provides an automated method for aligning token predictions with AST nodes, by extracting and aggregating normalized model logits within AST structures. To demonstrate the practical benefit of ASTxplainer, we illustrate the insights that our framework can provide by performing an empirical evaluation on 12 popular LLMs for code using a curated dataset of the most popular GitHub projects. Additionally, we perform a user study examining the usefulness of an ASTxplainer-derived visualization of model predictions aimed at enabling model users to explain predictions. The results of these studies illustrate the potential for ASTxplainer to provide insights into LLM effectiveness, and aid end-users in understanding predictions.

The increasing size of large language models (LLMs) has introduced challenges in their training and inference. Removing model components is perceived as a solution to tackle the large model sizes, however, existing pruning methods solely focus on performance, without considering an essential aspect for the responsible use of LLMs: model fairness. It is crucial to address the fairness of LLMs towards diverse groups, such as women, Black people, LGBTQ+, Jewish communities, among others, as they are being deployed and available to a wide audience. In this work, first, we investigate how attention heads impact fairness and performance in pre-trained transformer-based language models. We then propose a novel method to prune the attention heads that negatively impact fairness while retaining the heads critical for performance, i.e. language modeling capabilities. Our approach is practical in terms of time and resources, as it does not require fine-tuning the final pruned, and fairer, model. Our findings demonstrate a reduction in gender bias by 19%, 19.5%, 39.5%, 34.7%, 23%, and 8% for DistilGPT-2, GPT-2, GPT-Neo of two different sizes, GPT-J, and Llama 2 models, respectively, in comparison to the biased model, with only a slight decrease in performance.

Efficiently quantifying renal structures can provide distinct spatial context and facilitate biomarker discovery for kidney morphology. However, the development and evaluation of the transformer model to segment the renal cortex, medulla, and collecting system remains challenging due to data inefficiency. Inspired by the hierarchical structures in vision transformer, we propose a novel method using a 3D block aggregation transformer for segmenting kidney components on contrast-enhanced CT scans. We construct the first cohort of renal substructures segmentation dataset with 116 subjects under institutional review board (IRB) approval. Our method yields the state-of-the-art performance (Dice of 0.8467) against the baseline approach of 0.8308 with the data-efficient design. The Pearson R achieves 0.9891 between the proposed method and manual standards and indicates the strong correlation and reproducibility for volumetric analysis. We extend the proposed method to the public KiTS dataset, the method leads to improved accuracy compared to transformer-based approaches. We show that the 3D block aggregation transformer can achieve local communication between sequence representations without modifying self-attention, and it can serve as an accurate and efficient quantification tool for characterizing renal structures.

Transformers with linear recurrent modeling offer linear-time training and constant-memory inference. Despite their demonstrated efficiency and performance, pretraining such non-standard architectures from scratch remains costly and risky. The linearization of large language models (LLMs) transforms pretrained standard models into linear recurrent structures, enabling more efficient deployment. However, current linearization methods typically introduce additional feature map modules that require extensive fine-tuning and overlook the gating mechanisms used in state-of-the-art linear recurrent models. To address these issues, this paper presents Liger, short for Linearizing LLMs to gated recurrent structures. Liger is a novel approach for converting pretrained LLMs into gated linear recurrent models without adding extra parameters. It repurposes the pretrained key matrix weights to construct diverse gating mechanisms, facilitating the formation of various gated recurrent structures while avoiding the need to train additional components from scratch. Using lightweight fine-tuning with Low-Rank Adaptation (LoRA), Liger restores the performance of the linearized gated recurrent models to match that of the original LLMs. Additionally, we introduce Liger Attention, an intra-layer hybrid attention mechanism, which significantly recovers 93\% of the Transformer-based LLM at 0.02\% pre-training tokens during the linearization process, achieving competitive results across multiple benchmarks, as validated on models ranging from 1B to 8B parameters. Code is available at https://github.com/OpenSparseLLMs/Linearization.

Chain-of-Thought (CoT) is a robust approach for tackling LLM tasks that require intermediate reasoning steps prior to generating a final answer. In this paper, we present GreenMind-Medium-14B-R1, the Vietnamese reasoning model inspired by the finetuning strategy based on Group Relative Policy Optimization. We also leverage a high-quality Vietnamese synthesized reasoning dataset and design two reward functions to tackle the main limitations of this technique: (i) language mixing, where we explicitly detect the presence of biased language characters during the process of sampling tokens, and (ii) we leverage Sentence Transformer-based models to ensure that the generated reasoning content maintains factual correctness and does not distort the final output. Experimental results on the Vietnamese dataset from the VLSP 2023 Challenge demonstrate that our model outperforms prior works and enhances linguistic consistency in its responses. Furthermore, we extend our evaluation to SeaExam-a multilingual multiple-choice dataset, showing the effectiveness of our reasoning method compared to few-shot prompting techniques.

Transformer-based models trained on large and general purpose datasets consisting of molecular strings have recently emerged as a powerful tool for successfully modeling various structure-property relations. Inspired by this success, we extend the paradigm of training chemical language transformers on large-scale chemical datasets to generative tasks in this work. Specifically, we propose GP-MoLFormer, an autoregressive molecular string generator that is trained on more than 1.1B (billion) chemical SMILES. GP-MoLFormer uses a 46.8M parameter transformer decoder model with linear attention and rotary positional encodings as the base architecture. GP-MoLFormer's utility is evaluated and compared with that of existing baselines on three different tasks: de novo generation, scaffold-constrained molecular decoration, and unconstrained property-guided optimization. While the first two are handled with no additional training, we propose a parameter-efficient fine-tuning method for the last task, which uses property-ordered molecular pairs as input. We call this new approach pair-tuning. Our results show GP-MoLFormer performs better or comparable with baselines across all three tasks, demonstrating its general utility for a variety of molecular generation tasks. We further report strong memorization of training data in GP-MoLFormer generations, which has so far remained unexplored for chemical language models. Our analyses reveal that training data memorization and novelty in generations are impacted by the quality and scale of the training data; duplication bias in training data can enhance memorization at the cost of lowering novelty. We further establish a scaling law relating inference compute and novelty in generations.

HTML documents are an important medium for disseminating information on the Web for human consumption. An HTML document presents information in multiple text formats including unstructured text, structured key-value pairs, and tables. Effective representation of these documents is essential for machine understanding to enable a wide range of applications, such as Question Answering, Web Search, and Personalization. Existing work has either represented these documents using visual features extracted by rendering them in a browser, which is typically computationally expensive, or has simply treated them as plain text documents, thereby failing to capture useful information presented in their HTML structure. We argue that the text and HTML structure together convey important semantics of the content and therefore warrant a special treatment for their representation learning. In this paper, we introduce a novel representation learning approach for web pages, dubbed DOM-LM, which addresses the limitations of existing approaches by encoding both text and DOM tree structure with a transformer-based encoder and learning generalizable representations for HTML documents via self-supervised pre-training. We evaluate DOM-LM on a variety of webpage understanding tasks, including Attribute Extraction, Open Information Extraction, and Question Answering. Our extensive experiments show that DOM-LM consistently outperforms all baselines designed for these tasks. In particular, DOM-LM demonstrates better generalization performance both in few-shot and zero-shot settings, making it attractive for making it suitable for real-world application settings with limited labeled data.

Transformer-based vision models typically tokenize images into fixed-size square patches as input units, which lacks the adaptability to image content and overlooks the inherent pixel grouping structure. Inspired by the subword tokenization widely adopted in language models, we propose an image tokenizer at a subobject level, where the subobjects are represented by semantically meaningful image segments obtained by segmentation models (e.g., segment anything models). To implement a learning system based on subobject tokenization, we first introduced a Sequence-to-sequence AutoEncoder (SeqAE) to compress subobject segments of varying sizes and shapes into compact embedding vectors, then fed the subobject embeddings into a large language model for vision language learning. Empirical results demonstrated that our subobject-level tokenization significantly facilitates efficient learning of translating images into object and attribute descriptions compared to the traditional patch-level tokenization. Codes and models will be open-sourced at https://github.com/ChenDelong1999/subobjects.

While transformer-based language models have driven the AI revolution thus far, their computational complexity has spurred growing interest in viable alternatives, such as structured state space sequence models (SSMs) and Selective SSMs. Among these, Mamba (S6) and its variant Mamba-2 have shown remarkable inference speed ups over transformers while achieving comparable or superior performance on complex language modeling tasks. However, despite these architectural innovations and empirical successes, the fundamental learning capabilities of Mamba remain poorly understood. In this paper, we address this gap by studying in-context learning (ICL) on Markov chains and uncovering a surprising phenomenon: unlike transformers, even a single-layer Mamba efficiently learns the in-context Laplacian smoothing estimator, which is both Bayes and minimax optimal, for all Markovian orders. To explain this, we theoretically characterize the representation capacity of Mamba and reveal the fundamental role of convolution in enabling it to represent the optimal Laplacian smoothing. These theoretical insights align strongly with empirical results and, to the best of our knowledge, represent the first formal connection between Mamba and optimal statistical estimators. Finally, we outline promising research directions inspired by these findings.

Predicting disease trajectories from electronic health records (EHRs) is a complex task due to major challenges such as data non-stationarity, high granularity of medical codes, and integration of multimodal data. EHRs contain both structured data, such as diagnostic codes, and unstructured data, such as clinical notes, which hold essential information often overlooked. Current models, primarily based on structured data, struggle to capture the complete medical context of patients, resulting in a loss of valuable information. To address this issue, we propose an approach that integrates unstructured clinical notes into transformer-based deep learning models for sequential disease prediction. This integration enriches the representation of patients' medical histories, thereby improving the accuracy of diagnosis predictions. Experiments on MIMIC-IV datasets demonstrate that the proposed approach outperforms traditional models relying solely on structured data.

Multi-task robot learning holds significant importance in tackling diverse and complex scenarios. However, current approaches are hindered by performance issues and difficulties in collecting training datasets. In this paper, we propose GeRM (Generalist Robotic Model). We utilize offline reinforcement learning to optimize data utilization strategies to learn from both demonstrations and sub-optimal data, thus surpassing the limitations of human demonstrations. Thereafter, we employ a transformer-based VLA network to process multi-modal inputs and output actions. By introducing the Mixture-of-Experts structure, GeRM allows faster inference speed with higher whole model capacity, and thus resolves the issue of limited RL parameters, enhancing model performance in multi-task learning while controlling computational costs. Through a series of experiments, we demonstrate that GeRM outperforms other methods across all tasks, while also validating its efficiency in both training and inference processes. Additionally, we uncover its potential to acquire emergent skills. Additionally, we contribute the QUARD-Auto dataset, collected automatically to support our training approach and foster advancements in multi-task quadruped robot learning. This work presents a new paradigm for reducing the cost of collecting robot data and driving progress in the multi-task learning community.

Manual digitization of bibliographic metadata is time consuming and labor intensive, especially for historical and real-world archives with highly variable formatting across documents. Despite advances in machine learning, the absence of dedicated datasets for metadata extraction hinders automation. To address this gap, we introduce BiblioPage, a dataset of scanned title pages annotated with structured bibliographic metadata. The dataset consists of approximately 2,000 monograph title pages collected from 14 Czech libraries, spanning a wide range of publication periods, typographic styles, and layout structures. Each title page is annotated with 16 bibliographic attributes, including title, contributors, and publication metadata, along with precise positional information in the form of bounding boxes. To extract structured information from this dataset, we valuated object detection models such as YOLO and DETR combined with transformer-based OCR, achieving a maximum mAP of 52 and an F1 score of 59. Additionally, we assess the performance of various visual large language models, including LlamA 3.2-Vision and GPT-4o, with the best model reaching an F1 score of 67. BiblioPage serves as a real-world benchmark for bibliographic metadata extraction, contributing to document understanding, document question answering, and document information extraction. Dataset and evaluation scripts are availible at: https://github.com/DCGM/biblio-dataset

Recently, significant progress has been made applying machine learning to the problem of table structure inference and extraction from unstructured documents. However, one of the greatest challenges remains the creation of datasets with complete, unambiguous ground truth at scale. To address this, we develop a new, more comprehensive dataset for table extraction, called PubTables-1M. PubTables-1M contains nearly one million tables from scientific articles, supports multiple input modalities, and contains detailed header and location information for table structures, making it useful for a wide variety of modeling approaches. It also addresses a significant source of ground truth inconsistency observed in prior datasets called oversegmentation, using a novel canonicalization procedure. We demonstrate that these improvements lead to a significant increase in training performance and a more reliable estimate of model performance at evaluation for table structure recognition. Further, we show that transformer-based object detection models trained on PubTables-1M produce excellent results for all three tasks of detection, structure recognition, and functional analysis without the need for any special customization for these tasks. Data and code will be released at https://github.com/microsoft/table-transformer.

Many graph representation learning (GRL) problems are dynamic, with millions of edges added or removed per second. A fundamental workload in this setting is dynamic link prediction: using a history of graph updates to predict whether a given pair of vertices will become connected. Recent schemes for link prediction in such dynamic settings employ Transformers, modeling individual graph updates as single tokens. In this work, we propose HOT: a model that enhances this line of works by harnessing higher-order (HO) graph structures; specifically, k-hop neighbors and more general subgraphs containing a given pair of vertices. Harnessing such HO structures by encoding them into the attention matrix of the underlying Transformer results in higher accuracy of link prediction outcomes, but at the expense of increased memory pressure. To alleviate this, we resort to a recent class of schemes that impose hierarchy on the attention matrix, significantly reducing memory footprint. The final design offers a sweetspot between high accuracy and low memory utilization. HOT outperforms other dynamic GRL schemes, for example achieving 9%, 7%, and 15% higher accuracy than - respectively - DyGFormer, TGN, and GraphMixer, for the MOOC dataset. Our design can be seamlessly extended towards other dynamic GRL workloads.

Traditional drug design faces significant challenges due to inherent chemical and biological complexities, often resulting in high failure rates in clinical trials. Deep learning advancements, particularly generative models, offer potential solutions to these challenges. One promising algorithm is DrugGPT, a transformer-based model, that generates small molecules for input protein sequences. Although promising, it generates both chemically valid and invalid structures and does not incorporate the features of approved drugs, resulting in time-consuming and inefficient drug discovery. To address these issues, we introduce DrugGen, an enhanced model based on the DrugGPT structure. DrugGen is fine-tuned on approved drug-target interactions and optimized with proximal policy optimization. By giving reward feedback from protein-ligand binding affinity prediction using pre-trained transformers (PLAPT) and a customized invalid structure assessor, DrugGen significantly improves performance. Evaluation across multiple targets demonstrated that DrugGen achieves 100% valid structure generation compared to 95.5% with DrugGPT and produced molecules with higher predicted binding affinities (7.22 [6.30-8.07]) compared to DrugGPT (5.81 [4.97-6.63]) while maintaining diversity and novelty. Docking simulations further validate its ability to generate molecules targeting binding sites effectively. For example, in the case of fatty acid-binding protein 5 (FABP5), DrugGen generated molecules with superior docking scores (FABP5/11, -9.537 and FABP5/5, -8.399) compared to the reference molecule (Palmitic acid, -6.177). Beyond lead compound generation, DrugGen also shows potential for drug repositioning and creating novel pharmacophores for existing targets. By producing high-quality small molecules, DrugGen provides a high-performance medium for advancing pharmaceutical research and drug discovery.

Code search with natural language plays a crucial role in reusing existing code snippets and accelerating software development. Thanks to the Transformer-based pretraining models, the performance of code search has been improved significantly compared to traditional information retrieval (IR) based models. However, due to the quadratic complexity of multi-head self-attention, there is a limit on the input token length. For efficient training on standard GPUs like V100, existing pretrained code models, including GraphCodeBERT, CodeBERT, RoBERTa (code), take the first 256 tokens by default, which makes them unable to represent the complete information of long code that is greater than 256 tokens. Unlike long text paragraph that can be regarded as a whole with complete semantics, the semantics of long code is discontinuous as a piece of long code may contain different code modules. Therefore, it is unreasonable to directly apply the long text processing methods to long code. To tackle the long code problem, we propose SEA (Split, Encode and Aggregate for Long Code Search), which splits long code into code blocks, encodes these blocks into embeddings, and aggregates them to obtain a comprehensive long code representation. With SEA, we could directly use Transformer-based pretraining models to model long code without changing their internal structure and repretraining. Leveraging abstract syntax tree (AST) based splitting and attention-based aggregation methods, SEA achieves significant improvements in long code search performance. We also compare SEA with two sparse Trasnformer methods. With GraphCodeBERT as the encoder, SEA achieves an overall mean reciprocal ranking score of 0.785, which is 10.1% higher than GraphCodeBERT on the CodeSearchNet benchmark.

Generating motion for arbitrary skeletons is a longstanding challenge in computer graphics, remaining largely unexplored due to the scarcity of diverse datasets and the irregular nature of the data. In this work, we introduce AnyTop, a diffusion model that generates motions for diverse characters with distinct motion dynamics, using only their skeletal structure as input. Our work features a transformer-based denoising network, tailored for arbitrary skeleton learning, integrating topology information into the traditional attention mechanism. Additionally, by incorporating textual joint descriptions into the latent feature representation, AnyTop learns semantic correspondences between joints across diverse skeletons. Our evaluation demonstrates that AnyTop generalizes well, even with as few as three training examples per topology, and can produce motions for unseen skeletons as well. Furthermore, our model's latent space is highly informative, enabling downstream tasks such as joint correspondence, temporal segmentation and motion editing. Our webpage, https://anytop2025.github.io/Anytop-page, includes links to videos and code.

Diffusion models have shown exceptional performance in visual generation tasks. Recently, these models have shifted from traditional U-Shaped CNN-Attention hybrid structures to fully transformer-based isotropic architectures. While these transformers exhibit strong scalability and performance, their reliance on complicated self-attention operation results in slow inference speeds. Contrary to these works, we rethink one of the simplest yet fastest module in deep learning, 3x3 Convolution, to construct a scaled-up purely convolutional diffusion model. We first discover that an Encoder-Decoder Hourglass design outperforms scalable isotropic architectures for Conv3x3, but still under-performing our expectation. Further improving the architecture, we introduce sparse skip connections to reduce redundancy and improve scalability. Based on the architecture, we introduce conditioning improvements including stage-specific embeddings, mid-block condition injection, and conditional gating. These improvements lead to our proposed Diffusion CNN (DiC), which serves as a swift yet competitive diffusion architecture baseline. Experiments on various scales and settings show that DiC surpasses existing diffusion transformers by considerable margins in terms of performance while keeping a good speed advantage. Project page: https://github.com/YuchuanTian/DiC

Recent years have witnessed great progress in image restoration thanks to the advancements in modern deep neural networks e.g. Convolutional Neural Network and Transformer. However, existing restoration backbones are usually limited due to the inherent local reductive bias or quadratic computational complexity. Recently, Selective Structured State Space Model e.g., Mamba, has shown great potential for long-range dependencies modeling with linear complexity, but it is still under-explored in low-level computer vision. In this work, we introduce a simple but strong benchmark model, named MambaIR, for image restoration. In detail, we propose the Residual State Space Block as the core component, which employs convolution and channel attention to enhance the capabilities of the vanilla Mamba. In this way, our MambaIR takes advantage of local patch recurrence prior as well as channel interaction to produce restoration-specific feature representation. Extensive experiments demonstrate the superiority of our method, for example, MambaIR outperforms Transformer-based baseline SwinIR by up to 0.36dB, using similar computational cost but with a global receptive field. Code is available at https://github.com/csguoh/MambaIR.

Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown promise as tools to make sense of a range of multi-variate sequences from protein-structures, music, electronic health records to weather-forecasts. We can also represent human lives in a way that shares this structural similarity to language. From one perspective, lives are simply sequences of events: People are born, visit the pediatrician, start school, move to a new location, get married, and so on. Here, we exploit this similarity to adapt innovations from natural language processing to examine the evolution and predictability of human lives based on detailed event sequences. We do this by drawing on arguably the most comprehensive registry data in existence, available for an entire nation of more than six million individuals across decades. Our data include information about life-events related to health, education, occupation, income, address, and working hours, recorded with day-to-day resolution. We create embeddings of life-events in a single vector space showing that this embedding space is robust and highly structured. Our models allow us to predict diverse outcomes ranging from early mortality to personality nuances, outperforming state-of-the-art models by a wide margin. Using methods for interpreting deep learning models, we probe the algorithm to understand the factors that enable our predictions. Our framework allows researchers to identify new potential mechanisms that impact life outcomes and associated possibilities for personalized interventions.

Multiple business scenarios require an automated generation of descriptive human-readable text from structured input data. Hence, fact-to-text generation systems have been developed for various downstream tasks like generating soccer reports, weather and financial reports, medical reports, person biographies, etc. Unfortunately, previous work on fact-to-text (F2T) generation has focused primarily on English mainly due to the high availability of relevant datasets. Only recently, the problem of cross-lingual fact-to-text (XF2T) was proposed for generation across multiple languages alongwith a dataset, XALIGN for eight languages. However, there has been no rigorous work on the actual XF2T generation problem. We extend XALIGN dataset with annotated data for four more languages: Punjabi, Malayalam, Assamese and Oriya. We conduct an extensive study using popular Transformer-based text generation models on our extended multi-lingual dataset, which we call XALIGNV2. Further, we investigate the performance of different text generation strategies: multiple variations of pretraining, fact-aware embeddings and structure-aware input encoding. Our extensive experiments show that a multi-lingual mT5 model which uses fact-aware embeddings with structure-aware input encoding leads to best results on average across the twelve languages. We make our code, dataset and model publicly available, and hope that this will help advance further research in this critical area.

Graph Neural Networks (GNNs) that are based on the message passing (MP) paradigm generally exchange information between 1-hop neighbors to build node representations at each layer. In principle, such networks are not able to capture long-range interactions (LRI) that may be desired or necessary for learning a given task on graphs. Recently, there has been an increasing interest in development of Transformer-based methods for graphs that can consider full node connectivity beyond the original sparse structure, thus enabling the modeling of LRI. However, MP-GNNs that simply rely on 1-hop message passing often fare better in several existing graph benchmarks when combined with positional feature representations, among other innovations, hence limiting the perceived utility and ranking of Transformer-like architectures. Here, we present the Long Range Graph Benchmark (LRGB) with 5 graph learning datasets: PascalVOC-SP, COCO-SP, PCQM-Contact, Peptides-func and Peptides-struct that arguably require LRI reasoning to achieve strong performance in a given task. We benchmark both baseline GNNs and Graph Transformer networks to verify that the models which capture long-range dependencies perform significantly better on these tasks. Therefore, these datasets are suitable for benchmarking and exploration of MP-GNNs and Graph Transformer architectures that are intended to capture LRI.

Large diffusion models have been successful in text-to-audio (T2A) synthesis tasks, but they often suffer from common issues such as semantic misalignment and poor temporal consistency due to limited natural language understanding and data scarcity. Additionally, 2D spatial structures widely used in T2A works lead to unsatisfactory audio quality when generating variable-length audio samples since they do not adequately prioritize temporal information. To address these challenges, we propose Make-an-Audio 2, a latent diffusion-based T2A method that builds on the success of Make-an-Audio. Our approach includes several techniques to improve semantic alignment and temporal consistency: Firstly, we use pre-trained large language models (LLMs) to parse the text into structured <event & order> pairs for better temporal information capture. We also introduce another structured-text encoder to aid in learning semantic alignment during the diffusion denoising process. To improve the performance of variable length generation and enhance the temporal information extraction, we design a feed-forward Transformer-based diffusion denoiser. Finally, we use LLMs to augment and transform a large amount of audio-label data into audio-text datasets to alleviate the problem of scarcity of temporal data. Extensive experiments show that our method outperforms baseline models in both objective and subjective metrics, and achieves significant gains in temporal information understanding, semantic consistency, and sound quality.

Many existing end-to-end systems for hybrid question answering tasks can often be boiled down to a "prompt-and-pray" paradigm, where the user has limited control and insight into the intermediate reasoning steps used to achieve the final result. Additionally, due to the context size limitation of many transformer-based LLMs, it is often not reasonable to expect that the full structured and unstructured context will fit into a given prompt in a zero-shot setting, let alone a few-shot setting. We introduce BlendSQL, a superset of SQLite to act as a unified dialect for orchestrating reasoning across both unstructured and structured data. For hybrid question answering tasks involving multi-hop reasoning, we encode the full decomposed reasoning roadmap into a single interpretable BlendSQL query. Notably, we show that BlendSQL can scale to massive datasets and improve the performance of end-to-end systems while using 35% fewer tokens. Our code is available and installable as a package at https://github.com/parkervg/blendsql.

The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor generalization due to limited supervised data. In this paper, we propose to learn protein-ligand binding representation in a self-supervised learning manner. Different from existing pre-training approaches which treat proteins and ligands individually, we emphasize to discern the intricate binding patterns from fine-grained interactions. Specifically, this self-supervised learning problem is formulated as a prediction of the conclusive binding complex structure given a pocket and ligand with a Transformer based interaction module, which naturally emulates the binding process. To ensure the representation of rich binding information, we introduce two pre-training tasks, i.e.~atomic pairwise distance map prediction and mask ligand reconstruction, which comprehensively model the fine-grained interactions from both structure and feature space. Extensive experiments have demonstrated the superiority of our method across various binding tasks, including protein-ligand affinity prediction, virtual screening and protein-ligand docking.

Text-to-3D with diffusion models have achieved remarkable progress in recent years. However, existing methods either rely on score distillation-based optimization which suffer from slow inference, low diversity and Janus problems, or are feed-forward methods that generate low quality results due to the scarcity of 3D training data. In this paper, we propose Instant3D, a novel method that generates high-quality and diverse 3D assets from text prompts in a feed-forward manner. We adopt a two-stage paradigm, which first generates a sparse set of four structured and consistent views from text in one shot with a fine-tuned 2D text-to-image diffusion model, and then directly regresses the NeRF from the generated images with a novel transformer-based sparse-view reconstructor. Through extensive experiments, we demonstrate that our method can generate high-quality, diverse and Janus-free 3D assets within 20 seconds, which is two order of magnitude faster than previous optimization-based methods that can take 1 to 10 hours. Our project webpage: https://jiahao.ai/instant3d/.

Language models have demonstrated the ability to generate highly fluent text; however, it remains unclear whether their output retains coherent high-level structure (e.g., story progression). Here, we propose to apply a statistical tool, model criticism in latent space, to evaluate the high-level structure of the generated text. Model criticism compares the distributions between real and generated data in a latent space obtained according to an assumptive generative process. Different generative processes identify specific failure modes of the underlying model. We perform experiments on three representative aspects of high-level discourse -- coherence, coreference, and topicality -- and find that transformer-based language models are able to capture topical structures but have a harder time maintaining structural coherence or modeling coreference.

Automatic dependency parsing of Thai sentences has been underexplored, as evidenced by the lack of large Thai dependency treebanks with complete dependency structures and the lack of a published systematic evaluation of state-of-the-art models, especially transformer-based parsers. In this work, we address these problems by introducing Thai Universal Dependency Treebank (TUD), a new largest Thai treebank consisting of 3,627 trees annotated in accordance with the Universal Dependencies (UD) framework. We then benchmark dependency parsing models that incorporate pretrained transformers as encoders and train them on Thai-PUD and our TUD. The evaluation results show that most of our models can outperform other models reported in previous papers and provide insight into the optimal choices of components to include in Thai dependency parsers. The new treebank and every model's full prediction generated in our experiment are made available on a GitHub repository for further study.

Image inpainting has made significant advances in recent years. However, it is still challenging to recover corrupted images with both vivid textures and reasonable structures. Some specific methods only tackle regular textures while losing holistic structures due to the limited receptive fields of convolutional neural networks (CNNs). On the other hand, attention-based models can learn better long-range dependency for the structure recovery, but they are limited by the heavy computation for inference with large image sizes. To address these issues, we propose to leverage an additional structure restorer to facilitate the image inpainting incrementally. The proposed model restores holistic image structures with a powerful attention-based transformer model in a fixed low-resolution sketch space. Such a grayscale space is easy to be upsampled to larger scales to convey correct structural information. Our structure restorer can be integrated with other pretrained inpainting models efficiently with the zero-initialized residual addition. Furthermore, a masking positional encoding strategy is utilized to improve the performance with large irregular masks. Extensive experiments on various datasets validate the efficacy of our model compared with other competitors. Our codes are released in https://github.com/DQiaole/ZITS_inpainting.

Adapting Deep Learning (DL) techniques to automate non-trivial coding activities, such as code documentation and defect detection, has been intensively studied recently. Learning to predict code changes is one of the popular and essential investigations. Prior studies have shown that DL techniques such as Neural Machine Translation (NMT) can benefit meaningful code changes, including bug fixing and code refactoring. However, NMT models may encounter bottleneck when modeling long sequences, thus are limited in accurately predicting code changes. In this work, we design a Transformer-based approach, considering that Transformer has proven effective in capturing long-term dependencies. Specifically, we propose a novel model named DTrans. For better incorporating the local structure of code, i.e., statement-level information in this paper, DTrans is designed with dynamically relative position encoding in the multi-head attention of Transformer. Experiments on benchmark datasets demonstrate that DTrans can more accurately generate patches than the state-of-the-art methods, increasing the performance by at least 5.45\%-46.57\% in terms of the exact match metric on different datasets. Moreover, DTrans can locate the lines to change with 1.75\%-24.21\% higher accuracy than the existing methods.

A great number of deep learning based models have been recently proposed for automatic music composition. Among these models, the Transformer stands out as a prominent approach for generating expressive classical piano performance with a coherent structure of up to one minute. The model is powerful in that it learns abstractions of data on its own, without much human-imposed domain knowledge or constraints. In contrast with this general approach, this paper shows that Transformers can do even better for music modeling, when we improve the way a musical score is converted into the data fed to a Transformer model. In particular, we seek to impose a metrical structure in the input data, so that Transformers can be more easily aware of the beat-bar-phrase hierarchical structure in music. The new data representation maintains the flexibility of local tempo changes, and provides hurdles to control the rhythmic and harmonic structure of music. With this approach, we build a Pop Music Transformer that composes Pop piano music with better rhythmic structure than existing Transformer models.

Image inpainting is an important task in computer vision. As admirable methods are presented, the inpainted image is getting closer to reality. However, the result is still not good enough in the reconstructed texture and structure based on human vision. Although recent advances in computer hardware have enabled the development of larger and more complex models, there is still a need for lightweight models that can be used by individuals and small-sized institutions. Therefore, we propose a lightweight model that combines a specialized transformer with a traditional convolutional neural network (CNN). Furthermore, we have noticed most researchers only consider three primary colors (RGB) in inpainted images, but we think this is not enough. So we propose a new loss function to intensify color details. Extensive experiments on commonly seen datasets (Places2 and CelebA) validate the efficacy of our proposed model compared with other state-of-the-art methods. Index Terms: HSV color space, image inpainting, joint attention, stripe window, transformer

We report a series of deep learning models to solve complex forward and inverse design problems in molecular modeling and design. Using both diffusion models inspired by nonequilibrium thermodynamics and attention-based transformer architectures, we demonstrate a flexible framework to capture complex chemical structures. First trained on the QM9 dataset and a series of quantum mechanical properties (e.g. homo, lumo, free energy, heat capacity, etc.), we then generalize the model to study and design key properties of deep eutectic solvents. In addition to separate forward and inverse models, we also report an integrated fully prompt-based multi-task generative pretrained transformer model that solves multiple forward, inverse design, and prediction tasks, flexibly and within one model. We show that the multi-task generative model has the overall best performance and allows for flexible integration of multiple objectives, within one model, and for distinct chemistries, suggesting that synergies emerge during training of this large language model. Trained jointly in tasks related to the QM9 dataset and deep eutectic solvents (DESs), the model can predict various quantum mechanical properties and critical properties to achieve deep eutectic solvent behavior. Several novel combinations of DESs are proposed based on this framework.

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.

Modern Natural Language Processing (NLP) models based on Transformer structures represent the state of the art in terms of performance on very diverse tasks. However, these models are complex and represent several hundred million parameters for the smallest of them. This may hinder their adoption at the industrial level, making it difficult to scale up to a reasonable infrastructure and/or to comply with societal and environmental responsibilities. To this end, we present in this paper a model that drastically reduces the computational cost of a well-known French model (CamemBERT), while preserving good performance.

Humans can easily imagine the complete 3D geometry of occluded objects and scenes. This appealing ability is vital for recognition and understanding. To enable such capability in AI systems, we propose VoxFormer, a Transformer-based semantic scene completion framework that can output complete 3D volumetric semantics from only 2D images. Our framework adopts a two-stage design where we start from a sparse set of visible and occupied voxel queries from depth estimation, followed by a densification stage that generates dense 3D voxels from the sparse ones. A key idea of this design is that the visual features on 2D images correspond only to the visible scene structures rather than the occluded or empty spaces. Therefore, starting with the featurization and prediction of the visible structures is more reliable. Once we obtain the set of sparse queries, we apply a masked autoencoder design to propagate the information to all the voxels by self-attention. Experiments on SemanticKITTI show that VoxFormer outperforms the state of the art with a relative improvement of 20.0% in geometry and 18.1% in semantics and reduces GPU memory during training to less than 16GB. Our code is available on https://github.com/NVlabs/VoxFormer.

Document structure analysis, aka document layout analysis, is crucial for understanding both the physical layout and logical structure of documents, serving information retrieval, document summarization, knowledge extraction, etc. Hierarchical Document Structure Analysis (HDSA) specifically aims to restore the hierarchical structure of documents created using authoring software with hierarchical schemas. Previous research has primarily followed two approaches: one focuses on tackling specific subtasks of HDSA in isolation, such as table detection or reading order prediction, while the other adopts a unified framework that uses multiple branches or modules, each designed to address a distinct task. In this work, we propose a unified relation prediction approach for HDSA, called UniHDSA, which treats various HDSA sub-tasks as relation prediction problems and consolidates relation prediction labels into a unified label space. This allows a single relation prediction module to handle multiple tasks simultaneously, whether at a page-level or document-level structure analysis. To validate the effectiveness of UniHDSA, we develop a multimodal end-to-end system based on Transformer architectures. Extensive experimental results demonstrate that our approach achieves state-of-the-art performance on a hierarchical document structure analysis benchmark, Comp-HRDoc, and competitive results on a large-scale document layout analysis dataset, DocLayNet, effectively illustrating the superiority of our method across all sub-tasks. The Comp-HRDoc benchmark and UniHDSA's configurations are publicly available at https://github.com/microsoft/CompHRDoc.

To quantify how well natural language understanding models can capture consistency in a general conversation, we introduce the DialoguE COntradiction DEtection task (DECODE) and a new conversational dataset containing both human-human and human-bot contradictory dialogues. We then compare a structured utterance-based approach of using pre-trained Transformer models for contradiction detection with the typical unstructured approach. Results reveal that: (i) our newly collected dataset is notably more effective at providing supervision for the dialogue contradiction detection task than existing NLI data including those aimed to cover the dialogue domain; (ii) the structured utterance-based approach is more robust and transferable on both analysis and out-of-distribution dialogues than its unstructured counterpart. We also show that our best contradiction detection model correlates well with human judgments and further provide evidence for its usage in both automatically evaluating and improving the consistency of state-of-the-art generative chatbots.

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

Attention based language models have become a critical component in state-of-the-art natural language processing systems. However, these models have significant computational requirements, due to long training times, dense operations and large parameter count. In this work we demonstrate a set of modifications to the structure of a Transformer layer, producing a more efficient architecture. First, we add a convolutional module to complement the self-attention module, decoupling the learning of local and global interactions. Secondly, we rely on grouped transformations to reduce the computational cost of dense feed-forward layers and convolutions, while preserving the expressivity of the model. We apply the resulting architecture to language representation learning and demonstrate its superior performance compared to BERT models of different scales. We further highlight its improved efficiency, both in terms of floating-point operations (FLOPs) and time-to-train.

As ground-based all-sky astronomical surveys will gather millions of images in the coming years, a critical requirement emerges for the development of fast deconvolution algorithms capable of efficiently improving the spatial resolution of these images. By successfully recovering clean and high-resolution images from these surveys, the objective is to deepen the understanding of galaxy formation and evolution through accurate photometric measurements. We introduce a two-step deconvolution framework using a Swin Transformer architecture. Our study reveals that the deep learning-based solution introduces a bias, constraining the scope of scientific analysis. To address this limitation, we propose a novel third step relying on the active coefficients in the sparsity wavelet framework. We conducted a performance comparison between our deep learning-based method and Firedec, a classical deconvolution algorithm, based on an analysis of a subset of the EDisCS cluster samples. We demonstrate the advantage of our method in terms of resolution recovery, generalisation to different noise properties, and computational efficiency. The analysis of this cluster sample not only allowed us to assess the efficiency of our method, but it also enabled us to quantify the number of clumps within these galaxies in relation to their disc colour. This robust technique that we propose holds promise for identifying structures in the distant universe through ground-based images.

Image-based fashion design with AI techniques has attracted increasing attention in recent years. We focus on a new fashion design task, where we aim to transfer a reference appearance image onto a clothing image while preserving the structure of the clothing image. It is a challenging task since there are no reference images available for the newly designed output fashion images. Although diffusion-based image translation or neural style transfer (NST) has enabled flexible style transfer, it is often difficult to maintain the original structure of the image realistically during the reverse diffusion, especially when the referenced appearance image greatly differs from the common clothing appearance. To tackle this issue, we present a novel diffusion model-based unsupervised structure-aware transfer method to semantically generate new clothes from a given clothing image and a reference appearance image. In specific, we decouple the foreground clothing with automatically generated semantic masks by conditioned labels. And the mask is further used as guidance in the denoising process to preserve the structure information. Moreover, we use the pre-trained vision Transformer (ViT) for both appearance and structure guidance. Our experimental results show that the proposed method outperforms state-of-the-art baseline models, generating more realistic images in the fashion design task. Code and demo can be found at https://github.com/Rem105-210/DiffFashion.

Large pre-trained models have achieved outstanding results in sequence modeling. The Transformer block and its attention mechanism have been the main drivers of the success of these models. Recently, alternative architectures, such as Selective Structured State Space Models (SSMs), have been proposed to address the inefficiencies of Transformers. This paper explores the compression of SSM-based models, particularly Mamba and its hybrids. We study the sensitivity of these models to the removal of selected components at different granularities to reduce the model size and computational overhead, thus improving their efficiency while maintaining accuracy. The proposed solutions, collectively referred to as Mamba-Shedder, achieve a speedup of up to 1.4x during inference, demonstrating that model efficiency can be improved by eliminating several redundancies with minimal impact on the overall model performance. The code is available at https://github.com/IntelLabs/Hardware-Aware-Automated-Machine-Learning.

We present a new formulation for structured information extraction (SIE) from visually rich documents. It aims to address the limitations of existing IOB tagging or graph-based formulations, which are either overly reliant on the correct ordering of input text or struggle with decoding a complex graph. Instead, motivated by anchor-based object detectors in vision, we represent an entity as an anchor word and a bounding box, and represent entity linking as the association between anchor words. This is more robust to text ordering, and maintains a compact graph for entity linking. The formulation motivates us to introduce 1) a DOCument TRansformer (DocTr) that aims at detecting and associating entity bounding boxes in visually rich documents, and 2) a simple pre-training strategy that helps learn entity detection in the context of language. Evaluations on three SIE benchmarks show the effectiveness of the proposed formulation, and the overall approach outperforms existing solutions.

In deep learning theory, the covariance matrix of the representations serves as a proxy to examine the network's trainability. Motivated by the success of Transformers, we study the covariance matrix of a modified Softmax-based attention model with skip connections in the proportional limit of infinite-depth-and-width. We show that at initialization the limiting distribution can be described by a stochastic differential equation (SDE) indexed by the depth-to-width ratio. To achieve a well-defined stochastic limit, the Transformer's attention mechanism is modified by centering the Softmax output at identity, and scaling the Softmax logits by a width-dependent temperature parameter. We examine the stability of the network through the corresponding SDE, showing how the scale of both the drift and diffusion can be elegantly controlled with the aid of residual connections. The existence of a stable SDE implies that the covariance structure is well-behaved, even for very large depth and width, thus preventing the notorious issues of rank degeneracy in deep attention models. Finally, we show, through simulations, that the SDE provides a surprisingly good description of the corresponding finite-size model. We coin the name shaped Transformer for these architectural modifications.

The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction, directly generating diverse, novel protein structures from neural networks remains difficult. In this work, we present a new diffusion-based generative model that designs protein backbone structures via a procedure that mirrors the native folding process. We describe protein backbone structure as a series of consecutive angles capturing the relative orientation of the constituent amino acid residues, and generate new structures by denoising from a random, unfolded state towards a stable folded structure. Not only does this mirror how proteins biologically twist into energetically favorable conformations, the inherent shift and rotational invariance of this representation crucially alleviates the need for complex equivariant networks. We train a denoising diffusion probabilistic model with a simple transformer backbone and demonstrate that our resulting model unconditionally generates highly realistic protein structures with complexity and structural patterns akin to those of naturally-occurring proteins. As a useful resource, we release the first open-source codebase and trained models for protein structure diffusion.

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

Recent conditional image generation methods produce images of remarkable diversity, fidelity and realism. However, the majority of these methods allow conditioning only on labels or text prompts, which limits their level of control over the generation result. In this paper, we introduce MaskSketch, an image generation method that allows spatial conditioning of the generation result using a guiding sketch as an extra conditioning signal during sampling. MaskSketch utilizes a pre-trained masked generative transformer, requiring no model training or paired supervision, and works with input sketches of different levels of abstraction. We show that intermediate self-attention maps of a masked generative transformer encode important structural information of the input image, such as scene layout and object shape, and we propose a novel sampling method based on this observation to enable structure-guided generation. Our results show that MaskSketch achieves high image realism and fidelity to the guiding structure. Evaluated on standard benchmark datasets, MaskSketch outperforms state-of-the-art methods for sketch-to-image translation, as well as unpaired image-to-image translation approaches.

At present, different deep learning models are presenting high accuracy on popular inference datasets such as SNLI, MNLI, and SciTail. However, there are different indicators that those datasets can be exploited by using some simple linguistic patterns. This fact poses difficulties to our understanding of the actual capacity of machine learning models to solve the complex task of textual inference. We propose a new set of syntactic tasks focused on contradiction detection that require specific capacities over linguistic logical forms such as: Boolean coordination, quantifiers, definite description, and counting operators. We evaluate two kinds of deep learning models that implicitly exploit language structure: recurrent models and the Transformer network BERT. We show that although BERT is clearly more efficient to generalize over most logical forms, there is space for improvement when dealing with counting operators. Since the syntactic tasks can be implemented in different languages, we show a successful case of cross-lingual transfer learning between English and Portuguese.

Head and neck (H&N) cancers are among the most prevalent types of cancer worldwide, and [18F]F-FDG PET/CT is widely used for H&N cancer management. Recently, the diffusion model has demonstrated remarkable performance in various image-generation tasks. In this work, we proposed a 3D diffusion model to accurately perform H&N tumor segmentation from 3D PET and CT volumes. The 3D diffusion model was developed considering the 3D nature of PET and CT images acquired. During the reverse process, the model utilized a 3D UNet structure and took the concatenation of PET, CT, and Gaussian noise volumes as the network input to generate the tumor mask. Experiments based on the HECKTOR challenge dataset were conducted to evaluate the effectiveness of the proposed diffusion model. Several state-of-the-art techniques based on U-Net and Transformer structures were adopted as the reference methods. Benefits of employing both PET and CT as the network input as well as further extending the diffusion model from 2D to 3D were investigated based on various quantitative metrics and the uncertainty maps generated. Results showed that the proposed 3D diffusion model could generate more accurate segmentation results compared with other methods. Compared to the diffusion model in 2D format, the proposed 3D model yielded superior results. Our experiments also highlighted the advantage of utilizing dual-modality PET and CT data over only single-modality data for H&N tumor segmentation.

Causal inference is a critical task across fields such as healthcare, economics, and the social sciences. While recent advances in machine learning, especially those based on the deep-learning architectures, have shown potential in estimating causal effects, existing approaches often fall short in handling complex causal structures and lack adaptability across various causal scenarios. In this paper, we present a novel transformer-based method for causal inference that overcomes these challenges. The core innovation of our model lies in its integration of causal Directed Acyclic Graphs (DAGs) directly into the attention mechanism, enabling it to accurately model the underlying causal structure. This allows for flexible estimation of both average treatment effects (ATE) and conditional average treatment effects (CATE). Extensive experiments on both synthetic and real-world datasets demonstrate that our approach surpasses existing methods in estimating causal effects across a wide range of scenarios. The flexibility and robustness of our model make it a valuable tool for researchers and practitioners tackling complex causal inference problems.

Financial forecasting has been an important and active area of machine learning research because of the challenges it presents and the potential rewards that even minor improvements in prediction accuracy or forecasting may entail. Traditionally, financial forecasting has heavily relied on quantitative indicators and metrics derived from structured financial statements. Earnings conference call data, including text and audio, is an important source of unstructured data that has been used for various prediction tasks using deep earning and related approaches. However, current deep learning-based methods are limited in the way that they deal with numeric data; numbers are typically treated as plain-text tokens without taking advantage of their underlying numeric structure. This paper describes a numeric-oriented hierarchical transformer model to predict stock returns, and financial risk using multi-modal aligned earnings calls data by taking advantage of the different categories of numbers (monetary, temporal, percentages etc.) and their magnitude. We present the results of a comprehensive evaluation of NumHTML against several state-of-the-art baselines using a real-world publicly available dataset. The results indicate that NumHTML significantly outperforms the current state-of-the-art across a variety of evaluation metrics and that it has the potential to offer significant financial gains in a practical trading context.

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them struggle to handle protein understanding and generation tasks concurrently. We propose a unified protein language model, xTrimoPGLM, to address these two types of tasks simultaneously through an innovative pre-training framework. Our key technical contribution is an exploration of the compatibility and the potential for joint optimization of the two types of objectives, which has led to a strategy for training xTrimoPGLM at an unprecedented scale of 100 billion parameters and 1 trillion training tokens. Our extensive experiments reveal that 1) xTrimoPGLM significantly outperforms other advanced baselines in 18 protein understanding benchmarks across four categories. The model also facilitates an atomic-resolution view of protein structures, leading to an advanced 3D structural prediction model that surpasses existing language model-based tools. 2) xTrimoPGLM not only can generate de novo protein sequences following the principles of natural ones, but also can perform programmable generation after supervised fine-tuning (SFT) on curated sequences. These results highlight the substantial capability and versatility of xTrimoPGLM in understanding and generating protein sequences, contributing to the evolving landscape of foundation models in protein science.

Linear transformers aim to reduce the quadratic space-time complexity of vanilla transformers. However, they usually suffer from degraded performances on various tasks and corpus. In this paper, we examine existing kernel-based linear transformers and identify two key issues that lead to such performance gaps: 1) unbounded gradients in the attention computation adversely impact the convergence of linear transformer models; 2) attention dilution which trivially distributes attention scores over long sequences while neglecting neighbouring structures. To address these issues, we first identify that the scaling of attention matrices is the devil in unbounded gradients, which turns out unnecessary in linear attention as we show theoretically and empirically. To this end, we propose a new linear attention that replaces the scaling operation with a normalization to stabilize gradients. For the issue of attention dilution, we leverage a diagonal attention to confine attention to only neighbouring tokens in early layers. Benefiting from the stable gradients and improved attention, our new linear transformer model, transNormer, demonstrates superior performance on text classification and language modeling tasks, as well as on the challenging Long-Range Arena benchmark, surpassing vanilla transformer and existing linear variants by a clear margin while being significantly more space-time efficient. The code is available at https://github.com/OpenNLPLab/Transnormer .

Transformer models are deployed in a wide range of settings, from multi-accelerator clusters to standalone mobile phones. The diverse inference constraints in these scenarios necessitate practitioners to train foundation models such as PaLM 2, Llama, & ViTs as a series of models of varying sizes. Due to significant training costs, only a select few model sizes are trained and supported, limiting more fine-grained control over relevant tradeoffs, including latency, cost, and accuracy. This work introduces MatFormer, a nested Transformer architecture designed to offer elasticity in a variety of deployment constraints. Each Feed Forward Network (FFN) block of a MatFormer model is jointly optimized with a few nested smaller FFN blocks. This training procedure allows for the Mix'n'Match of model granularities across layers -- i.e., a trained universal MatFormer model enables extraction of hundreds of accurate smaller models, which were never explicitly optimized. We empirically demonstrate MatFormer's effectiveness across different model classes (decoders & encoders), modalities (language & vision), and scales (up to 2.6B parameters). We find that a 2.6B decoder-only MatFormer language model (MatLM) allows us to extract smaller models spanning from 1.5B to 2.6B, each exhibiting comparable validation loss and one-shot downstream evaluations to their independently trained counterparts. Furthermore, we observe that smaller encoders extracted from a universal MatFormer-based ViT (MatViT) encoder preserve the metric-space structure for adaptive large-scale retrieval. Finally, we showcase that speculative decoding with the accurate and consistent submodels extracted from MatFormer can further reduce inference latency.

We introduce a novel superpoint-based transformer architecture for efficient semantic segmentation of large-scale 3D scenes. Our method incorporates a fast algorithm to partition point clouds into a hierarchical superpoint structure, which makes our preprocessing 7 times faster than existing superpoint-based approaches. Additionally, we leverage a self-attention mechanism to capture the relationships between superpoints at multiple scales, leading to state-of-the-art performance on three challenging benchmark datasets: S3DIS (76.0% mIoU 6-fold validation), KITTI-360 (63.5% on Val), and DALES (79.6%). With only 212k parameters, our approach is up to 200 times more compact than other state-of-the-art models while maintaining similar performance. Furthermore, our model can be trained on a single GPU in 3 hours for a fold of the S3DIS dataset, which is 7x to 70x fewer GPU-hours than the best-performing methods. Our code and models are accessible at github.com/drprojects/superpoint_transformer.

Self-supervised speech representation learning has become essential for extracting meaningful features from untranscribed audio. Recent advances highlight the potential of deriving discrete symbols from the features correlated with linguistic units, which enables text-less training across diverse tasks. In particular, sentence-level Self-Distillation of the pretrained HuBERT (SD-HuBERT) induces syllabic structures within latent speech frame representations extracted from an intermediate Transformer layer. In SD-HuBERT, sentence-level representation is accumulated from speech frame features through self-attention layers using a special CLS token. However, we observe that the information aggregated in the CLS token correlates more with speaker identity than with linguistic content. To address this, we propose a speech-only self-supervised fine-tuning approach that separates syllabic units from speaker information. Our method introduces speaker perturbation as data augmentation and adopts a frame-level training objective to prevent the CLS token from aggregating paralinguistic information. Experimental results show that our approach surpasses the current state-of-the-art method in most syllable segmentation and syllabic unit quality metrics on Librispeech, underscoring its effectiveness in promoting syllabic organization within speech-only models.

Transformers yield state-of-the-art results across many tasks. However, their heuristically designed architecture impose huge computational costs during inference. This work aims on challenging the common design philosophy of the Vision Transformer (ViT) model with uniform dimension across all the stacked blocks in a model stage, where we redistribute the parameters both across transformer blocks and between different structures within the block via the first systematic attempt on global structural pruning. Dealing with diverse ViT structural components, we derive a novel Hessian-based structural pruning criteria comparable across all layers and structures, with latency-aware regularization for direct latency reduction. Performing iterative pruning on the DeiT-Base model leads to a new architecture family called NViT (Novel ViT), with a novel parameter redistribution that utilizes parameters more efficiently. On ImageNet-1K, NViT-Base achieves a 2.6x FLOPs reduction, 5.1x parameter reduction, and 1.9x run-time speedup over the DeiT-Base model in a near lossless manner. Smaller NViT variants achieve more than 1% accuracy gain at the same throughput of the DeiT Small/Tiny variants, as well as a lossless 3.3x parameter reduction over the SWIN-Small model. These results outperform prior art by a large margin. Further analysis is provided on the parameter redistribution insight of NViT, where we show the high prunability of ViT models, distinct sensitivity within ViT block, and unique parameter distribution trend across stacked ViT blocks. Our insights provide viability for a simple yet effective parameter redistribution rule towards more efficient ViTs for off-the-shelf performance boost.

Most existing forecasting systems are memory-based methods, which attempt to mimic human forecasting ability by employing various memory mechanisms and have progressed in temporal modeling for memory dependency. Nevertheless, an obvious weakness of this paradigm is that it can only model limited historical dependence and can not transcend the past. In this paper, we rethink the temporal dependence of event evolution and propose a novel memory-anticipation-based paradigm to model an entire temporal structure, including the past, present, and future. Based on this idea, we present Memory-and-Anticipation Transformer (MAT), a memory-anticipation-based approach, to address the online action detection and anticipation tasks. In addition, owing to the inherent superiority of MAT, it can process online action detection and anticipation tasks in a unified manner. The proposed MAT model is tested on four challenging benchmarks TVSeries, THUMOS'14, HDD, and EPIC-Kitchens-100, for online action detection and anticipation tasks, and it significantly outperforms all existing methods. Code is available at https://github.com/Echo0125/Memory-and-Anticipation-Transformer.

The excellent performance of Transformer in supervised learning has led to growing interest in its potential application to deep reinforcement learning (DRL) to achieve high performance on a wide variety of problems. However, the decision making of a DRL agent is a black box, which greatly hinders the application of the agent to real-world problems. To address this problem, we propose the Action Q-Transformer (AQT), which introduces a transformer encoder-decoder structure to Q-learning based DRL methods. In AQT, the encoder calculates the state value function and the decoder calculates the advantage function to promote the acquisition of different attentions indicating the agent's decision-making. The decoder in AQT utilizes action queries, which represent the information of each action, as queries. This enables us to obtain the attentions for the state value and for each action. By acquiring and visualizing these attentions that detail the agent's decision-making, we achieve a DRL model with high interpretability. In this paper, we show that visualization of attention in Atari 2600 games enables detailed analysis of agents' decision-making in various game tasks. Further, experimental results demonstrate that our method can achieve higher performance than the baseline in some games.

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

The Transformer architecture has become a dominant choice in many domains, such as natural language processing and computer vision. Yet, it has not achieved competitive performance on popular leaderboards of graph-level prediction compared to mainstream GNN variants. Therefore, it remains a mystery how Transformers could perform well for graph representation learning. In this paper, we solve this mystery by presenting Graphormer, which is built upon the standard Transformer architecture, and could attain excellent results on a broad range of graph representation learning tasks, especially on the recent OGB Large-Scale Challenge. Our key insight to utilizing Transformer in the graph is the necessity of effectively encoding the structural information of a graph into the model. To this end, we propose several simple yet effective structural encoding methods to help Graphormer better model graph-structured data. Besides, we mathematically characterize the expressive power of Graphormer and exhibit that with our ways of encoding the structural information of graphs, many popular GNN variants could be covered as the special cases of Graphormer.

This paper investigates the ability of transformer-based models to learn structural recursion from examples. Recursion is a universal concept in both natural and formal languages. Structural recursion is central to the programming language and formal mathematics tasks where symbolic tools currently excel beyond neural models, such as inferring semantic relations between datatypes and emulating program behavior. We introduce a general framework that nicely connects the abstract concepts of structural recursion in the programming language domain to concrete sequence modeling problems and learned models' behavior. The framework includes a representation that captures the general syntax of structural recursion, coupled with two different frameworks for understanding their semantics -- one that is more natural from a programming languages perspective and one that helps bridge that perspective with a mechanistic understanding of the underlying transformer architecture. With our framework as a powerful conceptual tool, we identify different issues under various set-ups. The models trained to emulate recursive computations cannot fully capture the recursion yet instead fit short-cut algorithms and thus cannot solve certain edge cases that are under-represented in the training distribution. In addition, it is difficult for state-of-the-art large language models (LLMs) to mine recursive rules from in-context demonstrations. Meanwhile, these LLMs fail in interesting ways when emulating reduction (step-wise computation) of the recursive function.

Predictive process monitoring is a process mining task aimed at forecasting information about a running process trace, such as the most correct next activity to be executed. In medical domains, predictive process monitoring can provide valuable decision support in atypical and nontrivial situations. Decision support and quality assessment in medicine cannot ignore domain knowledge, in order to be grounded on all the available information (which is not limited to data) and to be really acceptable by end users. In this paper, we propose a predictive process monitoring approach relying on the use of a {\em transformer}, a deep learning architecture based on the attention mechanism. A major contribution of our work lies in the incorporation of ontological domain-specific knowledge, carried out through a graph positional encoding technique. The paper presents and discusses the encouraging experimental result we are collecting in the domain of stroke management.

Multimodal knowledge graph completion (MMKGC) aims to predict missing links in multimodal knowledge graphs (MMKGs) by leveraging information from various modalities alongside structural data. Existing MMKGC approaches primarily extend traditional knowledge graph embedding (KGE) models, which often require creating an embedding for every entity. This results in large model sizes and inefficiencies in integrating multimodal information, particularly for real-world graphs. Meanwhile, Transformer-based models have demonstrated competitive performance in knowledge graph completion (KGC). However, their focus on single-modal knowledge limits their capacity to utilize cross-modal information. Recently, Large vision-language models (VLMs) have shown potential in cross-modal tasks but are constrained by the high cost of training. In this work, we propose a novel approach that integrates Transformer-based KGE models with cross-modal context generated by pre-trained VLMs, thereby extending their applicability to MMKGC. Specifically, we employ a pre-trained VLM to transform relevant visual information from entities and their neighbors into textual sequences. We then frame KGC as a sequence-to-sequence task, fine-tuning the model with the generated cross-modal context. This simple yet effective method significantly reduces model size compared to traditional KGE approaches while achieving competitive performance across multiple large-scale datasets with minimal hyperparameter tuning.

This study explores replacing Transformers in Visual Language Models (VLMs) with Mamba, a recent structured state space model (SSM) that demonstrates promising performance in sequence modeling. We test models up to 3B parameters under controlled conditions, showing that Mamba-based VLMs outperforms Transformers-based VLMs in captioning, question answering, and reading comprehension. However, we find that Transformers achieve greater performance in visual grounding and the performance gap widens with scale. We explore two hypotheses to explain this phenomenon: 1) the effect of task-agnostic visual encoding on the updates of the hidden states, and 2) the difficulty in performing visual grounding from the perspective of in-context multimodal retrieval. Our results indicate that a task-aware encoding yields minimal performance gains on grounding, however, Transformers significantly outperform Mamba at in-context multimodal retrieval. Overall, Mamba shows promising performance on tasks where the correct output relies on a summary of the image but struggles when retrieval of explicit information from the context is required.

Transformer-based Large Language Models (LLMs) have demonstrated remarkable success across various challenging tasks. However, the deployment of LLMs is hindered by their substantial parameter count and memory consumption. Recently, numerous studies have attempted to compress LLMs by pruning them using training-free methods. However, these pruned models often experience significant performance degradation on complex tasks. To address this issue, we propose a novel training pipeline for semi-structured sparse models, named Adaptive Sparse Trainer (AST). By distilling the knowledge stored in its dense counterpart, we prevent the sparse model from overfitting and ensure a stable training process. Moreover, AST allows the model to adaptively select better lottery tickets (e.g., masks) during training. Additionally, we discovered that adding extra well-initialized parameters can further enhance model performance with only a small increase in memory footprint. Our method significantly narrows the performance gap between dense and sparse models while maintaining limited computational cost. Furthermore, when combined with existing quantization methods, AST can compress language models by up to 16x compared to dense FP32 precision models with minimal performance loss. AST outperforms previous state-of-the-art methods by reducing the zero-shot accuracy gap between dense and semi-structured sparse models to 1.12% across multiple zero-shot tasks on Llama2-7B, using less than 0.4% of the pretraining tokens.

Acceleration of large language model pre-training is a critical issue in present NLP research. In this paper, we focus on speeding up pre-training by progressively growing from a small Transformer structure to a large one. There are two main research problems related to progressive growth: growth schedule and growth operator. For growth schedule, existing work has explored multi-stage expansion of depth and feedforward layers. However, the impact of each dimension on the schedule's efficiency is still an open question. For growth operator, existing work relies on the initialization of new weights to inherit knowledge, and achieve only non-strict function preservation, limiting further optimization of training dynamics. To address these issues, we propose Masked Structural Growth (MSG), including growth schedules involving all possible dimensions and strictly function-preserving growth operators that is independent of the initialization of new weights. Experiments show that MSG is significantly faster than related work: we achieve a speed-up of 80% for Bert-base and 120% for Bert-large pre-training. Moreover, MSG is able to improve fine-tuning performances at the same time.

The Multiplane Image (MPI), containing a set of fronto-parallel RGBA layers, is an effective and efficient representation for view synthesis from sparse inputs. Yet, its fixed structure limits the performance, especially for surfaces imaged at oblique angles. We introduce the Structural MPI (S-MPI), where the plane structure approximates 3D scenes concisely. Conveying RGBA contexts with geometrically-faithful structures, the S-MPI directly bridges view synthesis and 3D reconstruction. It can not only overcome the critical limitations of MPI, i.e., discretization artifacts from sloped surfaces and abuse of redundant layers, and can also acquire planar 3D reconstruction. Despite the intuition and demand of applying S-MPI, great challenges are introduced, e.g., high-fidelity approximation for both RGBA layers and plane poses, multi-view consistency, non-planar regions modeling, and efficient rendering with intersected planes. Accordingly, we propose a transformer-based network based on a segmentation model. It predicts compact and expressive S-MPI layers with their corresponding masks, poses, and RGBA contexts. Non-planar regions are inclusively handled as a special case in our unified framework. Multi-view consistency is ensured by sharing global proxy embeddings, which encode plane-level features covering the complete 3D scenes with aligned coordinates. Intensive experiments show that our method outperforms both previous state-of-the-art MPI-based view synthesis methods and planar reconstruction methods.

Transformers represent the state-of-the-art in Natural Language Processing (NLP) in recent years, proving effective even in tasks done in low-resource languages. While pretrained transformers for these languages can be made, it is challenging to measure their true performance and capacity due to the lack of hard benchmark datasets, as well as the difficulty and cost of producing them. In this paper, we present three contributions: First, we propose a methodology for automatically producing Natural Language Inference (NLI) benchmark datasets for low-resource languages using published news articles. Through this, we create and release NewsPH-NLI, the first sentence entailment benchmark dataset in the low-resource Filipino language. Second, we produce new pretrained transformers based on the ELECTRA technique to further alleviate the resource scarcity in Filipino, benchmarking them on our dataset against other commonly-used transfer learning techniques. Lastly, we perform analyses on transfer learning techniques to shed light on their true performance when operating in low-data domains through the use of degradation tests.

In medical applications, deep learning methods are built to automate diagnostic tasks. However, a clinically relevant question that practitioners usually face, is how to predict the future trajectory of a disease (prognosis). Current methods for such a problem often require domain knowledge, and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many forecasting problem from multimodal data. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner, we model a prognosis prediction problem with two transformer-based components that share information between each other. The first block in this model aims to analyze the imaging data, and the second block leverages the internal representations of the first one as inputs, also fusing them with auxiliary patient data. We show the effectiveness of our method in predicting the development of structural knee osteoarthritis changes over time. Our results show that the proposed method outperforms the state-of-the-art baselines in terms of various performance metrics. In addition, we empirically show that the existence of the multi-agent transformers with depths of 2 is sufficient to achieve good performances. Our code is publicly available at https://github.com/MIPT-Oulu/CLIMAT.

Open-domain question answering (QA) is known to involve several underlying knowledge and reasoning challenges, but are models actually learning such knowledge when trained on benchmark tasks? To investigate this, we introduce several new challenge tasks that probe whether state-of-the-art QA models have general knowledge about word definitions and general taxonomic reasoning, both of which are fundamental to more complex forms of reasoning and are widespread in benchmark datasets. As an alternative to expensive crowd-sourcing, we introduce a methodology for automatically building datasets from various types of expert knowledge (e.g., knowledge graphs and lexical taxonomies), allowing for systematic control over the resulting probes and for a more comprehensive evaluation. We find automatically constructing probes to be vulnerable to annotation artifacts, which we carefully control for. Our evaluation confirms that transformer-based QA models are already predisposed to recognize certain types of structural lexical knowledge. However, it also reveals a more nuanced picture: their performance degrades substantially with even a slight increase in the number of hops in the underlying taxonomic hierarchy, or as more challenging distractor candidate answers are introduced. Further, even when these models succeed at the standard instance-level evaluation, they leave much room for improvement when assessed at the level of clusters of semantically connected probes (e.g., all Isa questions about a concept).

In this paper, we propose SPBERT, a transformer-based language model pre-trained on massive SPARQL query logs. By incorporating masked language modeling objectives and the word structural objective, SPBERT can learn general-purpose representations in both natural language and SPARQL query language. We investigate how SPBERT and encoder-decoder architecture can be adapted for Knowledge-based QA corpora. We conduct exhaustive experiments on two additional tasks, including SPARQL Query Construction and Answer Verbalization Generation. The experimental results show that SPBERT can obtain promising results, achieving state-of-the-art BLEU scores on several of these tasks.

Automated computational analysis of the vast chemical space is critical for numerous fields of research such as drug discovery and material science. Representation learning techniques have recently been employed with the primary objective of generating compact and informative numerical expressions of complex data. One approach to efficiently learn molecular representations is processing string-based notations of chemicals via natural language processing (NLP) algorithms. Majority of the methods proposed so far utilize SMILES notations for this purpose; however, SMILES is associated with numerous problems related to validity and robustness, which may prevent the model from effectively uncovering the knowledge hidden in the data. In this study, we propose SELFormer, a transformer architecture-based chemical language model that utilizes a 100% valid, compact and expressive notation, SELFIES, as input, in order to learn flexible and high-quality molecular representations. SELFormer is pre-trained on two million drug-like compounds and fine-tuned for diverse molecular property prediction tasks. Our performance evaluation has revealed that, SELFormer outperforms all competing methods, including graph learning-based approaches and SMILES-based chemical language models, on predicting aqueous solubility of molecules and adverse drug reactions. We also visualized molecular representations learned by SELFormer via dimensionality reduction, which indicated that even the pre-trained model can discriminate molecules with differing structural properties. We shared SELFormer as a programmatic tool, together with its datasets and pre-trained models. Overall, our research demonstrates the benefit of using the SELFIES notations in the context of chemical language modeling and opens up new possibilities for the design and discovery of novel drug candidates with desired features.

Chip design relies heavily on generating Boolean circuits, such as AND-Inverter Graphs (AIGs), from functional descriptions like truth tables. While recent advances in deep learning have aimed to accelerate circuit design, these efforts have mostly focused on tasks other than synthesis, and traditional heuristic methods have plateaued. In this paper, we introduce ShortCircuit, a novel transformer-based architecture that leverages the structural properties of AIGs and performs efficient space exploration. Contrary to prior approaches attempting end-to-end generation of logic circuits using deep networks, ShortCircuit employs a two-phase process combining supervised with reinforcement learning to enhance generalization to unseen truth tables. We also propose an AlphaZero variant to handle the double exponentially large state space and the sparsity of the rewards, enabling the discovery of near-optimal designs. To evaluate the generative performance of our trained model , we extract 500 truth tables from a benchmark set of 20 real-world circuits. ShortCircuit successfully generates AIGs for 84.6% of the 8-input test truth tables, and outperforms the state-of-the-art logic synthesis tool, ABC, by 14.61% in terms of circuits size.

Efficiently supporting long context length is crucial for Transformer models. The quadratic complexity of the self-attention computation plagues traditional Transformers. Sliding window-based static sparse attention mitigates the problem by limiting the attention scope of the input tokens, reducing the theoretical complexity from quadratic to linear. Although the sparsity induced by window attention is highly structured, it does not align perfectly with the microarchitecture of the conventional accelerators, leading to suboptimal implementation. In response, we propose a dataflow-aware FPGA-based accelerator design, SWAT, that efficiently leverages the sparsity to achieve scalable performance for long input. The proposed microarchitecture is based on a design that maximizes data reuse by using a combination of row-wise dataflow, kernel fusion optimization, and an input-stationary design considering the distributed memory and computation resources of FPGA. Consequently, it achieves up to 22times and 5.7times improvement in latency and energy efficiency compared to the baseline FPGA-based accelerator and 15times energy efficiency compared to GPU-based solution.

In volume rendering, transfer functions are used to classify structures of interest, and to assign optical properties such as color and opacity. They are commonly defined as 1D or 2D functions that map simple features to these optical properties. As the process of designing a transfer function is typically tedious and unintuitive, several approaches have been proposed for their interactive specification. In this paper, we present a novel method to define transfer functions for volume rendering by leveraging the feature extraction capabilities of self-supervised pre-trained vision transformers. To design a transfer function, users simply select the structures of interest in a slice viewer, and our method automatically selects similar structures based on the high-level features extracted by the neural network. Contrary to previous learning-based transfer function approaches, our method does not require training of models and allows for quick inference, enabling an interactive exploration of the volume data. Our approach reduces the amount of necessary annotations by interactively informing the user about the current classification, so they can focus on annotating the structures of interest that still require annotation. In practice, this allows users to design transfer functions within seconds, instead of minutes. We compare our method to existing learning-based approaches in terms of annotation and compute time, as well as with respect to segmentation accuracy. Our accompanying video showcases the interactivity and effectiveness of our method.

Peptides are essential in biological processes and therapeutics. In this study, we introduce Multi-Peptide, an innovative approach that combines transformer-based language models with Graph Neural Networks (GNNs) to predict peptide properties. We combine PeptideBERT, a transformer model tailored for peptide property prediction, with a GNN encoder to capture both sequence-based and structural features. By employing Contrastive Language-Image Pre-training (CLIP), Multi-Peptide aligns embeddings from both modalities into a shared latent space, thereby enhancing the model's predictive accuracy. Evaluations on hemolysis and nonfouling datasets demonstrate Multi-Peptide's robustness, achieving state-of-the-art 86.185% accuracy in hemolysis prediction. This study highlights the potential of multimodal learning in bioinformatics, paving the way for accurate and reliable predictions in peptide-based research and applications.

The vision-based perception for autonomous driving has undergone a transformation from the bird-eye-view (BEV) representations to the 3D semantic occupancy. Compared with the BEV planes, the 3D semantic occupancy further provides structural information along the vertical direction. This paper presents OccFormer, a dual-path transformer network to effectively process the 3D volume for semantic occupancy prediction. OccFormer achieves a long-range, dynamic, and efficient encoding of the camera-generated 3D voxel features. It is obtained by decomposing the heavy 3D processing into the local and global transformer pathways along the horizontal plane. For the occupancy decoder, we adapt the vanilla Mask2Former for 3D semantic occupancy by proposing preserve-pooling and class-guided sampling, which notably mitigate the sparsity and class imbalance. Experimental results demonstrate that OccFormer significantly outperforms existing methods for semantic scene completion on SemanticKITTI dataset and for LiDAR semantic segmentation on nuScenes dataset. Code is available at https://github.com/zhangyp15/OccFormer.

Recent music generation methods based on transformers have a context window of up to a minute. The music generated by these methods is largely unstructured beyond the context window. With a longer context window, learning long-scale structures from musical data is a prohibitively challenging problem. This paper proposes integrating a text-to-music model with a large language model to generate music with form. The papers discusses the solutions to the challenges of such integration. The experimental results show that the proposed method can generate 2.5-minute-long music that is highly structured, strongly organized, and cohesive.

Lane detection, the process of identifying lane markings as approximated curves, is widely used for lane departure warning and adaptive cruise control in autonomous vehicles. The popular pipeline that solves it in two steps -- feature extraction plus post-processing, while useful, is too inefficient and flawed in learning the global context and lanes' long and thin structures. To tackle these issues, we propose an end-to-end method that directly outputs parameters of a lane shape model, using a network built with a transformer to learn richer structures and context. The lane shape model is formulated based on road structures and camera pose, providing physical interpretation for parameters of network output. The transformer models non-local interactions with a self-attention mechanism to capture slender structures and global context. The proposed method is validated on the TuSimple benchmark and shows state-of-the-art accuracy with the most lightweight model size and fastest speed. Additionally, our method shows excellent adaptability to a challenging self-collected lane detection dataset, showing its powerful deployment potential in real applications. Codes are available at https://github.com/liuruijin17/LSTR.

In recent years, there has been a growing emphasis on compressing large pre-trained transformer models for resource-constrained devices. However, traditional pruning methods often leave the embedding layer untouched, leading to model over-parameterization. Additionally, they require extensive compression time with large datasets to maintain performance in pruned models. To address these challenges, we propose VTrans, an iterative pruning framework guided by the Variational Information Bottleneck (VIB) principle. Our method compresses all structural components, including embeddings, attention heads, and layers using VIB-trained masks. This approach retains only essential weights in each layer, ensuring compliance with specified model size or computational constraints. Notably, our method achieves upto 70% more compression than prior state-of-the-art approaches, both task-agnostic and task-specific. We further propose faster variants of our method: Fast-VTrans utilizing only 3% of the data and Faster-VTrans, a time efficient alternative that involves exclusive finetuning of VIB masks, accelerating compression by upto 25 times with minimal performance loss compared to previous methods. Extensive experiments on BERT, ROBERTa, and GPT-2 models substantiate the efficacy of our method. Moreover, our method demonstrates scalability in compressing large models such as LLaMA-2-7B, achieving superior performance compared to previous pruning methods. Additionally, we use attention-based probing to qualitatively assess model redundancy and interpret the efficiency of our approach. Notably, our method considers heads with high attention to special and current tokens in un-pruned model as foremost candidates for pruning while retained heads are observed to attend more to task-critical keywords.

We present a new table structure recognition (TSR) approach, called TSRFormer, to robustly recognizing the structures of complex tables with geometrical distortions from various table images. Unlike previous methods, we formulate table separation line prediction as a line regression problem instead of an image segmentation problem and propose a new two-stage DETR based separator prediction approach, dubbed Separator REgression TRansformer (SepRETR), to predict separation lines from table images directly. To make the two-stage DETR framework work efficiently and effectively for the separation line prediction task, we propose two improvements: 1) A prior-enhanced matching strategy to solve the slow convergence issue of DETR; 2) A new cross attention module to sample features from a high-resolution convolutional feature map directly so that high localization accuracy is achieved with low computational cost. After separation line prediction, a simple relation network based cell merging module is used to recover spanning cells. With these new techniques, our TSRFormer achieves state-of-the-art performance on several benchmark datasets, including SciTSR, PubTabNet and WTW. Furthermore, we have validated the robustness of our approach to tables with complex structures, borderless cells, large blank spaces, empty or spanning cells as well as distorted or even curved shapes on a more challenging real-world in-house dataset.

The incredible success of transformers on sequence modeling tasks can be largely attributed to the self-attention mechanism, which allows information to be transferred between different parts of a sequence. Self-attention allows transformers to encode causal structure which makes them particularly suitable for sequence modeling. However, the process by which transformers learn such causal structure via gradient-based training algorithms remains poorly understood. To better understand this process, we introduce an in-context learning task that requires learning latent causal structure. We prove that gradient descent on a simplified two-layer transformer learns to solve this task by encoding the latent causal graph in the first attention layer. The key insight of our proof is that the gradient of the attention matrix encodes the mutual information between tokens. As a consequence of the data processing inequality, the largest entries of this gradient correspond to edges in the latent causal graph. As a special case, when the sequences are generated from in-context Markov chains, we prove that transformers learn an induction head (Olsson et al., 2022). We confirm our theoretical findings by showing that transformers trained on our in-context learning task are able to recover a wide variety of causal structures.

While the successes of transformers across many domains are indisputable, accurate understanding of the learning mechanics is still largely lacking. Their capabilities have been probed on benchmarks which include a variety of structured and reasoning tasks -- but mathematical understanding is lagging substantially behind. Recent lines of work have begun studying representational aspects of this question: that is, the size/depth/complexity of attention-based networks to perform certain tasks. However, there is no guarantee the learning dynamics will converge to the constructions proposed. In our paper, we provide fine-grained mechanistic understanding of how transformers learn "semantic structure", understood as capturing co-occurrence structure of words. Precisely, we show, through a combination of experiments on synthetic data modeled by Latent Dirichlet Allocation (LDA), Wikipedia data, and mathematical analysis that the embedding layer and the self-attention layer encode the topical structure. In the former case, this manifests as higher average inner product of embeddings between same-topic words. In the latter, it manifests as higher average pairwise attention between same-topic words. The mathematical results involve several assumptions to make the analysis tractable, which we verify on data, and might be of independent interest as well.

Effective modeling of complex spatiotemporal dependencies in long-form videos remains an open problem. The recently proposed Structured State-Space Sequence (S4) model with its linear complexity offers a promising direction in this space. However, we demonstrate that treating all image-tokens equally as done by S4 model can adversely affect its efficiency and accuracy. To address this limitation, we present a novel Selective S4 (i.e., S5) model that employs a lightweight mask generator to adaptively select informative image tokens resulting in more efficient and accurate modeling of long-term spatiotemporal dependencies in videos. Unlike previous mask-based token reduction methods used in transformers, our S5 model avoids the dense self-attention calculation by making use of the guidance of the momentum-updated S4 model. This enables our model to efficiently discard less informative tokens and adapt to various long-form video understanding tasks more effectively. However, as is the case for most token reduction methods, the informative image tokens could be dropped incorrectly. To improve the robustness and the temporal horizon of our model, we propose a novel long-short masked contrastive learning (LSMCL) approach that enables our model to predict longer temporal context using shorter input videos. We present extensive comparative results using three challenging long-form video understanding datasets (LVU, COIN and Breakfast), demonstrating that our approach consistently outperforms the previous state-of-the-art S4 model by up to 9.6% accuracy while reducing its memory footprint by 23%.

Transformer models can use two fundamentally different kinds of information: information stored in weights during training, and information provided ``in-context'' at inference time. In this work, we show that transformers exhibit different inductive biases in how they represent and generalize from the information in these two sources. In particular, we characterize whether they generalize via parsimonious rules (rule-based generalization) or via direct comparison with observed examples (exemplar-based generalization). This is of important practical consequence, as it informs whether to encode information in weights or in context, depending on how we want models to use that information. In transformers trained on controlled stimuli, we find that generalization from weights is more rule-based whereas generalization from context is largely exemplar-based. In contrast, we find that in transformers pre-trained on natural language, in-context learning is significantly rule-based, with larger models showing more rule-basedness. We hypothesise that rule-based generalization from in-context information might be an emergent consequence of large-scale training on language, which has sparse rule-like structure. Using controlled stimuli, we verify that transformers pretrained on data containing sparse rule-like structure exhibit more rule-based generalization.

As transformers are equivariant to the permutation of input tokens, encoding the positional information of tokens is necessary for many tasks. However, since existing positional encoding schemes have been initially designed for NLP tasks, their suitability for vision tasks, which typically exhibit different structural properties in their data, is questionable. We argue that existing positional encoding schemes are suboptimal for 3D vision tasks, as they do not respect their underlying 3D geometric structure. Based on this hypothesis, we propose a geometry-aware attention mechanism that encodes the geometric structure of tokens as relative transformation determined by the geometric relationship between queries and key-value pairs. By evaluating on multiple novel view synthesis (NVS) datasets in the sparse wide-baseline multi-view setting, we show that our attention, called Geometric Transform Attention (GTA), improves learning efficiency and performance of state-of-the-art transformer-based NVS models without any additional learned parameters and only minor computational overhead.

Removing noise from images is a challenging and fundamental problem in the field of computer vision. Images captured by modern cameras are inevitably degraded by noise which limits the accuracy of any quantitative measurements on those images. In this project, we propose a novel image reconstruction framework which can be used for tasks such as image denoising, deblurring or inpainting. The model proposed in this project is based on Vision Transformer (ViT) that takes 2D images as input and outputs embeddings which can be used for reconstructing denoised images. We incorporate four additional optimization techniques in the framework to improve the model reconstruction capability, namely Locality Sensitive Attention (LSA), Shifted Patch Tokenization (SPT), Rotary Position Embeddings (RoPE) and adversarial loss function inspired from Generative Adversarial Networks (GANs). LSA, SPT and RoPE enable the transformer to learn from the dataset more efficiently, while the adversarial loss function enhances the resolution of the reconstructed images. Based on our experiments, the proposed architecture outperforms the benchmark U-Net model by more than 3.5\% structural similarity (SSIM) for the reconstruction tasks of image denoising and inpainting. The proposed enhancements further show an improvement of \textasciitilde5\% SSIM over the benchmark for both tasks.

Previous works on Treatment Effect Estimation (TEE) are not in widespread use because they are predominantly theoretical, where strong parametric assumptions are made but untractable for practical application. Recent work uses multilayer perceptron (MLP) for modeling casual relationships, however, MLPs lag far behind recent advances in ML methodology, which limits their applicability and generalizability. To extend beyond the single domain formulation and towards more realistic learning scenarios, we explore model design spaces beyond MLPs, i.e., transformer backbones, which provide flexibility where attention layers govern interactions among treatments and covariates to exploit structural similarities of potential outcomes for confounding control. Through careful model design, Transformers as Treatment Effect Estimators (TransTEE) is proposed. We show empirically that TransTEE can: (1) serve as a general purpose treatment effect estimator that significantly outperforms competitive baselines in a variety of challenging TEE problems (e.g., discrete, continuous, structured, or dosage-associated treatments) and is applicable to both when covariates are tabular and when they consist of structural data (e.g., texts, graphs); (2) yield multiple advantages: compatibility with propensity score modeling, parameter efficiency, robustness to continuous treatment value distribution shifts, explainable in covariate adjustment, and real-world utility in auditing pre-trained language models

We present a new class of fast polylog-linear algorithms based on the theory of structured matrices (in particular low displacement rank) for integrating tensor fields defined on weighted trees. Several applications of the resulting fast tree-field integrators (FTFIs) are presented, including (a) approximation of graph metrics with tree metrics, (b) graph classification, (c) modeling on meshes, and finally (d) Topological Transformers (TTs) (Choromanski et al., 2022) for images. For Topological Transformers, we propose new relative position encoding (RPE) masking mechanisms with as few as three extra learnable parameters per Transformer layer, leading to 1.0-1.5%+ accuracy gains. Importantly, most of FTFIs are exact methods, thus numerically equivalent to their brute-force counterparts. When applied to graphs with thousands of nodes, those exact algorithms provide 5.7-13x speedups. We also provide an extensive theoretical analysis of our methods.

Structured state space sequence (S4) models have recently achieved state-of-the-art performance on long-range sequence modeling tasks. These models also have fast inference speeds and parallelisable training, making them potentially useful in many reinforcement learning settings. We propose a modification to a variant of S4 that enables us to initialise and reset the hidden state in parallel, allowing us to tackle reinforcement learning tasks. We show that our modified architecture runs asymptotically faster than Transformers in sequence length and performs better than RNN's on a simple memory-based task. We evaluate our modified architecture on a set of partially-observable environments and find that, in practice, our model outperforms RNN's while also running over five times faster. Then, by leveraging the model's ability to handle long-range sequences, we achieve strong performance on a challenging meta-learning task in which the agent is given a randomly-sampled continuous control environment, combined with a randomly-sampled linear projection of the environment's observations and actions. Furthermore, we show the resulting model can adapt to out-of-distribution held-out tasks. Overall, the results presented in this paper show that structured state space models are fast and performant for in-context reinforcement learning tasks. We provide code at https://github.com/luchris429/popjaxrl.

Structured dropout approaches, such as attention dropout and DropHead, have been investigated to regularize the multi-head attention mechanism in Transformers. In this paper, we propose a new regularization scheme based on token-level rather than structure-level to reduce overfitting. Specifically, we devise a novel Token-Level Masking (TLM) training strategy for Transformers to regularize the connections of self-attention, which consists of two masking techniques that are effective and easy to implement. The underlying idea is to manipulate the connections between tokens in the multi-head attention via masking, where the networks are forced to exploit partial neighbors' information to produce a meaningful representation. The generality and effectiveness of TLM are thoroughly evaluated via extensive experiments on 4 diversified NLP tasks across 18 datasets, including natural language understanding benchmark GLUE, ChineseGLUE, Chinese Grammatical Error Correction, and data-to-text generation. The results indicate that TLM can consistently outperform attention dropout and DropHead, e.g., it increases by 0.5 points relative to DropHead with BERT-large on GLUE. Moreover, TLM can establish a new record on the data-to-text benchmark Rotowire (18.93 BLEU). Our code will be publicly available at https://github.com/Young1993/tlm.

Code retrieval is a crucial component in modern software development, particularly in large-scale projects. However, existing approaches relying on sequence-based models often fail to fully exploit the structural dependencies inherent in code, leading to suboptimal retrieval performance, particularly with structurally complex code fragments. In this paper, we introduce GNN-Coder, a novel framework based on Graph Neural Network (GNN) to utilize Abstract Syntax Tree (AST). We make the first attempt to study how GNN-integrated Transformer can promote the development of semantic retrieval tasks by capturing the structural and semantic features of code. We further propose an innovative graph pooling method tailored for AST, utilizing the number of child nodes as a key feature to highlight the intrinsic topological relationships within the AST. This design effectively integrates both sequential and hierarchical representations, enhancing the model's ability to capture code structure and semantics. Additionally, we introduce the Mean Angular Margin (MAM), a novel metric for quantifying the uniformity of code embedding distributions, providing a standardized measure of feature separability. The proposed method achieves a lower MAM, indicating a more discriminative feature representation. This underscores GNN-Coder's superior ability to distinguish between code snippets, thereby enhancing retrieval accuracy. Experimental results show that GNN-Coder significantly boosts retrieval performance, with a 1\%-10\% improvement in MRR on the CSN dataset, and a notable 20\% gain in zero-shot performance on the CosQA dataset.

Score-based diffusion models have captured widespread attention and funded fast progress of recent vision generative tasks. In this paper, we focus on diffusion model backbone which has been much neglected before. We systematically explore vision Transformers as diffusion learners for various generative tasks. With our improvements the performance of vanilla ViT-based backbone (IU-ViT) is boosted to be on par with traditional U-Net-based methods. We further provide a hypothesis on the implication of disentangling the generative backbone as an encoder-decoder structure and show proof-of-concept experiments verifying the effectiveness of a stronger encoder for generative tasks with ASymmetriC ENcoder Decoder (ASCEND). Our improvements achieve competitive results on CIFAR-10, CelebA, LSUN, CUB Bird and large-resolution text-to-image tasks. To the best of our knowledge, we are the first to successfully train a single diffusion model on text-to-image task beyond 64x64 resolution. We hope this will motivate people to rethink the modeling choices and the training pipelines for diffusion-based generative models.

Sequence modeling is a crucial area across various domains, including Natural Language Processing (NLP), speech recognition, time series forecasting, music generation, and bioinformatics. Recurrent Neural Networks (RNNs) and Long Short Term Memory Networks (LSTMs) have historically dominated sequence modeling tasks like Machine Translation, Named Entity Recognition (NER), etc. However, the advancement of transformers has led to a shift in this paradigm, given their superior performance. Yet, transformers suffer from O(N^2) attention complexity and challenges in handling inductive bias. Several variations have been proposed to address these issues which use spectral networks or convolutions and have performed well on a range of tasks. However, they still have difficulty in dealing with long sequences. State Space Models(SSMs) have emerged as promising alternatives for sequence modeling paradigms in this context, especially with the advent of S4 and its variants, such as S4nd, Hippo, Hyena, Diagnol State Spaces (DSS), Gated State Spaces (GSS), Linear Recurrent Unit (LRU), Liquid-S4, Mamba, etc. In this survey, we categorize the foundational SSMs based on three paradigms namely, Gating architectures, Structural architectures, and Recurrent architectures. This survey also highlights diverse applications of SSMs across domains such as vision, video, audio, speech, language (especially long sequence modeling), medical (including genomics), chemical (like drug design), recommendation systems, and time series analysis, including tabular data. Moreover, we consolidate the performance of SSMs on benchmark datasets like Long Range Arena (LRA), WikiText, Glue, Pile, ImageNet, Kinetics-400, sstv2, as well as video datasets such as Breakfast, COIN, LVU, and various time series datasets. The project page for Mamba-360 work is available on this webpage.https://github.com/badripatro/mamba360.

Vision Transformers (ViTs) have demonstrated powerful representation ability in various visual tasks thanks to their intrinsic data-hungry nature. However, we unexpectedly find that ViTs perform vulnerably when applied to face recognition (FR) scenarios with extremely large datasets. We investigate the reasons for this phenomenon and discover that the existing data augmentation approach and hard sample mining strategy are incompatible with ViTs-based FR backbone due to the lack of tailored consideration on preserving face structural information and leveraging each local token information. To remedy these problems, this paper proposes a superior FR model called TransFace, which employs a patch-level data augmentation strategy named DPAP and a hard sample mining strategy named EHSM. Specially, DPAP randomly perturbs the amplitude information of dominant patches to expand sample diversity, which effectively alleviates the overfitting problem in ViTs. EHSM utilizes the information entropy in the local tokens to dynamically adjust the importance weight of easy and hard samples during training, leading to a more stable prediction. Experiments on several benchmarks demonstrate the superiority of our TransFace. Code and models are available at https://github.com/DanJun6737/TransFace.

Structural pruning enables model acceleration by removing structurally-grouped parameters from neural networks. However, the parameter-grouping patterns vary widely across different models, making architecture-specific pruners, which rely on manually-designed grouping schemes, non-generalizable to new architectures. In this work, we study a highly-challenging yet barely-explored task, any structural pruning, to tackle general structural pruning of arbitrary architecture like CNNs, RNNs, GNNs and Transformers. The most prominent obstacle towards this goal lies in the structural coupling, which not only forces different layers to be pruned simultaneously, but also expects all removed parameters to be consistently unimportant, thereby avoiding structural issues and significant performance degradation after pruning. To address this problem, we propose a general and {fully automatic} method, Dependency Graph (DepGraph), to explicitly model the dependency between layers and comprehensively group coupled parameters for pruning. In this work, we extensively evaluate our method on several architectures and tasks, including ResNe(X)t, DenseNet, MobileNet and Vision transformer for images, GAT for graph, DGCNN for 3D point cloud, alongside LSTM for language, and demonstrate that, even with a simple norm-based criterion, the proposed method consistently yields gratifying performances.

We present Arabic-Nougat, a suite of OCR models for converting Arabic book pages into structured Markdown text. Based on Meta's Nougat architecture, Arabic-Nougat includes three specialized models: arabic-small-nougat, arabic-base-nougat, and arabic-large-nougat. These models are fine-tuned on a synthetic dataset, arabic-img2md, comprising 13.7k pairs of Arabic book pages and their Markdown representations. Key contributions include the Aranizer-PBE-86k tokenizer, designed for efficient tokenization, and the use of torch.bfloat16 precision with Flash Attention 2 for optimized training and inference. Our models achieve state-of-the-art performance, with arabic-large-nougat delivering the highest Markdown Structure Accuracy and the lowest Character Error Rate. Additionally, we release a large-scale dataset containing 1.1 billion Arabic tokens extracted from over 8,500 books using our best-performing model, providing a valuable resource for Arabic OCR research. All models, datasets, and code are open-sourced and available at https://github.com/MohamedAliRashad/arabic-nougat.

This paper investigates the capability of plain Vision Transformers (ViTs) for semantic segmentation using the encoder-decoder framework and introduces SegViTv2. In this study, we introduce a novel Attention-to-Mask (\atm) module to design a lightweight decoder effective for plain ViT. The proposed ATM converts the global attention map into semantic masks for high-quality segmentation results. Our decoder outperforms the popular decoder UPerNet using various ViT backbones while consuming only about 5% of the computational cost. For the encoder, we address the concern of the relatively high computational cost in the ViT-based encoders and propose a Shrunk++ structure that incorporates edge-aware query-based down-sampling (EQD) and query-based upsampling (QU) modules. The Shrunk++ structure reduces the computational cost of the encoder by up to 50% while maintaining competitive performance. Furthermore, we propose to adapt SegViT for continual semantic segmentation, demonstrating nearly zero forgetting of previously learned knowledge. Experiments show that our proposed SegViTv2 surpasses recent segmentation methods on three popular benchmarks including ADE20k, COCO-Stuff-10k and PASCAL-Context datasets. The code is available through the following link: https://github.com/zbwxp/SegVit.

We explore the capability of plain Vision Transformers (ViTs) for semantic segmentation and propose the SegVit. Previous ViT-based segmentation networks usually learn a pixel-level representation from the output of the ViT. Differently, we make use of the fundamental component -- attention mechanism, to generate masks for semantic segmentation. Specifically, we propose the Attention-to-Mask (ATM) module, in which the similarity maps between a set of learnable class tokens and the spatial feature maps are transferred to the segmentation masks. Experiments show that our proposed SegVit using the ATM module outperforms its counterparts using the plain ViT backbone on the ADE20K dataset and achieves new state-of-the-art performance on COCO-Stuff-10K and PASCAL-Context datasets. Furthermore, to reduce the computational cost of the ViT backbone, we propose query-based down-sampling (QD) and query-based up-sampling (QU) to build a Shrunk structure. With the proposed Shrunk structure, the model can save up to 40% computations while maintaining competitive performance.

Methods for designing organic materials with desired properties have high potential impact across fields such as medicine, renewable energy, petrochemical engineering, and agriculture. However, using generative modeling to design substances with desired properties is difficult because candidate compounds must satisfy multiple constraints, including synthetic accessibility and other metrics that are intuitive to domain experts but challenging to quantify. We propose C5T5, a novel self-supervised pretraining method that enables transformers to make zero-shot select-and-replace edits, altering organic substances towards desired property values. C5T5 operates on IUPAC names -- a standardized molecular representation that intuitively encodes rich structural information for organic chemists but that has been largely ignored by the ML community. Our technique requires no edited molecule pairs to train and only a rough estimate of molecular properties, and it has the potential to model long-range dependencies and symmetric molecular structures more easily than graph-based methods. C5T5 also provides a powerful interface to domain experts: it grants users fine-grained control over the generative process by selecting and replacing IUPAC name fragments, which enables experts to leverage their intuitions about structure-activity relationships. We demonstrate C5T5's effectiveness on four physical properties relevant for drug discovery, showing that it learns successful and chemically intuitive strategies for altering molecules towards desired property values.

The current large language models are mainly based on decode-only structure transformers, which have great in-context learning (ICL) capabilities. It is generally believed that the important foundation of its ICL capability is the induction heads mechanism, which requires at least two layers attention. In order to more efficiently implement the ability of the model's induction, we revisit the induction heads mechanism and proposed a KV shifting attention. We theoretically prove that the KV shifting attention reducing the model's requirements for the depth and width of the induction heads mechanism. Our experimental results demonstrate that KV shifting attention is beneficial to learning induction heads and language modeling, which lead to better performance or faster convergence from toy models to the pre-training models with more than 10 B parameters.

Sentences that present a complex syntax act as a major stumbling block for downstream Natural Language Processing applications whose predictive quality deteriorates with sentence length and complexity. The task of Text Simplification (TS) may remedy this situation. It aims to modify sentences in order to make them easier to process, using a set of rewriting operations, such as reordering, deletion, or splitting. State-of-the-art syntactic TS approaches suffer from two major drawbacks: first, they follow a very conservative approach in that they tend to retain the input rather than transforming it, and second, they ignore the cohesive nature of texts, where context spread across clauses or sentences is needed to infer the true meaning of a statement. To address these problems, we present a discourse-aware TS approach that splits and rephrases complex English sentences within the semantic context in which they occur. Based on a linguistically grounded transformation stage that uses clausal and phrasal disembedding mechanisms, complex sentences are transformed into shorter utterances with a simple canonical structure that can be easily analyzed by downstream applications. With sentence splitting, we thus address a TS task that has hardly been explored so far. Moreover, we introduce the notion of minimality in this context, as we aim to decompose source sentences into a set of self-contained minimal semantic units. To avoid breaking down the input into a disjointed sequence of statements that is difficult to interpret because important contextual information is missing, we incorporate the semantic context between the split propositions in the form of hierarchical structures and semantic relationships. In that way, we generate a semantic hierarchy of minimal propositions that leads to a novel representation of complex assertions that puts a semantic layer on top of the simplified sentences.

In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about synthetic procedures. By taking advantage of recent advances in natural language processing for procedural texts, SynKB supports more flexible queries about reaction conditions, and thus has the potential to help chemists search the literature for conditions used in relevant reactions as they design new synthetic routes. Using customized Transformer models to automatically extract information from 6 million synthesis procedures described in U.S. and EU patents, we show that for many queries, SynKB has higher recall than Reaxsys, while maintaining high precision. We plan to make SynKB available as an open-source tool; in contrast, proprietary chemistry databases require costly subscriptions.

Semantic answer type prediction (SMART) is known to be a useful step towards effective question answering (QA) systems. The SMART task involves predicting the top-k knowledge graph (KG) types for a given natural language question. This is challenging due to the large number of types in KGs. In this paper, we propose use of extreme multi-label classification using Transformer models (XBERT) by clustering KG types using structural and semantic features based on question text. We specifically improve the clustering stage of the XBERT pipeline using textual and structural features derived from KGs. We show that these features can improve end-to-end performance for the SMART task, and yield state-of-the-art results.

Transformers are widely used to extract semantic meanings from input tokens, yet they usually operate as black-box models. In this paper, we present a simple yet informative decomposition of hidden states (or embeddings) of trained transformers into interpretable components. For any layer, embedding vectors of input sequence samples are represented by a tensor h in R^{C times T times d}. Given embedding vector h_{c,t} in R^d at sequence position t le T in a sequence (or context) c le C, extracting the mean effects yields the decomposition \[ h_{c,t} = \mu + pos_t + ctx_c + resid_{c,t} \] where mu is the global mean vector, pos_t and ctx_c are the mean vectors across contexts and across positions respectively, and resid_{c,t} is the residual vector. For popular transformer architectures and diverse text datasets, empirically we find pervasive mathematical structure: (1) (pos_t)_{t} forms a low-dimensional, continuous, and often spiral shape across layers, (2) (ctx_c)_c shows clear cluster structure that falls into context topics, and (3) (pos_t)_{t} and (ctx_c)_c are mutually nearly orthogonal. We argue that smoothness is pervasive and beneficial to transformers trained on languages, and our decomposition leads to improved model interpretability.

The transformer is a neural network component that can be used to learn useful representations of sequences or sets of data-points. The transformer has driven recent advances in natural language processing, computer vision, and spatio-temporal modelling. There are many introductions to transformers, but most do not contain precise mathematical descriptions of the architecture and the intuitions behind the design choices are often also missing. Moreover, as research takes a winding path, the explanations for the components of the transformer can be idiosyncratic. In this note we aim for a mathematically precise, intuitive, and clean description of the transformer architecture. We will not discuss training as this is rather standard. We assume that the reader is familiar with fundamental topics in machine learning including multi-layer perceptrons, linear transformations, softmax functions and basic probability.

Attention-based transformers have become the standard architecture in many deep learning fields, primarily due to their ability to model long-range dependencies and handle variable-length input sequences. However, the attention mechanism with its quadratic complexity is a significant bottleneck in the transformer architecture. This algorithm is only uni-directional in the decoder and converges to a static pattern in over-parametrized decoder-only models. I address this issue by developing a generative function as attention or activation replacement. It still has the auto-regressive character by comparing each token with the previous one. In my test setting with nanoGPT this yields a smaller loss while having a smaller model. The loss further drops by incorporating an average context vector. This concept of attention replacement is distributed under the GNU AGPL v3 license at https://gitlab.com/Bachstelze/causal_generation.

The Transformer is a sequence model that forgoes traditional recurrent architectures in favor of a fully attention-based approach. Besides improving performance, an advantage of using attention is that it can also help to interpret a model by showing how the model assigns weight to different input elements. However, the multi-layer, multi-head attention mechanism in the Transformer model can be difficult to decipher. To make the model more accessible, we introduce an open-source tool that visualizes attention at multiple scales, each of which provides a unique perspective on the attention mechanism. We demonstrate the tool on BERT and OpenAI GPT-2 and present three example use cases: detecting model bias, locating relevant attention heads, and linking neurons to model behavior.

Transformers have achieved great success in many artificial intelligence fields, such as natural language processing, computer vision, and audio processing. Therefore, it is natural to attract lots of interest from academic and industry researchers. Up to the present, a great variety of Transformer variants (a.k.a. X-formers) have been proposed, however, a systematic and comprehensive literature review on these Transformer variants is still missing. In this survey, we provide a comprehensive review of various X-formers. We first briefly introduce the vanilla Transformer and then propose a new taxonomy of X-formers. Next, we introduce the various X-formers from three perspectives: architectural modification, pre-training, and applications. Finally, we outline some potential directions for future research.

Transformer is a deep neural network that employs a self-attention mechanism to comprehend the contextual relationships within sequential data. Unlike conventional neural networks or updated versions of Recurrent Neural Networks (RNNs) such as Long Short-Term Memory (LSTM), transformer models excel in handling long dependencies between input sequence elements and enable parallel processing. As a result, transformer-based models have attracted substantial interest among researchers in the field of artificial intelligence. This can be attributed to their immense potential and remarkable achievements, not only in Natural Language Processing (NLP) tasks but also in a wide range of domains, including computer vision, audio and speech processing, healthcare, and the Internet of Things (IoT). Although several survey papers have been published highlighting the transformer's contributions in specific fields, architectural differences, or performance evaluations, there is still a significant absence of a comprehensive survey paper encompassing its major applications across various domains. Therefore, we undertook the task of filling this gap by conducting an extensive survey of proposed transformer models from 2017 to 2022. Our survey encompasses the identification of the top five application domains for transformer-based models, namely: NLP, Computer Vision, Multi-Modality, Audio and Speech Processing, and Signal Processing. We analyze the impact of highly influential transformer-based models in these domains and subsequently classify them based on their respective tasks using a proposed taxonomy. Our aim is to shed light on the existing potential and future possibilities of transformers for enthusiastic researchers, thus contributing to the broader understanding of this groundbreaking technology.

Transformer is a new kind of neural architecture which encodes the input data as powerful features via the attention mechanism. Basically, the visual transformers first divide the input images into several local patches and then calculate both representations and their relationship. Since natural images are of high complexity with abundant detail and color information, the granularity of the patch dividing is not fine enough for excavating features of objects in different scales and locations. In this paper, we point out that the attention inside these local patches are also essential for building visual transformers with high performance and we explore a new architecture, namely, Transformer iN Transformer (TNT). Specifically, we regard the local patches (e.g., 16times16) as "visual sentences" and present to further divide them into smaller patches (e.g., 4times4) as "visual words". The attention of each word will be calculated with other words in the given visual sentence with negligible computational costs. Features of both words and sentences will be aggregated to enhance the representation ability. Experiments on several benchmarks demonstrate the effectiveness of the proposed TNT architecture, e.g., we achieve an 81.5% top-1 accuracy on the ImageNet, which is about 1.7% higher than that of the state-of-the-art visual transformer with similar computational cost. The PyTorch code is available at https://github.com/huawei-noah/CV-Backbones, and the MindSpore code is available at https://gitee.com/mindspore/models/tree/master/research/cv/TNT.

Recurrent neural networks are effective models to process sequences. However, they are unable to learn long-term dependencies because of their inherent sequential nature. As a solution, Vaswani et al. introduced the Transformer, a model solely based on the attention mechanism that is able to relate any two positions of the input sequence, hence modelling arbitrary long dependencies. The Transformer has improved the state-of-the-art across numerous sequence modelling tasks. However, its effectiveness comes at the expense of a quadratic computational and memory complexity with respect to the sequence length, hindering its adoption. Fortunately, the deep learning community has always been interested in improving the models' efficiency, leading to a plethora of solutions such as parameter sharing, pruning, mixed-precision, and knowledge distillation. Recently, researchers have directly addressed the Transformer's limitation by designing lower-complexity alternatives such as the Longformer, Reformer, Linformer, and Performer. However, due to the wide range of solutions, it has become challenging for researchers and practitioners to determine which methods to apply in practice in order to meet the desired trade-off between capacity, computation, and memory. This survey addresses this issue by investigating popular approaches to make Transformers faster and lighter and by providing a comprehensive explanation of the methods' strengths, limitations, and underlying assumptions.

Transformer architecture currently represents the main driver behind many successes in a variety of tasks addressed by deep learning, especially the recent advances in natural language processing (NLP) culminating with large language models (LLM). In addition, transformer architecture has found a wide spread of interest from computer vision (CV) researchers and practitioners, allowing for many advancements in vision-related tasks and opening the door for multi-task and multi-modal deep learning architectures that share the same principle of operation. One drawback to these architectures is their reliance on the scaled dot product attention mechanism with the softmax activation function, which is computationally expensive and requires large compute capabilities both for training and inference. This paper investigates substituting the attention mechanism usually adopted for transformer architecture with an architecture incorporating gated linear unit (GLU) activation within a multi-layer perceptron (MLP) structure in conjunction with the default MLP incorporated in the traditional transformer design. Another step forward taken by this paper is to eliminate the second non-gated MLP to further reduce the computational cost. Experimental assessments conducted by this research show that both proposed modifications and reductions offer competitive performance in relation to baseline architectures, in support of the aims of this work in establishing a more efficient yet capable alternative to the traditional attention mechanism as the core component in designing transformer architectures.

Although purely transformer-based architectures showed promising performance in many computer vision tasks, many hybrid models consisting of CNN and transformer blocks are introduced to fit more specialized tasks. Nevertheless, despite the performance gain of both pure and hybrid transformer-based architectures compared to CNNs in medical imaging segmentation, their high training cost and complexity make it challenging to use them in real scenarios. In this work, we propose simple architectures based on purely convolutional layers, and show that by just taking advantage of the attention map visualizations obtained from a self-supervised pretrained vision transformer network (e.g., DINO) one can outperform complex transformer-based networks with much less computation costs. The proposed architecture is composed of two encoder branches with the original image as input in one branch and the attention map visualizations of the same image from multiple self-attention heads from a pre-trained DINO model (as multiple channels) in the other branch. The results of our experiments on two publicly available medical imaging datasets show that the proposed pipeline outperforms U-Net and the state-of-the-art medical image segmentation models.

Transformers have become one of the dominant architectures in deep learning, particularly as a powerful alternative to convolutional neural networks (CNNs) in computer vision. However, Transformer training and inference in previous works can be prohibitively expensive due to the quadratic complexity of self-attention over a long sequence of representations, especially for high-resolution dense prediction tasks. To this end, we present a novel Less attention vIsion Transformer (LIT), building upon the fact that the early self-attention layers in Transformers still focus on local patterns and bring minor benefits in recent hierarchical vision Transformers. Specifically, we propose a hierarchical Transformer where we use pure multi-layer perceptrons (MLPs) to encode rich local patterns in the early stages while applying self-attention modules to capture longer dependencies in deeper layers. Moreover, we further propose a learned deformable token merging module to adaptively fuse informative patches in a non-uniform manner. The proposed LIT achieves promising performance on image recognition tasks, including image classification, object detection and instance segmentation, serving as a strong backbone for many vision tasks. Code is available at: https://github.com/zhuang-group/LIT

Transformers have demonstrated effectiveness in in-context solving data-fitting problems from various (latent) models, as reported by Garg et al. However, the absence of an inherent iterative structure in the transformer architecture presents a challenge in emulating the iterative algorithms, which are commonly employed in traditional machine learning methods. To address this, we propose the utilization of looped transformer architecture and its associated training methodology, with the aim of incorporating iterative characteristics into the transformer architectures. Experimental results suggest that the looped transformer achieves performance comparable to the standard transformer in solving various data-fitting problems, while utilizing less than 10\% of the parameter count.

Transformers are central to recent successes in natural language processing and computer vision. Transformers have a mostly uniform backbone where layers alternate between feed-forward and self-attention in order to build a deep network. Here we investigate this design choice and find that more complex blocks that have different permutations of layer primitives can be more efficient. Using this insight, we develop a complex block, named Brainformer, that consists of a diverse sets of layers such as sparsely gated feed-forward layers, dense feed-forward layers, attention layers, and various forms of layer normalization and activation functions. Brainformer consistently outperforms the state-of-the-art dense and sparse Transformers, in terms of both quality and efficiency. A Brainformer model with 8 billion activated parameters per token demonstrates 2x faster training convergence and 5x faster step time compared to its GLaM counterpart. In downstream task evaluation, Brainformer also demonstrates a 3% higher SuperGLUE score with fine-tuning compared to GLaM with a similar number of activated parameters. Finally, Brainformer largely outperforms a Primer dense model derived with NAS with similar computation per token on fewshot evaluations.

Humans can easily understand a single image as depicting multiple potential objects permitting interaction. We use this skill to plan our interactions with the world and accelerate understanding new objects without engaging in interaction. In this paper, we would like to endow machines with the similar ability, so that intelligent agents can better explore the 3D scene or manipulate objects. Our approach is a transformer-based model that predicts the 3D location, physical properties and affordance of objects. To power this model, we collect a dataset with Internet videos, egocentric videos and indoor images to train and validate our approach. Our model yields strong performance on our data, and generalizes well to robotics data.

Transformer architecture has widespread applications, particularly in Natural Language Processing and computer vision. Recently Transformers have been employed in various aspects of time-series analysis. This tutorial provides an overview of the Transformer architecture, its applications, and a collection of examples from recent research papers in time-series analysis. We delve into an explanation of the core components of the Transformer, including the self-attention mechanism, positional encoding, multi-head, and encoder/decoder. Several enhancements to the initial, Transformer architecture are highlighted to tackle time-series tasks. The tutorial also provides best practices and techniques to overcome the challenge of effectively training Transformers for time-series analysis.

The transformer architecture by Vaswani et al. (2017) is now ubiquitous across application domains, from natural language processing to speech processing and image understanding. We propose DenseFormer, a simple modification to the standard architecture that improves the perplexity of the model without increasing its size -- adding a few thousand parameters for large-scale models in the 100B parameters range. Our approach relies on an additional averaging step after each transformer block, which computes a weighted average of current and past representations -- we refer to this operation as Depth-Weighted-Average (DWA). The learned DWA weights exhibit coherent patterns of information flow, revealing the strong and structured reuse of activations from distant layers. Experiments demonstrate that DenseFormer is more data efficient, reaching the same perplexity of much deeper transformer models, and that for the same perplexity, these new models outperform transformer baselines in terms of memory efficiency and inference time.

The integration of syntactic structures into Transformer machine translation has shown positive results, but to our knowledge, no work has attempted to do so with semantic structures. In this work we propose two novel parameter-free methods for injecting semantic information into Transformers, both rely on semantics-aware masking of (some of) the attention heads. One such method operates on the encoder, through a Scene-Aware Self-Attention (SASA) head. Another on the decoder, through a Scene-Aware Cross-Attention (SACrA) head. We show a consistent improvement over the vanilla Transformer and syntax-aware models for four language pairs. We further show an additional gain when using both semantic and syntactic structures in some language pairs.

Large models based on the Transformer architecture play increasingly vital roles in artificial intelligence, particularly within the realms of natural language processing (NLP) and computer vision (CV). Model compression methods reduce their memory and computational cost, which is a necessary step to implement the transformer models on practical devices. Given the unique architecture of transformer, featuring alternative attention and Feedforward Neural Network (FFN) modules, specific compression techniques are required. The efficiency of these compression methods is also paramount, as it is usually impractical to retrain large models on the entire training dataset.This survey provides a comprehensive review of recent compression methods, with a specific focus on their application to transformer models. The compression methods are primarily categorized into pruning, quantization, knowledge distillation, and efficient architecture design. In each category, we discuss compression methods for both CV and NLP tasks, highlighting common underlying principles. At last, we delve into the relation between various compression methods, and discuss the further directions in this domain.

Transformer networks have lead to important progress in language modeling and machine translation. These models include two consecutive modules, a feed-forward layer and a self-attention layer. The latter allows the network to capture long term dependencies and are often regarded as the key ingredient in the success of Transformers. Building upon this intuition, we propose a new model that solely consists of attention layers. More precisely, we augment the self-attention layers with persistent memory vectors that play a similar role as the feed-forward layer. Thanks to these vectors, we can remove the feed-forward layer without degrading the performance of a transformer. Our evaluation shows the benefits brought by our model on standard character and word level language modeling benchmarks.

Foundation models, now powering most of the exciting applications in deep learning, are almost universally based on the Transformer architecture and its core attention module. Many subquadratic-time architectures such as linear attention, gated convolution and recurrent models, and structured state space models (SSMs) have been developed to address Transformers' computational inefficiency on long sequences, but they have not performed as well as attention on important modalities such as language. We identify that a key weakness of such models is their inability to perform content-based reasoning, and make several improvements. First, simply letting the SSM parameters be functions of the input addresses their weakness with discrete modalities, allowing the model to selectively propagate or forget information along the sequence length dimension depending on the current token. Second, even though this change prevents the use of efficient convolutions, we design a hardware-aware parallel algorithm in recurrent mode. We integrate these selective SSMs into a simplified end-to-end neural network architecture without attention or even MLP blocks (Mamba). Mamba enjoys fast inference (5times higher throughput than Transformers) and linear scaling in sequence length, and its performance improves on real data up to million-length sequences. As a general sequence model backbone, Mamba achieves state-of-the-art performance across several modalities such as language, audio, and genomics. On language modeling, our Mamba-3B model outperforms Transformers of the same size and matches Transformers twice its size, both in pretraining and downstream evaluation.

The Transformer architecture processes sequences by implementing a form of neural message-passing that consists of iterative information retrieval (attention), followed by local processing (position-wise MLP). Two types of information are essential under this general computational paradigm: "sensory" information about individual objects, and "relational" information describing the relationships between objects. Standard attention naturally encodes the former, but does not explicitly encode the latter. In this paper, we present an extension of Transformers where multi-head attention is augmented with two distinct types of attention heads, each routing information of a different type. The first type is the standard attention mechanism of Transformers, which captures object-level features, while the second type is a novel attention mechanism we propose to explicitly capture relational information. The two types of attention heads each possess different inductive biases, giving the resulting architecture greater efficiency and versatility. The promise of this approach is demonstrated empirically across a range of tasks.

Besides natural language processing, transformers exhibit extraordinary performance in solving broader applications, including scientific computing and computer vision. Previous works try to explain this from the expressive power and capability perspectives that standard transformers are capable of performing some algorithms. To empower transformers with algorithmic capabilities and motivated by the recently proposed looped transformer (Yang et al., 2024; Giannou et al., 2023), we design a novel transformer block, dubbed Algorithm Transformer (abbreviated as AlgoFormer). Compared with the standard transformer and vanilla looped transformer, the proposed AlgoFormer can achieve significantly higher expressiveness in algorithm representation when using the same number of parameters. In particular, inspired by the structure of human-designed learning algorithms, our transformer block consists of a pre-transformer that is responsible for task pre-processing, a looped transformer for iterative optimization algorithms, and a post-transformer for producing the desired results after post-processing. We provide theoretical evidence of the expressive power of the AlgoFormer in solving some challenging problems, mirroring human-designed algorithms. Furthermore, some theoretical and empirical results are presented to show that the designed transformer has the potential to be smarter than human-designed algorithms. Experimental results demonstrate the empirical superiority of the proposed transformer in that it outperforms the standard transformer and vanilla looped transformer in some challenging tasks.

For humans, language production and comprehension is sensitive to the hierarchical structure of sentences. In natural language processing, past work has questioned how effectively neural sequence models like transformers capture this hierarchical structure when generalizing to structurally novel inputs. We show that transformer language models can learn to generalize hierarchically after training for extremely long periods -- far beyond the point when in-domain accuracy has saturated. We call this phenomenon structural grokking. On multiple datasets, structural grokking exhibits inverted U-shaped scaling in model depth: intermediate-depth models generalize better than both very deep and very shallow transformers. When analyzing the relationship between model-internal properties and grokking, we find that optimal depth for grokking can be identified using the tree-structuredness metric of murty2023projections. Overall, our work provides strong evidence that, with extended training, vanilla transformers discover and use hierarchical structure.

We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections between the words in a sequence. Such architecture does not leverage the graph connectivity inductive bias, and can perform poorly when the graph topology is important and has not been encoded into the node features. We introduce a graph transformer with four new properties compared to the standard model. First, the attention mechanism is a function of the neighborhood connectivity for each node in the graph. Second, the positional encoding is represented by the Laplacian eigenvectors, which naturally generalize the sinusoidal positional encodings often used in NLP. Third, the layer normalization is replaced by a batch normalization layer, which provides faster training and better generalization performance. Finally, the architecture is extended to edge feature representation, which can be critical to tasks s.a. chemistry (bond type) or link prediction (entity relationship in knowledge graphs). Numerical experiments on a graph benchmark demonstrate the performance of the proposed graph transformer architecture. This work closes the gap between the original transformer, which was designed for the limited case of line graphs, and graph neural networks, that can work with arbitrary graphs. As our architecture is simple and generic, we believe it can be used as a black box for future applications that wish to consider transformer and graphs.

Recent years have seen a phenomenal rise in performance and applications of transformer neural networks. The family of transformer networks, including Bidirectional Encoder Representations from Transformer (BERT), Generative Pretrained Transformer (GPT) and Vision Transformer (ViT), have shown their effectiveness across Natural Language Processing (NLP) and Computer Vision (CV) domains. Transformer-based networks such as ChatGPT have impacted the lives of common men. However, the quest for high predictive performance has led to an exponential increase in transformers' memory and compute footprint. Researchers have proposed techniques to optimize transformer inference at all levels of abstraction. This paper presents a comprehensive survey of techniques for optimizing the inference phase of transformer networks. We survey techniques such as knowledge distillation, pruning, quantization, neural architecture search and lightweight network design at the algorithmic level. We further review hardware-level optimization techniques and the design of novel hardware accelerators for transformers. We summarize the quantitative results on the number of parameters/FLOPs and accuracy of several models/techniques to showcase the tradeoff exercised by them. We also outline future directions in this rapidly evolving field of research. We believe that this survey will educate both novice and seasoned researchers and also spark a plethora of research efforts in this field.

The Transformer architecture has two main non-embedding components: Attention and the Feed Forward Network (FFN). Attention captures interdependencies between words regardless of their position, while the FFN non-linearly transforms each input token independently. In this work we explore the role of the FFN, and find that despite taking up a significant fraction of the model's parameters, it is highly redundant. Concretely, we are able to substantially reduce the number of parameters with only a modest drop in accuracy by removing the FFN on the decoder layers and sharing a single FFN across the encoder. Finally we scale this architecture back to its original size by increasing the hidden dimension of the shared FFN, achieving substantial gains in both accuracy and latency with respect to the original Transformer Big.

What is the computational model behind a Transformer? Where recurrent neural networks have direct parallels in finite state machines, allowing clear discussion and thought around architecture variants or trained models, Transformers have no such familiar parallel. In this paper we aim to change that, proposing a computational model for the transformer-encoder in the form of a programming language. We map the basic components of a transformer-encoder -- attention and feed-forward computation -- into simple primitives, around which we form a programming language: the Restricted Access Sequence Processing Language (RASP). We show how RASP can be used to program solutions to tasks that could conceivably be learned by a Transformer, and how a Transformer can be trained to mimic a RASP solution. In particular, we provide RASP programs for histograms, sorting, and Dyck-languages. We further use our model to relate their difficulty in terms of the number of required layers and attention heads: analyzing a RASP program implies a maximum number of heads and layers necessary to encode a task in a transformer. Finally, we see how insights gained from our abstraction might be used to explain phenomena seen in recent works.

Understanding Transformer-based models has attracted significant attention, as they lie at the heart of recent technological advances across machine learning. While most interpretability methods rely on running models over inputs, recent work has shown that a zero-pass approach, where parameters are interpreted directly without a forward/backward pass is feasible for some Transformer parameters, and for two-layer attention networks. In this work, we present a theoretical analysis where all parameters of a trained Transformer are interpreted by projecting them into the embedding space, that is, the space of vocabulary items they operate on. We derive a simple theoretical framework to support our arguments and provide ample evidence for its validity. First, an empirical analysis showing that parameters of both pretrained and fine-tuned models can be interpreted in embedding space. Second, we present two applications of our framework: (a) aligning the parameters of different models that share a vocabulary, and (b) constructing a classifier without training by ``translating'' the parameters of a fine-tuned classifier to parameters of a different model that was only pretrained. Overall, our findings open the door to interpretation methods that, at least in part, abstract away from model specifics and operate in the embedding space only.

In this work we introduce KERNELIZED TRANSFORMER, a generic, scalable, data driven framework for learning the kernel function in Transformers. Our framework approximates the Transformer kernel as a dot product between spectral feature maps and learns the kernel by learning the spectral distribution. This not only helps in learning a generic kernel end-to-end, but also reduces the time and space complexity of Transformers from quadratic to linear. We show that KERNELIZED TRANSFORMERS achieve performance comparable to existing efficient Transformer architectures, both in terms of accuracy as well as computational efficiency. Our study also demonstrates that the choice of the kernel has a substantial impact on performance, and kernel learning variants are competitive alternatives to fixed kernel Transformers, both in long as well as short sequence tasks.

Transformers generalize to novel compositions of structures and entities after being trained on a complex dataset, but easily overfit on datasets of insufficient complexity. We observe that when the training set is sufficiently complex, the model encodes sentences that have a common syntactic structure using a systematic attention pattern. Inspired by this observation, we propose SQ-Transformer (Structurally Quantized) that explicitly encourages systematicity in the embeddings and attention layers, even with a training set of low complexity. At the embedding level, we introduce Structure-oriented Vector Quantization (SoVQ) to cluster word embeddings into several classes of structurally equivalent entities. At the attention level, we devise the Systematic Attention Layer (SAL) and an alternative, Systematically Regularized Layer (SRL) that operate on the quantized word embeddings so that sentences of the same structure are encoded with invariant or similar attention patterns. Empirically, we show that SQ-Transformer achieves stronger compositional generalization than the vanilla Transformer on multiple low-complexity semantic parsing and machine translation datasets. In our analysis, we show that SoVQ indeed learns a syntactically clustered embedding space and SAL/SRL induces generalizable attention patterns, which lead to improved systematicity.

Transformer layers, which use an alternating pattern of multi-head attention and multi-layer perceptron (MLP) layers, provide an effective tool for a variety of machine learning problems. As the transformer layers use residual connections to avoid the problem of vanishing gradients, they can be viewed as the numerical integration of a differential equation. In this extended abstract, we build upon this connection and propose a modification of the internal architecture of a transformer layer. The proposed model places the multi-head attention sublayer and the MLP sublayer parallel to each other. Our experiments show that this simple modification improves the performance of transformer networks in multiple tasks. Moreover, for the image classification task, we show that using neural ODE solvers with a sophisticated integration scheme further improves performance.

Transformers provide a class of expressive architectures that are extremely effective for sequence modeling. However, the key limitation of transformers is their quadratic memory and time complexity O(L^2) with respect to the sequence length in attention layers, which restricts application in extremely long sequences. Most existing approaches leverage sparsity or low-rank assumptions in the attention matrix to reduce cost, but sacrifice expressiveness. Instead, we propose Combiner, which provides full attention capability in each attention head while maintaining low computation and memory complexity. The key idea is to treat the self-attention mechanism as a conditional expectation over embeddings at each location, and approximate the conditional distribution with a structured factorization. Each location can attend to all other locations, either via direct attention, or through indirect attention to abstractions, which are again conditional expectations of embeddings from corresponding local regions. We show that most sparse attention patterns used in existing sparse transformers are able to inspire the design of such factorization for full attention, resulting in the same sub-quadratic cost (O(Llog(L)) or O(LL)). Combiner is a drop-in replacement for attention layers in existing transformers and can be easily implemented in common frameworks. An experimental evaluation on both autoregressive and bidirectional sequence tasks demonstrates the effectiveness of this approach, yielding state-of-the-art results on several image and text modeling tasks.

Transformer-based architectures achieved breakthrough performance in natural language processing and computer vision, yet they remain inferior to simpler linear baselines in multivariate long-term forecasting. To better understand this phenomenon, we start by studying a toy linear forecasting problem for which we show that transformers are incapable of converging to their true solution despite their high expressive power. We further identify the attention of transformers as being responsible for this low generalization capacity. Building upon this insight, we propose a shallow lightweight transformer model that successfully escapes bad local minima when optimized with sharpness-aware optimization. We empirically demonstrate that this result extends to all commonly used real-world multivariate time series datasets. In particular, SAMformer surpasses current state-of-the-art methods and is on par with the biggest foundation model MOIRAI while having significantly fewer parameters. The code is available at https://github.com/romilbert/samformer.

Transformer-like models for vision tasks have recently proven effective for a wide range of downstream applications such as segmentation and detection. Previous works have shown that segmentation properties emerge in vision transformers (ViTs) trained using self-supervised methods such as DINO, but not in those trained on supervised classification tasks. In this study, we probe whether segmentation emerges in transformer-based models solely as a result of intricate self-supervised learning mechanisms, or if the same emergence can be achieved under much broader conditions through proper design of the model architecture. Through extensive experimental results, we demonstrate that when employing a white-box transformer-like architecture known as CRATE, whose design explicitly models and pursues low-dimensional structures in the data distribution, segmentation properties, at both the whole and parts levels, already emerge with a minimalistic supervised training recipe. Layer-wise finer-grained analysis reveals that the emergent properties strongly corroborate the designed mathematical functions of the white-box network. Our results suggest a path to design white-box foundation models that are simultaneously highly performant and mathematically fully interpretable. Code is at https://github.com/Ma-Lab-Berkeley/CRATE.

Transformer-based methods have exhibited remarkable potential in single image super-resolution (SISR) by effectively extracting long-range dependencies. However, most of the current research in this area has prioritized the design of transformer blocks to capture global information, while overlooking the importance of incorporating high-frequency priors, which we believe could be beneficial. In our study, we conducted a series of experiments and found that transformer structures are more adept at capturing low-frequency information, but have limited capacity in constructing high-frequency representations when compared to their convolutional counterparts. Our proposed solution, the cross-refinement adaptive feature modulation transformer (CRAFT), integrates the strengths of both convolutional and transformer structures. It comprises three key components: the high-frequency enhancement residual block (HFERB) for extracting high-frequency information, the shift rectangle window attention block (SRWAB) for capturing global information, and the hybrid fusion block (HFB) for refining the global representation. Our experiments on multiple datasets demonstrate that CRAFT outperforms state-of-the-art methods by up to 0.29dB while using fewer parameters. The source code will be made available at: https://github.com/AVC2-UESTC/CRAFT-SR.git.

Recent progress in natural language processing has been driven by advances in both model architecture and model pretraining. Transformer architectures have facilitated building higher-capacity models and pretraining has made it possible to effectively utilize this capacity for a wide variety of tasks. Transformers is an open-source library with the goal of opening up these advances to the wider machine learning community. The library consists of carefully engineered state-of-the art Transformer architectures under a unified API. Backing this library is a curated collection of pretrained models made by and available for the community. Transformers is designed to be extensible by researchers, simple for practitioners, and fast and robust in industrial deployments. The library is available at https://github.com/huggingface/transformers.

Transformer-based models consist of interleaved feed-forward blocks - that capture content meaning, and relatively more expensive self-attention blocks - that capture context meaning. In this paper, we explored trade-offs and ordering of the blocks to improve upon the current Transformer architecture and proposed PAR Transformer. It needs 35% lower compute time than Transformer-XL achieved by replacing ~63% of the self-attention blocks with feed-forward blocks, and retains the perplexity on WikiText-103 language modelling benchmark. We further validated our results on text8 and enwiki8 datasets, as well as on the BERT model.

Transformers have greatly advanced the state-of-the-art in Natural Language Processing (NLP) in recent years, but present very large computation and storage requirements. We observe that the design process of Transformers (pre-train a foundation model on a large dataset in a self-supervised manner, and subsequently fine-tune it for different downstream tasks) leads to task-specific models that are highly over-parameterized, adversely impacting both accuracy and inference efficiency. We propose AxFormer, a systematic framework that applies accuracy-driven approximations to create optimized transformer models for a given downstream task. AxFormer combines two key optimizations -- accuracy-driven pruning and selective hard attention. Accuracy-driven pruning identifies and removes parts of the fine-tuned transformer that hinder performance on the given downstream task. Sparse hard-attention optimizes attention blocks in selected layers by eliminating irrelevant word aggregations, thereby helping the model focus only on the relevant parts of the input. In effect, AxFormer leads to models that are more accurate, while also being faster and smaller. Our experiments on GLUE and SQUAD tasks show that AxFormer models are up to 4.5% more accurate, while also being up to 2.5X faster and up to 3.2X smaller than conventional fine-tuned models. In addition, we demonstrate that AxFormer can be combined with previous efforts such as distillation or quantization to achieve further efficiency gains.

With Artificial Intelligence (AI) increasingly permeating various aspects of society, including healthcare, the adoption of the Transformers neural network architecture is rapidly changing many applications. Transformer is a type of deep learning architecture initially developed to solve general-purpose Natural Language Processing (NLP) tasks and has subsequently been adapted in many fields, including healthcare. In this survey paper, we provide an overview of how this architecture has been adopted to analyze various forms of data, including medical imaging, structured and unstructured Electronic Health Records (EHR), social media, physiological signals, and biomolecular sequences. Those models could help in clinical diagnosis, report generation, data reconstruction, and drug/protein synthesis. We identified relevant studies using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We also discuss the benefits and limitations of using transformers in healthcare and examine issues such as computational cost, model interpretability, fairness, alignment with human values, ethical implications, and environmental impact.

Transformers have become the predominant architecture in foundation models due to their excellent performance across various domains. However, the substantial cost of scaling these models remains a significant concern. This problem arises primarily from their dependence on a fixed number of parameters within linear projections. When architectural modifications (e.g., channel dimensions) are introduced, the entire model typically requires retraining from scratch. As model sizes continue growing, this strategy results in increasingly high computational costs and becomes unsustainable. To overcome this problem, we introduce TokenFormer, a natively scalable architecture that leverages the attention mechanism not only for computations among input tokens but also for interactions between tokens and model parameters, thereby enhancing architectural flexibility. By treating model parameters as tokens, we replace all the linear projections in Transformers with our token-parameter attention layer, where input tokens act as queries and model parameters as keys and values. This reformulation allows for progressive and efficient scaling without necessitating retraining from scratch. Our model scales from 124M to 1.4B parameters by incrementally adding new key-value parameter pairs, achieving performance comparable to Transformers trained from scratch while greatly reducing training costs. Code and models are available at https://github.com/Haiyang-W/TokenFormer.

Vision Transformer (ViT) extends the application range of transformers from language processing to computer vision tasks as being an alternative architecture against the existing convolutional neural networks (CNN). Since the transformer-based architecture has been innovative for computer vision modeling, the design convention towards an effective architecture has been less studied yet. From the successful design principles of CNN, we investigate the role of spatial dimension conversion and its effectiveness on transformer-based architecture. We particularly attend to the dimension reduction principle of CNNs; as the depth increases, a conventional CNN increases channel dimension and decreases spatial dimensions. We empirically show that such a spatial dimension reduction is beneficial to a transformer architecture as well, and propose a novel Pooling-based Vision Transformer (PiT) upon the original ViT model. We show that PiT achieves the improved model capability and generalization performance against ViT. Throughout the extensive experiments, we further show PiT outperforms the baseline on several tasks such as image classification, object detection, and robustness evaluation. Source codes and ImageNet models are available at https://github.com/naver-ai/pit

Transformer architectures rely on explicit position encodings in order to preserve a notion of word order. In this paper, we argue that existing work does not fully utilize position information. For example, the initial proposal of a sinusoid embedding is fixed and not learnable. In this paper, we first review absolute position embeddings and existing methods for relative position embeddings. We then propose new techniques that encourage increased interaction between query, key and relative position embeddings in the self-attention mechanism. Our most promising approach is a generalization of the absolute position embedding, improving results on SQuAD1.1 compared to previous position embeddings approaches. In addition, we address the inductive property of whether a position embedding can be robust enough to handle long sequences. We demonstrate empirically that our relative position embedding method is reasonably generalized and robust from the inductive perspective. Finally, we show that our proposed method can be adopted as a near drop-in replacement for improving the accuracy of large models with a small computational budget.

A simple design recipe for deep Transformers is to compose identical building blocks. But standard transformer blocks are far from simple, interweaving attention and MLP sub-blocks with skip connections & normalisation layers in precise arrangements. This complexity leads to brittle architectures, where seemingly minor changes can significantly reduce training speed, or render models untrainable. In this work, we ask to what extent the standard transformer block can be simplified? Combining signal propagation theory and empirical observations, we motivate modifications that allow many block components to be removed with no loss of training speed, including skip connections, projection or value parameters, sequential sub-blocks and normalisation layers. In experiments on both autoregressive decoder-only and BERT encoder-only models, our simplified transformers emulate the per-update training speed and performance of standard transformers, while enjoying 15% faster training throughput, and using 15% fewer parameters.

An emerging solution for explaining Transformer-based models is to use vector-based analysis on how the representations are formed. However, providing a faithful vector-based explanation for a multi-layer model could be challenging in three aspects: (1) Incorporating all components into the analysis, (2) Aggregating the layer dynamics to determine the information flow and mixture throughout the entire model, and (3) Identifying the connection between the vector-based analysis and the model's predictions. In this paper, we present DecompX to tackle these challenges. DecompX is based on the construction of decomposed token representations and their successive propagation throughout the model without mixing them in between layers. Additionally, our proposal provides multiple advantages over existing solutions for its inclusion of all encoder components (especially nonlinear feed-forward networks) and the classification head. The former allows acquiring precise vectors while the latter transforms the decomposition into meaningful prediction-based values, eliminating the need for norm- or summation-based vector aggregation. According to the standard faithfulness evaluations, DecompX consistently outperforms existing gradient-based and vector-based approaches on various datasets. Our code is available at https://github.com/mohsenfayyaz/DecompX.

The Transformer is an extremely powerful and prominent deep learning architecture. In this work, we challenge the commonly held belief in deep learning that going deeper is better, and show an alternative design approach that is building wider attention Transformers. We demonstrate that wide single layer Transformer models can compete with or outperform deeper ones in a variety of Natural Language Processing (NLP) tasks when both are trained from scratch. The impact of changing the model aspect ratio on Transformers is then studied systematically. This ratio balances the number of layers and the number of attention heads per layer while keeping the total number of attention heads and all other hyperparameters constant. On average, across 4 NLP tasks and 10 attention types, single layer wide models perform 0.3% better than their deep counterparts. We show an in-depth evaluation and demonstrate how wide models require a far smaller memory footprint and can run faster on commodity hardware, in addition, these wider models are also more interpretable. For example, a single layer Transformer on the IMDb byte level text classification has 3.1x faster inference latency on a CPU than its equally accurate deeper counterpart, and is half the size. We therefore put forward wider and shallower models as a viable and desirable alternative for small models on NLP tasks, and as an important area of research for domains beyond this.

Transformers, which are popular for language modeling, have been explored for solving vision tasks recently, e.g., the Vision Transformer (ViT) for image classification. The ViT model splits each image into a sequence of tokens with fixed length and then applies multiple Transformer layers to model their global relation for classification. However, ViT achieves inferior performance to CNNs when trained from scratch on a midsize dataset like ImageNet. We find it is because: 1) the simple tokenization of input images fails to model the important local structure such as edges and lines among neighboring pixels, leading to low training sample efficiency; 2) the redundant attention backbone design of ViT leads to limited feature richness for fixed computation budgets and limited training samples. To overcome such limitations, we propose a new Tokens-To-Token Vision Transformer (T2T-ViT), which incorporates 1) a layer-wise Tokens-to-Token (T2T) transformation to progressively structurize the image to tokens by recursively aggregating neighboring Tokens into one Token (Tokens-to-Token), such that local structure represented by surrounding tokens can be modeled and tokens length can be reduced; 2) an efficient backbone with a deep-narrow structure for vision transformer motivated by CNN architecture design after empirical study. Notably, T2T-ViT reduces the parameter count and MACs of vanilla ViT by half, while achieving more than 3.0\% improvement when trained from scratch on ImageNet. It also outperforms ResNets and achieves comparable performance with MobileNets by directly training on ImageNet. For example, T2T-ViT with comparable size to ResNet50 (21.5M parameters) can achieve 83.3\% top1 accuracy in image resolution 384times384 on ImageNet. (Code: https://github.com/yitu-opensource/T2T-ViT)

This document aims to be a self-contained, mathematically precise overview of transformer architectures and algorithms (*not* results). It covers what transformers are, how they are trained, what they are used for, their key architectural components, and a preview of the most prominent models. The reader is assumed to be familiar with basic ML terminology and simpler neural network architectures such as MLPs.

We present FIT: a transformer-based architecture with efficient self-attention and adaptive computation. Unlike original transformers, which operate on a single sequence of data tokens, we divide the data tokens into groups, with each group being a shorter sequence of tokens. We employ two types of transformer layers: local layers operate on data tokens within each group, while global layers operate on a smaller set of introduced latent tokens. These layers, comprising the same set of self-attention and feed-forward layers as standard transformers, are interleaved, and cross-attention is used to facilitate information exchange between data and latent tokens within the same group. The attention complexity is O(n^2) locally within each group of size n, but can reach O(L^{{4}/{3}}) globally for sequence length of L. The efficiency can be further enhanced by relying more on global layers that perform adaptive computation using a smaller set of latent tokens. FIT is a versatile architecture and can function as an encoder, diffusion decoder, or autoregressive decoder. We provide initial evidence demonstrating its effectiveness in high-resolution image understanding and generation tasks. Notably, FIT exhibits potential in performing end-to-end training on gigabit-scale data, such as 6400times6400 images, or 160K tokens (after patch tokenization), within a memory capacity of 16GB, without requiring specific optimizations or model parallelism.

A big convergence of model architectures across language, vision, speech, and multimodal is emerging. However, under the same name "Transformers", the above areas use different implementations for better performance, e.g., Post-LayerNorm for BERT, and Pre-LayerNorm for GPT and vision Transformers. We call for the development of Foundation Transformer for true general-purpose modeling, which serves as a go-to architecture for various tasks and modalities with guaranteed training stability. In this work, we introduce a Transformer variant, named Magneto, to fulfill the goal. Specifically, we propose Sub-LayerNorm for good expressivity, and the initialization strategy theoretically derived from DeepNet for stable scaling up. Extensive experiments demonstrate its superior performance and better stability than the de facto Transformer variants designed for various applications, including language modeling (i.e., BERT, and GPT), machine translation, vision pretraining (i.e., BEiT), speech recognition, and multimodal pretraining (i.e., BEiT-3).

The Transformer architecture is widely used in natural language processing. Despite its success, the design principle of the Transformer remains elusive. In this paper, we provide a novel perspective towards understanding the architecture: we show that the Transformer can be mathematically interpreted as a numerical Ordinary Differential Equation (ODE) solver for a convection-diffusion equation in a multi-particle dynamic system. In particular, how words in a sentence are abstracted into contexts by passing through the layers of the Transformer can be interpreted as approximating multiple particles' movement in the space using the Lie-Trotter splitting scheme and the Euler's method. Given this ODE's perspective, the rich literature of numerical analysis can be brought to guide us in designing effective structures beyond the Transformer. As an example, we propose to replace the Lie-Trotter splitting scheme by the Strang-Marchuk splitting scheme, a scheme that is more commonly used and with much lower local truncation errors. The Strang-Marchuk splitting scheme suggests that the self-attention and position-wise feed-forward network (FFN) sub-layers should not be treated equally. Instead, in each layer, two position-wise FFN sub-layers should be used, and the self-attention sub-layer is placed in between. This leads to a brand new architecture. Such an FFN-attention-FFN layer is "Macaron-like", and thus we call the network with this new architecture the Macaron Net. Through extensive experiments, we show that the Macaron Net is superior to the Transformer on both supervised and unsupervised learning tasks. The reproducible codes and pretrained models can be found at https://github.com/zhuohan123/macaron-net

While the Transformer architecture has become the de-facto standard for natural language processing tasks, its applications to computer vision remain limited. In vision, attention is either applied in conjunction with convolutional networks, or used to replace certain components of convolutional networks while keeping their overall structure in place. We show that this reliance on CNNs is not necessary and a pure transformer applied directly to sequences of image patches can perform very well on image classification tasks. When pre-trained on large amounts of data and transferred to multiple mid-sized or small image recognition benchmarks (ImageNet, CIFAR-100, VTAB, etc.), Vision Transformer (ViT) attains excellent results compared to state-of-the-art convolutional networks while requiring substantially fewer computational resources to train.

Transformer is a transformative framework that models sequential data and has achieved remarkable performance on a wide range of tasks, but with high computational and energy cost. To improve its efficiency, a popular choice is to compress the models via binarization which constrains the floating-point values into binary ones to save resource consumption owing to cheap bitwise operations significantly. However, existing binarization methods only aim at minimizing the information loss for the input distribution statistically, while ignoring the pairwise similarity modeling at the core of the attention. To this end, we propose a new binarization paradigm customized to high-dimensional softmax attention via kernelized hashing, called EcoFormer, to map the original queries and keys into low-dimensional binary codes in Hamming space. The kernelized hash functions are learned to match the ground-truth similarity relations extracted from the attention map in a self-supervised way. Based on the equivalence between the inner product of binary codes and the Hamming distance as well as the associative property of matrix multiplication, we can approximate the attention in linear complexity by expressing it as a dot-product of binary codes. Moreover, the compact binary representations of queries and keys enable us to replace most of the expensive multiply-accumulate operations in attention with simple accumulations to save considerable on-chip energy footprint on edge devices. Extensive experiments on both vision and language tasks show that EcoFormer consistently achieves comparable performance with standard attentions while consuming much fewer resources. For example, based on PVTv2-B0 and ImageNet-1K, Ecoformer achieves a 73% on-chip energy footprint reduction with only a 0.33% performance drop compared to the standard attention. Code is available at https://github.com/ziplab/EcoFormer.

Transformers have achieved superior performances in many tasks in natural language processing and computer vision, which also triggered great interest in the time series community. Among multiple advantages of Transformers, the ability to capture long-range dependencies and interactions is especially attractive for time series modeling, leading to exciting progress in various time series applications. In this paper, we systematically review Transformer schemes for time series modeling by highlighting their strengths as well as limitations. In particular, we examine the development of time series Transformers in two perspectives. From the perspective of network structure, we summarize the adaptations and modifications that have been made to Transformers in order to accommodate the challenges in time series analysis. From the perspective of applications, we categorize time series Transformers based on common tasks including forecasting, anomaly detection, and classification. Empirically, we perform robust analysis, model size analysis, and seasonal-trend decomposition analysis to study how Transformers perform in time series. Finally, we discuss and suggest future directions to provide useful research guidance. To the best of our knowledge, this paper is the first work to comprehensively and systematically summarize the recent advances of Transformers for modeling time series data. We hope this survey will ignite further research interests in time series Transformers.

Hierarchical structures are popular in recent vision transformers, however, they require sophisticated designs and massive datasets to work well. In this paper, we explore the idea of nesting basic local transformers on non-overlapping image blocks and aggregating them in a hierarchical way. We find that the block aggregation function plays a critical role in enabling cross-block non-local information communication. This observation leads us to design a simplified architecture that requires minor code changes upon the original vision transformer. The benefits of the proposed judiciously-selected design are threefold: (1) NesT converges faster and requires much less training data to achieve good generalization on both ImageNet and small datasets like CIFAR; (2) when extending our key ideas to image generation, NesT leads to a strong decoder that is 8times faster than previous transformer-based generators; and (3) we show that decoupling the feature learning and abstraction processes via this nested hierarchy in our design enables constructing a novel method (named GradCAT) for visually interpreting the learned model. Source code is available https://github.com/google-research/nested-transformer.

Recently, diffusion transformers have gained wide attention with its excellent performance in text-to-image and text-to-vidoe models, emphasizing the need for transformers as backbone for diffusion models. Transformer-based models have shown better generalization capability compared to CNN-based models for general vision tasks. However, much less has been explored in the existing literature regarding the capabilities of transformer-based diffusion backbones and expanding their generative prowess to other datasets. This paper focuses on enabling a single pre-trained diffusion transformer model to scale across multiple datasets swiftly, allowing for the completion of diverse generative tasks using just one model. To this end, we propose DiffScaler, an efficient scaling strategy for diffusion models where we train a minimal amount of parameters to adapt to different tasks. In particular, we learn task-specific transformations at each layer by incorporating the ability to utilize the learned subspaces of the pre-trained model, as well as the ability to learn additional task-specific subspaces, which may be absent in the pre-training dataset. As these parameters are independent, a single diffusion model with these task-specific parameters can be used to perform multiple tasks simultaneously. Moreover, we find that transformer-based diffusion models significantly outperform CNN-based diffusion models methods while performing fine-tuning over smaller datasets. We perform experiments on four unconditional image generation datasets. We show that using our proposed method, a single pre-trained model can scale up to perform these conditional and unconditional tasks, respectively, with minimal parameter tuning while performing as close as fine-tuning an entire diffusion model for that particular task.

Transformer training is notoriously difficult, requiring a careful design of optimizers and use of various heuristics. We make progress towards understanding the subtleties of training Transformers by carefully studying a simple yet canonical linearized shallow Transformer model. Specifically, we train linear Transformers to solve regression tasks, inspired by J.~von Oswald et al.~(ICML 2023), and K.~Ahn et al.~(NeurIPS 2023). Most importantly, we observe that our proposed linearized models can reproduce several prominent aspects of Transformer training dynamics. Consequently, the results obtained in this paper suggest that a simple linearized Transformer model could actually be a valuable, realistic abstraction for understanding Transformer optimization.

Transformer model architectures have garnered immense interest lately due to their effectiveness across a range of domains like language, vision and reinforcement learning. In the field of natural language processing for example, Transformers have become an indispensable staple in the modern deep learning stack. Recently, a dizzying number of "X-former" models have been proposed - Reformer, Linformer, Performer, Longformer, to name a few - which improve upon the original Transformer architecture, many of which make improvements around computational and memory efficiency. With the aim of helping the avid researcher navigate this flurry, this paper characterizes a large and thoughtful selection of recent efficiency-flavored "X-former" models, providing an organized and comprehensive overview of existing work and models across multiple domains.

Transformers use the dense self-attention mechanism which gives a lot of flexibility for long-range connectivity. Over multiple layers of a deep transformer, the number of possible connectivity patterns increases exponentially. However, very few of these contribute to the performance of the network, and even fewer are essential. We hypothesize that there are sparsely connected sub-networks within a transformer, called information pathways which can be trained independently. However, the dynamic (i.e., input-dependent) nature of these pathways makes it difficult to prune dense self-attention during training. But the overall distribution of these pathways is often predictable. We take advantage of this fact to propose Stochastically Subsampled self-Attention (SSA) - a general-purpose training strategy for transformers that can reduce both the memory and computational cost of self-attention by 4 to 8 times during training while also serving as a regularization method - improving generalization over dense training. We show that an ensemble of sub-models can be formed from the subsampled pathways within a network, which can achieve better performance than its densely attended counterpart. We perform experiments on a variety of NLP, computer vision and graph learning tasks in both generative and discriminative settings to provide empirical evidence for our claims and show the effectiveness of the proposed method.

Transformer-based models have gained increasing popularity achieving state-of-the-art performance in many research fields including speech translation. However, Transformer's quadratic complexity with respect to the input sequence length prevents its adoption as is with audio signals, which are typically represented by long sequences. Current solutions resort to an initial sub-optimal compression based on a fixed sampling of raw audio features. Therefore, potentially useful linguistic information is not accessible to higher-level layers in the architecture. To solve this issue, we propose Speechformer, an architecture that, thanks to reduced memory usage in the attention layers, avoids the initial lossy compression and aggregates information only at a higher level according to more informed linguistic criteria. Experiments on three language pairs (en->de/es/nl) show the efficacy of our solution, with gains of up to 0.8 BLEU on the standard MuST-C corpus and of up to 4.0 BLEU in a low resource scenario.

In order to reduce the computational complexity of large language models, great efforts have been made to to improve the efficiency of transformer models such as linear attention and flash-attention. However, the model size and corresponding computational complexity are constantly scaled up in pursuit of higher performance. In this work, we present MemoryFormer, a novel transformer architecture which significantly reduces the computational complexity (FLOPs) from a new perspective. We eliminate nearly all the computations of the transformer model except for the necessary computation required by the multi-head attention operation. This is made possible by utilizing an alternative method for feature transformation to replace the linear projection of fully-connected layers. Specifically, we first construct a group of in-memory lookup tables that store a large amount of discrete vectors to replace the weight matrix used in linear projection. We then use a hash algorithm to retrieve a correlated subset of vectors dynamically based on the input embedding. The retrieved vectors combined together will form the output embedding, which provides an estimation of the result of matrix multiplication operation in a fully-connected layer. Compared to conducting matrix multiplication, retrieving data blocks from memory is a much cheaper operation which requires little computations. We train MemoryFormer from scratch and conduct extensive experiments on various benchmarks to demonstrate the effectiveness of the proposed model.

Transformer-based language models have recently been at the forefront of active research in text generation. However, these models' advances come at the price of prohibitive training costs, with parameter counts in the billions and compute requirements measured in petaflop/s-decades. In this paper, we investigate transformer-based architectures for improving model performance in a low-data regime by selectively replacing attention layers with feed-forward and quasi-recurrent neural network layers. We test these architectures on the standard Enwik8 and Wikitext-103 corpora. Our results show that our reduced architectures outperform existing models with a comparable number of parameters, and obtain comparable performance to larger models while significantly reducing the number of parameters.

Transformer structure, stacked by a sequence of encoder and decoder network layers, achieves significant development in neural machine translation. However, vanilla Transformer mainly exploits the top-layer representation, assuming the lower layers provide trivial or redundant information and thus ignoring the bottom-layer feature that is potentially valuable. In this work, we propose the Group-Transformer model (GTrans) that flexibly divides multi-layer representations of both encoder and decoder into different groups and then fuses these group features to generate target words. To corroborate the effectiveness of the proposed method, extensive experiments and analytic experiments are conducted on three bilingual translation benchmarks and two multilingual translation tasks, including the IWLST-14, IWLST-17, LDC, WMT-14 and OPUS-100 benchmark. Experimental and analytical results demonstrate that our model outperforms its Transformer counterparts by a consistent gain. Furthermore, it can be successfully scaled up to 60 encoder layers and 36 decoder layers.

In this paper, we propose the Hierarchical Document Transformer (HDT), a novel sparse Transformer architecture tailored for structured hierarchical documents. Such documents are extremely important in numerous domains, including science, law or medicine. However, most existing solutions are inefficient and fail to make use of the structure inherent to documents. HDT exploits document structure by introducing auxiliary anchor tokens and redesigning the attention mechanism into a sparse multi-level hierarchy. This approach facilitates information exchange between tokens at different levels while maintaining sparsity, thereby enhancing computational and memory efficiency while exploiting the document structure as an inductive bias. We address the technical challenge of implementing HDT's sample-dependent hierarchical attention pattern by developing a novel sparse attention kernel that considers the hierarchical structure of documents. As demonstrated by our experiments, utilizing structural information present in documents leads to faster convergence, higher sample efficiency and better performance on downstream tasks.

As the rapid progression of practical applications based on Large Language Models continues, the importance of extrapolating performance has grown exponentially in the research domain. In our study, we identified an anomalous behavior in Transformer models that had been previously overlooked, leading to a chaos around closest tokens which carried the most important information. We've coined this discovery the "headache of Transformers". To address this at its core, we introduced a novel self-attention structure named Collinear Constrained Attention (CoCA). This structure can be seamlessly integrated with existing extrapolation, interpolation methods, and other optimization strategies designed for traditional Transformer models. We have achieved excellent extrapolating performance even for 16 times to 24 times of sequence lengths during inference without any fine-tuning on our model. We have also enhanced CoCA's computational and spatial efficiency to ensure its practicality. We plan to open-source CoCA shortly. In the meantime, we've made our code available in the appendix for reappearing experiments.

This work presents an analysis of the effectiveness of using standard shallow feed-forward networks to mimic the behavior of the attention mechanism in the original Transformer model, a state-of-the-art architecture for sequence-to-sequence tasks. We substitute key elements of the attention mechanism in the Transformer with simple feed-forward networks, trained using the original components via knowledge distillation. Our experiments, conducted on the IWSLT2017 dataset, reveal the capacity of these "attentionless Transformers" to rival the performance of the original architecture. Through rigorous ablation studies, and experimenting with various replacement network types and sizes, we offer insights that support the viability of our approach. This not only sheds light on the adaptability of shallow feed-forward networks in emulating attention mechanisms but also underscores their potential to streamline complex architectures for sequence-to-sequence tasks.

Transformers were originally proposed as a sequence-to-sequence model for text but have become vital for a wide range of modalities, including images, audio, video, and undirected graphs. However, transformers for directed graphs are a surprisingly underexplored topic, despite their applicability to ubiquitous domains including source code and logic circuits. In this work, we propose two direction- and structure-aware positional encodings for directed graphs: (1) the eigenvectors of the Magnetic Laplacian - a direction-aware generalization of the combinatorial Laplacian; (2) directional random walk encodings. Empirically, we show that the extra directionality information is useful in various downstream tasks, including correctness testing of sorting networks and source code understanding. Together with a data-flow-centric graph construction, our model outperforms the prior state of the art on the Open Graph Benchmark Code2 relatively by 14.7%.

This paper reveals a novel linear characteristic exclusive to transformer decoders, including models such as GPT, LLaMA, OPT, BLOOM and others. We analyze embedding transformations between sequential layers, uncovering a near-perfect linear relationship (Procrustes similarity score of 0.99). However, linearity decreases when the residual component is removed due to a consistently low output norm of the transformer layer. Our experiments show that removing or linearly approximating some of the most linear blocks of transformers does not affect significantly the loss or model performance. Moreover, in our pretraining experiments on smaller models we introduce a cosine-similarity-based regularization, aimed at reducing layer linearity. This regularization improves performance metrics on benchmarks like Tiny Stories and SuperGLUE and as well successfully decreases the linearity of the models. This study challenges the existing understanding of transformer architectures, suggesting that their operation may be more linear than previously assumed.

Attention layers, as commonly used in transformers, form the backbone of modern deep learning, yet there is no mathematical description of their benefits and deficiencies as compared with other architectures. In this work we establish both positive and negative results on the representation power of attention layers, with a focus on intrinsic complexity parameters such as width, depth, and embedding dimension. On the positive side, we present a sparse averaging task, where recurrent networks and feedforward networks all have complexity scaling polynomially in the input size, whereas transformers scale merely logarithmically in the input size; furthermore, we use the same construction to show the necessity and role of a large embedding dimension in a transformer. On the negative side, we present a triple detection task, where attention layers in turn have complexity scaling linearly in the input size; as this scenario seems rare in practice, we also present natural variants that can be efficiently solved by attention layers. The proof techniques emphasize the value of communication complexity in the analysis of transformers and related models, and the role of sparse averaging as a prototypical attention task, which even finds use in the analysis of triple detection.

Transformer has been considered the dominating neural architecture in NLP and CV, mostly under supervised settings. Recently, a similar surge of using Transformers has appeared in the domain of reinforcement learning (RL), but it is faced with unique design choices and challenges brought by the nature of RL. However, the evolution of Transformers in RL has not yet been well unraveled. In this paper, we seek to systematically review motivations and progress on using Transformers in RL, provide a taxonomy on existing works, discuss each sub-field, and summarize future prospects.

After their initial success in natural language processing, transformer architectures have rapidly gained traction in computer vision, providing state-of-the-art results for tasks such as image classification, detection, segmentation, and video analysis. We offer three insights based on simple and easy to implement variants of vision transformers. (1) The residual layers of vision transformers, which are usually processed sequentially, can to some extent be processed efficiently in parallel without noticeably affecting the accuracy. (2) Fine-tuning the weights of the attention layers is sufficient to adapt vision transformers to a higher resolution and to other classification tasks. This saves compute, reduces the peak memory consumption at fine-tuning time, and allows sharing the majority of weights across tasks. (3) Adding MLP-based patch pre-processing layers improves Bert-like self-supervised training based on patch masking. We evaluate the impact of these design choices using the ImageNet-1k dataset, and confirm our findings on the ImageNet-v2 test set. Transfer performance is measured across six smaller datasets.

Transformers have gained increasing popularity in a wide range of applications, including Natural Language Processing (NLP), Computer Vision and Speech Recognition, because of their powerful representational capacity. However, harnessing this representational capacity effectively requires a large amount of data, strong regularization, or both, to mitigate overfitting. Recently, the power of the Transformer has been unlocked by self-supervised pretraining strategies based on masked autoencoders which rely on reconstructing masked inputs, directly, or contrastively from unmasked content. This pretraining strategy which has been used in BERT models in NLP, Wav2Vec models in Speech and, recently, in MAE models in Vision, forces the model to learn about relationships between the content in different parts of the input using autoencoding related objectives. In this paper, we propose a novel, but surprisingly simple alternative to content reconstruction~-- that of predicting locations from content, without providing positional information for it. Doing so requires the Transformer to understand the positional relationships between different parts of the input, from their content alone. This amounts to an efficient implementation where the pretext task is a classification problem among all possible positions for each input token. We experiment on both Vision and Speech benchmarks, where our approach brings improvements over strong supervised training baselines and is comparable to modern unsupervised/self-supervised pretraining methods. Our method also enables Transformers trained without position embeddings to outperform ones trained with full position information.

Understanding the transformer architecture and its workings is essential for machine learning (ML) engineers. However, truly understanding the transformer architecture can be demanding, even if you have a solid background in machine learning or deep learning. The main working horse is attention, which yields to the transformer encoder-decoder structure. However, putting attention aside leaves several programming components that are easy to implement but whose role for the whole is unclear. These components are 'tokenization', 'embedding' ('un-embedding'), 'masking', 'positional encoding', and 'padding'. The focus of this work is on understanding them. To keep things simple, the understanding is built incrementally by adding components one by one, and after each step investigating what is doable and what is undoable with the current model. Simple sequences of zeros (0) and ones (1) are used to study the workings of each step.

As we show in this paper, the prediction for output token n+1 of Transformer architectures without one of the mechanisms of positional encodings and causal attention is invariant to permutations of input tokens 1, 2, ..., n-1. Usually, both mechanisms are employed and the symmetry with respect to the input tokens is broken. Recently, it has been shown that one can train Transformers without positional encodings. This must be enabled by the causal attention mechanism. In this paper, we elaborate on the argument that the causal connection mechanism must be responsible for the fact that Transformers are able to model input sequences where the order is important. Vertical "slices" of Transformers are all encouraged to represent the same location k in the input sequence. We hypothesize that residual connections contribute to this phenomenon, and demonstrate evidence for this.

State-of-the-art LLMs often rely on scale with high computational costs, which has sparked a research agenda to reduce parameter counts and costs without significantly impacting performance. Our study focuses on Transformer-based LLMs, specifically applying low-rank parametrization to the computationally intensive feedforward networks (FFNs), which are less studied than attention blocks. In contrast to previous works, (i) we explore low-rank parametrization at scale, up to 1.3B parameters; (ii) within Transformer language models rather than convolutional architectures; and (iii) starting from training from scratch. Experiments on the large RefinedWeb dataset show that low-rank parametrization is both efficient (e.g., 2.6times FFN speed-up with 32\% parameters) and effective during training. Interestingly, these structured FFNs exhibit steeper scaling curves than the original models. Motivated by this finding, we develop the wide and structured networks surpassing the current medium-sized and large-sized Transformer in perplexity and throughput performance. Our code is available at https://github.com/CLAIRE-Labo/StructuredFFN/tree/main.

We present a neat yet effective recursive operation on vision transformers that can improve parameter utilization without involving additional parameters. This is achieved by sharing weights across the depth of transformer networks. The proposed method can obtain a substantial gain (~2%) simply using naive recursive operation, requires no special or sophisticated knowledge for designing principles of networks, and introduces minimal computational overhead to the training procedure. To reduce the additional computation caused by recursive operation while maintaining the superior accuracy, we propose an approximating method through multiple sliced group self-attentions across recursive layers which can reduce the cost consumption by 10~30% with minimal performance loss. We call our model Sliced Recursive Transformer (SReT), a novel and parameter-efficient vision transformer design that is compatible with a broad range of other designs for efficient ViT architectures. Our best model establishes significant improvement on ImageNet-1K over state-of-the-art methods while containing fewer parameters. The proposed weight sharing mechanism by sliced recursion structure allows us to build a transformer with more than 100 or even 1000 shared layers with ease while keeping a compact size (13~15M), to avoid optimization difficulties when the model is too large. The flexible scalability has shown great potential for scaling up models and constructing extremely deep vision transformers. Code is available at https://github.com/szq0214/SReT.

This paper introduces the sparse modular addition task and examines how transformers learn it. We focus on transformers with embeddings in R^2 and introduce a visual sandbox that provides comprehensive visualizations of each layer throughout the training process. We reveal a type of circuit, called "clustering heads," which learns the problem's invariants. We analyze the training dynamics of these circuits, highlighting two-stage learning, loss spikes due to high curvature or normalization layers, and the effects of initialization and curriculum learning.

Transformer architecture has shown impressive performance in multiple research domains and has become the backbone of many neural network models. However, there is limited understanding on how it works. In particular, with a simple predictive loss, how the representation emerges from the gradient training dynamics remains a mystery. In this paper, for 1-layer transformer with one self-attention layer plus one decoder layer, we analyze its SGD training dynamics for the task of next token prediction in a mathematically rigorous manner. We open the black box of the dynamic process of how the self-attention layer combines input tokens, and reveal the nature of underlying inductive bias. More specifically, with the assumption (a) no positional encoding, (b) long input sequence, and (c) the decoder layer learns faster than the self-attention layer, we prove that self-attention acts as a discriminative scanning algorithm: starting from uniform attention, it gradually attends more to distinct key tokens for a specific next token to be predicted, and pays less attention to common key tokens that occur across different next tokens. Among distinct tokens, it progressively drops attention weights, following the order of low to high co-occurrence between the key and the query token in the training set. Interestingly, this procedure does not lead to winner-takes-all, but decelerates due to a phase transition that is controllable by the learning rates of the two layers, leaving (almost) fixed token combination. We verify this \emph{scan and snap} dynamics on synthetic and real-world data (WikiText).

Transformers have achieved remarkable success across diverse domains, but their monolithic architecture presents challenges in interpretability, adaptability, and scalability. This paper introduces a novel modular Transformer architecture that explicitly decouples knowledge and reasoning through a generalized cross-attention mechanism to a globally shared knowledge base with layer-specific transformations, specifically designed for effective knowledge retrieval. Critically, we provide a rigorous mathematical derivation demonstrating that the Feed-Forward Network (FFN) in a standard Transformer is a specialized case (a closure) of this generalized cross-attention, revealing its role in implicit knowledge retrieval and validating our design. This theoretical framework provides a new lens for understanding FFNs and lays the foundation for future research exploring enhanced interpretability, adaptability, and scalability, enabling richer interplay with external knowledge bases and other systems.

We present a framework for using transformer networks as universal computers by programming them with specific weights and placing them in a loop. Our input sequence acts as a punchcard, consisting of instructions and memory for data read/writes. We demonstrate that a constant number of encoder layers can emulate basic computing blocks, including embedding edit operations, non-linear functions, function calls, program counters, and conditional branches. Using these building blocks, we emulate a small instruction-set computer. This allows us to map iterative algorithms to programs that can be executed by a looped, 13-layer transformer. We show how this transformer, instructed by its input, can emulate a basic calculator, a basic linear algebra library, and in-context learning algorithms that employ backpropagation. Our work highlights the versatility of the attention mechanism, and demonstrates that even shallow transformers can execute full-fledged, general-purpose programs.

Models need appropriate inductive biases to effectively learn from small amounts of data and generalize systematically outside of the training distribution. While Transformers are highly versatile and powerful, they can still benefit from enhanced structural inductive biases for seq2seq tasks, especially those involving syntactic transformations, such as converting active to passive voice or semantic parsing. In this paper, we propose to strengthen the structural inductive bias of a Transformer by intermediate pre-training to perform synthetically generated syntactic transformations of dependency trees given a description of the transformation. Our experiments confirm that this helps with few-shot learning of syntactic tasks such as chunking, and also improves structural generalization for semantic parsing. Our analysis shows that the intermediate pre-training leads to attention heads that keep track of which syntactic transformation needs to be applied to which token, and that the model can leverage these attention heads on downstream tasks.

Transformer models are revolutionizing machine learning, but their inner workings remain mysterious. In this work, we present a new visualization technique designed to help researchers understand the self-attention mechanism in transformers that allows these models to learn rich, contextual relationships between elements of a sequence. The main idea behind our method is to visualize a joint embedding of the query and key vectors used by transformer models to compute attention. Unlike previous attention visualization techniques, our approach enables the analysis of global patterns across multiple input sequences. We create an interactive visualization tool, AttentionViz, based on these joint query-key embeddings, and use it to study attention mechanisms in both language and vision transformers. We demonstrate the utility of our approach in improving model understanding and offering new insights about query-key interactions through several application scenarios and expert feedback.

Transformer models are foundational to natural language processing (NLP) and computer vision. Despite various recent works devoted to reducing the quadratic cost of such models (as a function of the sequence length n), dealing with ultra long sequences efficiently (e.g., with more than 16K tokens) remains challenging. Applications such as answering questions based on an entire book or summarizing a scientific article are inefficient or infeasible. In this paper, we propose to significantly reduce the dependency of a Transformer model's complexity on n, by compressing the input into a representation whose size r is independent of n at each layer. Specifically, by exploiting the fact that in many tasks, only a small subset of special tokens (we call VIP-tokens) are most relevant to the final prediction, we propose a VIP-token centric compression (Vcc) scheme which selectively compresses the input sequence based on their impact on approximating the representation of these VIP-tokens. Compared with competitive baselines, the proposed algorithm not only is efficient (achieving more than 3times efficiency improvement compared to baselines on 4K and 16K lengths), but also achieves competitive or better performance on a large number of tasks. Further, we show that our algorithm can be scaled to 128K tokens (or more) while consistently offering accuracy improvement.

Incorporating modular designs into neural networks demonstrates superior out-of-generalization, learning efficiency, etc. Existing modular neural networks are generally explicit because their modular architectures are pre-defined, and individual modules are expected to implement distinct functions. Conversely, recent works reveal that there exist implicit modular structures in standard pre-trained transformers, namely Emergent Modularity. They indicate that such modular structures exhibit during the early pre-training phase and are totally spontaneous. However, most transformers are still treated as monolithic models with their modular natures underutilized. Therefore, given the excellent properties of explicit modular architecture, we explore whether and how dense pre-trained transformers can benefit from emergent modular structures. To study this question, we construct Emergent Mixture-of-Experts (EMoE). Without introducing additional parameters, EMoE can be seen as the modular counterpart of the original model and can be effortlessly incorporated into downstream tuning. Extensive experiments (we tune 1785 models) on various downstream tasks (vision and language) and models (22M to1.5B) demonstrate that EMoE effectively boosts in-domain and out-of-domain generalization abilities. Further analysis and ablation study suggest that EMoE mitigates negative knowledge transfer and is robust to various configurations. Code is available at https://github.com/qiuzh20/EMoE

Vision transformers have excelled in various computer vision tasks but mostly rely on rigid input sampling using a fixed-size grid of patches. This limits their applicability in real-world problems, such as in the field of robotics and UAVs, where one can utilize higher input elasticity to boost model performance and efficiency. Our paper addresses this limitation by formalizing the concept of input elasticity for vision transformers and introducing an evaluation protocol, including dedicated metrics for measuring input elasticity. Moreover, we propose modifications to the transformer architecture and training regime, which increase its elasticity. Through extensive experimentation, we spotlight opportunities and challenges associated with input sampling strategies.

Transformers have shown improved performance when compared to previous architectures for sequence processing such as RNNs. Despite their sizeable performance gains, as recently suggested, the model is computationally expensive to train and with a high parameter budget. In light of this, we explore parameter-sharing methods in Transformers with a specific focus on generative models. We perform an analysis of different parameter sharing/reduction methods and develop the Subformer. Our model combines sandwich-style parameter sharing, which overcomes naive cross-layer parameter sharing in generative models, and self-attentive embedding factorization (SAFE). Experiments on machine translation, abstractive summarization and language modeling show that the Subformer can outperform the Transformer even when using significantly fewer parameters.

Fusion is a technique for merging multiple independently-trained neural networks in order to combine their capabilities. Past attempts have been restricted to the case of fully-connected, convolutional, and residual networks. In this paper, we present a systematic approach for fusing two or more transformer-based networks exploiting Optimal Transport to (soft-)align the various architectural components. We flesh out an abstraction for layer alignment, that can generalize to arbitrary architectures -- in principle -- and we apply this to the key ingredients of Transformers such as multi-head self-attention, layer-normalization, and residual connections, and we discuss how to handle them via various ablation studies. Furthermore, our method allows the fusion of models of different sizes (heterogeneous fusion), providing a new and efficient way for compression of Transformers. The proposed approach is evaluated on both image classification tasks via Vision Transformer and natural language modeling tasks using BERT. Our approach consistently outperforms vanilla fusion, and, after a surprisingly short finetuning, also outperforms the individual converged parent models. In our analysis, we uncover intriguing insights about the significant role of soft alignment in the case of Transformers. Our results showcase the potential of fusing multiple Transformers, thus compounding their expertise, in the budding paradigm of model fusion and recombination.

The execution of graph algorithms using neural networks has recently attracted significant interest due to promising empirical progress. This motivates further understanding of how neural networks can replicate reasoning steps with relational data. In this work, we study the ability of transformer networks to simulate algorithms on graphs from a theoretical perspective. The architecture that we utilize is a looped transformer with extra attention heads that interact with the graph. We prove by construction that this architecture can simulate algorithms such as Dijkstra's shortest path algorithm, Breadth- and Depth-First Search, and Kosaraju's strongly connected components algorithm. The width of the network does not increase with the size of the input graph, which implies that the network can simulate the above algorithms for any graph. Despite this property, we show that there is a limit to simulation in our solution due to finite precision. Finally, we show a Turing Completeness result with constant width when the extra attention heads are utilized.

Large transformer models have shown extraordinary success in achieving state-of-the-art results in many natural language processing applications. However, training and deploying these models can be prohibitively costly for long sequences, as the standard self-attention mechanism of the Transformer uses O(n^2) time and space with respect to sequence length. In this paper, we demonstrate that the self-attention mechanism can be approximated by a low-rank matrix. We further exploit this finding to propose a new self-attention mechanism, which reduces the overall self-attention complexity from O(n^2) to O(n) in both time and space. The resulting linear transformer, the Linformer, performs on par with standard Transformer models, while being much more memory- and time-efficient.

The transformer model has gained widespread adoption in computer vision tasks in recent times. However, due to the quadratic time and memory complexity of self-attention, which is proportional to the number of input tokens, most existing Vision Transformers (ViTs) encounter challenges in achieving efficient performance in practical industrial deployment scenarios, such as TensorRT and CoreML, where traditional CNNs excel. Although some recent attempts have been made to design CNN-Transformer hybrid architectures to tackle this problem, their overall performance has not met expectations. To tackle these challenges, we propose an efficient hybrid ViT architecture named FMViT. This approach enhances the model's expressive power by blending high-frequency features and low-frequency features with varying frequencies, enabling it to capture both local and global information effectively. Additionally, we introduce deploy-friendly mechanisms such as Convolutional Multigroup Reparameterization (gMLP), Lightweight Multi-head Self-Attention (RLMHSA), and Convolutional Fusion Block (CFB) to further improve the model's performance and reduce computational overhead. Our experiments demonstrate that FMViT surpasses existing CNNs, ViTs, and CNNTransformer hybrid architectures in terms of latency/accuracy trade-offs for various vision tasks. On the TensorRT platform, FMViT outperforms Resnet101 by 2.5% (83.3% vs. 80.8%) in top-1 accuracy on the ImageNet dataset while maintaining similar inference latency. Moreover, FMViT achieves comparable performance with EfficientNet-B5, but with a 43% improvement in inference speed. On CoreML, FMViT outperforms MobileOne by 2.6% in top-1 accuracy on the ImageNet dataset, with inference latency comparable to MobileOne (78.5% vs. 75.9%). Our code can be found at https://github.com/tany0699/FMViT.

Ever since their conception, Transformers have taken over traditional sequence models in many tasks, such as NLP, image classification, and video/audio processing, for their fast training and superior performance. Much of the merit is attributable to positional encoding and multi-head attention. However, Transformers fall short in learning long-range dependencies mainly due to the quadratic complexity scaled with context length, in terms of both time and space. Consequently, over the past five years, a myriad of methods has been proposed to make Transformers more efficient. In this work, we first take a step back, study and compare existing solutions to long-sequence modeling in terms of their pure mathematical formulation. Specifically, we summarize them using a unified template, given their shared nature of token mixing. Through benchmarks, we then demonstrate that long context length does yield better performance, albeit application-dependent, and traditional Transformer models fall short in taking advantage of long-range dependencies. Next, inspired by emerging sparse models of huge capacity, we propose a machine learning system for handling million-scale dependencies. As a proof of concept, we evaluate the performance of one essential component of this system, namely, the distributed multi-head attention. We show that our algorithm can scale up attention computation by almost 40times using four GeForce RTX 4090 GPUs, compared to vanilla multi-head attention mechanism. We believe this study is an instrumental step towards modeling million-scale dependencies.

Transformers play a central role in the inner workings of large language models. We develop a mathematical framework for analyzing Transformers based on their interpretation as interacting particle systems, which reveals that clusters emerge in long time. Our study explores the underlying theory and offers new perspectives for mathematicians as well as computer scientists.

The recent boom of linear forecasting models questions the ongoing passion for architectural modifications of Transformer-based forecasters. These forecasters leverage Transformers to model the global dependencies over temporal tokens of time series, with each token formed by multiple variates of the same timestamp. However, Transformers are challenged in forecasting series with larger lookback windows due to performance degradation and computation explosion. Besides, the embedding for each temporal token fuses multiple variates that represent potential delayed events and distinct physical measurements, which may fail in learning variate-centric representations and result in meaningless attention maps. In this work, we reflect on the competent duties of Transformer components and repurpose the Transformer architecture without any modification to the basic components. We propose iTransformer that simply applies the attention and feed-forward network on the inverted dimensions. Specifically, the time points of individual series are embedded into variate tokens which are utilized by the attention mechanism to capture multivariate correlations; meanwhile, the feed-forward network is applied for each variate token to learn nonlinear representations. The iTransformer model achieves state-of-the-art on challenging real-world datasets, which further empowers the Transformer family with promoted performance, generalization ability across different variates, and better utilization of arbitrary lookback windows, making it a nice alternative as the fundamental backbone of time series forecasting. Code is available at this repository: https://github.com/thuml/iTransformer.

Plenty of existing work has analyzed the abilities of the transformer architecture by describing its representational capacity with formal models of computation. However, the focus so far has been on analyzing the architecture in terms of language acceptance. We contend that this is an ill-suited problem in the study of language models (LMs), which are definitionally probability distributions over strings. In this paper, we focus on the relationship between transformer LMs and n-gram LMs, a simple and historically relevant class of language models. We show that transformer LMs using the hard or sparse attention mechanisms can exactly represent any n-gram LM, giving us a concrete lower bound on their probabilistic representational capacity. This provides a first step towards understanding the mechanisms that transformer LMs can use to represent probability distributions over strings.

Transformer first appears in the field of natural language processing and is later migrated to the computer vision domain, where it demonstrates excellent performance in vision tasks. However, recently, Retentive Network (RetNet) has emerged as an architecture with the potential to replace Transformer, attracting widespread attention in the NLP community. Therefore, we raise the question of whether transferring RetNet's idea to vision can also bring outstanding performance to vision tasks. To address this, we combine RetNet and Transformer to propose RMT. Inspired by RetNet, RMT introduces explicit decay into the vision backbone, bringing prior knowledge related to spatial distances to the vision model. This distance-related spatial prior allows for explicit control of the range of tokens that each token can attend to. Additionally, to reduce the computational cost of global modeling, we decompose this modeling process along the two coordinate axes of the image. Abundant experiments have demonstrated that our RMT exhibits exceptional performance across various computer vision tasks. For example, RMT achieves 84.1% Top1-acc on ImageNet-1k using merely 4.5G FLOPs. To the best of our knowledge, among all models, RMT achieves the highest Top1-acc when models are of similar size and trained with the same strategy. Moreover, RMT significantly outperforms existing vision backbones in downstream tasks such as object detection, instance segmentation, and semantic segmentation. Our work is still in progress.

Transformers have emerged as the prevailing standard solution for various AI tasks, including computer vision and natural language processing. The widely adopted Query, Key, and Value formulation (QKV) has played a significant role in this. Nevertheless, no research has examined the essentiality of these three components for transformer performance. Therefore, we conducted an evaluation of the key-value formulation (KV), which generates symmetric attention maps, along with an asymmetric version that incorporates a 2D positional encoding into the attention matrix. Remarkably, this transformer requires fewer parameters and computation than the original one. Through experiments encompassing three task types -- synthetics (such as reversing or sorting a list), vision (mnist or cifar classification), and NLP (character generation and translation) -- we discovered that the KV transformer occasionally outperforms the QKV transformer. However, it also exhibits instances of underperformance compared to QKV, making it challenging to draw a definitive conclusion. Nonetheless, we consider the reported results to be encouraging and anticipate that they may pave the way for more efficient transformers in the future.

Recent research in mechanistic interpretability has attempted to reverse-engineer Transformer models by carefully inspecting network weights and activations. However, these approaches require considerable manual effort and still fall short of providing complete, faithful descriptions of the underlying algorithms. In this work, we introduce a procedure for training Transformers that are mechanistically interpretable by design. We build on RASP [Weiss et al., 2021], a programming language that can be compiled into Transformer weights. Instead of compiling human-written programs into Transformers, we design a modified Transformer that can be trained using gradient-based optimization and then automatically converted into a discrete, human-readable program. We refer to these models as Transformer Programs. To validate our approach, we learn Transformer Programs for a variety of problems, including an in-context learning task, a suite of algorithmic problems (e.g. sorting, recognizing Dyck languages), and NLP tasks including named entity recognition and text classification. The Transformer Programs can automatically find reasonable solutions, performing on par with standard Transformers of comparable size; and, more importantly, they are easy to interpret. To demonstrate these advantages, we convert Transformers into Python programs and use off-the-shelf code analysis tools to debug model errors and identify the "circuits" used to solve different sub-problems. We hope that Transformer Programs open a new path toward the goal of intrinsically interpretable machine learning.

Since its inception in "Attention Is All You Need", transformer architecture has led to revolutionary advancements in NLP. The attention layer within the transformer admits a sequence of input tokens X and makes them interact through pairwise similarities computed as softmax(XQK^top X^top), where (K,Q) are the trainable key-query parameters. In this work, we establish a formal equivalence between the optimization geometry of self-attention and a hard-margin SVM problem that separates optimal input tokens from non-optimal tokens using linear constraints on the outer-products of token pairs. This formalism allows us to characterize the implicit bias of 1-layer transformers optimized with gradient descent: (1) Optimizing the attention layer with vanishing regularization, parameterized by (K,Q), converges in direction to an SVM solution minimizing the nuclear norm of the combined parameter W=KQ^top. Instead, directly parameterizing by W minimizes a Frobenius norm objective. We characterize this convergence, highlighting that it can occur toward locally-optimal directions rather than global ones. (2) Complementing this, we prove the local/global directional convergence of gradient descent under suitable geometric conditions. Importantly, we show that over-parameterization catalyzes global convergence by ensuring the feasibility of the SVM problem and by guaranteeing a benign optimization landscape devoid of stationary points. (3) While our theory applies primarily to linear prediction heads, we propose a more general SVM equivalence that predicts the implicit bias with nonlinear heads. Our findings are applicable to arbitrary datasets and their validity is verified via experiments. We also introduce several open problems and research directions. We believe these findings inspire the interpretation of transformers as a hierarchy of SVMs that separates and selects optimal tokens.

Transformer-based end-to-end speech recognition has achieved great success. However, the large footprint and computational overhead make it difficult to deploy these models in some real-world applications. Model compression techniques can reduce the model size and speed up inference, but the compressed model has a fixed architecture which might be suboptimal. We propose a novel Transformer encoder with Input-Dependent Dynamic Depth (I3D) to achieve strong performance-efficiency trade-offs. With a similar number of layers at inference time, I3D-based models outperform the vanilla Transformer and the static pruned model via iterative layer pruning. We also present interesting analysis on the gate probabilities and the input-dependency, which helps us better understand deep encoders.

Transformers rely on both content-based and position-based addressing mechanisms to make predictions, but existing positional encoding techniques often diminish the effectiveness of position-based addressing. Many current methods enforce rigid patterns in attention maps, limiting the ability to model long-range dependencies and adapt to diverse tasks. Additionally, most positional encodings are learned as general biases, lacking the specialization required for different instances within a dataset. To address this, we propose conTextualized equivariAnt Position Embedding (TAPE), a novel framework that enhances positional embeddings by incorporating sequence content across layers. TAPE introduces dynamic, context-aware positional encodings, overcoming the constraints of traditional fixed patterns. By enforcing permutation and orthogonal equivariance, TAPE ensures the stability of positional encodings during updates, improving robustness and adaptability. Our method can be easily integrated into pre-trained transformers, offering parameter-efficient fine-tuning with minimal overhead. Extensive experiments shows that TAPE achieves superior performance in language modeling, arithmetic reasoning, and long-context retrieval tasks compared to existing positional embedding techniques.

Transformers are widely used for solving tasks in natural language processing, computer vision, speech, and music domains. In this paper, we talk about the efficiency of transformers in terms of memory (the number of parameters), computation cost (number of floating points operations), and performance of models, including accuracy, the robustness of the model, and fair \& bias-free features. We mainly discuss the vision transformer for the image classification task. Our contribution is to introduce an efficient 360 framework, which includes various aspects of the vision transformer, to make it more efficient for industrial applications. By considering those applications, we categorize them into multiple dimensions such as privacy, robustness, transparency, fairness, inclusiveness, continual learning, probabilistic models, approximation, computational complexity, and spectral complexity. We compare various vision transformer models based on their performance, the number of parameters, and the number of floating point operations (FLOPs) on multiple datasets.

Transformers have shown great potential in computer vision tasks. A common belief is their attention-based token mixer module contributes most to their competence. However, recent works show the attention-based module in Transformers can be replaced by spatial MLPs and the resulted models still perform quite well. Based on this observation, we hypothesize that the general architecture of the Transformers, instead of the specific token mixer module, is more essential to the model's performance. To verify this, we deliberately replace the attention module in Transformers with an embarrassingly simple spatial pooling operator to conduct only basic token mixing. Surprisingly, we observe that the derived model, termed as PoolFormer, achieves competitive performance on multiple computer vision tasks. For example, on ImageNet-1K, PoolFormer achieves 82.1% top-1 accuracy, surpassing well-tuned Vision Transformer/MLP-like baselines DeiT-B/ResMLP-B24 by 0.3%/1.1% accuracy with 35%/52% fewer parameters and 50%/62% fewer MACs. The effectiveness of PoolFormer verifies our hypothesis and urges us to initiate the concept of "MetaFormer", a general architecture abstracted from Transformers without specifying the token mixer. Based on the extensive experiments, we argue that MetaFormer is the key player in achieving superior results for recent Transformer and MLP-like models on vision tasks. This work calls for more future research dedicated to improving MetaFormer instead of focusing on the token mixer modules. Additionally, our proposed PoolFormer could serve as a starting baseline for future MetaFormer architecture design. Code is available at https://github.com/sail-sg/poolformer.

In contrast to RNNs, which compress previous tokens into a single hidden state, Transformers can attend to all previous tokens directly. However, standard Transformers only use representations from the immediately preceding layer. In this paper, we show that this design choice causes representation collapse and leads to suboptimal performance. To address this issue, we introduce Layer-Integrated Memory (LIMe), a simple yet powerful approach that preserves the model's overall memory footprint while expanding its representational capacity by allowing access to hidden states from earlier layers. Through extensive experiments across various architectures and different lookup mechanisms, we demonstrate consistent performance improvements on a wide range of tasks. Moreover, our analysis of the learned representation dynamics and our exploration of depthwise circuits reveal how LIMe integrates information across layers, pointing to promising directions for future research.