Daily Papers

Merging Large Language Models (LLMs) is a cost-effective technique for combining multiple expert LLMs into a single versatile model, retaining the expertise of the original ones. However, current approaches often overlook the importance of safety alignment during merging, leading to highly misaligned models. This work investigates the effects of model merging on alignment. We evaluate several popular model merging techniques, demonstrating that existing methods do not only transfer domain expertise but also propagate misalignment. We propose a simple two-step approach to address this problem: (i) generating synthetic safety and domain-specific data, and (ii) incorporating these generated data into the optimization process of existing data-aware model merging techniques. This allows us to treat alignment as a skill that can be maximized in the resulting merged LLM. Our experiments illustrate the effectiveness of integrating alignment-related data during merging, resulting in models that excel in both domain expertise and alignment.

Contrastive Language-Image Pre-training (CLIP) excels in multimodal tasks such as image-text retrieval and zero-shot classification but struggles with fine-grained understanding due to its focus on coarse-grained short captions. To address this, we propose Fine-Grained CLIP (FG-CLIP), which enhances fine-grained understanding through three key innovations. First, we leverage large multimodal models to generate 1.6 billion long caption-image pairs for capturing global-level semantic details. Second, a high-quality dataset is constructed with 12 million images and 40 million region-specific bounding boxes aligned with detailed captions to ensure precise, context-rich representations. Third, 10 million hard fine-grained negative samples are incorporated to improve the model's ability to distinguish subtle semantic differences. Corresponding training methods are meticulously designed for these data. Extensive experiments demonstrate that FG-CLIP outperforms the original CLIP and other state-of-the-art methods across various downstream tasks, including fine-grained understanding, open-vocabulary object detection, image-text retrieval, and general multimodal benchmarks. These results highlight FG-CLIP's effectiveness in capturing fine-grained image details and improving overall model performance. The related data, code, and models are available at https://github.com/360CVGroup/FG-CLIP.

Large Reasoning Models (LRMs) like DeepSeek-R1 and OpenAI-o1 have demonstrated remarkable reasoning capabilities, raising important questions about their biases in LLM-as-a-judge settings. We present a comprehensive benchmark comparing judging biases between LLMs and LRMs across both subjective preference-alignment datasets and objective fact-based datasets. Through investigation of bandwagon, authority, position, and distraction biases, we uncover four key findings: (1) despite their advanced reasoning capabilities, LRMs remain susceptible to the above biases; (2) LRMs demonstrate better robustness than LLMs specifically on fact-related datasets; (3) LRMs exhibit notable position bias, preferring options in later positions; and (4) we identify a novel "superficial reflection bias" where phrases mimicking reasoning (e.g., "wait, let me think...") significantly influence model judgments. To address these biases, we design and evaluate three mitigation strategies: specialized system prompts that reduce judging biases by up to 19\% in preference alignment datasets and 14\% in fact-related datasets, in-context learning that provides up to 27\% improvement on preference tasks but shows inconsistent results on factual tasks, and a self-reflection mechanism that reduces biases by up to 10\% in preference datasets and 16\% in fact-related datasets, with self-reflection proving particularly effective for LRMs. Our work provides crucial insights for developing more reliable LLM-as-a-Judge frameworks, especially as LRMs become increasingly deployed as automated judges.

Reward models (RMs) guide the alignment of large language models (LLMs), steering them toward behaviors preferred by humans. Evaluating RMs is the key to better aligning LLMs. However, the current evaluation of RMs may not directly correspond to their alignment performance due to the limited distribution of evaluation data and evaluation methods that are not closely related to alignment objectives. To address these limitations, we propose RMB, a comprehensive RM benchmark that covers over 49 real-world scenarios and includes both pairwise and Best-of-N (BoN) evaluations to better reflect the effectiveness of RMs in guiding alignment optimization. We demonstrate a positive correlation between our benchmark and the downstream alignment task performance. Based on our benchmark, we conduct extensive analysis on the state-of-the-art RMs, revealing their generalization defects that were not discovered by previous benchmarks, and highlighting the potential of generative RMs. Furthermore, we delve into open questions in reward models, specifically examining the effectiveness of majority voting for the evaluation of reward models and analyzing the impact factors of generative RMs, including the influence of evaluation criteria and instructing methods. Our evaluation code and datasets are available at https://github.com/Zhou-Zoey/RMB-Reward-Model-Benchmark.

One of the central tasks in software maintenance is being able to understand and develop code changes. Thus, given a natural language description of the desired new operation of a function, an agent (human or AI) might be asked to generate the set of edits to that function to implement the desired new operation; likewise, given a set of edits to a function, an agent might be asked to generate a changed description, of that function's new workings. Thus, there is an incentive to train a neural model for change-related tasks. Motivated by this, we offer a new, "natural", large dataset of coupled changes to code and documentation mined from actual high-quality GitHub projects, where each sample represents a single commit where the code and the associated docstring were changed together. We present the methodology for gathering the dataset, and some sample, challenging (but realistic) tasks where our dataset provides opportunities for both learning and evaluation. We find that current models (specifically Llama-3.1 405B, Mixtral 8times22B) do find these maintenance-related tasks challenging.

AI alignment refers to models acting towards human-intended goals, preferences, or ethical principles. Given that most large-scale deep learning models act as black boxes and cannot be manually controlled, analyzing the similarity between models and humans can be a proxy measure for ensuring AI safety. In this paper, we focus on the models' visual perception alignment with humans, further referred to as AI-human visual alignment. Specifically, we propose a new dataset for measuring AI-human visual alignment in terms of image classification, a fundamental task in machine perception. In order to evaluate AI-human visual alignment, a dataset should encompass samples with various scenarios that may arise in the real world and have gold human perception labels. Our dataset consists of three groups of samples, namely Must-Act (i.e., Must-Classify), Must-Abstain, and Uncertain, based on the quantity and clarity of visual information in an image and further divided into eight categories. All samples have a gold human perception label; even Uncertain (severely blurry) sample labels were obtained via crowd-sourcing. The validity of our dataset is verified by sampling theory, statistical theories related to survey design, and experts in the related fields. Using our dataset, we analyze the visual alignment and reliability of five popular visual perception models and seven abstention methods. Our code and data is available at https://github.com/jiyounglee-0523/VisAlign.

As Large Language Models (LLMs) and generative AI become increasingly widespread, concerns about content safety have grown in parallel. Currently, there is a clear lack of high-quality, human-annotated datasets that address the full spectrum of LLM-related safety risks and are usable for commercial applications. To bridge this gap, we propose a comprehensive and adaptable taxonomy for categorizing safety risks, structured into 12 top-level hazard categories with an extension to 9 fine-grained subcategories. This taxonomy is designed to meet the diverse requirements of downstream users, offering more granular and flexible tools for managing various risk types. Using a hybrid data generation pipeline that combines human annotations with a multi-LLM "jury" system to assess the safety of responses, we obtain Aegis 2.0, a carefully curated collection of 34,248 samples of human-LLM interactions, annotated according to our proposed taxonomy. To validate its effectiveness, we demonstrate that several lightweight models, trained using parameter-efficient techniques on Aegis 2.0, achieve performance competitive with leading safety models fully fine-tuned on much larger, non-commercial datasets. In addition, we introduce a novel training blend that combines safety with topic following data.This approach enhances the adaptability of guard models, enabling them to generalize to new risk categories defined during inference. We plan to open-source Aegis 2.0 data and models to the research community to aid in the safety guardrailing of LLMs.

With the release of ever more capable large language models (LLMs), researchers in NLP and related disciplines have started to explore the usability of LLMs for a wide variety of different annotation tasks. Very recently, a lot of this attention has shifted to tasks that are subjective in nature. Given that the latest generations of LLMs have digested and encoded extensive knowledge about different human subpopulations and individuals, the hope is that these models can be trained, tuned or prompted to align with a wide range of different human perspectives. While researchers already evaluate the success of this alignment via surveys and tests, there is a lack of resources to evaluate the alignment on what oftentimes matters the most in NLP; the actual downstream tasks. To fill this gap we present SubData, a Python library that offers researchers working on topics related to subjectivity in annotation tasks a convenient way of collecting, combining and using a range of suitable datasets.

Large Language Models (LLMs) are increasingly leveraged for translation tasks but often fall short when translating inclusive language -- such as texts containing the singular 'they' pronoun or otherwise reflecting fair linguistic protocols. Because these challenges span both computational and societal domains, it is imperative to critically evaluate how well LLMs handle inclusive translation with a well-founded framework. This paper presents FairTranslate, a novel, fully human-annotated dataset designed to evaluate non-binary gender biases in machine translation systems from English to French. FairTranslate includes 2418 English-French sentence pairs related to occupations, annotated with rich metadata such as the stereotypical alignment of the occupation, grammatical gender indicator ambiguity, and the ground-truth gender label (male, female, or inclusive). We evaluate four leading LLMs (Gemma2-2B, Mistral-7B, Llama3.1-8B, Llama3.3-70B) on this dataset under different prompting procedures. Our results reveal substantial biases in gender representation across LLMs, highlighting persistent challenges in achieving equitable outcomes in machine translation. These findings underscore the need for focused strategies and interventions aimed at ensuring fair and inclusive language usage in LLM-based translation systems. We make the FairTranslate dataset publicly available on Hugging Face, and disclose the code for all experiments on GitHub.

Large-scale language models like ChatGPT and GPT-4 have gained attention for their impressive conversational and generative capabilities. However, the creation of supervised paired question-answering data for instruction tuning presents formidable challenges. This endeavor necessitates substantial human effort for data annotation and wrestles with issues concerning data quality, diversity, accuracy, and other related factors. To overcome these obstacles, we introduce an innovative framework named Self-QA, which replaces the traditional practice of human-written instruction seeds with a vast amount of unsupervised knowledge, enabling the model to generate a larger quantity of correct and domain-specific instruction data. The effectiveness of our proposed method is demonstrated through experiments conducted on unsupervised corpora from various domains.

Do machines and humans process language in similar ways? A recent line of research has hinted in the affirmative, demonstrating that human brain signals can be effectively predicted using the internal representations of language models (LMs). This is thought to reflect shared computational principles between LMs and human language processing. However, there are also clear differences in how LMs and humans acquire and use language, even if the final task they are performing is the same. Despite this, there is little work exploring systematic differences between human and machine language processing using brain data. To address this question, we examine the differences between LM representations and the human brain's responses to language, specifically by examining a dataset of Magnetoencephalography (MEG) responses to a written narrative. In doing so we identify three phenomena that, in prior work, LMs have been found to not capture well: emotional understanding, figurative language processing, and physical commonsense. By fine-tuning LMs on datasets related to these phenomena, we observe that fine-tuned LMs show improved alignment with human brain responses across these tasks. Our study implies that the observed divergences between LMs and human brains may stem from LMs' inadequate representation of these specific types of knowledge.

We present a new financial domain large language model, InvestLM, tuned on LLaMA-65B (Touvron et al., 2023), using a carefully curated instruction dataset related to financial investment. Inspired by less-is-more-for-alignment (Zhou et al., 2023), we manually curate a small yet diverse instruction dataset, covering a wide range of financial related topics, from Chartered Financial Analyst (CFA) exam questions to SEC filings to Stackexchange quantitative finance discussions. InvestLM shows strong capabilities in understanding financial text and provides helpful responses to investment related questions. Financial experts, including hedge fund managers and research analysts, rate InvestLM's response as comparable to those of state-of-the-art commercial models (GPT-3.5, GPT-4 and Claude-2). Zero-shot evaluation on a set of financial NLP benchmarks demonstrates strong generalizability. From a research perspective, this work suggests that a high-quality domain specific LLM can be tuned using a small set of carefully curated instructions on a well-trained foundation model, which is consistent with the Superficial Alignment Hypothesis (Zhou et al., 2023). From a practical perspective, this work develops a state-of-the-art financial domain LLM with superior capability in understanding financial texts and providing helpful investment advice, potentially enhancing the work efficiency of financial professionals. We release the model parameters to the research community.

Recently, self-supervised learning has attracted great attention, since it only requires unlabeled data for model training. Contrastive learning is one popular method for self-supervised learning and has achieved promising empirical performance. However, the theoretical understanding of its generalization ability is still limited. To this end, we define a kind of (sigma,delta)-measure to mathematically quantify the data augmentation, and then provide an upper bound of the downstream classification error rate based on the measure. It reveals that the generalization ability of contrastive self-supervised learning is related to three key factors: alignment of positive samples, divergence of class centers, and concentration of augmented data. The first two factors are properties of learned representations, while the third one is determined by pre-defined data augmentation. We further investigate two canonical contrastive losses, InfoNCE and cross-correlation, to show how they provably achieve the first two factors. Moreover, we conduct experiments to study the third factor, and observe a strong correlation between downstream performance and the concentration of augmented data.

Alignment is the most critical step in building large language models (LLMs) that meet human needs. With the rapid development of LLMs gradually surpassing human capabilities, traditional alignment methods based on human-annotation are increasingly unable to meet the scalability demands. Therefore, there is an urgent need to explore new sources of automated alignment signals and technical approaches. In this paper, we systematically review the recently emerging methods of automated alignment, attempting to explore how to achieve effective, scalable, automated alignment once the capabilities of LLMs exceed those of humans. Specifically, we categorize existing automated alignment methods into 4 major categories based on the sources of alignment signals and discuss the current status and potential development of each category. Additionally, we explore the underlying mechanisms that enable automated alignment and discuss the essential factors that make automated alignment technologies feasible and effective from the fundamental role of alignment.

Cross-lingual alignment, the meaningful similarity of representations across languages in multilingual language models, has been an active field of research in recent years. We survey the literature of techniques to improve cross-lingual alignment, providing a taxonomy of methods and summarising insights from throughout the field. We present different understandings of cross-lingual alignment and their limitations. We provide a qualitative summary of results from a large number of surveyed papers. Finally, we discuss how these insights may be applied not only to encoder models, where this topic has been heavily studied, but also to encoder-decoder or even decoder-only models, and argue that an effective trade-off between language-neutral and language-specific information is key.

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

String similarity models are vital for record linkage, entity resolution, and search. In this work, we present STANCE --a learned model for computing the similarity of two strings. Our approach encodes the characters of each string, aligns the encodings using Sinkhorn Iteration (alignment is posed as an instance of optimal transport) and scores the alignment with a convolutional neural network. We evaluate STANCE's ability to detect whether two strings can refer to the same entity--a task we term alias detection. We construct five new alias detection datasets (and make them publicly available). We show that STANCE or one of its variants outperforms both state-of-the-art and classic, parameter-free similarity models on four of the five datasets. We also demonstrate STANCE's ability to improve downstream tasks by applying it to an instance of cross-document coreference and show that it leads to a 2.8 point improvement in B^3 F1 over the previous state-of-the-art approach.

Word alignments are useful for tasks like statistical and neural machine translation (NMT) and cross-lingual annotation projection. Statistical word aligners perform well, as do methods that extract alignments jointly with translations in NMT. However, most approaches require parallel training data, and quality decreases as less training data is available. We propose word alignment methods that require no parallel data. The key idea is to leverage multilingual word embeddings, both static and contextualized, for word alignment. Our multilingual embeddings are created from monolingual data only without relying on any parallel data or dictionaries. We find that alignments created from embeddings are superior for four and comparable for two language pairs compared to those produced by traditional statistical aligners, even with abundant parallel data; e.g., contextualized embeddings achieve a word alignment F1 for English-German that is 5 percentage points higher than eflomal, a high-quality statistical aligner, trained on 100k parallel sentences.

Monolingual word alignment is crucial to model semantic interactions between sentences. In particular, null alignment, a phenomenon in which words have no corresponding counterparts, is pervasive and critical in handling semantically divergent sentences. Identification of null alignment is useful on its own to reason about the semantic similarity of sentences by indicating there exists information inequality. To achieve unbalanced word alignment that values both alignment and null alignment, this study shows that the family of optimal transport (OT), i.e., balanced, partial, and unbalanced OT, are natural and powerful approaches even without tailor-made techniques. Our extensive experiments covering unsupervised and supervised settings indicate that our generic OT-based alignment methods are competitive against the state-of-the-arts specially designed for word alignment, remarkably on challenging datasets with high null alignment frequencies.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

Instruction tuning is a standard technique employed to align large language models to end tasks and user preferences after the initial pretraining phase. Recent research indicates the critical role of data engineering in instruction tuning -- when appropriately selected, only limited data is necessary to achieve superior performance. However, we still lack a principled understanding of what makes good instruction tuning data for alignment, and how we should select data automatically and effectively. In this work, we delve deeply into automatic data selection strategies for alignment. We start with controlled studies to measure data across three dimensions: complexity, quality, and diversity, along which we examine existing methods and introduce novel techniques for enhanced data measurement. Subsequently, we propose a simple strategy to select data samples based on the measurement. We present deita (short for Data-Efficient Instruction Tuning for Alignment), a series of models fine-tuned from LLaMA and Mistral models using data samples automatically selected with our proposed approach. Empirically, deita performs better or on par with the state-of-the-art open-source alignment models with only 6K SFT training data samples -- over 10x less than the data used in the baselines. When further trained with direct preference optimization (DPO), deita-Mistral-7B + DPO trained with 6K SFT and 10K DPO samples achieve 7.55 MT-Bench and 90.06% AlpacaEval scores. We anticipate this work to provide tools on automatic data selection, facilitating data-efficient alignment. We release our models as well as the selected datasets for future researches to effectively align models more efficiently.

We test similarity-based word alignment models (SimAlign and awesome-align) in combination with word embeddings from mBERT and XLM-R on parallel sentences in German and Romansh. Since Romansh is an unseen language, we are dealing with a zero-shot setting. Using embeddings from mBERT, both models reach an alignment error rate of 0.22, which outperforms fast_align, a statistical model, and is on par with similarity-based word alignment for seen languages. We interpret these results as evidence that mBERT contains information that can be meaningful and applicable to Romansh. To evaluate performance, we also present a new trilingual corpus, which we call the DERMIT (DE-RM-IT) corpus, containing press releases made by the Canton of Grisons in German, Romansh and Italian in the past 25 years. The corpus contains 4 547 parallel documents and approximately 100 000 sentence pairs in each language combination. We additionally present a gold standard for German-Romansh word alignment. The data is available at https://github.com/eyldlv/DERMIT-Corpus.

Word alignment over parallel corpora has a wide variety of applications, including learning translation lexicons, cross-lingual transfer of language processing tools, and automatic evaluation or analysis of translation outputs. The great majority of past work on word alignment has worked by performing unsupervised learning on parallel texts. Recently, however, other work has demonstrated that pre-trained contextualized word embeddings derived from multilingually trained language models (LMs) prove an attractive alternative, achieving competitive results on the word alignment task even in the absence of explicit training on parallel data. In this paper, we examine methods to marry the two approaches: leveraging pre-trained LMs but fine-tuning them on parallel text with objectives designed to improve alignment quality, and proposing methods to effectively extract alignments from these fine-tuned models. We perform experiments on five language pairs and demonstrate that our model can consistently outperform previous state-of-the-art models of all varieties. In addition, we demonstrate that we are able to train multilingual word aligners that can obtain robust performance on different language pairs. Our aligner, AWESOME (Aligning Word Embedding Spaces of Multilingual Encoders), with pre-trained models is available at https://github.com/neulab/awesome-align

Real world deployments of word alignment are almost certain to cover both high and low resource languages. However, the state-of-the-art for this task recommends a different model class depending on the availability of gold alignment training data for a particular language pair. We propose BinaryAlign, a novel word alignment technique based on binary sequence labeling that outperforms existing approaches in both scenarios, offering a unifying approach to the task. Additionally, we vary the specific choice of multilingual foundation model, perform stratified error analysis over alignment error type, and explore the performance of BinaryAlign on non-English language pairs. We make our source code publicly available.

We present 20min-XD (20 Minuten cross-lingual document-level), a French-German, document-level comparable corpus of news articles, sourced from the Swiss online news outlet 20 Minuten/20 minutes. Our dataset comprises around 15,000 article pairs spanning 2015 to 2024, automatically aligned based on semantic similarity. We detail the data collection process and alignment methodology. Furthermore, we provide a qualitative and quantitative analysis of the corpus. The resulting dataset exhibits a broad spectrum of cross-lingual similarity, ranging from near-translations to loosely related articles, making it valuable for various NLP applications and broad linguistically motivated studies. We publicly release the dataset in document- and sentence-aligned versions and code for the described experiments.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

The most common tools for word-alignment rely on a large amount of parallel sentences, which are then usually processed according to one of the IBM model algorithms. The training data is, however, the same as for machine translation (MT) systems, especially for neural MT (NMT), which itself is able to produce word-alignments using the trained attention heads. This is convenient because word-alignment is theoretically a viable byproduct of any attention-based NMT, which is also able to provide decoder scores for a translated sentence pair. We summarize different approaches on how word-alignment can be extracted from alignment scores and then explore ways in which scores can be extracted from NMT, focusing on inferring the word-alignment scores based on output sentence and token probabilities. We compare this to the extraction of alignment scores from attention. We conclude with aggregating all of the sources of alignment scores into a simple feed-forward network which achieves the best results when combined alignment extractors are used.

The word alignment task, despite its prominence in the era of statistical machine translation (SMT), is niche and under-explored today. In this two-part tutorial, we argue for the continued relevance for word alignment. The first part provides a historical background to word alignment as a core component of the traditional SMT pipeline. We zero-in on GIZA++, an unsupervised, statistical word aligner with surprising longevity. Jumping forward to the era of neural machine translation (NMT), we show how insights from word alignment inspired the attention mechanism fundamental to present-day NMT. The second part shifts to a survey approach. We cover neural word aligners, showing the slow but steady progress towards surpassing GIZA++ performance. Finally, we cover the present-day applications of word alignment, from cross-lingual annotation projection, to improving translation.

This article introduces contrastive alignment instructions (AlignInstruct) to address two challenges in machine translation (MT) on large language models (LLMs). One is the expansion of supported languages to previously unseen ones. The second relates to the lack of data in low-resource languages. Model fine-tuning through MT instructions (MTInstruct) is a straightforward approach to the first challenge. However, MTInstruct is limited by weak cross-lingual signals inherent in the second challenge. AlignInstruct emphasizes cross-lingual supervision via a cross-lingual discriminator built using statistical word alignments. Our results based on fine-tuning the BLOOMZ models (1b1, 3b, and 7b1) in up to 24 unseen languages showed that: (1) LLMs can effectively translate unseen languages using MTInstruct; (2) AlignInstruct led to consistent improvements in translation quality across 48 translation directions involving English; (3) Discriminator-based instructions outperformed their generative counterparts as cross-lingual instructions; (4) AlignInstruct improved performance in 30 zero-shot directions.

Creating an abridged version of a text involves shortening it while maintaining its linguistic qualities. In this paper, we examine this task from an NLP perspective for the first time. We present a new resource, AbLit, which is derived from abridged versions of English literature books. The dataset captures passage-level alignments between the original and abridged texts. We characterize the linguistic relations of these alignments, and create automated models to predict these relations as well as to generate abridgements for new texts. Our findings establish abridgement as a challenging task, motivating future resources and research. The dataset is available at github.com/roemmele/AbLit.

Multi-modal 3D object understanding has gained significant attention, yet current approaches often assume complete data availability and rigid alignment across all modalities. We present CrossOver, a novel framework for cross-modal 3D scene understanding via flexible, scene-level modality alignment. Unlike traditional methods that require aligned modality data for every object instance, CrossOver learns a unified, modality-agnostic embedding space for scenes by aligning modalities - RGB images, point clouds, CAD models, floorplans, and text descriptions - with relaxed constraints and without explicit object semantics. Leveraging dimensionality-specific encoders, a multi-stage training pipeline, and emergent cross-modal behaviors, CrossOver supports robust scene retrieval and object localization, even with missing modalities. Evaluations on ScanNet and 3RScan datasets show its superior performance across diverse metrics, highlighting adaptability for real-world applications in 3D scene understanding.

The Scielo database is an important source of scientific information in Latin America, containing articles from several research domains. A striking characteristic of Scielo is that many of its full-text contents are presented in more than one language, thus being a potential source of parallel corpora. In this article, we present the development of a parallel corpus from Scielo in three languages: English, Portuguese, and Spanish. Sentences were automatically aligned using the Hunalign algorithm for all language pairs, and for a subset of trilingual articles also. We demonstrate the capabilities of our corpus by training a Statistical Machine Translation system (Moses) for each language pair, which outperformed related works on scientific articles. Sentence alignment was also manually evaluated, presenting an average of 98.8% correctly aligned sentences across all languages. Our parallel corpus is freely available in the TMX format, with complementary information regarding article metadata.

Recent studies have shown that post-aligning multilingual pretrained language models (mPLMs) using alignment objectives on both original and transliterated data can improve crosslingual alignment. This improvement further leads to better crosslingual transfer performance. However, it remains unclear how and why a better crosslingual alignment is achieved, as this technique only involves transliterations, and does not use any parallel data. This paper attempts to explicitly evaluate the crosslingual alignment and identify the key elements in transliteration-based approaches that contribute to better performance. For this, we train multiple models under varying setups for two pairs of related languages: (1) Polish and Ukrainian and (2) Hindi and Urdu. To assess alignment, we define four types of similarities based on sentence representations. Our experiments show that adding transliterations alone improves the overall similarities, even for random sentence pairs. With the help of auxiliary alignment objectives, especially the contrastive objective, the model learns to distinguish matched from random pairs, leading to better alignments. However, we also show that better alignment does not always yield better downstream performance, suggesting that further research is needed to clarify the connection between alignment and performance.

Non-autoregressive translation (NAT) models are typically trained with the cross-entropy loss, which forces the model outputs to be aligned verbatim with the target sentence and will highly penalize small shifts in word positions. Latent alignment models relax the explicit alignment by marginalizing out all monotonic latent alignments with the CTC loss. However, they cannot handle non-monotonic alignments, which is non-negligible as there is typically global word reordering in machine translation. In this work, we explore non-monotonic latent alignments for NAT. We extend the alignment space to non-monotonic alignments to allow for the global word reordering and further consider all alignments that overlap with the target sentence. We non-monotonically match the alignments to the target sentence and train the latent alignment model to maximize the F1 score of non-monotonic matching. Extensive experiments on major WMT benchmarks show that our method substantially improves the translation performance of CTC-based models. Our best model achieves 30.06 BLEU on WMT14 En-De with only one-iteration decoding, closing the gap between non-autoregressive and autoregressive models.

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a novel numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including 3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at https://github.com/QizhiPei/BioT5.

For tasks like code synthesis from natural language, code retrieval, and code summarization, data-driven models have shown great promise. However, creating these models require parallel data between natural language (NL) and code with fine-grained alignments. Stack Overflow (SO) is a promising source to create such a data set: the questions are diverse and most of them have corresponding answers with high-quality code snippets. However, existing heuristic methods (e.g., pairing the title of a post with the code in the accepted answer) are limited both in their coverage and the correctness of the NL-code pairs obtained. In this paper, we propose a novel method to mine high-quality aligned data from SO using two sets of features: hand-crafted features considering the structure of the extracted snippets, and correspondence features obtained by training a probabilistic model to capture the correlation between NL and code using neural networks. These features are fed into a classifier that determines the quality of mined NL-code pairs. Experiments using Python and Java as test beds show that the proposed method greatly expands coverage and accuracy over existing mining methods, even when using only a small number of labeled examples. Further, we find that reasonable results are achieved even when training the classifier on one language and testing on another, showing promise for scaling NL-code mining to a wide variety of programming languages beyond those for which we are able to annotate data.

Image captioning is one of the straightforward tasks that can take advantage of large-scale web-crawled data which provides rich knowledge about the visual world for a captioning model. However, since web-crawled data contains image-text pairs that are aligned at different levels, the inherent noises (e.g., misaligned pairs) make it difficult to learn a precise captioning model. While the filtering strategy can effectively remove noisy data, however, it leads to a decrease in learnable knowledge and sometimes brings about a new problem of data deficiency. To take the best of both worlds, we propose a noise-aware learning framework, which learns rich knowledge from the whole web-crawled data while being less affected by the noises. This is achieved by the proposed quality controllable model, which is learned using alignment levels of the image-text pairs as an additional control signal during training. The alignment-conditioned training allows the model to generate high-quality captions of well-aligned by simply setting the control signal to desired alignment level at inference time. Through in-depth analysis, we show that our controllable captioning model is effective in handling noise. In addition, with two tasks of zero-shot captioning and text-to-image retrieval using generated captions (i.e., self-retrieval), we also demonstrate our model can produce high-quality captions in terms of descriptiveness and distinctiveness. Code is available at https://github.com/kakaobrain/noc.

Recent approaches to large language model (LLM) alignment typically require millions of human annotations or rely on external aligned models for synthetic data generation. This paper introduces ALMA: Alignment with Minimal Annotation, demonstrating that effective alignment can be achieved using only 9,000 labeled examples -- less than 1% of conventional approaches. ALMA generates large amounts of high-quality synthetic alignment data through new techniques: diverse prompt synthesis via few-shot learning, diverse response generation with multiple model checkpoints, and judge (reward model) enhancement through score aggregation and self-distillation. Using only a pretrained Llama3 base model, 5,000 SFT examples, and 4,000 judge annotations, ALMA achieves performance close to Llama3-Instruct across diverse alignment benchmarks (e.g., 0.1% difference on AlpacaEval 2.0 score). These results are achieved with a multi-round, self-bootstrapped data synthesis and training recipe that continues to improve for 10 rounds, surpassing the typical 3-round ceiling of previous methods. These results suggest that base models already possess sufficient knowledge for effective alignment, and that synthetic data generation methods can expose it.

The advancement of transformer neural networks has significantly elevated the capabilities of sentence similarity models, particularly in creating effective vector representations of natural language inputs. However, these models face notable challenges in domain-specific contexts, especially in highly specialized scientific sub-fields. Traditional methods often struggle in this regime, either overgeneralizing similarities within a niche or being overly sensitive to minor differences, resulting in inaccurate text classification and subpar vector representation. In an era where retrieval augmentation and search are increasingly crucial, precise and concise numerical representations are essential. In this paper, we target this issue by assembling niche datasets using co-citations as a similarity metric, focusing on biomedical domains. We employ two key strategies for fine-tuning state-of-the-art models: 1. Domain-specific Fine-Tuning, which tailors pretrained models to a single domain, and 2. Universal Applicability with Mixture of Experts (MoE), adapting pretrained models with enforced routing for multiple domains simultaneously. Our training approach emphasizes the use of abstracts for faster training, incorporating Multiple Negative Rankings loss for efficient contrastive learning. Notably, our MoE variants, equipped with N experts, achieve the efficacy of N individual models, heralding a new era of versatile, One-Size-Fits-All transformer networks for various tasks. This methodology marks significant advancements in scientific text classification metrics and holds promise for enhancing vector database search and compilation.

Word alignment, which aims to align translationally equivalent words between source and target sentences, plays an important role in many natural language processing tasks. Current unsupervised neural alignment methods focus on inducing alignments from neural machine translation models, which does not leverage the full context in the target sequence. In this paper, we propose Mask-Align, a self-supervised word alignment model that takes advantage of the full context on the target side. Our model masks out each target token and predicts it conditioned on both source and the remaining target tokens. This two-step process is based on the assumption that the source token contributing most to recovering the masked target token should be aligned. We also introduce an attention variant called leaky attention, which alleviates the problem of unexpected high cross-attention weights on special tokens such as periods. Experiments on four language pairs show that our model outperforms previous unsupervised neural aligners and obtains new state-of-the-art results.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Since their inception, embeddings have become a primary ingredient in many flavours of Natural Language Processing (NLP) tasks supplanting earlier types of representation. Even though multilingual embeddings have been used for the increasing number of multilingual tasks, due to the scarcity of parallel training data, low-resource languages such as Sinhala, tend to focus more on monolingual embeddings. Then when it comes to the aforementioned multi-lingual tasks, it is challenging to utilize these monolingual embeddings given that even if the embedding spaces have a similar geometric arrangement due to an identical training process, the embeddings of the languages considered are not aligned. This is solved by the embedding alignment task. Even in this, high-resource language pairs are in the limelight while low-resource languages such as Sinhala which is in dire need of help seem to have fallen by the wayside. In this paper, we try to align Sinhala and English word embedding spaces based on available alignment techniques and introduce a benchmark for Sinhala language embedding alignment. In addition to that, to facilitate the supervised alignment, as an intermediate task, we also introduce Sinhala-English alignment datasets. These datasets serve as our anchor datasets for supervised word embedding alignment. Even though we do not obtain results comparable to the high-resource languages such as French, German, or Chinese, we believe our work lays the groundwork for more specialized alignment between English and Sinhala embeddings.

Despite their remarkable ability to capture linguistic nuances across diverse languages, questions persist regarding the degree of alignment between languages in multilingual embeddings. Drawing inspiration from research on high-dimensional representations in neural language models, we employ clustering to uncover latent concepts within multilingual models. Our analysis focuses on quantifying the alignment and overlap of these concepts across various languages within the latent space. To this end, we introduce two metrics and aimed at quantifying these aspects, enabling a deeper exploration of multilingual embeddings. Our study encompasses three multilingual models (mT5, mBERT, and XLM-R) and three downstream tasks (Machine Translation, Named Entity Recognition, and Sentiment Analysis). Key findings from our analysis include: i) deeper layers in the network demonstrate increased cross-lingual alignment due to the presence of language-agnostic concepts, ii) fine-tuning of the models enhances alignment within the latent space, and iii) such task-specific calibration helps in explaining the emergence of zero-shot capabilities in the models.The code is available at \url{https://github.com/baselmousi/multilingual-latent-concepts}

We present a new scientific document similarity model based on matching fine-grained aspects of texts. To train our model, we exploit a naturally-occurring source of supervision: sentences in the full-text of papers that cite multiple papers together (co-citations). Such co-citations not only reflect close paper relatedness, but also provide textual descriptions of how the co-cited papers are related. This novel form of textual supervision is used for learning to match aspects across papers. We develop multi-vector representations where vectors correspond to sentence-level aspects of documents, and present two methods for aspect matching: (1) A fast method that only matches single aspects, and (2) a method that makes sparse multiple matches with an Optimal Transport mechanism that computes an Earth Mover's Distance between aspects. Our approach improves performance on document similarity tasks in four datasets. Further, our fast single-match method achieves competitive results, paving the way for applying fine-grained similarity to large scientific corpora. Code, data, and models available at: https://github.com/allenai/aspire

We introduce an architecture to learn joint multilingual sentence representations for 93 languages, belonging to more than 30 different families and written in 28 different scripts. Our system uses a single BiLSTM encoder with a shared BPE vocabulary for all languages, which is coupled with an auxiliary decoder and trained on publicly available parallel corpora. This enables us to learn a classifier on top of the resulting embeddings using English annotated data only, and transfer it to any of the 93 languages without any modification. Our experiments in cross-lingual natural language inference (XNLI dataset), cross-lingual document classification (MLDoc dataset) and parallel corpus mining (BUCC dataset) show the effectiveness of our approach. We also introduce a new test set of aligned sentences in 112 languages, and show that our sentence embeddings obtain strong results in multilingual similarity search even for low-resource languages. Our implementation, the pre-trained encoder and the multilingual test set are available at https://github.com/facebookresearch/LASER

Synthetic data generation has become an increasingly popular way of training models without the need for large, manually labeled datasets. For tasks like text embedding, synthetic data offers diverse and scalable training examples, significantly reducing the cost of human annotation. However, most current approaches rely heavily on proprietary models like GPT-4, which are expensive and inefficient for generating large-scale embedding data. In this paper, we introduce SPEED, a framework that aligns open-source small models (8B) to efficiently generate large-scale synthetic embedding data. Through supervised fine-tuning, preference optimization, and self-improvement, SPEED enables small open-source models to produce high-quality data. Remarkably, SPEED uses only less than 1/10 of the GPT API calls, outperforming the state-of-the-art embedding model E5_mistral when both are trained solely on their synthetic data. Using this efficient generator, we conduct a comprehensive study on how various factors within the alignment pipeline impact data quality and reveal the scaling law for synthetic embedding data.

We consider the problem of translating high-level textual descriptions to formal representations in technical documentation as part of an effort to model the meaning of such documentation. We focus specifically on the problem of learning translational correspondences between text descriptions and grounded representations in the target documentation, such as formal representation of functions or code templates. Our approach exploits the parallel nature of such documentation, or the tight coupling between high-level text and the low-level representations we aim to learn. Data is collected by mining technical documents for such parallel text-representation pairs, which we use to train a simple semantic parsing model. We report new baseline results on sixteen novel datasets, including the standard library documentation for nine popular programming languages across seven natural languages, and a small collection of Unix utility manuals.

Entity alignment is to find identical entities in different knowledge graphs (KGs) that refer to the same real-world object. Embedding-based entity alignment techniques have been drawing a lot of attention recently because they can help solve the issue of symbolic heterogeneity in different KGs. However, in this paper, we show that the progress made in the past was due to biased and unchallenging evaluation. We highlight two major flaws in existing datasets that favor embedding-based entity alignment techniques, i.e., the isomorphic graph structures in relation triples and the weak heterogeneity in attribute triples. Towards a critical evaluation of embedding-based entity alignment methods, we construct a new dataset with heterogeneous relations and attributes based on event-centric KGs. We conduct extensive experiments to evaluate existing popular methods, and find that they fail to achieve promising performance. As a new approach to this difficult problem, we propose a time-aware literal encoder for entity alignment. The dataset and source code are publicly available to foster future research. Our work calls for more effective and practical embedding-based solutions to entity alignment.

We study unsupervised multilingual alignment, the problem of finding word-to-word translations between multiple languages without using any parallel data. One popular strategy is to reduce multilingual alignment to the much simplified bilingual setting, by picking one of the input languages as the pivot language that we transit through. However, it is well-known that transiting through a poorly chosen pivot language (such as English) may severely degrade the translation quality, since the assumed transitive relations among all pairs of languages may not be enforced in the training process. Instead of going through a rather arbitrarily chosen pivot language, we propose to use the Wasserstein barycenter as a more informative "mean" language: it encapsulates information from all languages and minimizes all pairwise transportation costs. We evaluate our method on standard benchmarks and demonstrate state-of-the-art performances.

Mining parallel document pairs poses a significant challenge because existing sentence embedding models often have limited context windows, preventing them from effectively capturing document-level information. Another overlooked issue is the lack of concrete evaluation benchmarks comprising high-quality parallel document pairs for assessing document-level mining approaches, particularly for Indic languages. In this study, we introduce Pralekha, a large-scale benchmark for document-level alignment evaluation. Pralekha includes over 2 million documents, with a 1:2 ratio of unaligned to aligned pairs, covering 11 Indic languages and English. Using Pralekha, we evaluate various document-level mining approaches across three dimensions: the embedding models, the granularity levels, and the alignment algorithm. To address the challenge of aligning documents using sentence and chunk-level alignments, we propose a novel scoring method, Document Alignment Coefficient (DAC). DAC demonstrates substantial improvements over baseline pooling approaches, particularly in noisy scenarios, achieving average gains of 20-30% in precision and 15-20% in F1 score. These results highlight DAC's effectiveness in parallel document mining for Indic languages.

Recently, there has been a significant upsurge of interest in leveraging large language models (LLMs) to assist scientific discovery. However, most LLMs only focus on general science, while they lack domain-specific knowledge, such as chemical molecules and amino acid sequences. To bridge these gaps, we introduce SciDFM, a mixture-of-experts LLM, which is trained from scratch and is able to conduct college-level scientific reasoning and understand molecules and amino acid sequences. We collect a large-scale training corpus containing numerous scientific papers and books from different disciplines as well as data from domain-specific databases. We further fine-tune the pre-trained model on lots of instruction data to improve performances on downstream benchmarks. From experiment results, we show that SciDFM achieves strong performance on general scientific benchmarks such as SciEval and SciQ, and it reaches a SOTA performance on domain-specific benchmarks among models of similar size. We further analyze the expert layers and show that the results of expert selection vary with data from different disciplines. To benefit the broader research community, we open-source SciDFM at https://huggingface.co/OpenDFM/SciDFM-MoE-A5.6B-v1.0.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

The massive growth of image-text data through web crawling inherently presents the challenge of variability in data quality. This paper introduces a novel algorithm, rooted in human knowledge, to compress this vast corpus of web-crawled image-text datasets to a compact and high-quality form. Our method unfolds in three major steps. First, we collect an image-text dataset, wherein each image is associated with multiple captions sourced from diverse origins. Then, to systemically capture human preferences regarding the best caption paired with each image, we establish a comprehensive set of both subjective and objective criteria for critically guiding the alignment assessment from labelers. Lastly, we train a reward model on the annotated dataset to internalize the nuanced human understanding of image-text alignment. The resulting reward model thus can act as a human-like referee to filter misaligned/low-quality image-text pairs. Extensive experiments demonstrate that we are able to secure (or even improve) model performance by compressing the image-text datasets up to ~90%. An impressive example is that, by aggressively reducing the total training sample from 130M to 15.5M (e.g., ~9x smaller), our BLIP-B/16 models still consistently show superior performance compared with the full-size-dataset counterpart on image-text retrieval (Flickr30K, COCO) by ~2.5% in Recall@1, and on image-captioning (Nocaps, COCO) by ~10.0% in CIDEr and ~2.7% in SPICE.

One of the most important problems in machine translation (MT) evaluation is to evaluate the similarity between translation hypotheses with different surface forms from the reference, especially at the segment level. We propose to use word embeddings to perform word alignment for segment-level MT evaluation. We performed experiments with three types of alignment methods using word embeddings. We evaluated our proposed methods with various translation datasets. Experimental results show that our proposed methods outperform previous word embeddings-based methods.

Connectionist Temporal Classification (CTC) is a widely used criterion for training supervised sequence-to-sequence (seq2seq) models. It enables learning the relations between input and output sequences, termed alignments, by marginalizing over perfect alignments (that yield the ground truth), at the expense of imperfect alignments. This binary differentiation of perfect and imperfect alignments falls short of capturing other essential alignment properties that hold significance in other real-world applications. Here we propose Align With Purpose, a general Plug-and-Play framework for enhancing a desired property in models trained with the CTC criterion. We do that by complementing the CTC with an additional loss term that prioritizes alignments according to a desired property. Our method does not require any intervention in the CTC loss function, enables easy optimization of a variety of properties, and allows differentiation between both perfect and imperfect alignments. We apply our framework in the domain of Automatic Speech Recognition (ASR) and show its generality in terms of property selection, architectural choice, and scale of training dataset (up to 280,000 hours). To demonstrate the effectiveness of our framework, we apply it to two unrelated properties: emission time and word error rate (WER). For the former, we report an improvement of up to 570ms in latency optimization with a minor reduction in WER, and for the latter, we report a relative improvement of 4.5% WER over the baseline models. To the best of our knowledge, these applications have never been demonstrated to work on a scale of data as large as ours. Notably, our method can be implemented using only a few lines of code, and can be extended to other alignment-free loss functions and to domains other than ASR.

Large language models (LLMs) usually fall short on information extraction (IE) tasks and struggle to follow the complex instructions of IE tasks. This primarily arises from LLMs not being aligned with humans, as mainstream alignment datasets typically do not include IE data. In this paper, we introduce ADELIE (Aligning large language moDELs on Information Extraction), an aligned LLM that effectively solves various IE tasks, including closed IE, open IE, and on-demand IE. We first collect and construct a high-quality alignment corpus IEInstruct for IE. Then we train ADELIE_SFT using instruction tuning on IEInstruct. We further train ADELIE_SFT with direct preference optimization (DPO) objective, resulting in ADELIE_DPO. Extensive experiments on various held-out IE datasets demonstrate that our models (ADELIE_SFT and ADELIE_DPO) achieve state-of-the-art (SoTA) performance among open-source models. We further explore the general capabilities of ADELIE, and experimental results reveal that their general capabilities do not exhibit a noticeable decline. We will release the code, data, and models to facilitate further research.

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in comprehending protein sequences remains an open question, largely due to the absence of datasets linking protein sequences to descriptive text. Researchers have then attempted to adapt LLMs for protein understanding by integrating a protein sequence encoder with a pre-trained LLM. However, this adaptation raises a fundamental question: "Can LLMs, originally designed for NLP, effectively comprehend protein sequences as a form of language?" Current datasets fall short in addressing this question due to the lack of a direct correlation between protein sequences and corresponding text descriptions, limiting the ability to train and evaluate LLMs for protein understanding effectively. To bridge this gap, we introduce ProteinLMDataset, a dataset specifically designed for further self-supervised pretraining and supervised fine-tuning (SFT) of LLMs to enhance their capability for protein sequence comprehension. Specifically, ProteinLMDataset includes 17.46 billion tokens for pretraining and 893,000 instructions for SFT. Additionally, we present ProteinLMBench, the first benchmark dataset consisting of 944 manually verified multiple-choice questions for assessing the protein understanding capabilities of LLMs. ProteinLMBench incorporates protein-related details and sequences in multiple languages, establishing a new standard for evaluating LLMs' abilities in protein comprehension. The large language model InternLM2-7B, pretrained and fine-tuned on the ProteinLMDataset, outperforms GPT-4 on ProteinLMBench, achieving the highest accuracy score. The dataset and the benchmark are available at https://huggingface.co/datasets/tsynbio/ProteinLMBench.

Vector representations of natural language are ubiquitous in search applications. Recently, various methods based on contrastive learning have been proposed to learn textual representations from unlabelled data; by maximizing alignment between minimally-perturbed embeddings of the same text, and encouraging a uniform distribution of embeddings across a broader corpus. Differently, we propose maximizing alignment between texts and a composition of their phrasal constituents. We consider several realizations of this objective and elaborate the impact on representations in each case. Experimental results on semantic textual similarity tasks show improvements over baselines that are comparable with state-of-the-art approaches. Moreover, this work is the first to do so without incurring costs in auxiliary training objectives or additional network parameters.

The success of a text simplification system heavily depends on the quality and quantity of complex-simple sentence pairs in the training corpus, which are extracted by aligning sentences between parallel articles. To evaluate and improve sentence alignment quality, we create two manually annotated sentence-aligned datasets from two commonly used text simplification corpora, Newsela and Wikipedia. We propose a novel neural CRF alignment model which not only leverages the sequential nature of sentences in parallel documents but also utilizes a neural sentence pair model to capture semantic similarity. Experiments demonstrate that our proposed approach outperforms all the previous work on monolingual sentence alignment task by more than 5 points in F1. We apply our CRF aligner to construct two new text simplification datasets, Newsela-Auto and Wiki-Auto, which are much larger and of better quality compared to the existing datasets. A Transformer-based seq2seq model trained on our datasets establishes a new state-of-the-art for text simplification in both automatic and human evaluation.

Large Language Models (LLMs) have achieved significant advancements, however, the common learning paradigm treats LLMs as passive information repositories, neglecting their potential for active learning and alignment. Some approaches train LLMs using their own generated synthetic data, exploring the possibility of active alignment. However, there is still a huge gap between these one-time alignment methods and the continuous automatic alignment of humans. In this paper, we introduce I-SHEEP, an Iterative Self-EnHancEmEnt Paradigm.This human-like paradigm enables LLMs to continuously self-align from scratch with nothing. Compared to the one-time alignment method Dromedary sun2023principledriven, which refers to the first iteration in this paper, I-SHEEP can significantly enhance capacities on both Qwen and Llama models. I-SHEEP achieves a maximum relative improvement of 78.2\% in the Alpaca Eval, 24.0\% in the MT Bench, and an absolute increase of 8.88\% in the IFEval accuracy over subsequent iterations in Qwen-1.5 72B model. Additionally, I-SHEEP surpasses the base model in various standard benchmark generation tasks, achieving an average improvement of 24.77\% in code generation tasks, 12.04\% in TrivialQA, and 20.29\% in SQuAD. We also provide new insights based on the experiment results. Our codes, datasets, and models are available at https://anonymous.4open.science/r/I-SHEEP.

Phrase representations play an important role in data science and natural language processing, benefiting various tasks like Entity Alignment, Record Linkage, Fuzzy Joins, and Paraphrase Classification. The current state-of-the-art method involves fine-tuning pre-trained language models for phrasal embeddings using contrastive learning. However, we have identified areas for improvement. First, these pre-trained models tend to be unnecessarily complex and require to be pre-trained on a corpus with context sentences. Second, leveraging the phrase type and morphology gives phrase representations that are both more precise and more flexible. We propose an improved framework to learn phrase representations in a context-free fashion. The framework employs phrase type classification as an auxiliary task and incorporates character-level information more effectively into the phrase representation. Furthermore, we design three granularities of data augmentation to increase the diversity of training samples. Our experiments across a wide range of tasks show that our approach generates superior phrase embeddings compared to previous methods while requiring a smaller model size. The code is available at \faGithub~ https://github.com/tigerchen52/PEARL abstract

The availability of parallel texts is crucial to the performance of machine translation models. However, most of the world's languages face the predominant challenge of data scarcity. In this paper, we propose strategies to synthesize parallel data relying on morpho-syntactic information and using bilingual lexicons along with a small amount of seed parallel data. Our methodology adheres to a realistic scenario backed by the small parallel seed data. It is linguistically informed, as it aims to create augmented data that is more likely to be grammatically correct. We analyze how our synthetic data can be combined with raw parallel data and demonstrate a consistent improvement in performance in our experiments on 14 languages (28 English <-> X pairs) ranging from well- to very low-resource ones. Our method leads to improvements even when using only five seed sentences and a bilingual lexicon.

Data selection is crucial for optimizing language model (LM) performance on specific tasks, yet most existing methods fail to effectively consider the target task distribution. Current approaches either ignore task-specific requirements entirely or rely on approximations that fail to capture the nuanced patterns needed for tasks like Autoformalization or code generation. Methods that do consider the target distribution often rely on simplistic, sometimes noisy, representations, like hashed n-gram features, which can lead to collisions and introduce noise. We introduce ZIP-FIT, a data selection framework that uses gzip compression to directly measure alignment between potential training data and the target task distribution. In extensive evaluations on Autoformalization and Python code generation, ZIP-FIT significantly outperforms leading baselines like DSIR and D4. Models trained on ZIP-FIT-selected data achieve their lowest cross-entropy loss up to 85.1\% faster than baselines, demonstrating that better task alignment leads to more efficient learning. In addition, ZIP-FIT performs selection up to 65.8\% faster than DSIR and two orders of magnitude faster than D4. Notably, ZIP-FIT shows that smaller, well-aligned datasets often outperform larger but less targeted ones, demonstrating that a small amount of higher quality data is superior to a large amount of lower quality data. Our results imply that task-aware data selection is crucial for efficient domain adaptation, and that compression offers a principled way to measure task alignment. By showing that targeted data selection can dramatically improve task-specific performance, our work provides new insights into the relationship between data quality, task alignment, and model learning efficiency.

Large language models have already demonstrated their formidable capabilities in general domains, ushering in a revolutionary transformation. However, exploring and exploiting the extensive knowledge of these models to comprehend multi-omics biology remains underexplored. To fill this research gap, we first introduce Biology-Instructions, the first large-scale multi-omics biological sequences-related instruction-tuning dataset including DNA, RNA, proteins, and multi-molecules, designed to bridge the gap between large language models (LLMs) and complex biological sequences-related tasks. This dataset can enhance the versatility of LLMs by integrating diverse biological sequenced-based prediction tasks with advanced reasoning capabilities, while maintaining conversational fluency. Additionally, we reveal significant performance limitations in even state-of-the-art LLMs on biological sequence-related multi-omics tasks without specialized pre-training and instruction-tuning. We further develop a strong baseline called ChatMultiOmics with a novel three-stage training pipeline, demonstrating the powerful ability to understand biology by using Biology-Instructions. Biology-Instructions and ChatMultiOmics are publicly available and crucial resources for enabling more effective integration of LLMs with multi-omics sequence analysis.

Large Language Models (LLMs) trained on extensive textual corpora have emerged as leading solutions for a broad array of Natural Language Processing (NLP) tasks. Despite their notable performance, these models are prone to certain limitations such as misunderstanding human instructions, generating potentially biased content, or factually incorrect (hallucinated) information. Hence, aligning LLMs with human expectations has become an active area of interest within the research community. This survey presents a comprehensive overview of these alignment technologies, including the following aspects. (1) Data collection: the methods for effectively collecting high-quality instructions for LLM alignment, including the use of NLP benchmarks, human annotations, and leveraging strong LLMs. (2) Training methodologies: a detailed review of the prevailing training methods employed for LLM alignment. Our exploration encompasses Supervised Fine-tuning, both Online and Offline human preference training, along with parameter-efficient training mechanisms. (3) Model Evaluation: the methods for evaluating the effectiveness of these human-aligned LLMs, presenting a multifaceted approach towards their assessment. In conclusion, we collate and distill our findings, shedding light on several promising future research avenues in the field. This survey, therefore, serves as a valuable resource for anyone invested in understanding and advancing the alignment of LLMs to better suit human-oriented tasks and expectations. An associated GitHub link collecting the latest papers is available at https://github.com/GaryYufei/AlignLLMHumanSurvey.

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

Causal abstraction is a promising theoretical framework for explainable artificial intelligence that defines when an interpretable high-level causal model is a faithful simplification of a low-level deep learning system. However, existing causal abstraction methods have two major limitations: they require a brute-force search over alignments between the high-level model and the low-level one, and they presuppose that variables in the high-level model will align with disjoint sets of neurons in the low-level one. In this paper, we present distributed alignment search (DAS), which overcomes these limitations. In DAS, we find the alignment between high-level and low-level models using gradient descent rather than conducting a brute-force search, and we allow individual neurons to play multiple distinct roles by analyzing representations in non-standard bases-distributed representations. Our experiments show that DAS can discover internal structure that prior approaches miss. Overall, DAS removes previous obstacles to conducting causal abstraction analyses and allows us to find conceptual structure in trained neural nets.

Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement. Conclusions: SourceData-NLP's scale highlights the value of integrating curation into publishing. Models trained with SourceData-NLP will furthermore enable the development of tools able to extract causal hypotheses from the literature and assemble them into knowledge graphs.

Multiple sequence alignments (MSAs) of proteins encode rich biological information and have been workhorses in bioinformatic methods for tasks like protein design and protein structure prediction for decades. Recent breakthroughs like AlphaFold2 that use transformers to attend directly over large quantities of raw MSAs have reaffirmed their importance. Generation of MSAs is highly computationally intensive, however, and no datasets comparable to those used to train AlphaFold2 have been made available to the research community, hindering progress in machine learning for proteins. To remedy this problem, we introduce OpenProteinSet, an open-source corpus of more than 16 million MSAs, associated structural homologs from the Protein Data Bank, and AlphaFold2 protein structure predictions. We have previously demonstrated the utility of OpenProteinSet by successfully retraining AlphaFold2 on it. We expect OpenProteinSet to be broadly useful as training and validation data for 1) diverse tasks focused on protein structure, function, and design and 2) large-scale multimodal machine learning research.

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in distinguishing sequences from varied species like chimpanzees, dogs, and humans, becoming a staple in contemporary genomic research. However, these approaches often demand extensive computational resources, posing a challenge in terms of scalability and efficiency. Addressing this issue, our study introduces a novel adaptation of Jiang et al.'s compressor-based, parameter-free classification method, specifically tailored for DNA sequence analysis. This innovative approach utilizes a variety of compression algorithms, such as Gzip, Brotli, and LZMA, to efficiently process and classify genomic sequences. Not only does this method align with the current state-of-the-art in terms of accuracy, but it also offers a more resource-efficient alternative to traditional machine learning methods. Our comprehensive evaluation demonstrates the proposed method's effectiveness in accurately classifying DNA sequences from multiple species. We present a detailed analysis of the performance of each algorithm used, highlighting the strengths and limitations of our approach in various genomic contexts. Furthermore, we discuss the broader implications of our findings for bioinformatics, particularly in genomic data processing and analysis. The results of our study pave the way for more efficient and scalable DNA sequence classification methods, offering significant potential for advancements in genomic research and applications.

Speech-to-Speech and Speech-to-Text translation are currently dynamic areas of research. To contribute to these fields, we present SpeechAlign, a framework to evaluate the underexplored field of source-target alignment in speech models. Our framework has two core components. First, to tackle the absence of suitable evaluation datasets, we introduce the Speech Gold Alignment dataset, built upon a English-German text translation gold alignment dataset. Secondly, we introduce two novel metrics, Speech Alignment Error Rate (SAER) and Time-weighted Speech Alignment Error Rate (TW-SAER), to evaluate alignment quality in speech models. By publishing SpeechAlign we provide an accessible evaluation framework for model assessment, and we employ it to benchmark open-source Speech Translation models.

We present a corpus of sentence-aligned triples of German audio, German text, and English translation, based on German audiobooks. The speech translation data consist of 110 hours of audio material aligned to over 50k parallel sentences. An even larger dataset comprising 547 hours of German speech aligned to German text is available for speech recognition. The audio data is read speech and thus low in disfluencies. The quality of audio and sentence alignments has been checked by a manual evaluation, showing that speech alignment quality is in general very high. The sentence alignment quality is comparable to well-used parallel translation data and can be adjusted by cutoffs on the automatic alignment score. To our knowledge, this corpus is to date the largest resource for German speech recognition and for end-to-end German-to-English speech translation.

Despite the remarkable advances in language modeling, current mainstream decoding methods still struggle to generate texts that align with human texts across different aspects. In particular, sampling-based methods produce less-repetitive texts which are often disjunctive in discourse, while search-based methods maintain topic coherence at the cost of increased repetition. Overall, these methods fall short in achieving holistic alignment across a broad range of aspects. In this work, we frame decoding from a language model as an optimization problem with the goal of strictly matching the expected performance with human texts measured by multiple metrics of desired aspects simultaneously. The resulting decoding distribution enjoys an analytical solution that scales the input language model distribution via a sequence-level energy function defined by these metrics. And most importantly, we prove that this induced distribution is guaranteed to improve the perplexity on human texts, which suggests a better approximation to the underlying distribution of human texts. To facilitate tractable sampling from this globally normalized distribution, we adopt the Sampling-Importance-Resampling technique. Experiments on various domains and model scales demonstrate the superiority of our method in metrics alignment with human texts and human evaluation over strong baselines.

Entity resolution is a widely studied problem with several proposals to match records across relations. Matching textual content is a widespread task in many applications, such as question answering and search. While recent methods achieve promising results for these two tasks, there is no clear solution for the more general problem of matching textual content and structured data. We introduce a framework that supports this new task in an unsupervised setting for any pair of corpora, being relational tables or text documents. Our method builds a fine-grained graph over the content of the corpora and derives word embeddings to represent the objects to match in a low dimensional space. The learned representation enables effective and efficient matching at different granularity, from relational tuples to text sentences and paragraphs. Our flexible framework can exploit pre-trained resources, but it does not depends on their existence and achieves better quality performance in matching content when the vocabulary is domain specific. We also introduce optimizations in the graph creation process with an "expand and compress" approach that first identifies new valid relationships across elements, to improve matching, and then prunes nodes and edges, to reduce the graph size. Experiments on real use cases and public datasets show that our framework produces embeddings that outperform word embeddings and fine-tuned language models both in results' quality and in execution times.

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at https://github.com/PharMolix/OpenBioMed.

This paper delves into the continuous post-training optimization methods for small language models, and proposes a continuous post-training alignment data construction method for small language models. The core of this method is based on the data guidance of large models, optimizing the diversity and accuracy of alignment data. In addition, to verify the effectiveness of the methods in this paper, we used Qwen2-0.5B-Instruct model as the baseline model for small language models, using the alignment dataset constructed by our proposed method, we trained and compared several groups of experiments, including SFT (Supervised Fine Tuning) post-training experiment and KTO (Kahneman Tversky optimization) post-training experiment, as well as SFT-KTO two-stage post-training experiment and model weight fusion experiment. Finally, we evaluated and analyzed the performance of post-training models, and confirmed that the continuous post-training optimization method proposed by us can significantly improve the performance of small language models.

The rapid expansion of scientific literature in computer science presents challenges in tracking research trends and extracting key insights. Existing datasets provide metadata but lack structured summaries that capture core contributions and methodologies. We introduce CS-PaperSum, a large-scale dataset of 91,919 papers from 31 top-tier computer science conferences, enriched with AI-generated structured summaries using ChatGPT. To assess summary quality, we conduct embedding alignment analysis and keyword overlap analysis, demonstrating strong preservation of key concepts. We further present a case study on AI research trends, highlighting shifts in methodologies and interdisciplinary crossovers, including the rise of self-supervised learning, retrieval-augmented generation, and multimodal AI. Our dataset enables automated literature analysis, research trend forecasting, and AI-driven scientific discovery, providing a valuable resource for researchers, policymakers, and scientific information retrieval systems.

Recent significant improvements in speech and language technologies come both from self-supervised approaches over raw language data as well as various types of explicit supervision. To ensure high-quality processing of spoken data, the most useful type of explicit supervision is still the alignment between the speech signal and its corresponding text transcript, which is a data type that is not available for many languages. In this paper, we present our approach to building large and open speech-and-text-aligned datasets of less-resourced languages based on transcripts of parliamentary proceedings and their recordings. Our starting point are the ParlaMint comparable corpora of transcripts of parliamentary proceedings of 26 national European parliaments. In the pilot run on expanding the ParlaMint corpora with aligned publicly available recordings, we focus on three Slavic languages, namely Croatian, Polish, and Serbian. The main challenge of our approach is the lack of any global alignment between the ParlaMint texts and the available recordings, as well as the sometimes varying data order in each of the modalities, which requires a novel approach in aligning long sequences of text and audio in a large search space. The results of this pilot run are three high-quality datasets that span more than 5,000 hours of speech and accompanying text transcripts. Although these datasets already make a huge difference in the availability of spoken and textual data for the three languages, we want to emphasize the potential of the presented approach in building similar datasets for many more languages.

Despite the considerable advancements in English LLMs, the progress in building comparable models for other languages has been hindered due to the scarcity of tailored resources. Our work aims to bridge this divide by introducing an expansive suite of resources specifically designed for the development of Indic LLMs, covering 22 languages, containing a total of 251B tokens and 74.8M instruction-response pairs. Recognizing the importance of both data quality and quantity, our approach combines highly curated manually verified data, unverified yet valuable data, and synthetic data. We build a clean, open-source pipeline for curating pre-training data from diverse sources, including websites, PDFs, and videos, incorporating best practices for crawling, cleaning, flagging, and deduplication. For instruction-fine tuning, we amalgamate existing Indic datasets, translate/transliterate English datasets into Indian languages, and utilize LLaMa2 and Mixtral models to create conversations grounded in articles from Indian Wikipedia and Wikihow. Additionally, we address toxicity alignment by generating toxic prompts for multiple scenarios and then generate non-toxic responses by feeding these toxic prompts to an aligned LLaMa2 model. We hope that the datasets, tools, and resources released as a part of this work will not only propel the research and development of Indic LLMs but also establish an open-source blueprint for extending such efforts to other languages. The data and other artifacts created as part of this work are released with permissive licenses.

Static and contextual multilingual embeddings have complementary strengths. Static embeddings, while less expressive than contextual language models, can be more straightforwardly aligned across multiple languages. We combine the strengths of static and contextual models to improve multilingual representations. We extract static embeddings for 40 languages from XLM-R, validate those embeddings with cross-lingual word retrieval, and then align them using VecMap. This results in high-quality, highly multilingual static embeddings. Then we apply a novel continued pre-training approach to XLM-R, leveraging the high quality alignment of our static embeddings to better align the representation space of XLM-R. We show positive results for multiple complex semantic tasks. We release the static embeddings and the continued pre-training code. Unlike most previous work, our continued pre-training approach does not require parallel text.

The absence of explicitly tailored, accessible annotated datasets for educational purposes presents a notable obstacle for NLP tasks in languages with limited resources.This study initially explores the feasibility of using machine translation (MT) to convert an existing dataset into a Tigrinya dataset in SQuAD format. As a result, we present TIGQA, an expert annotated educational dataset consisting of 2.68K question-answer pairs covering 122 diverse topics such as climate, water, and traffic. These pairs are from 537 context paragraphs in publicly accessible Tigrinya and Biology books. Through comprehensive analyses, we demonstrate that the TIGQA dataset requires skills beyond simple word matching, requiring both single-sentence and multiple-sentence inference abilities. We conduct experiments using state-of-the art MRC methods, marking the first exploration of such models on TIGQA. Additionally, we estimate human performance on the dataset and juxtapose it with the results obtained from pretrained models.The notable disparities between human performance and best model performance underscore the potential for further enhancements to TIGQA through continued research. Our dataset is freely accessible via the provided link to encourage the research community to address the challenges in the Tigrinya MRC.

The degree of semantic relatedness of two units of language has long been considered fundamental to understanding meaning. Additionally, automatically determining relatedness has many applications such as question answering and summarization. However, prior NLP work has largely focused on semantic similarity, a subset of relatedness, because of a lack of relatedness datasets. In this paper, we introduce a dataset for Semantic Textual Relatedness, STR-2022, that has 5,500 English sentence pairs manually annotated using a comparative annotation framework, resulting in fine-grained scores. We show that human intuition regarding relatedness of sentence pairs is highly reliable, with a repeat annotation correlation of 0.84. We use the dataset to explore questions on what makes sentences semantically related. We also show the utility of STR-2022 for evaluating automatic methods of sentence representation and for various downstream NLP tasks. Our dataset, data statement, and annotation questionnaire can be found at: https://doi.org/10.5281/zenodo.7599667

Scholars studying organizations often work with multiple datasets lacking shared unique identifiers or covariates. In such situations, researchers may turn to approximate string matching methods to combine datasets. String matching, although useful, faces fundamental challenges. Even when two strings appear similar to humans, fuzzy matching often does not work because it fails to adapt to the informativeness of the character combinations presented. Worse, many entities have multiple names that are dissimilar (e.g., "Fannie Mae" and "Federal National Mortgage Association"), a case where string matching has little hope of succeeding. This paper introduces data from a prominent employment-related networking site (LinkedIn) as a tool to address these problems. We propose interconnected approaches to leveraging the massive amount of information from LinkedIn regarding organizational name-to-name links. The first approach builds a machine learning model for predicting matches from character strings, treating the trillions of user-contributed organizational name pairs as a training corpus: this approach constructs a string matching metric that explicitly maximizes match probabilities. A second approach identifies relationships between organization names using network representations of the LinkedIn data. A third approach combines the first and second. We document substantial improvements over fuzzy matching in applications, making all methods accessible in open-source software ("LinkOrgs").

The crux of learning vision-language models is to extract semantically aligned information from visual and linguistic data. Existing attempts usually face the problem of coarse alignment, e.g., the vision encoder struggles in localizing an attribute-specified object. In this work, we propose an embarrassingly simple approach to better align image and text features with no need of additional data formats other than image-text pairs. Concretely, given an image and its paired text, we manage to parse objects (e.g., cat) and attributes (e.g., black) from the description, which are highly likely to exist in the image. It is noteworthy that the parsing pipeline is fully automatic and thus enjoys good scalability. With these parsed semantics as supervision signals, we can complement the commonly used image-text contrastive loss with the multi-tag classification loss. Extensive experimental results on a broad suite of semantic segmentation datasets substantiate the average 3.65\% improvement of our framework over existing alternatives. Furthermore, the visualization results indicate that attribute supervision makes vision-language models accurately localize attribute-specified objects. Project page and code can be found at https://qinying-liu.github.io/Tag-Align.

Recent research in representation learning utilizes large databases of proteins or molecules to acquire knowledge of drug and protein structures through unsupervised learning techniques. These pre-trained representations have proven to significantly enhance the accuracy of subsequent tasks, such as predicting the affinity between drugs and target proteins. In this study, we demonstrate that by incorporating knowledge graphs from diverse sources and modalities into the sequences or SMILES representation, we can further enrich the representation and achieve state-of-the-art results on established benchmark datasets. We provide preprocessed and integrated data obtained from 7 public sources, which encompass over 30M triples. Additionally, we make available the pre-trained models based on this data, along with the reported outcomes of their performance on three widely-used benchmark datasets for drug-target binding affinity prediction found in the Therapeutic Data Commons (TDC) benchmarks. Additionally, we make the source code for training models on benchmark datasets publicly available. Our objective in releasing these pre-trained models, accompanied by clean data for model pretraining and benchmark results, is to encourage research in knowledge-enhanced representation learning.

Recent breakthroughs in large language modeling have facilitated rigorous exploration of their application in diverse tasks related to tabular data modeling, such as prediction, tabular data synthesis, question answering, and table understanding. Each task presents unique challenges and opportunities. However, there is currently a lack of comprehensive review that summarizes and compares the key techniques, metrics, datasets, models, and optimization approaches in this research domain. This survey aims to address this gap by consolidating recent progress in these areas, offering a thorough survey and taxonomy of the datasets, metrics, and methodologies utilized. It identifies strengths, limitations, unexplored territories, and gaps in the existing literature, while providing some insights for future research directions in this vital and rapidly evolving field. It also provides relevant code and datasets references. Through this comprehensive review, we hope to provide interested readers with pertinent references and insightful perspectives, empowering them with the necessary tools and knowledge to effectively navigate and address the prevailing challenges in the field.

Word2vec is one of the most used algorithms to generate word embeddings because of a good mix of efficiency, quality of the generated representations and cognitive grounding. However, word meaning is not static and depends on the context in which words are used. Differences in word meaning that depends on time, location, topic, and other factors, can be studied by analyzing embeddings generated from different corpora in collections that are representative of these factors. For example, language evolution can be studied using a collection of news articles published in different time periods. In this paper, we present a general framework to support cross-corpora language studies with word embeddings, where embeddings generated from different corpora can be compared to find correspondences and differences in meaning across the corpora. CADE is the core component of our framework and solves the key problem of aligning the embeddings generated from different corpora. In particular, we focus on providing solid evidence about the effectiveness, generality, and robustness of CADE. To this end, we conduct quantitative and qualitative experiments in different domains, from temporal word embeddings to language localization and topical analysis. The results of our experiments suggest that CADE achieves state-of-the-art or superior performance on tasks where several competing approaches are available, yet providing a general method that can be used in a variety of domains. Finally, our experiments shed light on the conditions under which the alignment is reliable, which substantially depends on the degree of cross-corpora vocabulary overlap.

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization. Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates 28 distinct datasets across 7 tasks, with input lengths ranging from 70 to 1000. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with 21 times fewer parameters and approximately 56 times less GPU time in pre-training.

Pretext training followed by task-specific fine-tuning has been a successful approach in vision and language domains. This paper proposes a self-supervised pretext training framework tailored to event sequence data. We introduce a novel alignment verification task that is specialized to event sequences, building on good practices in masked reconstruction and contrastive learning. Our pretext tasks unlock foundational representations that are generalizable across different down-stream tasks, including next-event prediction for temporal point process models, event sequence classification, and missing event interpolation. Experiments on popular public benchmarks demonstrate the potential of the proposed method across different tasks and data domains.

Aligning sentences in a reference summary with their counterparts in source documents was shown as a useful auxiliary summarization task, notably for generating training data for salience detection. Despite its assessed utility, the alignment step was mostly approached with heuristic unsupervised methods, typically ROUGE-based, and was never independently optimized or evaluated. In this paper, we propose establishing summary-source alignment as an explicit task, while introducing two major novelties: (1) applying it at the more accurate proposition span level, and (2) approaching it as a supervised classification task. To that end, we created a novel training dataset for proposition-level alignment, derived automatically from available summarization evaluation data. In addition, we crowdsourced dev and test datasets, enabling model development and proper evaluation. Utilizing these data, we present a supervised proposition alignment baseline model, showing improved alignment-quality over the unsupervised approach.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

Recent studies have demonstrated the cross-lingual alignment ability of multilingual pretrained language models. In this work, we found that the cross-lingual alignment can be further improved by training seq2seq models on sentence pairs mined using their own encoder outputs. We utilized these findings to develop a new approach -- cross-lingual retrieval for iterative self-supervised training (CRISS), where mining and training processes are applied iteratively, improving cross-lingual alignment and translation ability at the same time. Using this method, we achieved state-of-the-art unsupervised machine translation results on 9 language directions with an average improvement of 2.4 BLEU, and on the Tatoeba sentence retrieval task in the XTREME benchmark on 16 languages with an average improvement of 21.5% in absolute accuracy. Furthermore, CRISS also brings an additional 1.8 BLEU improvement on average compared to mBART, when finetuned on supervised machine translation downstream tasks.

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

We introduce ParaNames, a massively multilingual parallel name resource consisting of 140 million names spanning over 400 languages. Names are provided for 16.8 million entities, and each entity is mapped from a complex type hierarchy to a standard type (PER/LOC/ORG). Using Wikidata as a source, we create the largest resource of this type to date. We describe our approach to filtering and standardizing the data to provide the best quality possible. ParaNames is useful for multilingual language processing, both in defining tasks for name translation/transliteration and as supplementary data for tasks such as named entity recognition and linking. We demonstrate the usefulness of ParaNames on two tasks. First, we perform canonical name translation between English and 17 other languages. Second, we use it as a gazetteer for multilingual named entity recognition, obtaining performance improvements on all 10 languages evaluated.

Mathematical symbols and descriptions appear in various forms across document section boundaries without explicit markup. In this paper, we present a new large-scale dataset that emphasizes extracting symbols and descriptions in scientific documents. Symlink annotates scientific papers of 5 different domains (i.e., computer science, biology, physics, mathematics, and economics). Our experiments on Symlink demonstrate the challenges of the symbol-description linking task for existing models and call for further research effort in this area. We will publicly release Symlink to facilitate future research.

Recent works have demonstrated the effectiveness of self-alignment in which a large language model is, by itself, aligned to follow general instructions through the automatic generation of instructional data using a handful of human-written seeds. Instead of general alignment, in this work, we focus on self-alignment for expert domain specialization (e.g., biomedicine), discovering it to be very effective for improving zero-shot and few-shot performance in target domains of interest. As a preliminary, we first present the benchmark results of existing aligned models within a specialized domain, which reveals the marginal effect that "generic" instruction-following training has on downstream expert domains' performance. To remedy this, we explore self-specialization that leverages domain-specific unlabelled data and a few labeled seeds for the self-alignment process. When augmented with retrieval to reduce hallucination and enhance concurrency of the alignment, self-specialization offers an effective (and efficient) way of "carving out" an expert model out of a "generalist", pre-trained LLM where different domains of expertise are originally combined in a form of "superposition". Our experimental results on a biomedical domain show that our self-specialized model (30B) outperforms its base model, MPT-30B by a large margin and even surpasses larger popular models based on LLaMA-65B, highlighting its potential and practicality for specialization, especially considering its efficiency in terms of data and parameters.

Joint representation learning over multi-sourced knowledge graphs (KGs) yields transferable and expressive embeddings that improve downstream tasks. Entity alignment (EA) is a critical step in this process. Despite recent considerable research progress in embedding-based EA, how it works remains to be explored. In this paper, we provide a similarity flooding perspective to explain existing translation-based and aggregation-based EA models. We prove that the embedding learning process of these models actually seeks a fixpoint of pairwise similarities between entities. We also provide experimental evidence to support our theoretical analysis. We propose two simple but effective methods inspired by the fixpoint computation in similarity flooding, and demonstrate their effectiveness on benchmark datasets. Our work bridges the gap between recent embedding-based models and the conventional similarity flooding algorithm. It would improve our understanding of and increase our faith in embedding-based EA.

Large Language Models (LLMs), particularly those similar to ChatGPT, have significantly influenced the field of Natural Language Processing (NLP). While these models excel in general language tasks, their performance in domain-specific downstream tasks such as biomedical and clinical Named Entity Recognition (NER), Relation Extraction (RE), and Medical Natural Language Inference (NLI) is still evolving. In this context, our study investigates the potential of instruction tuning for biomedical language processing, applying this technique to two general LLMs of substantial scale. We present a comprehensive, instruction-based model trained on a dataset that consists of approximately 200,000 instruction-focused samples. This dataset represents a carefully curated compilation of existing data, meticulously adapted and reformatted to align with the specific requirements of our instruction-based tasks. This initiative represents an important step in utilising such models to achieve results on par with specialised encoder-only models like BioBERT and BioClinicalBERT for various classical biomedical NLP tasks. Our work includes an analysis of the dataset's composition and its impact on model performance, providing insights into the intricacies of instruction tuning. By sharing our codes, models, and the distinctively assembled instruction-based dataset, we seek to encourage ongoing research and development in this area.

The advancement of natural language processing (NLP) in biology hinges on models' ability to interpret intricate biomedical literature. Traditional models often struggle with the complex and domain-specific language in this field. In this paper, we present BioMamba, a pre-trained model specifically designed for biomedical text mining. BioMamba builds upon the Mamba architecture and is pre-trained on an extensive corpus of biomedical literature. Our empirical studies demonstrate that BioMamba significantly outperforms models like BioBERT and general-domain Mamba across various biomedical tasks. For instance, BioMamba achieves a 100 times reduction in perplexity and a 4 times reduction in cross-entropy loss on the BioASQ test set. We provide an overview of the model architecture, pre-training process, and fine-tuning techniques. Additionally, we release the code and trained model to facilitate further research.

Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models nucleotide evolution on phylogenetic trees using multispecies whole-genome alignments. Our approach integrates an alignment into the loss function during training but does not require it for making predictions, thereby enhancing the model's applicability. We applied this framework to train PhyloGPN, a model that excels at predicting functionally disruptive variants from a single sequence alone and demonstrates strong transfer learning capabilities.

We present sentence aligned parallel corpora across 10 Indian Languages - Hindi, Telugu, Tamil, Malayalam, Gujarati, Urdu, Bengali, Oriya, Marathi, Punjabi, and English - many of which are categorized as low resource. The corpora are compiled from online sources which have content shared across languages. The corpora presented significantly extends present resources that are either not large enough or are restricted to a specific domain (such as health). We also provide a separate test corpus compiled from an independent online source that can be independently used for validating the performance in 10 Indian languages. Alongside, we report on the methods of constructing such corpora using tools enabled by recent advances in machine translation and cross-lingual retrieval using deep neural network based methods.

Motivation: The gut microbiota has recently emerged as a key factor that underpins certain connections between diet and human health. A tremendous amount of knowledge has been amassed from experimental studies on diet, human metabolism and microbiome. However, this evidence remains mostly buried in scientific publications, and biomedical literature mining in this domain remains scarce. We developed DiMB-RE, a comprehensive corpus annotated with 15 entity types (e.g., Nutrient, Microorganism) and 13 relation types (e.g., increases, improves) capturing diet-microbiome associations. We also trained and evaluated state-of-the-art natural language processing (NLP) models for named entity, trigger, and relation extraction as well as factuality detection using DiMB-RE. Results: DiMB-RE consists of 14,450 entities and 4,206 relationships from 165 articles. While NLP models performed reasonably well for named entity recognition (0.760 F_{1}), end-to-end relation extraction performance was modest (0.356 F_{1}), partly due to missed entities and triggers as well as cross-sentence relations. Conclusions: To our knowledge, DiMB-RE is largest and most diverse dataset focusing on diet-microbiome interactions. It can serve as a benchmark corpus for biomedical literature mining. Availability: DiMB-RE and the NLP models are available at https://github.com/ScienceNLP-Lab/DiMB-RE.

This paper presents BOUQuET, a multicentric and multi-register/domain dataset and benchmark, and its broader collaborative extension initiative. This dataset is handcrafted in non-English languages first, each of these source languages being represented among the 23 languages commonly used by half of the world's population and therefore having the potential to serve as pivot languages that will enable more accurate translations. The dataset is specially designed to avoid contamination and be multicentric, so as to enforce representation of multilingual language features. In addition, the dataset goes beyond the sentence level, as it is organized in paragraphs of various lengths. Compared with related machine translation (MT) datasets, we show that BOUQuET has a broader representation of domains while simplifying the translation task for non-experts. Therefore, BOUQuET is specially suitable for the open initiative and call for translation participation that we are launching to extend it to a multi-way parallel corpus to any written language.

Antibodies are proteins produced by the immune system that can identify and neutralise a wide variety of antigens with high specificity and affinity, and constitute the most successful class of biotherapeutics. With the advent of next-generation sequencing, billions of antibody sequences have been collected in recent years, though their application in the design of better therapeutics has been constrained by the sheer volume and complexity of the data. To address this challenge, we present IgBert and IgT5, the best performing antibody-specific language models developed to date which can consistently handle both paired and unpaired variable region sequences as input. These models are trained comprehensively using the more than two billion unpaired sequences and two million paired sequences of light and heavy chains present in the Observed Antibody Space dataset. We show that our models outperform existing antibody and protein language models on a diverse range of design and regression tasks relevant to antibody engineering. This advancement marks a significant leap forward in leveraging machine learning, large scale data sets and high-performance computing for enhancing antibody design for therapeutic development.

We present Samanantar, the largest publicly available parallel corpora collection for Indic languages. The collection contains a total of 49.7 million sentence pairs between English and 11 Indic languages (from two language families). Specifically, we compile 12.4 million sentence pairs from existing, publicly-available parallel corpora, and additionally mine 37.4 million sentence pairs from the web, resulting in a 4x increase. We mine the parallel sentences from the web by combining many corpora, tools, and methods: (a) web-crawled monolingual corpora, (b) document OCR for extracting sentences from scanned documents, (c) multilingual representation models for aligning sentences, and (d) approximate nearest neighbor search for searching in a large collection of sentences. Human evaluation of samples from the newly mined corpora validate the high quality of the parallel sentences across 11 languages. Further, we extract 83.4 million sentence pairs between all 55 Indic language pairs from the English-centric parallel corpus using English as the pivot language. We trained multilingual NMT models spanning all these languages on Samanantar, which outperform existing models and baselines on publicly available benchmarks, such as FLORES, establishing the utility of Samanantar. Our data and models are available publicly at https://indicnlp.ai4bharat.org/samanantar/ and we hope they will help advance research in NMT and multilingual NLP for Indic languages.

Soccer is a globally popular sport with a vast audience, in this paper, we consider constructing an automatic soccer game commentary model to improve the audiences' viewing experience. In general, we make the following contributions: First, observing the prevalent video-text misalignment in existing datasets, we manually annotate timestamps for 49 matches, establishing a more robust benchmark for soccer game commentary generation, termed as SN-Caption-test-align; Second, we propose a multi-modal temporal alignment pipeline to automatically correct and filter the existing dataset at scale, creating a higher-quality soccer game commentary dataset for training, denoted as MatchTime; Third, based on our curated dataset, we train an automatic commentary generation model, named MatchVoice. Extensive experiments and ablation studies have demonstrated the effectiveness of our alignment pipeline, and training model on the curated datasets achieves state-of-the-art performance for commentary generation, showcasing that better alignment can lead to significant performance improvements in downstream tasks.

A popular natural language processing task decades ago, word alignment has been dominated until recently by GIZA++, a statistical method based on the 30-year-old IBM models. New methods that outperform GIZA++ primarily rely on large machine translation models, massively multilingual language models, or supervision from GIZA++ alignments itself. We introduce Embedding-Enhanced GIZA++, and outperform GIZA++ without any of the aforementioned factors. Taking advantage of monolingual embedding spaces of source and target language only, we exceed GIZA++'s performance in every tested scenario for three languages pairs. In the lowest-resource setting, we outperform GIZA++ by 8.5, 10.9, and 12 AER for Ro-En, De-En, and En-Fr, respectively. We release our code at https://github.com/kellymarchisio/ee-giza.

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation techniques. To facilitate progress in this field, we introduce the Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. We curate tasks into specific training, validation, and test splits to ensure that each task tests biologically relevant generalization that transfers to real-life scenarios. We benchmark a range of approaches to semi-supervised protein representation learning, which span recent work as well as canonical sequence learning techniques. We find that self-supervised pretraining is helpful for almost all models on all tasks, more than doubling performance in some cases. Despite this increase, in several cases features learned by self-supervised pretraining still lag behind features extracted by state-of-the-art non-neural techniques. This gap in performance suggests a huge opportunity for innovative architecture design and improved modeling paradigms that better capture the signal in biological sequences. TAPE will help the machine learning community focus effort on scientifically relevant problems. Toward this end, all data and code used to run these experiments are available at https://github.com/songlab-cal/tape.

Enterprises often own large collections of structured data in the form of large databases or an enterprise data lake. Such data collections come with limited metadata and strict access policies that could limit access to the data contents and, therefore, limit the application of classic retrieval and analysis solutions. As a result, there is a need for solutions that can effectively utilize the available metadata. In this paper, we study the problem of matching table metadata to a business glossary containing data labels and descriptions. The resulting matching enables the use of an available or curated business glossary for retrieval and analysis without or before requesting access to the data contents. One solution to this problem is to use manually-defined rules or similarity measures on column names and glossary descriptions (or their vector embeddings) to find the closest match. However, such approaches need to be tuned through manual labeling and cannot handle many business glossaries that contain a combination of simple as well as complex and long descriptions. In this work, we leverage the power of large language models (LLMs) to design generic matching methods that do not require manual tuning and can identify complex relations between column names and glossaries. We propose methods that utilize LLMs in two ways: a) by generating additional context for column names that can aid with matching b) by using LLMs to directly infer if there is a relation between column names and glossary descriptions. Our preliminary experimental results show the effectiveness of our proposed methods.

This paper embarks on an exploration into the Large Language Model (LLM) datasets, which play a crucial role in the remarkable advancements of LLMs. The datasets serve as the foundational infrastructure analogous to a root system that sustains and nurtures the development of LLMs. Consequently, examination of these datasets emerges as a critical topic in research. In order to address the current lack of a comprehensive overview and thorough analysis of LLM datasets, and to gain insights into their current status and future trends, this survey consolidates and categorizes the fundamental aspects of LLM datasets from five perspectives: (1) Pre-training Corpora; (2) Instruction Fine-tuning Datasets; (3) Preference Datasets; (4) Evaluation Datasets; (5) Traditional Natural Language Processing (NLP) Datasets. The survey sheds light on the prevailing challenges and points out potential avenues for future investigation. Additionally, a comprehensive review of the existing available dataset resources is also provided, including statistics from 444 datasets, covering 8 language categories and spanning 32 domains. Information from 20 dimensions is incorporated into the dataset statistics. The total data size surveyed surpasses 774.5 TB for pre-training corpora and 700M instances for other datasets. We aim to present the entire landscape of LLM text datasets, serving as a comprehensive reference for researchers in this field and contributing to future studies. Related resources are available at: https://github.com/lmmlzn/Awesome-LLMs-Datasets.

Large Language Models (LLMs) and LLM-based agents show great promise in accelerating scientific research. Existing benchmarks for measuring this potential and guiding future development continue to evolve from pure recall and rote knowledge tasks, towards more practical work such as literature review and experimental planning. Bioinformatics is a domain where fully autonomous AI-driven discovery may be near, but no extensive benchmarks for measuring progress have been introduced to date. We therefore present the Bioinformatics Benchmark (BixBench), a dataset comprising over 50 real-world scenarios of practical biological data analysis with nearly 300 associated open-answer questions designed to measure the ability of LLM-based agents to explore biological datasets, perform long, multi-step analytical trajectories, and interpret the nuanced results of those analyses. We evaluate the performance of two frontier LLMs (GPT-4o and Claude 3.5 Sonnet) using a custom agent framework we open source. We find that even the latest frontier models only achieve 17% accuracy in the open-answer regime, and no better than random in a multiple-choice setting. By exposing the current limitations of frontier models, we hope BixBench can spur the development of agents capable of conducting rigorous bioinformatic analysis and accelerate scientific discovery.

Molecule discovery is a pivotal research field, impacting everything from the medicines we take to the materials we use. Recently, Large Language Models (LLMs) have been widely adopted in molecule understanding and generation, yet the alignments between molecules and their corresponding captions remain a significant challenge. Previous endeavours often treat the molecule as a general SMILES string or molecular graph, neglecting the fine-grained alignments between the molecular sub-structures and the descriptive textual phrases, which are crucial for accurate and explainable predictions. In this case, we introduce MolReFlect, a novel teacher-student framework designed to contextually perform the molecule-caption alignments in a fine-grained way. Our approach initially leverages a larger teacher LLM to label the detailed alignments by directly extracting critical phrases from molecule captions or SMILES strings and implying them to corresponding sub-structures or characteristics. To refine these alignments, we propose In-Context Selective Reflection, which retrieves previous extraction results as context examples for teacher LLM to reflect and lets a smaller student LLM select from in-context reflection and previous extraction results. Finally, we enhance the learning process of the student LLM through Chain-of-Thought In-Context Molecule Tuning, integrating the fine-grained alignments and the reasoning processes within the Chain-of-Thought format. Our experimental results demonstrate that MolReFlect enables LLMs like Mistral-7B to significantly outperform the previous baselines, achieving SOTA performance on the ChEBI-20 dataset. This advancement not only enhances the generative capabilities of LLMs in the molecule-caption translation task, but also contributes to a more explainable framework.

We present PhiloBERTA, a cross-lingual transformer model that measures semantic relationships between ancient Greek and Latin lexicons. Through analysis of selected term pairs from classical texts, we use contextual embeddings and angular similarity metrics to identify precise semantic alignments. Our results show that etymologically related pairs demonstrate significantly higher similarity scores, particularly for abstract philosophical concepts such as epist\=em\=e (scientia) and dikaiosyn\=e (iustitia). Statistical analysis reveals consistent patterns in these relationships (p = 0.012), with etymologically related pairs showing remarkably stable semantic preservation compared to control pairs. These findings establish a quantitative framework for examining how philosophical concepts moved between Greek and Latin traditions, offering new methods for classical philological research.

Many text generation applications require the generated text to be factually consistent with input information. Automatic evaluation of factual consistency is challenging. Previous work has developed various metrics that often depend on specific functions, such as natural language inference (NLI) or question answering (QA), trained on limited data. Those metrics thus can hardly assess diverse factual inconsistencies (e.g., contradictions, hallucinations) that occur in varying inputs/outputs (e.g., sentences, documents) from different tasks. In this paper, we propose AlignScore, a new holistic metric that applies to a variety of factual inconsistency scenarios as above. AlignScore is based on a general function of information alignment between two arbitrary text pieces. Crucially, we develop a unified training framework of the alignment function by integrating a large diversity of data sources, resulting in 4.7M training examples from 7 well-established tasks (NLI, QA, paraphrasing, fact verification, information retrieval, semantic similarity, and summarization). We conduct extensive experiments on large-scale benchmarks including 22 evaluation datasets, where 19 of the datasets were never seen in the alignment training. AlignScore achieves substantial improvement over a wide range of previous metrics. Moreover, AlignScore (355M parameters) matches or even outperforms metrics based on ChatGPT and GPT-4 that are orders of magnitude larger.

This paper describes the system we developed for SemEval-2024 Task 1, "Semantic Textual Relatedness for African and Asian Languages." The aim of the task is to build a model that can identify semantic textual relatedness (STR) between two sentences of a target language belonging to a collection of African and Asian languages. We participated in Subtasks A and C and explored supervised and cross-lingual training leveraging large language models (LLMs). Pre-trained large language models have been extensively used for machine translation and semantic similarity. Using a combination of machine translation and sentence embedding LLMs, we developed a unified STR model, TranSem, for subtask A and fine-tuned the T5 family of models on the STR data, FineSem, for use in subtask C. Our model results for 7 languages in subtask A were better than the official baseline for 3 languages and on par with the baseline for the remaining 4 languages. Our model results for the 12 languages in subtask C resulted in 1st place for Africaans, 2nd place for Indonesian, and 3rd place for English with low performance for the remaining 9 languages.

Previous works on knowledge-to-text generation take as input a few RDF triples or key-value pairs conveying the knowledge of some entities to generate a natural language description. Existing datasets, such as WIKIBIO, WebNLG, and E2E, basically have a good alignment between an input triple/pair set and its output text. However, in practice, the input knowledge could be more than enough, since the output description may only cover the most significant knowledge. In this paper, we introduce a large-scale and challenging dataset to facilitate the study of such a practical scenario in KG-to-text. Our dataset involves retrieving abundant knowledge of various types of main entities from a large knowledge graph (KG), which makes the current graph-to-sequence models severely suffer from the problems of information loss and parameter explosion while generating the descriptions. We address these challenges by proposing a multi-graph structure that is able to represent the original graph information more comprehensively. Furthermore, we also incorporate aggregation methods that learn to extract the rich graph information. Extensive experiments demonstrate the effectiveness of our model architecture.

Text Summarization is a popular task and an active area of research for the Natural Language Processing community. By definition, it requires to account for long input texts, a characteristic which poses computational challenges for neural models. Moreover, real-world documents come in a variety of complex, visually-rich, layouts. This information is of great relevance, whether to highlight salient content or to encode long-range interactions between textual passages. Yet, all publicly available summarization datasets only provide plain text content. To facilitate research on how to exploit visual/layout information to better capture long-range dependencies in summarization models, we present LoRaLay, a collection of datasets for long-range summarization with accompanying visual/layout information. We extend existing and popular English datasets (arXiv and PubMed) with layout information and propose four novel datasets -- consistently built from scholar resources -- covering French, Spanish, Portuguese, and Korean languages. Further, we propose new baselines merging layout-aware and long-range models -- two orthogonal approaches -- and obtain state-of-the-art results, showing the importance of combining both lines of research.

Pre-trained LLMs have demonstrated substantial capabilities across a range of conventional natural language processing (NLP) tasks, such as summarization and entity recognition. In this paper, we explore the application of LLMs in the generation of high-quality protein sequences. Specifically, we adopt a suite of pre-trained LLMs, including Mistral-7B1, Llama-2-7B2, Llama-3-8B3, and gemma-7B4, to produce valid protein sequences. All of these models are publicly available.5 Unlike previous work in this field, our approach utilizes a relatively small dataset comprising 42,000 distinct human protein sequences. We retrain these models to process protein-related data, ensuring the generation of biologically feasible protein structures. Our findings demonstrate that even with limited data, the adapted models exhibit efficiency comparable to established protein-focused models such as ProGen varieties, ProtGPT2, and ProLLaMA, which were trained on millions of protein sequences. To validate and quantify the performance of our models, we conduct comparative analyses employing standard metrics such as pLDDT, RMSD, TM-score, and REU. Furthermore, we commit to making the trained versions of all four models publicly available, fostering greater transparency and collaboration in the field of computational biology.

Sentence embeddings are commonly used in text clustering and semantic retrieval tasks. State-of-the-art sentence representation methods are based on artificial neural networks fine-tuned on large collections of manually labeled sentence pairs. Sufficient amount of annotated data is available for high-resource languages such as English or Chinese. In less popular languages, multilingual models have to be used, which offer lower performance. In this publication, we address this problem by proposing a method for training effective language-specific sentence encoders without manually labeled data. Our approach is to automatically construct a dataset of paraphrase pairs from sentence-aligned bilingual text corpora. We then use the collected data to fine-tune a Transformer language model with an additional recurrent pooling layer. Our sentence encoder can be trained in less than a day on a single graphics card, achieving high performance on a diverse set of sentence-level tasks. We evaluate our method on eight linguistic tasks in Polish, comparing it with the best available multilingual sentence encoders.

Word evolution refers to the changing meanings and associations of words throughout time, as a byproduct of human language evolution. By studying word evolution, we can infer social trends and language constructs over different periods of human history. However, traditional techniques such as word representation learning do not adequately capture the evolving language structure and vocabulary. In this paper, we develop a dynamic statistical model to learn time-aware word vector representation. We propose a model that simultaneously learns time-aware embeddings and solves the resulting "alignment problem". This model is trained on a crawled NYTimes dataset. Additionally, we develop multiple intuitive evaluation strategies of temporal word embeddings. Our qualitative and quantitative tests indicate that our method not only reliably captures this evolution over time, but also consistently outperforms state-of-the-art temporal embedding approaches on both semantic accuracy and alignment quality.

We introduce ParaNames, a multilingual parallel name resource consisting of 118 million names spanning across 400 languages. Names are provided for 13.6 million entities which are mapped to standardized entity types (PER/LOC/ORG). Using Wikidata as a source, we create the largest resource of this type to-date. We describe our approach to filtering and standardizing the data to provide the best quality possible. ParaNames is useful for multilingual language processing, both in defining tasks for name translation/transliteration and as supplementary data for tasks such as named entity recognition and linking. We demonstrate an application of ParaNames by training a multilingual model for canonical name translation to and from English. Our resource is released under a Creative Commons license (CC BY 4.0) at https://github.com/bltlab/paranames.

In the domain of semantic parsing, significant progress has been achieved in Text-to-SQL and question-answering tasks, both of which focus on extracting information from data sources in their native formats. However, the inherent constraints of their formal meaning representations, such as SQL programming language or basic logical forms, hinder their ability to analyze data from various perspectives, such as conducting statistical analyses. To address this limitation and inspire research in this field, we design SIGMA, a new dataset for Text-to-Code semantic parsing with statistical analysis. SIGMA comprises 6000 questions with corresponding Python code labels, spanning across 160 databases. Half of the questions involve query types, which return information in its original format, while the remaining 50% are statistical analysis questions, which perform statistical operations on the data. The Python code labels in our dataset cover 4 types of query types and 40 types of statistical analysis patterns. We evaluated the SIGMA dataset using three different baseline models: LGESQL, SmBoP, and SLSQL. The experimental results show that the LGESQL model with ELECTRA outperforms all other models, achieving 83.37% structure accuracy. In terms of execution accuracy, the SmBoP model, when combined with GraPPa and T5, reaches 76.38%.

Recent advances in machine learning have significantly improved the understanding of source code data and achieved good performance on a number of downstream tasks. Open source repositories like GitHub enable this process with rich unlabeled code data. However, the lack of high quality labeled data has largely hindered the progress of several code related tasks, such as program translation, summarization, synthesis, and code search. This paper introduces XLCoST, Cross-Lingual Code SnippeT dataset, a new benchmark dataset for cross-lingual code intelligence. Our dataset contains fine-grained parallel data from 8 languages (7 commonly used programming languages and English), and supports 10 cross-lingual code tasks. To the best of our knowledge, it is the largest parallel dataset for source code both in terms of size and the number of languages. We also provide the performance of several state-of-the-art baseline models for each task. We believe this new dataset can be a valuable asset for the research community and facilitate the development and validation of new methods for cross-lingual code intelligence.

Multilingual Large Language Models are capable of using powerful Large Language Models to handle and respond to queries in multiple languages, which achieves remarkable success in multilingual natural language processing tasks. Despite these breakthroughs, there still remains a lack of a comprehensive survey to summarize existing approaches and recent developments in this field. To this end, in this paper, we present a thorough review and provide a unified perspective to summarize the recent progress as well as emerging trends in multilingual large language models (MLLMs) literature. The contributions of this paper can be summarized: (1) First survey: to our knowledge, we take the first step and present a thorough review in MLLMs research field according to multi-lingual alignment; (2) New taxonomy: we offer a new and unified perspective to summarize the current progress of MLLMs; (3) New frontiers: we highlight several emerging frontiers and discuss the corresponding challenges; (4) Abundant resources: we collect abundant open-source resources, including relevant papers, data corpora, and leaderboards. We hope our work can provide the community with quick access and spur breakthrough research in MLLMs.

The ability of generative large language models (LLMs) to perform in-context learning has given rise to a large body of research into how best to prompt models for various natural language processing tasks. In this paper, we focus on machine translation (MT), a task that has been shown to benefit from in-context translation examples. However no systematic studies have been published on how best to select examples, and mixed results have been reported on the usefulness of similarity-based selection over random selection. We provide a study covering multiple LLMs and multiple in-context example retrieval strategies, comparing multilingual sentence embeddings. We cover several language directions, representing different levels of language resourcedness (English into French, German, Swahili and Wolof). Contrarily to previously published results, we find that sentence embedding similarity can improve MT, especially for low-resource language directions, and discuss the balance between selection pool diversity and quality. We also highlight potential problems with the evaluation of LLM-based MT and suggest a more appropriate evaluation protocol, adapting the COMET metric to the evaluation of LLMs. Code and outputs are freely available at https://github.com/ArmelRandy/ICL-MT.

We present Platypus, a family of fine-tuned and merged Large Language Models (LLMs) that achieves the strongest performance and currently stands at first place in HuggingFace's Open LLM Leaderboard as of the release date of this work. In this work we describe (1) our curated dataset Open-Platypus, that is a subset of other open datasets and which we release to the public (2) our process of fine-tuning and merging LoRA modules in order to conserve the strong prior of pretrained LLMs, while bringing specific domain knowledge to the surface (3) our efforts in checking for test data leaks and contamination in the training data, which can inform future research. Specifically, the Platypus family achieves strong performance in quantitative LLM metrics across model sizes, topping the global Open LLM leaderboard while using just a fraction of the fine-tuning data and overall compute that are required for other state-of-the-art fine-tuned LLMs. In particular, a 13B Platypus model can be trained on a single A100 GPU using 25k questions in 5 hours. This is a testament of the quality of our Open-Platypus dataset, and opens opportunities for more improvements in the field. Project page: https://platypus-llm.github.io

This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a phylogenetic distance metrics based on the similarity of LLMs' output. The resulting metric is then used to construct dendrograms, which satisfactorily capture known relationships across a set of 111 open-source and 45 closed models. Furthermore, our phylogenetic distance predicts performance in standard benchmarks, thus demonstrating its functional validity and paving the way for a time and cost-effective estimation of LLM capabilities. To sum up, by translating population genetic concepts to machine learning, we propose and validate a tool to evaluate LLM development, relationships and capabilities, even in the absence of transparent training information.

As large language models (LLMs) continue to advance, ensuring their alignment with human values becomes increasingly critical. Traditional alignment methods heavily rely on human feedback to fine-tune models. With the emergence of superhuman models whose outputs may surpass human understanding, evaluating and aligning these models using human judgments poses significant challenges. To address the challenges, recent works use weak supervisors to elicit knowledge from much stronger models. However, there are important disanalogies between the empirical setup in the existing works and the genuine goal of alignment. We remark that existing works investigate the phenomenon of weak-to-strong generation in analogous setup (i.e., binary classification), rather than practical alignment-relevant tasks (e.g., safety). In this paper, we bridge this gap by extending weak-to-strong generation to the context of practical alignment. We empirically demonstrate the widespread phenomenon of weak-to-strong generation in three complicated alignment tasks: safety, toxicity, and legal reasoning}. Furthermore, we explore efficient strategies for improving alignment performance to enhance the quality of model outcomes. Lastly, we summarize and analyze the challenges and potential solutions in regard to specific alignment tasks, which we hope to catalyze the research progress on the topic of weak-to-strong generalization. Our code is released at https://github.com/yeruimeng/WTS.git.

We introduce ChatGLM, an evolving family of large language models that we have been developing over time. This report primarily focuses on the GLM-4 language series, which includes GLM-4, GLM-4-Air, and GLM-4-9B. They represent our most capable models that are trained with all the insights and lessons gained from the preceding three generations of ChatGLM. To date, the GLM-4 models are pre-trained on ten trillions of tokens mostly in Chinese and English, along with a small set of corpus from 24 languages, and aligned primarily for Chinese and English usage. The high-quality alignment is achieved via a multi-stage post-training process, which involves supervised fine-tuning and learning from human feedback. Evaluations show that GLM-4 1) closely rivals or outperforms GPT-4 in terms of general metrics such as MMLU, GSM8K, MATH, BBH, GPQA, and HumanEval, 2) gets close to GPT-4-Turbo in instruction following as measured by IFEval, 3) matches GPT-4 Turbo (128K) and Claude 3 for long context tasks, and 4) outperforms GPT-4 in Chinese alignments as measured by AlignBench. The GLM-4 All Tools model is further aligned to understand user intent and autonomously decide when and which tool(s) touse -- including web browser, Python interpreter, text-to-image model, and user-defined functions -- to effectively complete complex tasks. In practical applications, it matches and even surpasses GPT-4 All Tools in tasks like accessing online information via web browsing and solving math problems using Python interpreter. Over the course, we have open-sourced a series of models, including ChatGLM-6B (three generations), GLM-4-9B (128K, 1M), GLM-4V-9B, WebGLM, and CodeGeeX, attracting over 10 million downloads on Hugging face in the year 2023 alone. The open models can be accessed through https://github.com/THUDM and https://huggingface.co/THUDM.

Text-to-image generation has advanced rapidly, yet aligning complex textual prompts with generated visuals remains challenging, especially with intricate object relationships and fine-grained details. This paper introduces Fast Prompt Alignment (FPA), a prompt optimization framework that leverages a one-pass approach, enhancing text-to-image alignment efficiency without the iterative overhead typical of current methods like OPT2I. FPA uses large language models (LLMs) for single-iteration prompt paraphrasing, followed by fine-tuning or in-context learning with optimized prompts to enable real-time inference, reducing computational demands while preserving alignment fidelity. Extensive evaluations on the COCO Captions and PartiPrompts datasets demonstrate that FPA achieves competitive text-image alignment scores at a fraction of the processing time, as validated through both automated metrics (TIFA, VQA) and human evaluation. A human study with expert annotators further reveals a strong correlation between human alignment judgments and automated scores, underscoring the robustness of FPA's improvements. The proposed method showcases a scalable, efficient alternative to iterative prompt optimization, enabling broader applicability in real-time, high-demand settings. The codebase is provided to facilitate further research: https://github.com/tiktok/fast_prompt_alignment

In this report, we introduce SciFive, a domain-specific T5 model that has been pre-trained on large biomedical corpora. Our model outperforms the current SOTA methods (i.e. BERT, BioBERT, Base T5) on tasks in named entity relation, relation extraction, natural language inference, and question-answering. We show that text-generation methods have significant potential in a broad array of biomedical NLP tasks, particularly those requiring longer, more complex outputs. Our results support the exploration of more difficult text generation tasks and the development of new methods in this area

Lyrics alignment gained considerable attention in recent years. State-of-the-art systems either re-use established speech recognition toolkits, or design end-to-end solutions involving a Connectionist Temporal Classification (CTC) loss. However, both approaches suffer from specific weaknesses: toolkits are known for their complexity, and CTC systems use a loss designed for transcription which can limit alignment accuracy. In this paper, we use instead a contrastive learning procedure that derives cross-modal embeddings linking the audio and text domains. This way, we obtain a novel system that is simple to train end-to-end, can make use of weakly annotated training data, jointly learns a powerful text model, and is tailored to alignment. The system is not only the first to yield an average absolute error below 0.2 seconds on the standard Jamendo dataset but it is also robust to other languages, even when trained on English data only. Finally, we release word-level alignments for the JamendoLyrics Multi-Lang dataset.

Contextual language models have been trained on Classical languages, including Ancient Greek and Latin, for tasks such as lemmatization, morphological tagging, part of speech tagging, authorship attribution, and detection of scribal errors. However, high-quality sentence embedding models for these historical languages are significantly more difficult to achieve due to the lack of training data. In this work, we use a multilingual knowledge distillation approach to train BERT models to produce sentence embeddings for Ancient Greek text. The state-of-the-art sentence embedding approaches for high-resource languages use massive datasets, but our distillation approach allows our Ancient Greek models to inherit the properties of these models while using a relatively small amount of translated sentence data. We build a parallel sentence dataset using a sentence-embedding alignment method to align Ancient Greek documents with English translations, and use this dataset to train our models. We evaluate our models on translation search, semantic similarity, and semantic retrieval tasks and investigate translation bias. We make our training and evaluation datasets freely available at https://github.com/kevinkrahn/ancient-greek-datasets .

The evolution of Neural Machine Translation (NMT) has been significantly influenced by six core challenges (Koehn and Knowles, 2017), which have acted as benchmarks for progress in this field. This study revisits these challenges, offering insights into their ongoing relevance in the context of advanced Large Language Models (LLMs): domain mismatch, amount of parallel data, rare word prediction, translation of long sentences, attention model as word alignment, and sub-optimal beam search. Our empirical findings indicate that LLMs effectively lessen the reliance on parallel data for major languages in the pretraining phase. Additionally, the LLM-based translation system significantly enhances the translation of long sentences that contain approximately 80 words and shows the capability to translate documents of up to 512 words. However, despite these significant improvements, the challenges of domain mismatch and prediction of rare words persist. While the challenges of word alignment and beam search, specifically associated with NMT, may not apply to LLMs, we identify three new challenges for LLMs in translation tasks: inference efficiency, translation of low-resource languages in the pretraining phase, and human-aligned evaluation. The datasets and models are released at https://github.com/pangjh3/LLM4MT.

We show that margin-based bitext mining in a multilingual sentence space can be applied to monolingual corpora of billions of sentences. We are using ten snapshots of a curated common crawl corpus (Wenzek et al., 2019) totalling 32.7 billion unique sentences. Using one unified approach for 38 languages, we were able to mine 4.5 billions parallel sentences, out of which 661 million are aligned with English. 20 language pairs have more then 30 million parallel sentences, 112 more then 10 million, and most more than one million, including direct alignments between many European or Asian languages. To evaluate the quality of the mined bitexts, we train NMT systems for most of the language pairs and evaluate them on TED, WMT and WAT test sets. Using our mined bitexts only and no human translated parallel data, we achieve a new state-of-the-art for a single system on the WMT'19 test set for translation between English and German, Russian and Chinese, as well as German/French. In particular, our English/German system outperforms the best single one by close to 4 BLEU points and is almost on pair with best WMT'19 evaluation system which uses system combination and back-translation. We also achieve excellent results for distant languages pairs like Russian/Japanese, outperforming the best submission at the 2019 workshop on Asian Translation (WAT).

A plethora of sentence embedding models makes it challenging to choose one, especially for domains such as telecom, rich with specialized vocabulary. We evaluate multiple embeddings obtained from publicly available models and their domain-adapted variants, on both point retrieval accuracies as well as their (95\%) confidence intervals. We establish a systematic method to obtain thresholds for similarity scores for different embeddings. We observe that fine-tuning improves mean bootstrapped accuracies as well as tightens confidence intervals. The pre-training combined with fine-tuning makes confidence intervals even tighter. To understand these variations, we analyse and report significant correlations between the distributional overlap between top-K, correct and random sentence similarities with retrieval accuracies and similarity thresholds. Following current literature, we analyze if retrieval accuracy variations can be attributed to isotropy of embeddings. Our conclusions are that isotropy of embeddings (as measured by two independent state-of-the-art isotropy metric definitions) cannot be attributed to better retrieval performance. However, domain adaptation which improves retrieval accuracies also improves isotropy. We establish that domain adaptation moves domain specific embeddings further away from general domain embeddings.

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

Exploring and quantifying semantic relatedness is central to representing language. It holds significant implications across various NLP tasks, including offering insights into the capabilities and performance of Large Language Models (LLMs). While earlier NLP research primarily focused on semantic similarity, often within the English language context, we instead investigate the broader phenomenon of semantic relatedness. In this paper, we present SemRel, a new semantic relatedness dataset collection annotated by native speakers across 14 languages:Afrikaans, Algerian Arabic, Amharic, English, Hausa, Hindi, Indonesian, Kinyarwanda, Marathi, Moroccan Arabic, Modern Standard Arabic, Punjabi, Spanish, and Telugu. These languages originate from five distinct language families and are predominantly spoken in Africa and Asia -- regions characterised by a relatively limited availability of NLP resources. Each instance in the SemRel datasets is a sentence pair associated with a score that represents the degree of semantic textual relatedness between the two sentences. The scores are obtained using a comparative annotation framework. We describe the data collection and annotation processes, related challenges when building the datasets, and their impact and utility in NLP. We further report experiments for each language and across the different languages.

Extending large language models to effectively handle long contexts requires instruction fine-tuning on input sequences of similar length. To address this, we present LongAlign -- a recipe of the instruction data, training, and evaluation for long context alignment. First, we construct a long instruction-following dataset using Self-Instruct. To ensure the data diversity, it covers a broad range of tasks from various long context sources. Second, we adopt the packing and sorted batching strategies to speed up supervised fine-tuning on data with varied length distributions. Additionally, we develop a loss weighting method to balance the contribution to the loss across different sequences during packing training. Third, we introduce the LongBench-Chat benchmark for evaluating instruction-following capabilities on queries of 10k-100k in length. Experiments show that LongAlign outperforms existing recipes for LLMs in long context tasks by up to 30\%, while also maintaining their proficiency in handling short, generic tasks. The code, data, and long-aligned models are open-sourced at https://github.com/THUDM/LongAlign.

The proliferation of open-source scientific software for science and research presents opportunities and challenges. In this paper, we introduce the SciCat dataset -- a comprehensive collection of Free-Libre Open Source Software (FLOSS) projects, designed to address the need for a curated repository of scientific and research software. This collection is crucial for understanding the creation of scientific software and aiding in its development. To ensure extensive coverage, our approach involves selecting projects from a pool of 131 million deforked repositories from the World of Code data source. Subsequently, we analyze README.md files using OpenAI's advanced language models. Our classification focuses on software designed for scientific purposes, research-related projects, and research support software. The SciCat dataset aims to become an invaluable tool for researching science-related software, shedding light on emerging trends, prevalent practices, and challenges in the field of scientific software development. Furthermore, it includes data that can be linked to the World of Code, GitHub, and other platforms, providing a solid foundation for conducting comparative studies between scientific and non-scientific software.

Retrieval models are often evaluated on partially-annotated datasets. Each query is mapped to a few relevant texts and the remaining corpus is assumed to be irrelevant. As a result, models that successfully retrieve false negatives are punished in evaluation. Unfortunately, completely annotating all texts for every query is not resource efficient. In this work, we show that using partially-annotated datasets in evaluation can paint a distorted picture. We curate D-MERIT, a passage retrieval evaluation set from Wikipedia, aspiring to contain all relevant passages for each query. Queries describe a group (e.g., ``journals about linguistics'') and relevant passages are evidence that entities belong to the group (e.g., a passage indicating that Language is a journal about linguistics). We show that evaluating on a dataset containing annotations for only a subset of the relevant passages might result in misleading ranking of the retrieval systems and that as more relevant texts are included in the evaluation set, the rankings converge. We propose our dataset as a resource for evaluation and our study as a recommendation for balance between resource-efficiency and reliable evaluation when annotating evaluation sets for text retrieval.

There has been an increase of interest in code search using natural language. Assessing the performance of such code search models can be difficult without a readily available evaluation suite. In this paper, we present an evaluation dataset consisting of natural language query and code snippet pairs, with the hope that future work in this area can use this dataset as a common benchmark. We also provide the results of two code search models ([1] and [6]) from recent work. The evaluation dataset is available at https://github.com/facebookresearch/Neural-Code-Search-Evaluation-Dataset

We present the HPLT (High Performance Language Technologies) language resources, a new massive multilingual dataset including both monolingual and bilingual corpora extracted from CommonCrawl and previously unused web crawls from the Internet Archive. We describe our methods for data acquisition, management and processing of large corpora, which rely on open-source software tools and high-performance computing. Our monolingual collection focuses on low- to medium-resourced languages and covers 75 languages and a total of ~5.6 trillion word tokens de-duplicated on the document level. Our English-centric parallel corpus is derived from its monolingual counterpart and covers 18 language pairs and more than 96 million aligned sentence pairs with roughly 1.4 billion English tokens. The HPLT language resources are one of the largest open text corpora ever released, providing a great resource for language modeling and machine translation training. We publicly release the corpora, the software, and the tools used in this work.

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.

We present ALT (ALignment with Textual feedback), an approach that aligns language models with user preferences expressed in text. We argue that text offers greater expressiveness, enabling users to provide richer feedback than simple comparative preferences and this richer feedback can lead to more efficient and effective alignment. ALT aligns the model by conditioning its generation on the textual feedback. Our method relies solely on language modeling techniques and requires minimal hyper-parameter tuning, though it still presents the main benefits of RL-based alignment algorithms and can effectively learn from textual feedback. We explore the efficacy and efficiency of textual feedback across different tasks such as toxicity reduction, summarization, and dialog response generation. We find that ALT outperforms PPO for the task of toxicity reduction while being able to match its performance on summarization with only 20% of the samples. We also explore how ALT can be used with feedback provided by an existing LLM where we explore an LLM providing constrained and unconstrained textual feedback. We also outline future directions to align models with natural language feedback.

We develop high performance multilingualAbstract Meaning Representation (AMR) sys-tems by projecting English AMR annotationsto other languages with weak supervision. Weachieve this goal by bootstrapping transformer-based multilingual word embeddings, in partic-ular those from cross-lingual RoBERTa (XLM-R large). We develop a novel technique forforeign-text-to-English AMR alignment, usingthe contextual word alignment between En-glish and foreign language tokens. This wordalignment is weakly supervised and relies onthe contextualized XLM-R word embeddings.We achieve a highly competitive performancethat surpasses the best published results forGerman, Italian, Spanish and Chinese.

Understanding the performance of machine learning models across diverse data distributions is critically important for reliable applications. Motivated by this, there is a growing focus on curating benchmark datasets that capture distribution shifts. While valuable, the existing benchmarks are limited in that many of them only contain a small number of shifts and they lack systematic annotation about what is different across different shifts. We present MetaShift--a collection of 12,868 sets of natural images across 410 classes--to address this challenge. We leverage the natural heterogeneity of Visual Genome and its annotations to construct MetaShift. The key construction idea is to cluster images using its metadata, which provides context for each image (e.g. "cats with cars" or "cats in bathroom") that represent distinct data distributions. MetaShift has two important benefits: first, it contains orders of magnitude more natural data shifts than previously available. Second, it provides explicit explanations of what is unique about each of its data sets and a distance score that measures the amount of distribution shift between any two of its data sets. We demonstrate the utility of MetaShift in benchmarking several recent proposals for training models to be robust to data shifts. We find that the simple empirical risk minimization performs the best when shifts are moderate and no method had a systematic advantage for large shifts. We also show how MetaShift can help to visualize conflicts between data subsets during model training.

A key feature of neural models is that they can produce semantic vector representations of objects (texts, images, speech, etc.) ensuring that similar objects are close to each other in the vector space. While much work has focused on learning representations for other modalities, there are no aligned cross-modal representations for text and knowledge base (KB) elements. One challenge for learning such representations is the lack of parallel data, which we use contrastive training on heuristics-based datasets and data augmentation to overcome, training embedding models on (KB graph, text) pairs. On WebNLG, a cleaner manually crafted dataset, we show that they learn aligned representations suitable for retrieval. We then fine-tune on annotated data to create EREDAT (Ensembled Representations for Evaluation of DAta-to-Text), a similarity metric between English text and KB graphs. EREDAT outperforms or matches state-of-the-art metrics in terms of correlation with human judgments on WebNLG even though, unlike them, it does not require a reference text to compare against.

Intelligently extracting and linking complex scientific information from unstructured text is a challenging endeavor particularly for those inexperienced with natural language processing. Here, we present a simple sequence-to-sequence approach to joint named entity recognition and relation extraction for complex hierarchical information in scientific text. The approach leverages a pre-trained large language model (LLM), GPT-3, that is fine-tuned on approximately 500 pairs of prompts (inputs) and completions (outputs). Information is extracted either from single sentences or across sentences in abstracts/passages, and the output can be returned as simple English sentences or a more structured format, such as a list of JSON objects. We demonstrate that LLMs trained in this way are capable of accurately extracting useful records of complex scientific knowledge for three representative tasks in materials chemistry: linking dopants with their host materials, cataloging metal-organic frameworks, and general chemistry/phase/morphology/application information extraction. This approach represents a simple, accessible, and highly-flexible route to obtaining large databases of structured knowledge extracted from unstructured text. An online demo is available at http://www.matscholar.com/info-extraction.

The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler, or GME-sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the input abstracts text and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning as a generative task and few-shot learning with open Large Language Models (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open Large Language Models (Vicuna-13B) as synthetic data generator and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (f1-score=59.0) BioGPT-Large model for end-to-end RE of natural-products relationships along with all the generated synthetic data and the evaluation dataset. See more details at https://github.com/idiap/abroad-re.

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive dataset containing multi-modal information for over 5 million insect specimens, and it significantly expands existing image-based biological datasets by including taxonomic labels, raw nucleotide barcode sequences, assigned barcode index numbers, and geographical information. We propose three benchmark experiments to demonstrate the impact of the multi-modal data types on the classification and clustering accuracy. First, we pretrain a masked language model on the DNA barcode sequences of the BIOSCAN-5M dataset, and demonstrate the impact of using this large reference library on species- and genus-level classification performance. Second, we propose a zero-shot transfer learning task applied to images and DNA barcodes to cluster feature embeddings obtained from self-supervised learning, to investigate whether meaningful clusters can be derived from these representation embeddings. Third, we benchmark multi-modality by performing contrastive learning on DNA barcodes, image data, and taxonomic information. This yields a general shared embedding space enabling taxonomic classification using multiple types of information and modalities. The code repository of the BIOSCAN-5M Insect dataset is available at {https://github.com/zahrag/BIOSCAN-5M}

This paper presents a comprehensive overview of the data preparation pipeline developed for the OpenGPT-X project, a large-scale initiative aimed at creating open and high-performance multilingual large language models (LLMs). The project goal is to deliver models that cover all major European languages, with a particular focus on real-world applications within the European Union. We explain all data processing steps, starting with the data selection and requirement definition to the preparation of the final datasets for model training. We distinguish between curated data and web data, as each of these categories is handled by distinct pipelines, with curated data undergoing minimal filtering and web data requiring extensive filtering and deduplication. This distinction guided the development of specialized algorithmic solutions for both pipelines. In addition to describing the processing methodologies, we provide an in-depth analysis of the datasets, increasing transparency and alignment with European data regulations. Finally, we share key insights and challenges faced during the project, offering recommendations for future endeavors in large-scale multilingual data preparation for LLMs.

This paper presents Okapi, a new dataset for Natural Language to executable web Application Programming Interfaces (NL2API). This dataset is in English and contains 22,508 questions and 9,019 unique API calls, covering three domains. We define new compositional generalization tasks for NL2API which explore the models' ability to extrapolate from simple API calls in the training set to new and more complex API calls in the inference phase. Also, the models are required to generate API calls that execute correctly as opposed to the existing approaches which evaluate queries with placeholder values. Our dataset is different than most of the existing compositional semantic parsing datasets because it is a non-synthetic dataset studying the compositional generalization in a low-resource setting. Okapi is a step towards creating realistic datasets and benchmarks for studying compositional generalization alongside the existing datasets and tasks. We report the generalization capabilities of sequence-to-sequence baseline models trained on a variety of the SCAN and Okapi datasets tasks. The best model achieves 15\% exact match accuracy when generalizing from simple API calls to more complex API calls. This highlights some challenges for future research. Okapi dataset and tasks are publicly available at https://aka.ms/nl2api/data.

Scientific documents record research findings and valuable human knowledge, comprising a vast corpus of high-quality data. Leveraging multi-modality data extracted from these documents and assessing large models' abilities to handle scientific document-oriented tasks is therefore meaningful. Despite promising advancements, large models still perform poorly on multi-page scientific document extraction and understanding tasks, and their capacity to process within-document data formats such as charts and equations remains under-explored. To address these issues, we present DocGenome, a structured document benchmark constructed by annotating 500K scientific documents from 153 disciplines in the arXiv open-access community, using our custom auto-labeling pipeline. DocGenome features four key characteristics: 1) Completeness: It is the first dataset to structure data from all modalities including 13 layout attributes along with their LaTeX source codes. 2) Logicality: It provides 6 logical relationships between different entities within each scientific document. 3) Diversity: It covers various document-oriented tasks, including document classification, visual grounding, document layout detection, document transformation, open-ended single-page QA and multi-page QA. 4) Correctness: It undergoes rigorous quality control checks conducted by a specialized team. We conduct extensive experiments to demonstrate the advantages of DocGenome and objectively evaluate the performance of large models on our benchmark.

Artificial intelligence (AI) technologies should adhere to human norms to better serve our society and avoid disseminating harmful or misleading information, particularly in Conversational Information Retrieval (CIR). Previous work, including approaches and datasets, has not always been successful or sufficiently robust in taking human norms into consideration. To this end, we introduce a workflow that integrates ethical alignment, with an initial ethical judgment stage for efficient data screening. To address the need for ethical judgment in CIR, we present the QA-ETHICS dataset, adapted from the ETHICS benchmark, which serves as an evaluation tool by unifying scenarios and label meanings. However, each scenario only considers one ethical concept. Therefore, we introduce the MP-ETHICS dataset to evaluate a scenario under multiple ethical concepts, such as justice and Deontology. In addition, we suggest a new approach that achieves top performance in both binary and multi-label ethical judgment tasks. Our research provides a practical method for introducing ethical alignment into the CIR workflow. The data and code are available at https://github.com/wanng-ide/ealm .

Most large language models are fine-tuned using either expensive human-annotated data or GPT-4 generated data which cannot guarantee performance in certain domains. We argue that although the web-crawled data often has formatting errors causing semantic inaccuracies, it can still serve as a valuable source for high-quality supervised fine-tuning in specific domains without relying on advanced models like GPT-4. To this end, we create a paired training dataset automatically by aligning web-crawled data with a smaller set of high-quality data. By training a language model on this dataset, we can convert web data with irregular formats into high-quality ones. Our experiments show that training with the model-transformed data yields better results, surpassing training with only high-quality data by an average score of 9.4% in Chinese math problems. Additionally, our 7B model outperforms several open-source models larger than 32B and surpasses well-known closed-source models such as GPT-3.5, highlighting the efficacy of our approach.

We present Mr. TyDi, a multi-lingual benchmark dataset for mono-lingual retrieval in eleven typologically diverse languages, designed to evaluate ranking with learned dense representations. The goal of this resource is to spur research in dense retrieval techniques in non-English languages, motivated by recent observations that existing techniques for representation learning perform poorly when applied to out-of-distribution data. As a starting point, we provide zero-shot baselines for this new dataset based on a multi-lingual adaptation of DPR that we call "mDPR". Experiments show that although the effectiveness of mDPR is much lower than BM25, dense representations nevertheless appear to provide valuable relevance signals, improving BM25 results in sparse-dense hybrids. In addition to analyses of our results, we also discuss future challenges and present a research agenda in multi-lingual dense retrieval. Mr. TyDi can be downloaded at https://github.com/castorini/mr.tydi.

Multilingual semantic search is the task of retrieving relevant contents to a query expressed in different language combinations. This requires a better semantic understanding of the user's intent and its contextual meaning. Multilingual semantic search is less explored and more challenging than its monolingual or bilingual counterparts, due to the lack of multilingual parallel resources for this task and the need to circumvent "language bias". In this work, we propose an alignment approach: MAML-Align, specifically for low-resource scenarios. Our approach leverages meta-distillation learning based on MAML, an optimization-based Model-Agnostic Meta-Learner. MAML-Align distills knowledge from a Teacher meta-transfer model T-MAML, specialized in transferring from monolingual to bilingual semantic search, to a Student model S-MAML, which meta-transfers from bilingual to multilingual semantic search. To the best of our knowledge, we are the first to extend meta-distillation to a multilingual search application. Our empirical results show that on top of a strong baseline based on sentence transformers, our meta-distillation approach boosts the gains provided by MAML and significantly outperforms naive fine-tuning methods. Furthermore, multilingual meta-distillation learning improves generalization even to unseen languages.

In Brazil, the governmental body responsible for overseeing and coordinating post-graduate programs, CAPES, keeps records of all theses and dissertations presented in the country. Information regarding such documents can be accessed online in the Theses and Dissertations Catalog (TDC), which contains abstracts in Portuguese and English, and additional metadata. Thus, this database can be a potential source of parallel corpora for the Portuguese and English languages. In this article, we present the development of a parallel corpus from TDC, which is made available by CAPES under the open data initiative. Approximately 240,000 documents were collected and aligned using the Hunalign tool. We demonstrate the capability of our developed corpus by training Statistical Machine Translation (SMT) and Neural Machine Translation (NMT) models for both language directions, followed by a comparison with Google Translate (GT). Both translation models presented better BLEU scores than GT, with NMT system being the most accurate one. Sentence alignment was also manually evaluated, presenting an average of 82.30% correctly aligned sentences. Our parallel corpus is freely available in TMX format, with complementary information regarding document metadata

We propose procedures for evaluating and strengthening contextual embedding alignment and show that they are useful in analyzing and improving multilingual BERT. In particular, after our proposed alignment procedure, BERT exhibits significantly improved zero-shot performance on XNLI compared to the base model, remarkably matching pseudo-fully-supervised translate-train models for Bulgarian and Greek. Further, to measure the degree of alignment, we introduce a contextual version of word retrieval and show that it correlates well with downstream zero-shot transfer. Using this word retrieval task, we also analyze BERT and find that it exhibits systematic deficiencies, e.g. worse alignment for open-class parts-of-speech and word pairs written in different scripts, that are corrected by the alignment procedure. These results support contextual alignment as a useful concept for understanding large multilingual pre-trained models.

Machine translation is highly sensitive to the size and quality of the training data, which has led to an increasing interest in collecting and filtering large parallel corpora. In this paper, we propose a new method for this task based on multilingual sentence embeddings. In contrast to previous approaches, which rely on nearest neighbor retrieval with a hard threshold over cosine similarity, our proposed method accounts for the scale inconsistencies of this measure, considering the margin between a given sentence pair and its closest candidates instead. Our experiments show large improvements over existing methods. We outperform the best published results on the BUCC mining task and the UN reconstruction task by more than 10 F1 and 30 precision points, respectively. Filtering the English-German ParaCrawl corpus with our approach, we obtain 31.2 BLEU points on newstest2014, an improvement of more than one point over the best official filtered version.

Pathogen identification is pivotal in diagnosing, treating, and preventing diseases, crucial for controlling infections and safeguarding public health. Traditional alignment-based methods, though widely used, are computationally intense and reliant on extensive reference databases, often failing to detect novel pathogens due to their low sensitivity and specificity. Similarly, conventional machine learning techniques, while promising, require large annotated datasets and extensive feature engineering and are prone to overfitting. Addressing these challenges, we introduce PathoLM, a cutting-edge pathogen language model optimized for the identification of pathogenicity in bacterial and viral sequences. Leveraging the strengths of pre-trained DNA models such as the Nucleotide Transformer, PathoLM requires minimal data for fine-tuning, thereby enhancing pathogen detection capabilities. It effectively captures a broader genomic context, significantly improving the identification of novel and divergent pathogens. We developed a comprehensive data set comprising approximately 30 species of viruses and bacteria, including ESKAPEE pathogens, seven notably virulent bacterial strains resistant to antibiotics. Additionally, we curated a species classification dataset centered specifically on the ESKAPEE group. In comparative assessments, PathoLM dramatically outperforms existing models like DciPatho, demonstrating robust zero-shot and few-shot capabilities. Furthermore, we expanded PathoLM-Sp for ESKAPEE species classification, where it showed superior performance compared to other advanced deep learning methods, despite the complexities of the task.

Keeping track of all relevant recent publications and experimental results for a research area is a challenging task. Prior work has demonstrated the efficacy of information extraction models in various scientific areas. Recently, several datasets have been released for the yet understudied materials science domain. However, these datasets focus on sub-problems such as parsing synthesis procedures or on sub-domains, e.g., solid oxide fuel cells. In this resource paper, we present MuLMS, a new dataset of 50 open-access articles, spanning seven sub-domains of materials science. The corpus has been annotated by domain experts with several layers ranging from named entities over relations to frame structures. We present competitive neural models for all tasks and demonstrate that multi-task training with existing related resources leads to benefits.

For machine translation, a vast majority of language pairs in the world are considered low-resource because they have little parallel data available. Besides the technical challenges of learning with limited supervision, it is difficult to evaluate methods trained on low-resource language pairs because of the lack of freely and publicly available benchmarks. In this work, we introduce the FLoRes evaluation datasets for Nepali-English and Sinhala-English, based on sentences translated from Wikipedia. Compared to English, these are languages with very different morphology and syntax, for which little out-of-domain parallel data is available and for which relatively large amounts of monolingual data are freely available. We describe our process to collect and cross-check the quality of translations, and we report baseline performance using several learning settings: fully supervised, weakly supervised, semi-supervised, and fully unsupervised. Our experiments demonstrate that current state-of-the-art methods perform rather poorly on this benchmark, posing a challenge to the research community working on low-resource MT. Data and code to reproduce our experiments are available at https://github.com/facebookresearch/flores.

In drug-discovery-related tasks such as virtual screening, machine learning is emerging as a promising way to predict molecular properties. Conventionally, molecular fingerprints (numerical representations of molecules) are calculated through rule-based algorithms that map molecules to a sparse discrete space. However, these algorithms perform poorly for shallow prediction models or small datasets. To address this issue, we present SMILES Transformer. Inspired by Transformer and pre-trained language models from natural language processing, SMILES Transformer learns molecular fingerprints through unsupervised pre-training of the sequence-to-sequence language model using a huge corpus of SMILES, a text representation system for molecules. We performed benchmarks on 10 datasets against existing fingerprints and graph-based methods and demonstrated the superiority of the proposed algorithms in small-data settings where pre-training facilitated good generalization. Moreover, we define a novel metric to concurrently measure model accuracy and data efficiency.

Understanding biological processes, drug development, and biotechnological advancements requires detailed analysis of protein structures and sequences, a task in protein research that is inherently complex and time-consuming when performed manually. To streamline this process, we introduce ProteinGPT, a state-of-the-art multi-modal protein chat system, that allows users to upload protein sequences and/or structures for comprehensive protein analysis and responsive inquiries. ProteinGPT seamlessly integrates protein sequence and structure encoders with linear projection layers for precise representation adaptation, coupled with a large language model (LLM) to generate accurate and contextually relevant responses. To train ProteinGPT, we construct a large-scale dataset of 132,092 proteins with annotations, and optimize the instruction-tuning process using GPT-4o. This innovative system ensures accurate alignment between the user-uploaded data and prompts, simplifying protein analysis. Experiments show that ProteinGPT can produce promising responses to proteins and their corresponding questions.

Multilingual generative models obtain remarkable cross-lingual capabilities through pre-training on large-scale corpora. However, they still exhibit a performance bias toward high-resource languages, and learn isolated distributions of sentence representations across languages. To bridge this gap, we propose a simple yet effective alignment framework exploiting pairs of translation sentences. It aligns the internal sentence representations across different languages via multilingual contrastive learning and aligns model outputs by answering prompts in different languages. Experimental results demonstrate that even with less than 0.1 {\textperthousand} of pre-training tokens, our alignment framework significantly boosts the cross-lingual abilities of generative models and mitigates the performance gap. Further analysis reveals that it results in a better internal multilingual representation distribution of multilingual models.

A diversity of tasks use language models trained on semantic similarity data. While there are a variety of datasets that capture semantic similarity, they are either constructed from modern web data or are relatively small datasets created in the past decade by human annotators. This study utilizes a novel source, newly digitized articles from off-copyright, local U.S. newspapers, to assemble a massive-scale semantic similarity dataset spanning 70 years from 1920 to 1989 and containing nearly 400M positive semantic similarity pairs. Historically, around half of articles in U.S. local newspapers came from newswires like the Associated Press. While local papers reproduced articles from the newswire, they wrote their own headlines, which form abstractive summaries of the associated articles. We associate articles and their headlines by exploiting document layouts and language understanding. We then use deep neural methods to detect which articles are from the same underlying source, in the presence of substantial noise and abridgement. The headlines of reproduced articles form positive semantic similarity pairs. The resulting publicly available HEADLINES dataset is significantly larger than most existing semantic similarity datasets and covers a much longer span of time. It will facilitate the application of contrastively trained semantic similarity models to a variety of tasks, including the study of semantic change across space and time.

Modern machine learning relies on datasets to develop and validate research ideas. Given the growth of publicly available data, finding the right dataset to use is increasingly difficult. Any research question imposes explicit and implicit constraints on how well a given dataset will enable researchers to answer this question, such as dataset size, modality, and domain. We operationalize the task of recommending datasets given a short natural language description of a research idea, to help people find relevant datasets for their needs. Dataset recommendation poses unique challenges as an information retrieval problem; datasets are hard to directly index for search and there are no corpora readily available for this task. To facilitate this task, we build the DataFinder Dataset which consists of a larger automatically-constructed training set (17.5K queries) and a smaller expert-annotated evaluation set (392 queries). Using this data, we compare various information retrieval algorithms on our test set and present a superior bi-encoder retriever for text-based dataset recommendation. This system, trained on the DataFinder Dataset, finds more relevant search results than existing third-party dataset search engines. To encourage progress on dataset recommendation, we release our dataset and models to the public.

Training and evaluating language models increasingly requires the construction of meta-datasets --diverse collections of curated data with clear provenance. Natural language prompting has recently lead to improved zero-shot generalization by transforming existing, supervised datasets into a diversity of novel pretraining tasks, highlighting the benefits of meta-dataset curation. While successful in general-domain text, translating these data-centric approaches to biomedical language modeling remains challenging, as labeled biomedical datasets are significantly underrepresented in popular data hubs. To address this challenge, we introduce BigBIO a community library of 126+ biomedical NLP datasets, currently covering 12 task categories and 10+ languages. BigBIO facilitates reproducible meta-dataset curation via programmatic access to datasets and their metadata, and is compatible with current platforms for prompt engineering and end-to-end few/zero shot language model evaluation. We discuss our process for task schema harmonization, data auditing, contribution guidelines, and outline two illustrative use cases: zero-shot evaluation of biomedical prompts and large-scale, multi-task learning. BigBIO is an ongoing community effort and is available at https://github.com/bigscience-workshop/biomedical

While natural language processing tools have been developed extensively for some of the world's languages, a significant portion of the world's over 7000 languages are still neglected. One reason for this is that evaluation datasets do not yet cover a wide range of languages, including low-resource and endangered ones. We aim to address this issue by creating a text classification dataset encompassing a large number of languages, many of which currently have little to no annotated data available. We leverage parallel translations of the Bible to construct such a dataset by first developing applicable topics and employing a crowdsourcing tool to collect annotated data. By annotating the English side of the data and projecting the labels onto other languages through aligned verses, we generate text classification datasets for more than 1500 languages. We extensively benchmark several existing multilingual language models using our dataset. To facilitate the advancement of research in this area, we will release our dataset and code.

Machine learning has emerged as a powerful tool for scientific discovery, enabling researchers to extract meaningful insights from complex datasets. For instance, it has facilitated the identification of disease-predictive genes from gene expression data, significantly advancing healthcare. However, the traditional process for analyzing such datasets demands substantial human effort and expertise for the data selection, processing, and analysis. To address this challenge, we introduce a novel framework, a Team of AI-made Scientists (TAIS), designed to streamline the scientific discovery pipeline. TAIS comprises simulated roles, including a project manager, data engineer, and domain expert, each represented by a Large Language Model (LLM). These roles collaborate to replicate the tasks typically performed by data scientists, with a specific focus on identifying disease-predictive genes. Furthermore, we have curated a benchmark dataset to assess TAIS's effectiveness in gene identification, demonstrating our system's potential to significantly enhance the efficiency and scope of scientific exploration. Our findings represent a solid step towards automating scientific discovery through large language models.

We present a novel architecture, In-Database Entity Linking (IDEL), in which we integrate the analytics-optimized RDBMS MonetDB with neural text mining abilities. Our system design abstracts core tasks of most neural entity linking systems for MonetDB. To the best of our knowledge, this is the first defacto implemented system integrating entity-linking in a database. We leverage the ability of MonetDB to support in-database-analytics with user defined functions (UDFs) implemented in Python. These functions call machine learning libraries for neural text mining, such as TensorFlow. The system achieves zero cost for data shipping and transformation by utilizing MonetDB's ability to embed Python processes in the database kernel and exchange data in NumPy arrays. IDEL represents text and relational data in a joint vector space with neural embeddings and can compensate errors with ambiguous entity representations. For detecting matching entities, we propose a novel similarity function based on joint neural embeddings which are learned via minimizing pairwise contrastive ranking loss. This function utilizes a high dimensional index structures for fast retrieval of matching entities. Our first implementation and experiments using the WebNLG corpus show the effectiveness and the potentials of IDEL.

Building a general-purpose task model similar to ChatGPT has been an important research direction for gene large language models. Instruction fine-tuning is a key component in building ChatGPT, but existing instructions are primarily based on natural language. Natural language and gene sequences have significant differences in tokenization and encoding. Therefore, constructing a multilingual model that can handle both natural language and gene sequences is crucial for solving this problem.In this paper, we expand the capabilities of the LLaMA large language model to include gene language. This involves expanding the vocabulary using the Byte Pair Encoding (BPE) method, specifically tailored for DNA and protein sequences, and conducting further pre-training on these sequences. We then convert various downstream gene task data into a unified format for instruction fine-tuning and further fine-tune the model on this data.Our study demonstrates that a mixed model of gene and natural language, fine-tuned with instructions, achieves results comparable to the current state-of-the-art (SOTA) in tasks such as gene classification and gene sequence interaction. This provides a promising direction for building a unified large language model for gene tasks.

The output structure of database-like tables, consisting of values structured in horizontal rows and vertical columns identifiable by name, can cover a wide range of NLP tasks. Following this constatation, we propose a framework for text-to-table neural models applicable to problems such as extraction of line items, joint entity and relation extraction, or knowledge base population. The permutation-based decoder of our proposal is a generalized sequential method that comprehends information from all cells in the table. The training maximizes the expected log-likelihood for a table's content across all random permutations of the factorization order. During the content inference, we exploit the model's ability to generate cells in any order by searching over possible orderings to maximize the model's confidence and avoid substantial error accumulation, which other sequential models are prone to. Experiments demonstrate a high practical value of the framework, which establishes state-of-the-art results on several challenging datasets, outperforming previous solutions by up to 15%.

This work focuses on leveraging and selecting from vast, unlabeled, open data to pre-fine-tune a pre-trained language model. The goal is to minimize the need for costly domain-specific data for subsequent fine-tuning while achieving desired performance levels. While many data selection algorithms have been designed for small-scale applications, rendering them unsuitable for our context, some emerging methods do cater to language data scales. However, they often prioritize data that aligns with the target distribution. While this strategy may be effective when training a model from scratch, it can yield limited results when the model has already been pre-trained on a different distribution. Differing from prior work, our key idea is to select data that nudges the pre-training distribution closer to the target distribution. We show the optimality of this approach for fine-tuning tasks under certain conditions. We demonstrate the efficacy of our methodology across a diverse array of tasks (NLU, NLG, zero-shot) with models up to 2.7B, showing that it consistently surpasses other selection methods. Moreover, our proposed method is significantly faster than existing techniques, scaling to millions of samples within a single GPU hour. Our code is open-sourced (Code repository: https://anonymous.4open.science/r/DV4LLM-D761/ ). While fine-tuning offers significant potential for enhancing performance across diverse tasks, its associated costs often limit its widespread adoption; with this work, we hope to lay the groundwork for cost-effective fine-tuning, making its benefits more accessible.

Recent AI advances have enabled multi-modal systems to model and translate diverse information spaces. Extending beyond text and vision, we introduce OneProt, a multi-modal AI for proteins that integrates structural, sequence, alignment, and binding site data. Using the ImageBind framework, OneProt aligns the latent spaces of modality encoders along protein sequences. It demonstrates strong performance in retrieval tasks and surpasses state-of-the-art methods in various downstream tasks, including metal ion binding classification, gene-ontology annotation, and enzyme function prediction. This work expands multi-modal capabilities in protein models, paving the way for applications in drug discovery, biocatalytic reaction planning, and protein engineering.

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream tasks: molecular property prediction against up to 19 baseline methods across four datasets, plus zero-shot molecule-morphology matching.

Idiomatic expressions have always been a bottleneck for language comprehension and natural language understanding, specifically for tasks like Machine Translation(MT). MT systems predominantly produce literal translations of idiomatic expressions as they do not exhibit generic and linguistically deterministic patterns which can be exploited for comprehension of the non-compositional meaning of the expressions. These expressions occur in parallel corpora used for training, but due to the comparatively high occurrences of the constituent words of idiomatic expressions in literal context, the idiomatic meaning gets overpowered by the compositional meaning of the expression. State of the art Metaphor Detection Systems are able to detect non-compositional usage at word level but miss out on idiosyncratic phrasal idiomatic expressions. This creates a dire need for a dataset with a wider coverage and higher occurrence of commonly occurring idiomatic expressions, the spans of which can be used for Metaphor Detection. With this in mind, we present our English Possible Idiomatic Expressions(EPIE) corpus containing 25206 sentences labelled with lexical instances of 717 idiomatic expressions. These spans also cover literal usages for the given set of idiomatic expressions. We also present the utility of our dataset by using it to train a sequence labelling module and testing on three independent datasets with high accuracy, precision and recall scores.

Many organizations rely on data from government and third-party sources, and those sources rarely follow the same data formatting. This introduces challenges in integrating data from multiple sources or aligning external sources with internal databases. Commercial database systems do not offer adequate support for integrating data from heterogeneous sources, and manual integration is both time-consuming and inefficient. State-of-the-art data integration approaches that rely on similarity functions and textual transformations often fail to handle challenging cases where multiple mappings are required, or the mappings go beyond simple textual transformations. In this paper, we study the potentials of deep neural models for transforming tables for joinability. In particular, we cast the problem as a prediction task and develop a framework that leverages large deep-learning language models to transform tabular data from a source formatting to a desired target representation. Our framework can efficiently learn the patterns for mapping a source formatting into an expected target using just a few examples, which can then be used for tasks such as table joining, filling in missing values, and error detection. Compared to state-of-the-art mapping and joining approaches, our framework delivers noticeably more accurate and scalable performance on both real-world and synthetic datasets. Our experimental evaluation also shows that the performance of the proposed framework using our fine-tuned model is at par or better than large language models such as GPT-3, despite the significant difference in size, and that using large language models within our framework improves their performance.

During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based language models, many language models that learn characteristics of nucleotide sequences have also emerged. These models show good performance in classifying various features of nucleotide sequences. When classifying nucleotide sequences, not only the sequence itself, but also various background knowledge is utilized. In this study, we use not only a nucleotide sequence-based language model but also a text language model based on PubMed articles to reflect more biological background knowledge in the model. We propose a method to fine-tune the nucleotide sequence language model and the text language model based on various databases of antibiotic resistance genes. We also propose an LLM-based augmentation technique to supplement the data and an ensemble method to effectively combine the two models. We also propose a benchmark for evaluating the model. Our method achieved better performance than the nucleotide sequence language model in the drug resistance class prediction.

Multiple critical scenarios (like Wikipedia text generation given English Infoboxes) need automated generation of descriptive text in low resource (LR) languages from English fact triples. Previous work has focused on English fact-to-text (F2T) generation. To the best of our knowledge, there has been no previous attempt on cross-lingual alignment or generation for LR languages. Building an effective cross-lingual F2T (XF2T) system requires alignment between English structured facts and LR sentences. We propose two unsupervised methods for cross-lingual alignment. We contribute XALIGN, an XF2T dataset with 0.45M pairs across 8 languages, of which 5402 pairs have been manually annotated. We also train strong baseline XF2T generation models on the XAlign dataset.

A promising application of AI to healthcare is the retrieval of information from electronic health records (EHRs), e.g. to aid clinicians in finding relevant information for a consultation or to recruit suitable patients for a study. This requires search capabilities far beyond simple string matching, including the retrieval of concepts (diagnoses, symptoms, medications, etc.) related to the one in question. The suitability of AI methods for such applications is tested by predicting the relatedness of concepts with known relatedness scores. However, all existing biomedical concept relatedness datasets are notoriously small and consist of hand-picked concept pairs. We open-source a novel concept relatedness benchmark overcoming these issues: it is six times larger than existing datasets and concept pairs are chosen based on co-occurrence in EHRs, ensuring their relevance for the application of interest. We present an in-depth analysis of our new dataset and compare it to existing ones, highlighting that it is not only larger but also complements existing datasets in terms of the types of concepts included. Initial experiments with state-of-the-art embedding methods show that our dataset is a challenging new benchmark for testing concept relatedness models.

The choice of embedding model is a crucial step in the design of Retrieval Augmented Generation (RAG) systems. Given the sheer volume of available options, identifying clusters of similar models streamlines this model selection process. Relying solely on benchmark performance scores only allows for a weak assessment of model similarity. Thus, in this study, we evaluate the similarity of embedding models within the context of RAG systems. Our assessment is two-fold: We use Centered Kernel Alignment to compare embeddings on a pair-wise level. Additionally, as it is especially pertinent to RAG systems, we evaluate the similarity of retrieval results between these models using Jaccard and rank similarity. We compare different families of embedding models, including proprietary ones, across five datasets from the popular Benchmark Information Retrieval (BEIR). Through our experiments we identify clusters of models corresponding to model families, but interestingly, also some inter-family clusters. Furthermore, our analysis of top-k retrieval similarity reveals high-variance at low k values. We also identify possible open-source alternatives to proprietary models, with Mistral exhibiting the highest similarity to OpenAI models.

Despite the strong research interest in document-level Machine Translation (MT), the test sets dedicated to this task are still scarce. The existing test sets mainly cover topics from the general domain and fall short on specialised domains, such as legal and financial. Also, in spite of their document-level aspect, they still follow a sentence-level logic that does not allow for including certain linguistic phenomena such as information reorganisation. In this work, we aim to fill this gap by proposing a novel test set: DOLFIN. The dataset is built from specialised financial documents, and it makes a step towards true document-level MT by abandoning the paradigm of perfectly aligned sentences, presenting data in units of sections rather than sentences. The test set consists of an average of 1950 aligned sections for five language pairs. We present a detailed data collection pipeline that can serve as inspiration for aligning new document-level datasets. We demonstrate the usefulness and quality of this test set by evaluating a number of models. Our results show that the test set is able to discriminate between context-sensitive and context-agnostic models and shows the weaknesses when models fail to accurately translate financial texts. The test set is made public for the community.

This work introduces Salamandra, a suite of open-source decoder-only large language models available in three different sizes: 2, 7, and 40 billion parameters. The models were trained from scratch on highly multilingual data that comprises text in 35 European languages and code. Our carefully curated corpus is made exclusively from open-access data compiled from a wide variety of sources. Along with the base models, supplementary checkpoints that were fine-tuned on public-domain instruction data are also released for chat applications. Additionally, we also share our preliminary experiments on multimodality, which serve as proof-of-concept to showcase potential applications for the Salamandra family. Our extensive evaluations on multilingual benchmarks reveal that Salamandra has strong capabilities, achieving competitive performance when compared to similarly sized open-source models. We provide comprehensive evaluation results both on standard downstream tasks as well as key aspects related to bias and safety.With this technical report, we intend to promote open science by sharing all the details behind our design choices, data curation strategy and evaluation methodology. In addition to that, we deviate from the usual practice by making our training and evaluation scripts publicly accessible. We release all models under a permissive Apache 2.0 license in order to foster future research and facilitate commercial use, thereby contributing to the open-source ecosystem of large language models.

We introduce WikiLingua, a large-scale, multilingual dataset for the evaluation of crosslingual abstractive summarization systems. We extract article and summary pairs in 18 languages from WikiHow, a high quality, collaborative resource of how-to guides on a diverse set of topics written by human authors. We create gold-standard article-summary alignments across languages by aligning the images that are used to describe each how-to step in an article. As a set of baselines for further studies, we evaluate the performance of existing cross-lingual abstractive summarization methods on our dataset. We further propose a method for direct crosslingual summarization (i.e., without requiring translation at inference time) by leveraging synthetic data and Neural Machine Translation as a pre-training step. Our method significantly outperforms the baseline approaches, while being more cost efficient during inference.

In the field of language modeling, models augmented with retrieval components have emerged as a promising solution to address several challenges faced in the natural language processing (NLP) field, including knowledge grounding, interpretability, and scalability. Despite the primary focus on NLP, we posit that the paradigm of retrieval-enhancement can be extended to a broader spectrum of machine learning (ML) such as computer vision, time series prediction, and computational biology. Therefore, this work introduces a formal framework of this paradigm, Retrieval-Enhanced Machine Learning (REML), by synthesizing the literature in various domains in ML with consistent notations which is missing from the current literature. Also, we found that while a number of studies employ retrieval components to augment their models, there is a lack of integration with foundational Information Retrieval (IR) research. We bridge this gap between the seminal IR research and contemporary REML studies by investigating each component that comprises the REML framework. Ultimately, the goal of this work is to equip researchers across various disciplines with a comprehensive, formally structured framework of retrieval-enhanced models, thereby fostering interdisciplinary future research.

We present Spider, a large-scale, complex and cross-domain semantic parsing and text-to-SQL dataset annotated by 11 college students. It consists of 10,181 questions and 5,693 unique complex SQL queries on 200 databases with multiple tables, covering 138 different domains. We define a new complex and cross-domain semantic parsing and text-to-SQL task where different complex SQL queries and databases appear in train and test sets. In this way, the task requires the model to generalize well to both new SQL queries and new database schemas. Spider is distinct from most of the previous semantic parsing tasks because they all use a single database and the exact same programs in the train set and the test set. We experiment with various state-of-the-art models and the best model achieves only 12.4% exact matching accuracy on a database split setting. This shows that Spider presents a strong challenge for future research. Our dataset and task are publicly available at https://yale-lily.github.io/spider

Proteins are essential to life's processes, underpinning evolution and diversity. Advances in sequencing technology have revealed millions of proteins, underscoring the need for sophisticated pre-trained protein models for biological analysis and AI development. Facebook's ESM2, the most advanced protein language model to date, leverages a masked prediction task for unsupervised learning, crafting amino acid representations with notable biochemical accuracy. Yet, it lacks in delivering functional protein insights, signaling an opportunity for enhancing representation quality.Our study addresses this gap by incorporating protein family classification into ESM2's training.This approach, augmented with Community Propagation-Based Clustering Algorithm, improves global protein representations, while a contextual prediction task fine-tunes local amino acid accuracy. Significantly, our model achieved state-of-the-art results in several downstream experiments, demonstrating the power of combining global and local methodologies to substantially boost protein representation quality.

Despite Portuguese being one of the most spoken languages in the world, there is a lack of high-quality information retrieval datasets in that language. We present Quati, a dataset specifically designed for the Brazilian Portuguese language. It comprises a collection of queries formulated by native speakers and a curated set of documents sourced from a selection of high-quality Brazilian Portuguese websites. These websites are frequented more likely by real users compared to those randomly scraped, ensuring a more representative and relevant corpus. To label the query-document pairs, we use a state-of-the-art LLM, which shows inter-annotator agreement levels comparable to human performance in our assessments. We provide a detailed description of our annotation methodology to enable others to create similar datasets for other languages, providing a cost-effective way of creating high-quality IR datasets with an arbitrary number of labeled documents per query. Finally, we evaluate a diverse range of open-source and commercial retrievers to serve as baseline systems. Quati is publicly available at https://huggingface.co/datasets/unicamp-dl/quati and all scripts at https://github.com/unicamp-dl/quati .

High-quality text embedding is pivotal in improving semantic textual similarity (STS) tasks, which are crucial components in Large Language Model (LLM) applications. However, a common challenge existing text embedding models face is the problem of vanishing gradients, primarily due to their reliance on the cosine function in the optimization objective, which has saturation zones. To address this issue, this paper proposes a novel angle-optimized text embedding model called AnglE. The core idea of AnglE is to introduce angle optimization in a complex space. This novel approach effectively mitigates the adverse effects of the saturation zone in the cosine function, which can impede gradient and hinder optimization processes. To set up a comprehensive STS evaluation, we experimented on existing short-text STS datasets and a newly collected long-text STS dataset from GitHub Issues. Furthermore, we examine domain-specific STS scenarios with limited labeled data and explore how AnglE works with LLM-annotated data. Extensive experiments were conducted on various tasks including short-text STS, long-text STS, and domain-specific STS tasks. The results show that AnglE outperforms the state-of-the-art (SOTA) STS models that ignore the cosine saturation zone. These findings demonstrate the ability of AnglE to generate high-quality text embeddings and the usefulness of angle optimization in STS.

We introduce S2ORC, a large corpus of 81.1M English-language academic papers spanning many academic disciplines. The corpus consists of rich metadata, paper abstracts, resolved bibliographic references, as well as structured full text for 8.1M open access papers. Full text is annotated with automatically-detected inline mentions of citations, figures, and tables, each linked to their corresponding paper objects. In S2ORC, we aggregate papers from hundreds of academic publishers and digital archives into a unified source, and create the largest publicly-available collection of machine-readable academic text to date. We hope this resource will facilitate research and development of tools and tasks for text mining over academic text.

Similarity between training examples is used to curate pretraining datasets for language models by many methods -- for diversification and to select examples similar to high-quality data. However, similarity is typically measured with off-the-shelf embedding models that are generic or trained for tasks such as retrieval. This paper introduces a framework to analyze the suitability of embedding models specifically for data curation in the language model pretraining setting. We quantify the correlation between similarity in the embedding space to similarity in pretraining loss between different training examples, and how diversifying in the embedding space affects pretraining quality. We analyze a variety of embedding models in our framework, with experiments using the Pile dataset for pretraining a 1.7B parameter decoder-only language model. We find that the embedding models we consider are all useful for pretraining data curation. Moreover, a simple approach of averaging per-token embeddings proves to be surprisingly competitive with more sophisticated embedding models -- likely because the latter are not designed specifically for pretraining data curation. Indeed, we believe our analysis and evaluation framework can serve as a foundation for the design of embedding models that specifically reason about similarity in pretraining datasets.

We introduce SMUTF, a unique approach for large-scale tabular data schema matching (SM), which assumes that supervised learning does not affect performance in open-domain tasks, thereby enabling effective cross-domain matching. This system uniquely combines rule-based feature engineering, pre-trained language models, and generative large language models. In an innovative adaptation inspired by the Humanitarian Exchange Language, we deploy 'generative tags' for each data column, enhancing the effectiveness of SM. SMUTF exhibits extensive versatility, working seamlessly with any pre-existing pre-trained embeddings, classification methods, and generative models. Recognizing the lack of extensive, publicly available datasets for SM, we have created and open-sourced the HDXSM dataset from the public humanitarian data. We believe this to be the most exhaustive SM dataset currently available. In evaluations across various public datasets and the novel HDXSM dataset, SMUTF demonstrated exceptional performance, surpassing existing state-of-the-art models in terms of accuracy and efficiency, and} improving the F1 score by 11.84% and the AUC of ROC by 5.08%.

We introduce the first method for translating text embeddings from one vector space to another without any paired data, encoders, or predefined sets of matches. Our unsupervised approach translates any embedding to and from a universal latent representation (i.e., a universal semantic structure conjectured by the Platonic Representation Hypothesis). Our translations achieve high cosine similarity across model pairs with different architectures, parameter counts, and training datasets. The ability to translate unknown embeddings into a different space while preserving their geometry has serious implications for the security of vector databases. An adversary with access only to embedding vectors can extract sensitive information about the underlying documents, sufficient for classification and attribute inference.

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

This paper describes the development of a new benchmark for machine translation that provides training and test data for thousands of language pairs covering over 500 languages and tools for creating state-of-the-art translation models from that collection. The main goal is to trigger the development of open translation tools and models with a much broader coverage of the World's languages. Using the package it is possible to work on realistic low-resource scenarios avoiding artificially reduced setups that are common when demonstrating zero-shot or few-shot learning. For the first time, this package provides a comprehensive collection of diverse data sets in hundreds of languages with systematic language and script annotation and data splits to extend the narrow coverage of existing benchmarks. Together with the data release, we also provide a growing number of pre-trained baseline models for individual language pairs and selected language groups.

We propose ParaSCI, the first large-scale paraphrase dataset in the scientific field, including 33,981 paraphrase pairs from ACL (ParaSCI-ACL) and 316,063 pairs from arXiv (ParaSCI-arXiv). Digging into characteristics and common patterns of scientific papers, we construct this dataset though intra-paper and inter-paper methods, such as collecting citations to the same paper or aggregating definitions by scientific terms. To take advantage of sentences paraphrased partially, we put up PDBERT as a general paraphrase discovering method. The major advantages of paraphrases in ParaSCI lie in the prominent length and textual diversity, which is complementary to existing paraphrase datasets. ParaSCI obtains satisfactory results on human evaluation and downstream tasks, especially long paraphrase generation.

The paper focuses on deep learning semantic search algorithms applied in the HR domain. The aim of the article is developing a novel approach to training a Siamese network to link the skills mentioned in the job ad with the title. It has been shown that the title normalization process can be based either on classification or similarity comparison approaches. While classification algorithms strive to classify a sample into predefined set of categories, similarity search algorithms take a more flexible approach, since they are designed to find samples that are similar to a given query sample, without requiring pre-defined classes and labels. In this article semantic similarity search to find candidates for title normalization has been used. A pre-trained language model has been adapted while teaching it to match titles and skills based on co-occurrence information. For the purpose of this research fifty billion title-descriptions pairs had been collected for training the model and thirty three thousand title-description-normalized title triplets, where normalized job title was picked up manually by job ad creator for testing purposes. As baselines FastText, BERT, SentenceBert and JobBert have been used. As a metric of the accuracy of the designed algorithm is Recall in top one, five and ten model's suggestions. It has been shown that the novel training objective lets it achieve significant improvement in comparison to other generic and specific text encoders. Two settings with treating titles as standalone strings, and with included skills as additional features during inference have been used and the results have been compared in this article. Improvements by 10% and 21.5% have been achieved using VacancySBERT and VacancySBERT (with skills) respectively. The benchmark has been developed as open-source to foster further research in the area.

As opposed to scaling-up protein language models (PLMs), we seek improving performance via protein-specific optimization. Although the proportionality between the language model size and the richness of its learned representations is validated, we prioritize accessibility and pursue a path of data-efficient, cost-reduced, and knowledge-guided optimization. Through over twenty experiments ranging from masking, architecture, and pre-training data, we derive insights from protein-specific experimentation into building a model that interprets the language of life, optimally. We present Ankh, the first general-purpose PLM trained on Google's TPU-v4 surpassing the state-of-the-art performance with fewer parameters (<10% for pre-training, <7% for inference, and <30% for the embedding dimension). We provide a representative range of structure and function benchmarks where Ankh excels. We further provide a protein variant generation analysis on High-N and One-N input data scales where Ankh succeeds in learning protein evolutionary conservation-mutation trends and introducing functional diversity while retaining key structural-functional characteristics. We dedicate our work to promoting accessibility to research innovation via attainable resources.

We describe PARANMT-50M, a dataset of more than 50 million English-English sentential paraphrase pairs. We generated the pairs automatically by using neural machine translation to translate the non-English side of a large parallel corpus, following Wieting et al. (2017). Our hope is that ParaNMT-50M can be a valuable resource for paraphrase generation and can provide a rich source of semantic knowledge to improve downstream natural language understanding tasks. To show its utility, we use ParaNMT-50M to train paraphrastic sentence embeddings that outperform all supervised systems on every SemEval semantic textual similarity competition, in addition to showing how it can be used for paraphrase generation.