Daily Papers

In many machine learning for healthcare tasks, standard datasets are constructed by amassing data across many, often fundamentally dissimilar, sources. But when does adding more data help, and when does it hinder progress on desired model outcomes in real-world settings? We identify this situation as the Data Addition Dilemma, demonstrating that adding training data in this multi-source scaling context can at times result in reduced overall accuracy, uncertain fairness outcomes, and reduced worst-subgroup performance. We find that this possibly arises from an empirically observed trade-off between model performance improvements due to data scaling and model deterioration from distribution shift. We thus establish baseline strategies for navigating this dilemma, introducing distribution shift heuristics to guide decision-making on which data sources to add in data scaling, in order to yield the expected model performance improvements. We conclude with a discussion of the required considerations for data collection and suggestions for studying data composition and scale in the age of increasingly larger models.

Developing clinical prediction models (e.g., mortality prediction) based on electronic health records (EHRs) typically relies on expert opinion for feature selection and adjusting observation window size. This burdens experts and creates a bottleneck in the development process. We propose Retrieval-Enhanced Medical prediction model (REMed) to address such challenges. REMed can essentially evaluate an unlimited number of clinical events, select the relevant ones, and make predictions. This approach effectively eliminates the need for manual feature selection and enables an unrestricted observation window. We verified these properties through experiments on 27 clinical tasks and two independent cohorts from publicly available EHR datasets, where REMed outperformed other contemporary architectures that aim to handle as many events as possible. Notably, we found that the preferences of REMed align closely with those of medical experts. We expect our approach to significantly expedite the development of EHR prediction models by minimizing clinicians' need for manual involvement.

Curating a large scale medical imaging dataset for machine learning applications is both time consuming and expensive. Balancing the workload between model development, data collection and annotations is difficult for machine learning practitioners, especially under time constraints. Causal analysis is often used in medicine and economics to gain insights about the effects of actions and policies. In this paper we explore the effect of dataset interventions on the output of image classification models. Through a causal approach we investigate the effects of the quantity and type of data we need to incorporate in a dataset to achieve better performance for specific subtasks. The main goal of this paper is to highlight the potential of causal analysis as a tool for resource optimization for developing medical imaging ML applications. We explore this concept with a synthetic dataset and an exemplary use-case for Diabetic Retinopathy image analysis.

Large Vision-Language Models (LVLMs) have achieved significant progress in combining visual comprehension with language generation. Despite this success, the training data of LVLMs still suffers from Long-Tail (LT) problems, where the data distribution is highly imbalanced. Previous works have mainly focused on traditional VLM architectures, i.e., CLIP or ViT, and specific tasks such as recognition and classification. Nevertheless, the exploration of LVLM (e.g. LLaVA) and more general tasks (e.g. Visual Question Answering and Visual Reasoning) remains under-explored. In this paper, we first conduct an in-depth analysis of the LT issues in LVLMs and identify two core causes: the overrepresentation of head concepts and the underrepresentation of tail concepts. Based on the above observation, we propose an Adaptive Data Refinement Framework (ADR), which consists of two stages: Data Rebalancing (DR) and Data Synthesis (DS). In the DR stage, we adaptively rebalance the redundant data based on entity distributions, while in the DS stage, we leverage Denoising Diffusion Probabilistic Models (DDPMs) and scarce images to supplement underrepresented portions. Through comprehensive evaluations across eleven benchmarks, our proposed ADR effectively mitigates the long-tail problem in the training data, improving the average performance of LLaVA 1.5 relatively by 4.36%, without increasing the training data volume.

Automatic medical report generation (MRG) is of great research value as it has the potential to relieve radiologists from the heavy burden of report writing. Despite recent advancements, accurate MRG remains challenging due to the need for precise clinical understanding and the identification of clinical findings. Moreover, the imbalanced distribution of diseases makes the challenge even more pronounced, as rare diseases are underrepresented in training data, making their diagnostic performance unreliable. To address these challenges, we propose diagnosis-driven prompts for medical report generation (PromptMRG), a novel framework that aims to improve the diagnostic accuracy of MRG with the guidance of diagnosis-aware prompts. Specifically, PromptMRG is based on encoder-decoder architecture with an extra disease classification branch. When generating reports, the diagnostic results from the classification branch are converted into token prompts to explicitly guide the generation process. To further improve the diagnostic accuracy, we design cross-modal feature enhancement, which retrieves similar reports from the database to assist the diagnosis of a query image by leveraging the knowledge from a pre-trained CLIP. Moreover, the disease imbalanced issue is addressed by applying an adaptive logit-adjusted loss to the classification branch based on the individual learning status of each disease, which overcomes the barrier of text decoder's inability to manipulate disease distributions. Experiments on two MRG benchmarks show the effectiveness of the proposed method, where it obtains state-of-the-art clinical efficacy performance on both datasets.

Federated learning (FL) has been a promising approach in the field of medical imaging in recent years. A critical problem in FL, specifically in medical scenarios is to have a more accurate shared model which is robust to noisy and out-of distribution clients. In this work, we tackle the problem of statistical heterogeneity in data for FL which is highly plausible in medical data where for example the data comes from different sites with different scanner settings. We propose IDA (Inverse Distance Aggregation), a novel adaptive weighting approach for clients based on meta-information which handles unbalanced and non-iid data. We extensively analyze and evaluate our method against the well-known FL approach, Federated Averaging as a baseline.

Automating radiology report generation can significantly alleviate radiologists' workloads. Previous research has primarily focused on realizing highly concise observations while neglecting the precise attributes that determine the severity of diseases (e.g., small pleural effusion). Since incorrect attributes will lead to imprecise radiology reports, strengthening the generation process with precise attribute modeling becomes necessary. Additionally, the temporal information contained in the historical records, which is crucial in evaluating a patient's current condition (e.g., heart size is unchanged), has also been largely disregarded. To address these issues, we propose RECAP, which generates precise and accurate radiology reports via dynamic disease progression reasoning. Specifically, RECAP first predicts the observations and progressions (i.e., spatiotemporal information) given two consecutive radiographs. It then combines the historical records, spatiotemporal information, and radiographs for report generation, where a disease progression graph and dynamic progression reasoning mechanism are devised to accurately select the attributes of each observation and progression. Extensive experiments on two publicly available datasets demonstrate the effectiveness of our model.

The rapid advancement of large-scale vision-language models has showcased remarkable capabilities across various tasks. However, the lack of extensive and high-quality image-text data in medicine has greatly hindered the development of large-scale medical vision-language models. In this work, we present a diagnosis-guided bootstrapping strategy that exploits both image and label information to construct vision-language datasets. Based on the constructed dataset, we developed MedDr, a generalist foundation model for healthcare capable of handling diverse medical data modalities, including radiology, pathology, dermatology, retinography, and endoscopy. Moreover, during inference, we propose a simple but effective retrieval-augmented medical diagnosis strategy, which enhances the model's generalization ability. Extensive experiments on visual question answering, medical report generation, and medical image diagnosis demonstrate the superiority of our method.

Fairness or equity in machine learning is profoundly important for societal well-being, but limited public datasets hinder its progress, especially in the area of medicine. It is undeniable that fairness in medicine is one of the most important areas for fairness learning's applications. Currently, no large-scale public medical datasets with 3D imaging data for fairness learning are available, while 3D imaging data in modern clinics are standard tests for disease diagnosis. In addition, existing medical fairness datasets are actually repurposed datasets, and therefore they typically have limited demographic identity attributes with at most three identity attributes of age, gender, and race for fairness modeling. To address this gap, we introduce our Eye Fairness dataset with 30,000 subjects (Harvard-EF) covering three major eye diseases including age-related macular degeneration, diabetic retinopathy, and glaucoma affecting 380 million patients globally. Our Harvard-EF dataset includes both 2D fundus photos and 3D optical coherence tomography scans with six demographic identity attributes including age, gender, race, ethnicity, preferred language, and marital status. We also propose a fair identity scaling (FIS) approach combining group and individual scaling together to improve model fairness. Our FIS approach is compared with various state-of-the-art fairness learning methods with superior performance in the racial, gender, and ethnicity fairness tasks with 2D and 3D imaging data, which demonstrate the utilities of our Harvard-EF dataset for fairness learning. To facilitate fairness comparisons between different models, we propose performance-scaled disparity measures, which can be used to compare model fairness accounting for overall performance levels. The dataset and code are publicly accessible via https://ophai.hms.harvard.edu/datasets/harvard-ef30k.

Fairness is essential for machine learning systems deployed in high-stake applications. Among all fairness notions, individual fairness, deriving from a consensus that `similar individuals should be treated similarly,' is a vital notion to describe fair treatment for individual cases. Previous studies typically characterize individual fairness as a prediction-invariant problem when perturbing sensitive attributes on samples, and solve it by Distributionally Robust Optimization (DRO) paradigm. However, such adversarial perturbations along a direction covering sensitive information used in DRO do not consider the inherent feature correlations or innate data constraints, therefore could mislead the model to optimize at off-manifold and unrealistic samples. In light of this drawback, in this paper, we propose to learn and generate antidote data that approximately follows the data distribution to remedy individual unfairness. These generated on-manifold antidote data can be used through a generic optimization procedure along with original training data, resulting in a pure pre-processing approach to individual unfairness, or can also fit well with the in-processing DRO paradigm. Through extensive experiments on multiple tabular datasets, we demonstrate our method resists individual unfairness at a minimal or zero cost to predictive utility compared to baselines.

Background: Natural Language Processing (NLP) is widely used to extract clinical insights from Electronic Health Records (EHRs). However, the lack of annotated data, automated tools, and other challenges hinder the full utilisation of NLP for EHRs. Various Machine Learning (ML), Deep Learning (DL) and NLP techniques are studied and compared to understand the limitations and opportunities in this space comprehensively. Methodology: After screening 261 articles from 11 databases, we included 127 papers for full-text review covering seven categories of articles: 1) medical note classification, 2) clinical entity recognition, 3) text summarisation, 4) deep learning (DL) and transfer learning architecture, 5) information extraction, 6) Medical language translation and 7) other NLP applications. This study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Result and Discussion: EHR was the most commonly used data type among the selected articles, and the datasets were primarily unstructured. Various ML and DL methods were used, with prediction or classification being the most common application of ML or DL. The most common use cases were: the International Classification of Diseases, Ninth Revision (ICD-9) classification, clinical note analysis, and named entity recognition (NER) for clinical descriptions and research on psychiatric disorders. Conclusion: We find that the adopted ML models were not adequately assessed. In addition, the data imbalance problem is quite important, yet we must find techniques to address this underlining problem. Future studies should address key limitations in studies, primarily identifying Lupus Nephritis, Suicide Attempts, perinatal self-harmed and ICD-9 classification.

Underlying data structures, such as symmetries or invariances to transformations, are often exploited to improve the solution of learning tasks. However, embedding these properties in models or learning algorithms can be challenging and computationally intensive. Data augmentation, on the other hand, induces these symmetries during training by applying multiple transformations to the input data. Despite its ubiquity, its effectiveness depends on the choices of which transformations to apply, when to do so, and how often. In fact, there is both empirical and theoretical evidence that the indiscriminate use of data augmentation can introduce biases that outweigh its benefits. This work tackles these issues by automatically adapting the data augmentation while solving the learning task. To do so, it formulates data augmentation as an invariance-constrained learning problem and leverages Monte Carlo Markov Chain (MCMC) sampling to solve it. The result is a practical algorithm that not only does away with a priori searches for augmentation distributions, but also dynamically controls if and when data augmentation is applied. Our experiments illustrate the performance of this method, which achieves state-of-the-art results in automatic data augmentation benchmarks for CIFAR datasets. Furthermore, this approach can be used to gather insights on the actual symmetries underlying a learning task.

Addressing fairness in artificial intelligence (AI), particularly in medical AI, is crucial for ensuring equitable healthcare outcomes. Recent efforts to enhance fairness have introduced new methodologies and datasets in medical AI. However, the fairness issue under the setting of domain transfer is almost unexplored, while it is common that clinics rely on different imaging technologies (e.g., different retinal imaging modalities) for patient diagnosis. This paper presents FairDomain, a pioneering systemic study into algorithmic fairness under domain shifts, employing state-of-the-art domain adaptation (DA) and generalization (DG) algorithms for both medical segmentation and classification tasks to understand how biases are transferred between different domains. We also introduce a novel plug-and-play fair identity attention (FIA) module that adapts to various DA and DG algorithms to improve fairness by using self-attention to adjust feature importance based on demographic attributes. Additionally, we curate the first fairness-focused dataset with two paired imaging modalities for the same patient cohort on medical segmentation and classification tasks, to rigorously assess fairness in domain-shift scenarios. Excluding the confounding impact of demographic distribution variation between source and target domains will allow clearer quantification of the performance of domain transfer models. Our extensive evaluations reveal that the proposed FIA significantly enhances both model performance accounted for fairness across all domain shift settings (i.e., DA and DG) with respect to different demographics, which outperforms existing methods on both segmentation and classification. The code and data can be accessed at https://ophai.hms.harvard.edu/datasets/harvard-fairdomain20k.

Small sample sizes are common in many disciplines, which necessitates pooling roughly similar datasets across multiple institutions to study weak but relevant associations between images and disease outcomes. Such data often manifest shift/imbalance in covariates (i.e., secondary non-imaging data). Controlling for such nuisance variables is common within standard statistical analysis, but the ideas do not directly apply to overparameterized models. Consequently, recent work has shown how strategies from invariant representation learning provides a meaningful starting point, but the current repertoire of methods is limited to accounting for shifts/imbalances in just a couple of covariates at a time. In this paper, we show how viewing this problem from the perspective of Category theory provides a simple and effective solution that completely avoids elaborate multi-stage training pipelines that would otherwise be needed. We show the effectiveness of this approach via extensive experiments on real datasets. Further, we discuss how this style of formulation offers a unified perspective on at least 5+ distinct problem settings, from self-supervised learning to matching problems in 3D reconstruction.

Precise breast cancer classification on histopathological images has the potential to greatly improve the diagnosis and patient outcome in oncology. The data imbalance problem largely stems from the inherent imbalance within medical image datasets, where certain tumor subtypes may appear much less frequently. This constitutes a considerable limitation in biased model predictions that can overlook critical but rare classes. In this work, we adopted EfficientNet, a state-of-the-art convolutional neural network (CNN) model that balances high accuracy with computational cost efficiency. To address data imbalance, we introduce an intensive data augmentation pipeline and cost-sensitive learning, improving representation and ensuring that the model does not overly favor majority classes. This approach provides the ability to learn effectively from rare tumor types, improving its robustness. Additionally, we fine-tuned the model using transfer learning, where weights in the beginning trained on a binary classification task were adopted to multi-class classification, improving the capability to detect complex patterns within the BreakHis dataset. Our results underscore significant improvements in the binary classification performance, achieving an exceptional recall increase for benign cases from 0.92 to 0.95, alongside an accuracy enhancement from 97.35 % to 98.23%. Our approach improved the performance of multi-class tasks from 91.27% with regular augmentation to 94.54% with intensive augmentation, reaching 95.04% with transfer learning. This framework demonstrated substantial gains in precision in the minority classes, such as Mucinous carcinoma and Papillary carcinoma, while maintaining high recall consistently across these critical subtypes, as further confirmed by confusion matrix analysis.

Dynamic treatment regimes (DTRs) are personalized, adaptive, multi-stage treatment plans that adapt treatment decisions both to an individual's initial features and to intermediate outcomes and features at each subsequent stage, which are affected by decisions in prior stages. Examples include personalized first- and second-line treatments of chronic conditions like diabetes, cancer, and depression, which adapt to patient response to first-line treatment, disease progression, and individual characteristics. While existing literature mostly focuses on estimating the optimal DTR from offline data such as from sequentially randomized trials, we study the problem of developing the optimal DTR in an online manner, where the interaction with each individual affect both our cumulative reward and our data collection for future learning. We term this the DTR bandit problem. We propose a novel algorithm that, by carefully balancing exploration and exploitation, is guaranteed to achieve rate-optimal regret when the transition and reward models are linear. We demonstrate our algorithm and its benefits both in synthetic experiments and in a case study of adaptive treatment of major depressive disorder using real-world data.

With significant advancements in diffusion models, addressing the potential risks of dataset bias becomes increasingly important. Since generated outputs directly suffer from dataset bias, mitigating latent bias becomes a key factor in improving sample quality and proportion. This paper proposes time-dependent importance reweighting to mitigate the bias for the diffusion models. We demonstrate that the time-dependent density ratio becomes more precise than previous approaches, thereby minimizing error propagation in generative learning. While directly applying it to score-matching is intractable, we discover that using the time-dependent density ratio both for reweighting and score correction can lead to a tractable form of the objective function to regenerate the unbiased data density. Furthermore, we theoretically establish a connection with traditional score-matching, and we demonstrate its convergence to an unbiased distribution. The experimental evidence supports the usefulness of the proposed method, which outperforms baselines including time-independent importance reweighting on CIFAR-10, CIFAR-100, FFHQ, and CelebA with various bias settings. Our code is available at https://github.com/alsdudrla10/TIW-DSM.

In this paper, we introduce DRR-RATE, a large-scale synthetic chest X-ray dataset derived from the recently released CT-RATE dataset. DRR-RATE comprises of 50,188 frontal Digitally Reconstructed Radiographs (DRRs) from 21,304 unique patients. Each image is paired with a corresponding radiology text report and binary labels for 18 pathology classes. Given the controllable nature of DRR generation, it facilitates the inclusion of lateral view images and images from any desired viewing position. This opens up avenues for research into new and novel multimodal applications involving paired CT, X-ray images from various views, text, and binary labels. We demonstrate the applicability of DRR-RATE alongside existing large-scale chest X-ray resources, notably the CheXpert dataset and CheXnet model. Experiments demonstrate that CheXnet, when trained and tested on the DRR-RATE dataset, achieves sufficient to high AUC scores for the six common pathologies cited in common literature: Atelectasis, Cardiomegaly, Consolidation, Lung Lesion, Lung Opacity, and Pleural Effusion. Additionally, CheXnet trained on the CheXpert dataset can accurately identify several pathologies, even when operating out of distribution. This confirms that the generated DRR images effectively capture the essential pathology features from CT images. The dataset and labels are publicly accessible at https://huggingface.co/datasets/farrell236/DRR-RATE.

Gastrointestinal (GI) diseases represent a significant global health concern, with Capsule Endoscopy (CE) offering a non-invasive method for diagnosis by capturing a large number of GI tract images. However, the sheer volume of video frames necessitates automated analysis to reduce the workload on doctors and increase the diagnostic accuracy. In this paper, we present CapsuleNet, a deep learning model developed for the Capsule Vision 2024 Challenge, aimed at classifying 10 distinct GI abnormalities. Using a highly imbalanced dataset, we implemented various data augmentation strategies, reducing the data imbalance to a manageable level. Our model leverages a pretrained EfficientNet-b7 backbone, tuned with additional layers for classification and optimized with PReLU activation functions. The model demonstrated superior performance on validation data, achieving a micro accuracy of 84.5% and outperforming the VGG16 baseline across most classes. Despite these advances, challenges remain in classifying certain abnormalities, such as Erythema. Our findings suggest that CNN-based models like CapsuleNet can provide an efficient solution for GI tract disease classification, particularly when inference time is a critical factor.

Data augmentation (DA) is widely used to improve the generalization of neural networks by enforcing the invariances and symmetries to pre-defined transformations applied to input data. However, a fixed augmentation policy may have different effects on each sample in different training stages but existing approaches cannot adjust the policy to be adaptive to each sample and the training model. In this paper, we propose Model Adaptive Data Augmentation (MADAug) that jointly trains an augmentation policy network to teach the model when to learn what. Unlike previous work, MADAug selects augmentation operators for each input image by a model-adaptive policy varying between training stages, producing a data augmentation curriculum optimized for better generalization. In MADAug, we train the policy through a bi-level optimization scheme, which aims to minimize a validation-set loss of a model trained using the policy-produced data augmentations. We conduct an extensive evaluation of MADAug on multiple image classification tasks and network architectures with thorough comparisons to existing DA approaches. MADAug outperforms or is on par with other baselines and exhibits better fairness: it brings improvement to all classes and more to the difficult ones. Moreover, MADAug learned policy shows better performance when transferred to fine-grained datasets. In addition, the auto-optimized policy in MADAug gradually introduces increasing perturbations and naturally forms an easy-to-hard curriculum.

In the field of algorithmic fairness, significant attention has been put on group fairness criteria, such as Demographic Parity and Equalized Odds. Nevertheless, these objectives, measured as global averages, have raised concerns about persistent local disparities between sensitive groups. In this work, we address the problem of local fairness, which ensures that the predictor is unbiased not only in terms of expectations over the whole population, but also within any subregion of the feature space, unknown at training time. To enforce this objective, we introduce ROAD, a novel approach that leverages the Distributionally Robust Optimization (DRO) framework within a fair adversarial learning objective, where an adversary tries to infer the sensitive attribute from the predictions. Using an instance-level re-weighting strategy, ROAD is designed to prioritize inputs that are likely to be locally unfair, i.e. where the adversary faces the least difficulty in reconstructing the sensitive attribute. Numerical experiments demonstrate the effectiveness of our method: it achieves Pareto dominance with respect to local fairness and accuracy for a given global fairness level across three standard datasets, and also enhances fairness generalization under distribution shift.

Data imbalance is a common problem in machine learning that can have a critical effect on the performance of a model. Various solutions exist but their impact on the convergence of the learning dynamics is not understood. Here, we elucidate the significant negative impact of data imbalance on learning, showing that the learning curves for minority and majority classes follow sub-optimal trajectories when training with a gradient-based optimizer. This slowdown is related to the imbalance ratio and can be traced back to a competition between the optimization of different classes. Our main contribution is the analysis of the convergence of full-batch (GD) and stochastic gradient descent (SGD), and of variants that renormalize the contribution of each per-class gradient. We find that GD is not guaranteed to decrease the loss for each class but that this problem can be addressed by performing a per-class normalization of the gradient. With SGD, class imbalance has an additional effect on the direction of the gradients: the minority class suffers from a higher directional noise, which reduces the effectiveness of the per-class gradient normalization. Our findings not only allow us to understand the potential and limitations of strategies involving the per-class gradients, but also the reason for the effectiveness of previously used solutions for class imbalance such as oversampling.

We consider the task of evaluating policies of algorithmic resource allocation through randomized controlled trials (RCTs). Such policies are tasked with optimizing the utilization of limited intervention resources, with the goal of maximizing the benefits derived. Evaluation of such allocation policies through RCTs proves difficult, notwithstanding the scale of the trial, because the individuals' outcomes are inextricably interlinked through resource constraints controlling the policy decisions. Our key contribution is to present a new estimator leveraging our proposed novel concept, that involves retrospective reshuffling of participants across experimental arms at the end of an RCT. We identify conditions under which such reassignments are permissible and can be leveraged to construct counterfactual trials, whose outcomes can be accurately ascertained, for free. We prove theoretically that such an estimator is more accurate than common estimators based on sample means -- we show that it returns an unbiased estimate and simultaneously reduces variance. We demonstrate the value of our approach through empirical experiments on synthetic, semi-synthetic as well as real case study data and show improved estimation accuracy across the board.

Synthetic data generation offers a promising solution to enhance the usefulness of Electronic Healthcare Records (EHR) by generating realistic de-identified data. However, the existing literature primarily focuses on the quality of synthetic health data, neglecting the crucial aspect of fairness in downstream predictions. Consequently, models trained on synthetic EHR have faced criticism for producing biased outcomes in target tasks. These biases can arise from either spurious correlations between features or the failure of models to accurately represent sub-groups. To address these concerns, we present Bias-transforming Generative Adversarial Networks (Bt-GAN), a GAN-based synthetic data generator specifically designed for the healthcare domain. In order to tackle spurious correlations (i), we propose an information-constrained Data Generation Process that enables the generator to learn a fair deterministic transformation based on a well-defined notion of algorithmic fairness. To overcome the challenge of capturing exact sub-group representations (ii), we incentivize the generator to preserve sub-group densities through score-based weighted sampling. This approach compels the generator to learn from underrepresented regions of the data manifold. We conduct extensive experiments using the MIMIC-III database. Our results demonstrate that Bt-GAN achieves SOTA accuracy while significantly improving fairness and minimizing bias amplification. We also perform an in-depth explainability analysis to provide additional evidence supporting the validity of our study. In conclusion, our research introduces a novel and professional approach to addressing the limitations of synthetic data generation in the healthcare domain. By incorporating fairness considerations and leveraging advanced techniques such as GANs, we pave the way for more reliable and unbiased predictions in healthcare applications.

The meaningful use of electronic health records (EHR) continues to progress in the digital era with clinical decision support systems augmented by artificial intelligence. A priority in improving provider experience is to overcome information overload and reduce the cognitive burden so fewer medical errors and cognitive biases are introduced during patient care. One major type of medical error is diagnostic error due to systematic or predictable errors in judgment that rely on heuristics. The potential for clinical natural language processing (cNLP) to model diagnostic reasoning in humans with forward reasoning from data to diagnosis and potentially reduce the cognitive burden and medical error has not been investigated. Existing tasks to advance the science in cNLP have largely focused on information extraction and named entity recognition through classification tasks. We introduce a novel suite of tasks coined as Diagnostic Reasoning Benchmarks, DR.BENCH, as a new benchmark for developing and evaluating cNLP models with clinical diagnostic reasoning ability. The suite includes six tasks from ten publicly available datasets addressing clinical text understanding, medical knowledge reasoning, and diagnosis generation. DR.BENCH is the first clinical suite of tasks designed to be a natural language generation framework to evaluate pre-trained language models. Experiments with state-of-the-art pre-trained generative language models using large general domain models and models that were continually trained on a medical corpus demonstrate opportunities for improvement when evaluated in DR. BENCH. We share DR. BENCH as a publicly available GitLab repository with a systematic approach to load and evaluate models for the cNLP community.

Retrieval-augmented generation (RAG) is a well-suited technique for retrieving privacy-sensitive Electronic Health Records (EHR). It can serve as a key module of the healthcare copilot, helping reduce misdiagnosis for healthcare practitioners and patients. However, the diagnostic accuracy and specificity of existing heuristic-based RAG models used in the medical domain are inadequate, particularly for diseases with similar manifestations. This paper proposes MedRAG, a RAG model enhanced by knowledge graph (KG)-elicited reasoning for the medical domain that retrieves diagnosis and treatment recommendations based on manifestations. MedRAG systematically constructs a comprehensive four-tier hierarchical diagnostic KG encompassing critical diagnostic differences of various diseases. These differences are dynamically integrated with similar EHRs retrieved from an EHR database, and reasoned within a large language model. This process enables more accurate and specific decision support, while also proactively providing follow-up questions to enhance personalized medical decision-making. MedRAG is evaluated on both a public dataset DDXPlus and a private chronic pain diagnostic dataset (CPDD) collected from Tan Tock Seng Hospital, and its performance is compared against various existing RAG methods. Experimental results show that, leveraging the information integration and relational abilities of the KG, our MedRAG provides more specific diagnostic insights and outperforms state-of-the-art models in reducing misdiagnosis rates. Our code will be available at https://github.com/SNOWTEAM2023/MedRAG

Deep recommender systems (DRS) are intensively applied in modern web services. To deal with the massive web contents, DRS employs a two-stage workflow: retrieval and ranking, to generate its recommendation results. The retriever aims to select a small set of relevant candidates from the entire items with high efficiency; while the ranker, usually more precise but time-consuming, is supposed to further refine the best items from the retrieved candidates. Traditionally, the two components are trained either independently or within a simple cascading pipeline, which is prone to poor collaboration effect. Though some latest works suggested to train retriever and ranker jointly, there still exist many severe limitations: item distribution shift between training and inference, false negative, and misalignment of ranking order. As such, it remains to explore effective collaborations between retriever and ranker.

As the field of artificial intelligence progresses, assistive technologies are becoming more widely used across all industries. The healthcare industry is no different, with numerous studies being done to develop assistive tools for healthcare professionals. Automatic diagnostic systems are one such beneficial tool that can assist with a variety of tasks, including collecting patient information, analyzing test results, and diagnosing patients. However, the idea of developing systems that can provide a differential diagnosis has been largely overlooked in most of these research studies. In this study, we propose a transformer-based approach for providing differential diagnoses based on a patient's age, sex, medical history, and symptoms. We use the DDXPlus dataset, which provides differential diagnosis information for patients based on 49 disease types. Firstly, we propose a method to process the tabular patient data from the dataset and engineer them into patient reports to make them suitable for our research. In addition, we introduce two data modification modules to diversify the training data and consequently improve the robustness of the models. We approach the task as a multi-label classification problem and conduct extensive experiments using four transformer models. All the models displayed promising results by achieving over 97% F1 score on the held-out test set. Moreover, we design additional behavioral tests to get a broader understanding of the models. In particular, for one of our test cases, we prepared a custom test set of 100 samples with the assistance of a doctor. The results on the custom set showed that our proposed data modification modules improved the model's generalization capabilities. We hope our findings will provide future researchers with valuable insights and inspire them to develop reliable systems for automatic differential diagnosis.

Randomized controlled trials are susceptible to imbalance on covariates predictive of the outcome. Rerandomization and deterministic treatment assignment are two proposed solutions. This paper explores the relationship between rerandomization and deterministic assignment, showing how deterministic assignment is an extreme case of rerandomization. The paper argues that in small experiments, both fully randomized and fully deterministic assignment have limitations. Instead, the researcher should consider setting the rerandomization acceptance probability based on an analysis of covariates and assumptions about the data structure to achieve an optimal alignment between randomness and balance. This allows for the calculation of minimum p-values along with valid permutation tests and fiducial intervals. The paper also introduces tools, including a new, open-source R package named fastrerandomize, to implement rerandomization and explore options for optimal rerandomization acceptance thresholds.

Large recommendation models (LRMs) are fundamental to the multi-billion dollar online advertising industry, processing massive datasets of hundreds of billions of examples before transitioning to continuous online training to adapt to rapidly changing user behavior. The massive scale of data directly impacts both computational costs and the speed at which new methods can be evaluated (R&D velocity). This paper presents actionable principles and high-level frameworks to guide practitioners in optimizing training data requirements. These strategies have been successfully deployed in Google's largest Ads CTR prediction models and are broadly applicable beyond LRMs. We outline the concept of data convergence, describe methods to accelerate this convergence, and finally, detail how to optimally balance training data volume with model size.

Fairness in artificial intelligence models has gained significantly more attention in recent years, especially in the area of medicine, as fairness in medical models is critical to people's well-being and lives. High-quality medical fairness datasets are needed to promote fairness learning research. Existing medical fairness datasets are all for classification tasks, and no fairness datasets are available for medical segmentation, while medical segmentation is an equally important clinical task as classifications, which can provide detailed spatial information on organ abnormalities ready to be assessed by clinicians. In this paper, we propose the first fairness dataset for medical segmentation named Harvard-FairSeg with 10,000 subject samples. In addition, we propose a fair error-bound scaling approach to reweight the loss function with the upper error-bound in each identity group, using the segment anything model (SAM). We anticipate that the segmentation performance equity can be improved by explicitly tackling the hard cases with high training errors in each identity group. To facilitate fair comparisons, we utilize a novel equity-scaled segmentation performance metric to compare segmentation metrics in the context of fairness, such as the equity-scaled Dice coefficient. Through comprehensive experiments, we demonstrate that our fair error-bound scaling approach either has superior or comparable fairness performance to the state-of-the-art fairness learning models. The dataset and code are publicly accessible via https://ophai.hms.harvard.edu/datasets/harvard-fairseg10k.

The rehearsal strategy is widely used to alleviate the catastrophic forgetting problem in class incremental learning (CIL) by preserving limited exemplars from previous tasks. With imbalanced sample numbers between old and new classes, the classifier learning can be biased. Existing CIL methods exploit the long-tailed (LT) recognition techniques, e.g., the adjusted losses and the data re-sampling methods, to handle the data imbalance issue within each increment task. In this work, the dynamic nature of data imbalance in CIL is shown and a novel Dynamic Residual Classifier (DRC) is proposed to handle this challenging scenario. Specifically, DRC is built upon a recent advance residual classifier with the branch layer merging to handle the model-growing problem. Moreover, DRC is compatible with different CIL pipelines and substantially improves them. Combining DRC with the model adaptation and fusion (MAF) pipeline, this method achieves state-of-the-art results on both the conventional CIL and the LT-CIL benchmarks. Extensive experiments are also conducted for a detailed analysis. The code is publicly available.

Model selection/optimization in conformal inference is challenging, since it may break the exchangeability between labeled and unlabeled data. We study this problem in the context of conformal selection, which uses conformal p-values to select ``interesting'' instances with large unobserved labels from a pool of unlabeled data, while controlling the FDR in finite sample. For validity, existing solutions require the model choice to be independent of the data used to construct the p-values and calibrate the selection set. However, when presented with many model choices and limited labeled data, it is desirable to (i) select the best model in a data-driven manner, and (ii) mitigate power loss due to sample splitting. This paper presents OptCS, a general framework that allows valid statistical testing (selection) after flexible data-driven model optimization. We introduce general conditions under which OptCS constructs valid conformal p-values despite substantial data reuse and handles complex p-value dependencies to maintain finite-sample FDR control via a novel multiple testing procedure. We instantiate this general recipe to propose three FDR-controlling procedures, each optimizing the models differently: (i) selecting the most powerful one among multiple pre-trained candidate models, (ii) using all data for model fitting without sample splitting, and (iii) combining full-sample model fitting and selection. We demonstrate the efficacy of our methods via simulation studies and real applications in drug discovery and alignment of large language models in radiology report generation.

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.

The rapid development of large language models has led to the widespread adoption of Retrieval-Augmented Generation (RAG), which integrates external knowledge to alleviate knowledge bottlenecks and mitigate hallucinations. However, the existing RAG paradigm inevitably suffers from the impact of flawed information introduced during the retrieval phrase, thereby diminishing the reliability and correctness of the generated outcomes. In this paper, we propose Credibility-aware Generation (CAG), a universally applicable framework designed to mitigate the impact of flawed information in RAG. At its core, CAG aims to equip models with the ability to discern and process information based on its credibility. To this end, we propose an innovative data transformation framework that generates data based on credibility, thereby effectively endowing models with the capability of CAG. Furthermore, to accurately evaluate the models' capabilities of CAG, we construct a comprehensive benchmark covering three critical real-world scenarios. Experimental results demonstrate that our model can effectively understand and utilize credibility for generation, significantly outperform other models with retrieval augmentation, and exhibit resilience against the disruption caused by noisy documents, thereby maintaining robust performance. Moreover, our model supports customized credibility, offering a wide range of potential applications.

Bias in training datasets must be managed for various groups in classification tasks to ensure parity or equal treatment. With the recent growth in artificial intelligence models and their expanding role in automated decision-making, ensuring that these models are not biased is vital. There is an abundance of evidence suggesting that these models could contain or even amplify the bias present in the data on which they are trained, inherent to their objective function and learning algorithms; Many researchers direct their attention to this issue in different directions, namely, changing data to be statistically independent, adversarial training for restricting the capabilities of a particular competitor who aims to maximize parity, etc. These methods result in information loss and do not provide a suitable balance between accuracy and fairness or do not ensure limiting the biases in training. To this end, we propose a powerful strategy for training deep learning models called the Distraction module, which can be theoretically proven effective in controlling bias from affecting the classification results. This method can be utilized with different data types (e.g., Tabular, images, graphs, etc.). We demonstrate the potency of the proposed method by testing it on UCI Adult and Heritage Health datasets (tabular), POKEC-Z, POKEC-N and NBA datasets (graph), and CelebA dataset (vision). Using state-of-the-art methods proposed in the fairness literature for each dataset, we exhibit our model is superior to these proposed methods in minimizing bias and maintaining accuracy.

Radiology report generation (RRG) has attracted significant attention due to its potential to reduce the workload of radiologists. Current RRG approaches are still unsatisfactory against clinical standards. This paper introduces a novel RRG method, LM-RRG, that integrates large models (LMs) with clinical quality reinforcement learning to generate accurate and comprehensive chest X-ray radiology reports. Our method first designs a large language model driven feature extractor to analyze and interpret different regions of the chest X-ray image, emphasizing specific regions with medical significance. Next, based on the large model's decoder, we develop a multimodal report generator that leverages multimodal prompts from visual features and textual instruction to produce the radiology report in an auto-regressive way. Finally, to better reflect the clinical significant and insignificant errors that radiologists would normally assign in the report, we introduce a novel clinical quality reinforcement learning strategy. It utilizes the radiology report clinical quality (RadCliQ) metric as a reward function in the learning process. Extensive experiments on the MIMIC-CXR and IU-Xray datasets demonstrate the superiority of our method over the state of the art.

The demand for emergency department (ED) services is increasing across the globe, particularly during the current COVID-19 pandemic. Clinical triage and risk assessment have become increasingly challenging due to the shortage of medical resources and the strain on hospital infrastructure caused by the pandemic. As a result of the widespread use of electronic health records (EHRs), we now have access to a vast amount of clinical data, which allows us to develop predictive models and decision support systems to address these challenges. To date, however, there are no widely accepted benchmark ED triage prediction models based on large-scale public EHR data. An open-source benchmarking platform would streamline research workflows by eliminating cumbersome data preprocessing, and facilitate comparisons among different studies and methodologies. In this paper, based on the Medical Information Mart for Intensive Care IV Emergency Department (MIMIC-IV-ED) database, we developed a publicly available benchmark suite for ED triage predictive models and created a benchmark dataset that contains over 400,000 ED visits from 2011 to 2019. We introduced three ED-based outcomes (hospitalization, critical outcomes, and 72-hour ED reattendance) and implemented a variety of popular methodologies, ranging from machine learning methods to clinical scoring systems. We evaluated and compared the performance of these methods against benchmark tasks. Our codes are open-source, allowing anyone with MIMIC-IV-ED data access to perform the same steps in data processing, benchmark model building, and experiments. This study provides future researchers with insights, suggestions, and protocols for managing raw data and developing risk triaging tools for emergency care.

Model fairness is an essential element for Trustworthy AI. While many techniques for model fairness have been proposed, most of them assume that the training and deployment data distributions are identical, which is often not true in practice. In particular, when the bias between labels and sensitive groups changes, the fairness of the trained model is directly influenced and can worsen. We make two contributions for solving this problem. First, we analytically show that existing in-processing fair algorithms have fundamental limits in accuracy and group fairness. We introduce the notion of correlation shifts, which can explicitly capture the change of the above bias. Second, we propose a novel pre-processing step that samples the input data to reduce correlation shifts and thus enables the in-processing approaches to overcome their limitations. We formulate an optimization problem for adjusting the data ratio among labels and sensitive groups to reflect the shifted correlation. A key benefit of our approach lies in decoupling the roles of pre- and in-processing approaches: correlation adjustment via pre-processing and unfairness mitigation on the processed data via in-processing. Experiments show that our framework effectively improves existing in-processing fair algorithms w.r.t. accuracy and fairness, both on synthetic and real datasets.

Building deep reinforcement learning (RL) agents that find a good policy with few samples has proven notoriously challenging. To achieve sample efficiency, recent work has explored updating neural networks with large numbers of gradient steps for every new sample. While such high update-to-data (UTD) ratios have shown strong empirical performance, they also introduce instability to the training process. Previous approaches need to rely on periodic neural network parameter resets to address this instability, but restarting the training process is infeasible in many real-world applications and requires tuning the resetting interval. In this paper, we focus on one of the core difficulties of stable training with limited samples: the inability of learned value functions to generalize to unobserved on-policy actions. We mitigate this issue directly by augmenting the off-policy RL training process with a small amount of data generated from a learned world model. Our method, Model-Augmented Data for TD Learning (MAD-TD), uses small amounts of generated data to stabilize high UTD training and achieve competitive performance on the most challenging tasks in the DeepMind control suite. Our experiments further highlight the importance of employing a good model to generate data, MAD-TD's ability to combat value overestimation, and its practical stability gains for continued learning.

In many real-world applications, graph-structured data used for training and testing have differences in distribution, such as in high energy physics (HEP) where simulation data used for training may not match real experiments. Graph domain adaptation (GDA) is a method used to address these differences. However, current GDA primarily works by aligning the distributions of node representations output by a single graph neural network encoder shared across the training and testing domains, which may often yield sub-optimal solutions. This work examines different impacts of distribution shifts caused by either graph structure or node attributes and identifies a new type of shift, named conditional structure shift (CSS), which current GDA approaches are provably sub-optimal to deal with. A novel approach, called structural reweighting (StruRW), is proposed to address this issue and is tested on synthetic graphs, four benchmark datasets, and a new application in HEP. StruRW has shown significant performance improvement over the baselines in the settings with large graph structure shifts, and reasonable performance improvement when node attribute shift dominates.

Machine Learning methods can learn how to reconstruct Magnetic Resonance Images and thereby accelerate acquisition, which is of paramount importance to the clinical workflow. Physics-informed networks incorporate the forward model of accelerated MRI reconstruction in the learning process. With increasing network complexity, robustness is not ensured when reconstructing data unseen during training. We aim to embed data consistency (DC) in deep networks while balancing the degree of network complexity. While doing so, we will assess whether either explicit or implicit enforcement of DC in varying network architectures is preferred to optimize performance. We propose a scheme called Cascades of Independently Recurrent Inference Machines (CIRIM) to assess DC through unrolled optimization. Herein we assess DC both implicitly by gradient descent and explicitly by a designed term. Extensive comparison of the CIRIM to CS as well as to other methods is performed: the E2EVN, CascadeNet, KIKINet, LPDNet, RIM, IRIM, and UNet. Models were trained and evaluated on T1-weighted and FLAIR contrast brain data, and T2-weighted knee data. Both 1D and 2D undersampling patterns were evaluated. Robustness was tested by reconstructing 7.5x prospectively undersampled 3D FLAIR MRI data of Multiple Sclerosis (MS) patients with white matter lesions. The CIRIM performed best when implicitly enforcing DC, while the E2EVN required an explicit DC formulation. In reconstructing MS patient data, prospectively acquired with a sampling pattern unseen during model training, the CIRIM maintained lesion contrast while efficiently denoising the images. The CIRIM showed highly promising generalization capabilities maintaining a very fair trade-off between reconstructed image quality and fast reconstruction times, which is crucial in the clinical workflow.

Medical report generation from X-ray images is a challenging task, particularly in an unpaired setting where paired image-report data is unavailable for training. To address this challenge, we propose a novel model that leverages the available information in two distinct datasets, one comprising reports and the other consisting of images. The core idea of our model revolves around the notion that combining auto-encoding report generation with multi-modal (report-image) alignment can offer a solution. However, the challenge persists regarding how to achieve this alignment when pair correspondence is absent. Our proposed solution involves the use of auxiliary tasks, particularly contrastive learning and classification, to position related images and reports in close proximity to each other. This approach differs from previous methods that rely on pre-processing steps, such as using external information stored in a knowledge graph. Our model, named MedRAT, surpasses previous state-of-the-art methods, demonstrating the feasibility of generating comprehensive medical reports without the need for paired data or external tools.

Diabetic retinopathy (DR) is a growing health problem worldwide and is a leading cause of visual impairment and blindness, especially among working people aged 20-65. Its incidence is increasing along with the number of diabetes cases, and it is more common in developed countries than in developing countries. Recent research in the field of diabetic retinopathy diagnosis is using advanced technologies, such as analysis of images obtained by ophthalmoscopy. Automatic methods for analyzing eye images based on neural networks, deep learning and image analysis algorithms can improve the efficiency of diagnosis. This paper describes an automatic DR diagnosis method that includes processing and analysis of ophthalmoscopic images of the eye. It uses morphological algorithms to identify the optic disc and lesions characteristic of DR, such as microaneurysms, hemorrhages and exudates. Automated DR diagnosis has the potential to improve the efficiency of early detection of this disease and contribute to reducing the number of cases of diabetes-related visual impairment. The final step was to create an application with a graphical user interface that allowed retinal images taken at cooperating ophthalmology offices to be uploaded to the server. These images were then analyzed using a developed algorithm to make a diagnosis.

In the field of Computer Science, conference and workshop papers serve as important contributions, carrying substantial weight in research assessment processes, compared to other disciplines. However, a considerable number of these papers are not assigned a Digital Object Identifier (DOI), hence their citations are not reported in widely used citation datasets like OpenCitations and Crossref, raising limitations to citation analysis. While the Microsoft Academic Graph (MAG) previously addressed this issue by providing substantial coverage, its discontinuation has created a void in available data. BIP! NDR aims to alleviate this issue and enhance the research assessment processes within the field of Computer Science. To accomplish this, it leverages a workflow that identifies and retrieves Open Science papers lacking DOIs from the DBLP Corpus, and by performing text analysis, it extracts citation information directly from their full text. The current version of the dataset contains more than 510K citations made by approximately 60K open access Computer Science conference or workshop papers that, according to DBLP, do not have a DOI.

Various data augmentation techniques have been recently proposed in image-based deep reinforcement learning (DRL). Although they empirically demonstrate the effectiveness of data augmentation for improving sample efficiency or generalization, which technique should be preferred is not always clear. To tackle this question, we analyze existing methods to better understand them and to uncover how they are connected. Notably, by expressing the variance of the Q-targets and that of the empirical actor/critic losses of these methods, we can analyze the effects of their different components and compare them. We furthermore formulate an explanation about how these methods may be affected by choosing different data augmentation transformations in calculating the target Q-values. This analysis suggests recommendations on how to exploit data augmentation in a more principled way. In addition, we include a regularization term called tangent prop, previously proposed in computer vision, but whose adaptation to DRL is novel to the best of our knowledge. We evaluate our proposition and validate our analysis in several domains. Compared to different relevant baselines, we demonstrate that it achieves state-of-the-art performance in most environments and shows higher sample efficiency and better generalization ability in some complex environments.

How to ensure fairness is an important topic in federated learning (FL). Recent studies have investigated how to reward clients based on their contribution (collaboration fairness), and how to achieve uniformity of performance across clients (performance fairness). Despite achieving progress on either one, we argue that it is critical to consider them together, in order to engage and motivate more diverse clients joining FL to derive a high-quality global model. In this work, we propose a novel method to optimize both types of fairness simultaneously. Specifically, we propose to estimate client contribution in gradient and data space. In gradient space, we monitor the gradient direction differences of each client with respect to others. And in data space, we measure the prediction error on client data using an auxiliary model. Based on this contribution estimation, we propose a FL method, federated training via contribution estimation (FedCE), i.e., using estimation as global model aggregation weights. We have theoretically analyzed our method and empirically evaluated it on two real-world medical datasets. The effectiveness of our approach has been validated with significant performance improvements, better collaboration fairness, better performance fairness, and comprehensive analytical studies.

The recent success of Large Language Models (LLMs) has had a significant impact on the healthcare field, providing patients with medical advice, diagnostic information, and more. However, due to a lack of professional medical knowledge, patients are easily misled by generated erroneous information from LLMs, which may result in serious medical problems. To address this issue, we focus on tuning the LLMs to be medical assistants who collaborate with more experienced doctors. We first conduct a two-stage survey by inspiration-feedback to gain a broad understanding of the real needs of doctors for medical assistants. Based on this, we construct a Chinese medical dataset called DoctorFLAN to support the entire workflow of doctors, which includes 92K Q\&A samples from 22 tasks and 27 specialists. Moreover, we evaluate LLMs in doctor-oriented scenarios by constructing the DoctorFLAN-test containing 550 single-turn Q\&A and DotaBench containing 74 multi-turn conversations. The evaluation results indicate that being a medical assistant still poses challenges for existing open-source models, but DoctorFLAN can help them significantly. It demonstrates that the doctor-oriented dataset and benchmarks we construct can complement existing patient-oriented work and better promote medical LLMs research.

The digitization of medical records ushered in a new era of big data to clinical science, and with it the possibility that data could be shared, to multiply insights beyond what investigators could abstract from paper records. The need to share individual-level medical data to accelerate innovation in precision medicine continues to grow, and has never been more urgent, as scientists grapple with the COVID-19 pandemic. However, enthusiasm for the use of big data has been tempered by a fully appropriate concern for patient autonomy and privacy. That is, the ability to extract private or confidential information about an individual, in practice, renders it difficult to share data, since significant infrastructure and data governance must be established before data can be shared. Although HIPAA provided de-identification as an approved mechanism for data sharing, linkage attacks were identified as a major vulnerability. A variety of mechanisms have been established to avoid leaking private information, such as field suppression or abstraction, strictly limiting the amount of information that can be shared, or employing mathematical techniques such as differential privacy. Another approach, which we focus on here, is creating synthetic data that mimics the underlying data. For synthetic data to be a useful mechanism in support of medical innovation and a proxy for real-world evidence, one must demonstrate two properties of the synthetic dataset: (1) any analysis on the real data must be matched by analysis of the synthetic data (statistical fidelity) and (2) the synthetic data must preserve privacy, with minimal risk of re-identification (privacy guarantee). In this paper we propose a framework for quantifying the statistical fidelity and privacy preservation properties of synthetic datasets and demonstrate these metrics for synthetic data generated by Syntegra technology.

Concept shift is a prevailing problem in natural tasks like medical image segmentation where samples usually come from different subpopulations with variant correlations between features and labels. One common type of concept shift in medical image segmentation is the "information imbalance" between label-sparse samples with few (if any) segmentation labels and label-dense samples with plentiful labeled pixels. Existing distributionally robust algorithms have focused on adaptively truncating/down-weighting the "less informative" (i.e., label-sparse in our context) samples. To exploit data features of label-sparse samples more efficiently, we propose an adaptively weighted online optimization algorithm -- AdaWAC -- to incorporate data augmentation consistency regularization in sample reweighting. Our method introduces a set of trainable weights to balance the supervised loss and unsupervised consistency regularization of each sample separately. At the saddle point of the underlying objective, the weights assign label-dense samples to the supervised loss and label-sparse samples to the unsupervised consistency regularization. We provide a convergence guarantee by recasting the optimization as online mirror descent on a saddle point problem. Our empirical results demonstrate that AdaWAC not only enhances the segmentation performance and sample efficiency but also improves the robustness to concept shift on various medical image segmentation tasks with different UNet-style backbones.

Biomedical research is growing at such an exponential pace that scientists, researchers, and practitioners are no more able to cope with the amount of published literature in the domain. The knowledge presented in the literature needs to be systematized in such a way that claims and hypotheses can be easily found, accessed, and validated. Knowledge graphs can provide such a framework for semantic knowledge representation from literature. However, in order to build a knowledge graph, it is necessary to extract knowledge as relationships between biomedical entities and normalize both entities and relationship types. In this paper, we present and compare few rule-based and machine learning-based (Naive Bayes, Random Forests as examples of traditional machine learning methods and DistilBERT, PubMedBERT, T5 and SciFive-based models as examples of modern deep learning transformers) methods for scalable relationship extraction from biomedical literature, and for the integration into the knowledge graphs. We examine how resilient are these various methods to unbalanced and fairly small datasets. Our experiments show that transformer-based models handle well both small (due to pre-training on a large dataset) and unbalanced datasets. The best performing model was the PubMedBERT-based model fine-tuned on balanced data, with a reported F1-score of 0.92. DistilBERT-based model followed with F1-score of 0.89, performing faster and with lower resource requirements. BERT-based models performed better then T5-based generative models.

We focus on the Source Free Object Detection (SFOD) problem, when source data is unavailable during adaptation, and the model must adapt to the unlabeled target domain. In medical imaging, several approaches have leveraged a semi-supervised student-teacher architecture to bridge domain discrepancy. Context imbalance in labeled training data and significant domain shifts between domains can lead to biased teacher models that produce inaccurate pseudolabels, degrading the student model's performance and causing a mode collapse. Class imbalance, particularly when one class significantly outnumbers another, leads to contextual bias. To tackle the problem of context bias and the significant performance drop of the student model in the SFOD setting, we introduce Grounded Teacher (GT) as a standard framework. In this study, we model contextual relationships using a dedicated relational context module and leverage it to mitigate inherent biases in the model. This approach enables us to apply augmentations to closely related classes, across and within domains, enhancing the performance of underrepresented classes while keeping the effect on dominant classes minimal. We further improve the quality of predictions by implementing an expert foundational branch to supervise the student model. We validate the effectiveness of our approach in mitigating context bias under the SFOD setting through experiments on three medical datasets supported by comprehensive ablation studies. All relevant resources, including preprocessed data, trained model weights, and code, are publicly available at this https://github.com/Tajamul21/Grounded_Teacher.

As deep neural networks include a high number of parameters and operations, it can be a challenge to implement these models on devices with limited computational resources. Despite the development of novel pruning methods toward resource-efficient models, it has become evident that these models are not capable of handling "imbalanced" and "limited number of data points". We proposed a novel filter pruning method by considering the input and output of filters along with the values of the filters that deal with imbalanced datasets better than others. Our pruning method considers the fact that all information about the importance of a filter may not be reflected in the value of the filter. Instead, it is reflected in the changes made to the data after the filter is applied to it. In this work, three methods are compared with the same training conditions except for the ranking values of each method, and 14 methods are compared from other papers. We demonstrated that our model performed significantly better than other methods for imbalanced medical datasets. For example, when we removed up to 58% of FLOPs for the IDRID dataset and up to 45% for the ISIC dataset, our model was able to yield an equivalent (or even superior) result to the baseline model. To evaluate FLOP and parameter reduction using our model in real-world settings, we built a smartphone app, where we demonstrated a reduction of up to 79% in memory usage and 72% in prediction time. All codes and parameters for training different models are available at https://github.com/mohofar/Beta-Rank

In domains ranging from computer vision to natural language processing, machine learning models have been shown to exhibit stark disparities, often performing worse for members of traditionally underserved groups. One factor contributing to these performance gaps is a lack of representation in the data the models are trained on. It is often unclear, however, how to operationalize representativeness in specific applications. Here we formalize the problem of creating equitable training datasets, and propose a statistical framework for addressing this problem. We consider a setting where a model builder must decide how to allocate a fixed data collection budget to gather training data from different subgroups. We then frame dataset creation as a constrained optimization problem, in which one maximizes a function of group-specific performance metrics based on (estimated) group-specific learning rates and costs per sample. This flexible approach incorporates preferences of model-builders and other stakeholders, as well as the statistical properties of the learning task. When data collection decisions are made sequentially, we show that under certain conditions this optimization problem can be efficiently solved even without prior knowledge of the learning rates. To illustrate our approach, we conduct a simulation study of polygenic risk scores on synthetic genomic data -- an application domain that often suffers from non-representative data collection. We find that our adaptive sampling strategy outperforms several common data collection heuristics, including equal and proportional sampling, demonstrating the value of strategic dataset design for building equitable models.

As data becomes the fuel driving technological and economic growth, a fundamental challenge is how to quantify the value of data in algorithmic predictions and decisions. For example, in healthcare and consumer markets, it has been suggested that individuals should be compensated for the data that they generate, but it is not clear what is an equitable valuation for individual data. In this work, we develop a principled framework to address data valuation in the context of supervised machine learning. Given a learning algorithm trained on n data points to produce a predictor, we propose data Shapley as a metric to quantify the value of each training datum to the predictor performance. Data Shapley value uniquely satisfies several natural properties of equitable data valuation. We develop Monte Carlo and gradient-based methods to efficiently estimate data Shapley values in practical settings where complex learning algorithms, including neural networks, are trained on large datasets. In addition to being equitable, extensive experiments across biomedical, image and synthetic data demonstrate that data Shapley has several other benefits: 1) it is more powerful than the popular leave-one-out or leverage score in providing insight on what data is more valuable for a given learning task; 2) low Shapley value data effectively capture outliers and corruptions; 3) high Shapley value data inform what type of new data to acquire to improve the predictor.

Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the stringent inclusion and exclusion criteria of clinical trials. This process is manual, time-intensive, and challenging to scale up, resulting in many patients missing out on potential therapeutic options. Recent advancements in Large Language Models (LLMs) have made automating patient-trial matching possible, as shown in multiple concurrent research studies. However, the current approaches are confined to constrained, often synthetic datasets that do not adequately mirror the complexities encountered in real-world medical data. In this study, we present the first, end-to-end large-scale empirical evaluation of clinical trial matching using real-world EHRs. Our study showcases the capability of LLMs to accurately match patients with appropriate clinical trials. We perform experiments with proprietary LLMs, including GPT-4 and GPT-3.5, as well as our custom fine-tuned model called OncoLLM and show that OncoLLM, despite its significantly smaller size, not only outperforms GPT-3.5 but also matches the performance of qualified medical doctors. All experiments were carried out on real-world EHRs that include clinical notes and available clinical trials from a single cancer center in the United States.

Developing models with robust group fairness properties is paramount, particularly in ethically sensitive domains such as medical diagnosis. Recent approaches to achieving fairness in machine learning require a substantial amount of training data and depend on model retraining, which may not be practical in real-world scenarios. To mitigate these challenges, we propose Bias-based Weight Masking Fine-Tuning (BMFT), a novel post-processing method that enhances the fairness of a trained model in significantly fewer epochs without requiring access to the original training data. BMFT produces a mask over model parameters, which efficiently identifies the weights contributing the most towards biased predictions. Furthermore, we propose a two-step debiasing strategy, wherein the feature extractor undergoes initial fine-tuning on the identified bias-influenced weights, succeeded by a fine-tuning phase on a reinitialised classification layer to uphold discriminative performance. Extensive experiments across four dermatological datasets and two sensitive attributes demonstrate that BMFT outperforms existing state-of-the-art (SOTA) techniques in both diagnostic accuracy and fairness metrics. Our findings underscore the efficacy and robustness of BMFT in advancing fairness across various out-of-distribution (OOD) settings. Our code is available at: https://github.com/vios-s/BMFT

The current state of adoption of well-structured electronic health records and integration of digital methods for storing medical patient data in structured formats can often considered as inferior compared to the use of traditional, unstructured text based patient data documentation. Data mining in the field of medical data analysis often needs to rely solely on processing of unstructured data to retrieve relevant data. In natural language processing (NLP), statistical models have been shown successful in various tasks like part-of-speech tagging, relation extraction (RE) and named entity recognition (NER). In this work, we present GERNERMED, the first open, neural NLP model for NER tasks dedicated to detect medical entity types in German text data. Here, we avoid the conflicting goals of protection of sensitive patient data from training data extraction and the publication of the statistical model weights by training our model on a custom dataset that was translated from publicly available datasets in foreign language by a pretrained neural machine translation model. The sample code and the statistical model is available at: https://github.com/frankkramer-lab/GERNERMED

Automatic medical report generation (MRG), which possesses significant research value as it can aid radiologists in clinical diagnosis and report composition, has garnered increasing attention. Despite recent progress, generating accurate reports remains arduous due to the requirement for precise clinical comprehension and disease diagnosis inference. Furthermore, owing to the limited accessibility of medical data and the imbalanced distribution of diseases, the underrepresentation of rare diseases in training data makes large-scale medical visual language models (LVLMs) prone to hallucinations, such as omissions or fabrications, severely undermining diagnostic performance and further intensifying the challenges for MRG in practice. In this study, to effectively mitigate hallucinations in medical report generation, we propose a chain-of-medical-thought approach (CoMT), which intends to imitate the cognitive process of human doctors by decomposing diagnostic procedures. The radiological features with different importance are structured into fine-grained medical thought chains to enhance the inferential ability during diagnosis, thereby alleviating hallucination problems and enhancing the diagnostic accuracy of MRG. The code and dataset have been released at https://github.com/FRENKIE-CHIANG/CoMT.

Clustering non-Euclidean data is difficult, and one of the most used algorithms besides hierarchical clustering is the popular algorithm Partitioning Around Medoids (PAM), also simply referred to as k-medoids clustering. In Euclidean geometry the mean-as used in k-means-is a good estimator for the cluster center, but this does not exist for arbitrary dissimilarities. PAM uses the medoid instead, the object with the smallest dissimilarity to all others in the cluster. This notion of centrality can be used with any (dis-)similarity, and thus is of high relevance to many domains and applications. A key issue with PAM is its high run time cost. We propose modifications to the PAM algorithm that achieve an O(k)-fold speedup in the second ("SWAP") phase of the algorithm, but will still find the same results as the original PAM algorithm. If we relax the choice of swaps performed (while retaining comparable quality), we can further accelerate the algorithm by eagerly performing additional swaps in each iteration. With the substantially faster SWAP, we can now explore faster initialization strategies, because (i) the classic ("BUILD") initialization now becomes the bottleneck, and (ii) our swap is fast enough to compensate for worse starting conditions. We also show how the CLARA and CLARANS algorithms benefit from the proposed modifications. While we do not study the parallelization of our approach in this work, it can easily be combined with earlier approaches to use PAM and CLARA on big data (some of which use PAM as a subroutine, hence can immediately benefit from these improvements), where the performance with high k becomes increasingly important. In experiments on real data with k=100,200, we observed a 458x respectively 1191x speedup compared to the original PAM SWAP algorithm, making PAM applicable to larger data sets, and in particular to higher k.

Data sharding, a technique for partitioning and distributing data among multiple servers or nodes, offers enhancements in the scalability, performance, and fault tolerance of extensive distributed systems. Nonetheless, this strategy introduces novel challenges, including load balancing among shards, management of node failures and data loss, and adaptation to evolving data and workload patterns. This paper proposes an innovative approach to tackle these challenges by empowering self-healing nodes with adaptive data sharding. Leveraging concepts such as self-replication, fractal regeneration, sentient data sharding, and symbiotic node clusters, our approach establishes a dynamic and resilient data sharding scheme capable of addressing diverse scenarios and meeting varied requirements. Implementation and evaluation of our approach involve a prototype system simulating a large-scale distributed database across various data sharding scenarios. Comparative analyses against existing data sharding techniques highlight the superior scalability, performance, fault tolerance, and adaptability of our approach. Additionally, the paper delves into potential applications and limitations, providing insights into the future research directions that can further advance this innovative approach.

The Bhutanese government is increasing its utilization of technological approaches such as including Remote Sensing-based knowledge in their decision-making process. This study focuses on crop type and crop extent in Paro, one of the top rice-yielding districts in Bhutan, and employs publicly available NICFI high-resolution satellite imagery from Planet. Two Deep Learning (DL) approaches, point-based (DNN) and patch-based (U-Net), models were used in conjunction with cloud-computing platforms. Three different models per DL approaches (DNN and U-Net) were trained: 1) RGBN channels from Planet; 2) RGBN and elevation data (RGBNE); 3) RGBN and Sentinel-1 (S1) data (RGBNS), and RGBN with E and S1 data (RGBNES). From this comprehensive analysis, the U-Net displayed higher performance metrics across both model training and model validation efforts. Among the U-Net model sets, the RGBN, RGBNE, RGBNS, and RGBNES models had an F1-score of 0.8546, 0.8563, 0.8467, and 0.8500 respectively. An independent model evaluation was performed and found a high level of performance variation across all the metrics. For this independent model evaluation, the U-Net RGBN, RGBNE, RGBNES, and RGBN models displayed the F1-scores of 0.5935, 0.6154, 0.5882, and 0.6582, suggesting U-Net RGBNES as the best model. The study shows that the DL approaches can predict rice. Also, DL methods can be used with the survey-based approaches currently utilized by the Bhutan Department of Agriculture. Further, this study demonstrated the usage of regional land cover products such as SERVIR's RLCMS as a weak label approach to capture different strata addressing the class imbalance problem and improving the sampling design for DL application. Finally, through preliminary model testing and comparisons outlined it was shown that using additional features such as NDVI, EVI, and NDWI did not drastically improve model performance.

Clustering non-Euclidean data is difficult, and one of the most used algorithms besides hierarchical clustering is the popular algorithm Partitioning Around Medoids (PAM), also simply referred to as k-medoids. In Euclidean geometry the mean-as used in k-means-is a good estimator for the cluster center, but this does not hold for arbitrary dissimilarities. PAM uses the medoid instead, the object with the smallest dissimilarity to all others in the cluster. This notion of centrality can be used with any (dis-)similarity, and thus is of high relevance to many domains such as biology that require the use of Jaccard, Gower, or more complex distances. A key issue with PAM is its high run time cost. We propose modifications to the PAM algorithm to achieve an O(k)-fold speedup in the second SWAP phase of the algorithm, but will still find the same results as the original PAM algorithm. If we slightly relax the choice of swaps performed (at comparable quality), we can further accelerate the algorithm by performing up to k swaps in each iteration. With the substantially faster SWAP, we can now also explore alternative strategies for choosing the initial medoids. We also show how the CLARA and CLARANS algorithms benefit from these modifications. It can easily be combined with earlier approaches to use PAM and CLARA on big data (some of which use PAM as a subroutine, hence can immediately benefit from these improvements), where the performance with high k becomes increasingly important. In experiments on real data with k=100, we observed a 200-fold speedup compared to the original PAM SWAP algorithm, making PAM applicable to larger data sets as long as we can afford to compute a distance matrix, and in particular to higher k (at k=2, the new SWAP was only 1.5 times faster, as the speedup is expected to increase with k).

Social determinants of health (SDoH) have an important impact on patient outcomes but are incompletely collected from the electronic health records (EHR). This study researched the ability of large language models to extract SDoH from free text in EHRs, where they are most commonly documented, and explored the role of synthetic clinical text for improving the extraction of these scarcely documented, yet extremely valuable, clinical data. 800 patient notes were annotated for SDoH categories, and several transformer-based models were evaluated. The study also experimented with synthetic data generation and assessed for algorithmic bias. Our best-performing models were fine-tuned Flan-T5 XL (macro-F1 0.71) for any SDoH, and Flan-T5 XXL (macro-F1 0.70). The benefit of augmenting fine-tuning with synthetic data varied across model architecture and size, with smaller Flan-T5 models (base and large) showing the greatest improvements in performance (delta F1 +0.12 to +0.23). Model performance was similar on the in-hospital system dataset but worse on the MIMIC-III dataset. Our best-performing fine-tuned models outperformed zero- and few-shot performance of ChatGPT-family models for both tasks. These fine-tuned models were less likely than ChatGPT to change their prediction when race/ethnicity and gender descriptors were added to the text, suggesting less algorithmic bias (p<0.05). At the patient-level, our models identified 93.8% of patients with adverse SDoH, while ICD-10 codes captured 2.0%. Our method can effectively extracted SDoH information from clinic notes, performing better compare to GPT zero- and few-shot settings. These models could enhance real-world evidence on SDoH and aid in identifying patients needing social support.

Data diversity and volume are crucial to the success of training deep learning models, while in the medical imaging field, the difficulty and cost of data collection and annotation are especially huge. Specifically in robotic surgery, data scarcity and imbalance have heavily affected the model accuracy and limited the design and deployment of deep learning-based surgical applications such as surgical instrument segmentation. Considering this, we rethink the surgical instrument segmentation task and propose a one-to-many data generation solution that gets rid of the complicated and expensive process of data collection and annotation from robotic surgery. In our method, we only utilize a single surgical background tissue image and a few open-source instrument images as the seed images and apply multiple augmentations and blending techniques to synthesize amounts of image variations. In addition, we also introduce the chained augmentation mixing during training to further enhance the data diversities. The proposed approach is evaluated on the real datasets of the EndoVis-2018 and EndoVis-2017 surgical scene segmentation. Our empirical analysis suggests that without the high cost of data collection and annotation, we can achieve decent surgical instrument segmentation performance. Moreover, we also observe that our method can deal with novel instrument prediction in the deployment domain. We hope our inspiring results will encourage researchers to emphasize data-centric methods to overcome demanding deep learning limitations besides data shortage, such as class imbalance, domain adaptation, and incremental learning. Our code is available at https://github.com/lofrienger/Single_SurgicalScene_For_Segmentation.

Unequal access to costly datasets essential for empirical research has long hindered researchers from disadvantaged institutions, limiting their ability to contribute to their fields and advance their careers. Recent breakthroughs in Large Language Models (LLMs) have the potential to democratize data access by automating data collection from unstructured sources. We develop and evaluate a novel methodology using GPT-4o-mini within a Retrieval-Augmented Generation (RAG) framework to collect data from corporate disclosures. Our approach achieves human-level accuracy in collecting CEO pay ratios from approximately 10,000 proxy statements and Critical Audit Matters (CAMs) from more than 12,000 10-K filings, with LLM processing times of 9 and 40 minutes respectively, each at a cost under $10. This stands in stark contrast to the hundreds of hours needed for manual collection or the thousands of dollars required for commercial database subscriptions. To foster a more inclusive research community by empowering researchers with limited resources to explore new avenues of inquiry, we share our methodology and the resulting datasets.

This paper discusses pairing double/debiased machine learning (DDML) with stacking, a model averaging method for combining multiple candidate learners, to estimate structural parameters. In addition to conventional stacking, we consider two stacking variants available for DDML: short-stacking exploits the cross-fitting step of DDML to substantially reduce the computational burden and pooled stacking enforces common stacking weights over cross-fitting folds. Using calibrated simulation studies and two applications estimating gender gaps in citations and wages, we show that DDML with stacking is more robust to partially unknown functional forms than common alternative approaches based on single pre-selected learners. We provide Stata and R software implementing our proposals.

Diabetes, resulting from inadequate insulin production or utilization, causes extensive harm to the body. Existing diagnostic methods are often invasive and come with drawbacks, such as cost constraints. Although there are machine learning models like Classwise k Nearest Neighbor (CkNN) and General Regression Neural Network (GRNN), they struggle with imbalanced data and result in under-performance. Leveraging advancements in sensor technology and machine learning, we propose a non-invasive diabetes diagnosis using a Back Propagation Neural Network (BPNN) with batch normalization, incorporating data re-sampling and normalization for class balancing. Our method addresses existing challenges such as limited performance associated with traditional machine learning. Experimental results on three datasets show significant improvements in overall accuracy, sensitivity, and specificity compared to traditional methods. Notably, we achieve accuracies of 89.81% in Pima diabetes dataset, 75.49% in CDC BRFSS2015 dataset, and 95.28% in Mesra Diabetes dataset. This underscores the potential of deep learning models for robust diabetes diagnosis. See project website https://steve-zeyu-zhang.github.io/DiabetesDiagnosis/

Distribution shifts -- where the training distribution differs from the test distribution -- can substantially degrade the accuracy of machine learning (ML) systems deployed in the wild. Despite their ubiquity in the real-world deployments, these distribution shifts are under-represented in the datasets widely used in the ML community today. To address this gap, we present WILDS, a curated benchmark of 10 datasets reflecting a diverse range of distribution shifts that naturally arise in real-world applications, such as shifts across hospitals for tumor identification; across camera traps for wildlife monitoring; and across time and location in satellite imaging and poverty mapping. On each dataset, we show that standard training yields substantially lower out-of-distribution than in-distribution performance. This gap remains even with models trained by existing methods for tackling distribution shifts, underscoring the need for new methods for training models that are more robust to the types of distribution shifts that arise in practice. To facilitate method development, we provide an open-source package that automates dataset loading, contains default model architectures and hyperparameters, and standardizes evaluations. Code and leaderboards are available at https://wilds.stanford.edu.

Federated Domain Adaptation (FDA) describes the federated learning (FL) setting where source clients and a server work collaboratively to improve the performance of a target client where limited data is available. The domain shift between the source and target domains, coupled with limited data of the target client, makes FDA a challenging problem, e.g., common techniques such as federated averaging and fine-tuning fail due to domain shift and data scarcity. To theoretically understand the problem, we introduce new metrics that characterize the FDA setting and a theoretical framework with novel theorems for analyzing the performance of server aggregation rules. Further, we propose a novel lightweight aggregation rule, Federated Gradient Projection (FedGP), which significantly improves the target performance with domain shift and data scarcity. Moreover, our theory suggests an auto-weighting scheme that finds the optimal combinations of the source and target gradients. This scheme improves both FedGP and a simpler heuristic aggregation rule. Extensive experiments verify the theoretical insights and illustrate the effectiveness of the proposed methods in practice.

Biomedical imaging datasets are often small and biased, meaning that real-world performance of predictive models can be substantially lower than expected from internal testing. This work proposes using generative image editing to simulate dataset shifts and diagnose failure modes of biomedical vision models; this can be used in advance of deployment to assess readiness, potentially reducing cost and patient harm. Existing editing methods can produce undesirable changes, with spurious correlations learned due to the co-occurrence of disease and treatment interventions, limiting practical applicability. To address this, we train a text-to-image diffusion model on multiple chest X-ray datasets and introduce a new editing method RadEdit that uses multiple masks, if present, to constrain changes and ensure consistency in the edited images. We consider three types of dataset shifts: acquisition shift, manifestation shift, and population shift, and demonstrate that our approach can diagnose failures and quantify model robustness without additional data collection, complementing more qualitative tools for explainable AI.

To assess the effectiveness of any medical intervention, researchers must conduct a time-intensive and highly manual literature review. NLP systems can help to automate or assist in parts of this expensive process. In support of this goal, we release MS^2 (Multi-Document Summarization of Medical Studies), a dataset of over 470k documents and 20k summaries derived from the scientific literature. This dataset facilitates the development of systems that can assess and aggregate contradictory evidence across multiple studies, and is the first large-scale, publicly available multi-document summarization dataset in the biomedical domain. We experiment with a summarization system based on BART, with promising early results. We formulate our summarization inputs and targets in both free text and structured forms and modify a recently proposed metric to assess the quality of our system's generated summaries. Data and models are available at https://github.com/allenai/ms2

Digitally reconstructed radiographs (DRRs) are simulated 2D X-ray images generated from 3D CT volumes, widely used in preoperative settings but limited in intraoperative applications due to computational bottlenecks, especially for accurate but heavy physics-based Monte Carlo methods. While analytical DRR renderers offer greater efficiency, they overlook anisotropic X-ray image formation phenomena, such as Compton scattering. We present a novel approach that marries realistic physics-inspired X-ray simulation with efficient, differentiable DRR generation using 3D Gaussian splatting (3DGS). Our direction-disentangled 3DGS (DDGS) method separates the radiosity contribution into isotropic and direction-dependent components, approximating complex anisotropic interactions without intricate runtime simulations. Additionally, we adapt the 3DGS initialization to account for tomography data properties, enhancing accuracy and efficiency. Our method outperforms state-of-the-art techniques in image accuracy. Furthermore, our DDGS shows promise for intraoperative applications and inverse problems such as pose registration, delivering superior registration accuracy and runtime performance compared to analytical DRR methods.

Radiologists play a crucial role by translating medical images into medical reports. However, the field faces staffing shortages and increasing workloads. While automated approaches using vision-language models (VLMs) show promise as assistants, they require exceptionally high accuracy. Most current VLMs in radiology rely solely on supervised fine-tuning (SFT). Meanwhile, in the general domain, additional preference fine-tuning has become standard practice. The challenge in radiology lies in the prohibitive cost of obtaining radiologist feedback. We propose a scalable automated preference alignment technique for VLMs in radiology, focusing on chest X-ray (CXR) report generation. Our method leverages publicly available datasets with an LLM-as-a-Judge mechanism, eliminating the need for additional expert radiologist feedback. We evaluate and benchmark five direct alignment algorithms (DAAs). Our results show up to a 57.4% improvement in average GREEN scores, a LLM-based metric for evaluating CXR reports, and a 9.2% increase in an average across six metrics (domain specific and general), compared to the SFT baseline. We study reward overoptimization via length exploitation, with reports lengthening by up to 3.2x. To assess a potential alignment tax, we benchmark on six additional diverse tasks, finding no significant degradations. A reader study involving four board-certified radiologists indicates win rates of up to 0.62 over the SFT baseline, while significantly penalizing verbosity. Our analysis provides actionable insights for the development of VLMs in high-stakes fields like radiology.

The burgeoning integration of 3D medical imaging into healthcare has led to a substantial increase in the workload of medical professionals. To assist clinicians in their diagnostic processes and alleviate their workload, the development of a robust system for retrieving similar case studies presents a viable solution. While the concept holds great promise, the field of 3D medical text-image retrieval is currently limited by the absence of robust evaluation benchmarks and curated datasets. To remedy this, our study presents a groundbreaking dataset, BIMCV-R (This dataset will be released upon acceptance.), which includes an extensive collection of 8,069 3D CT volumes, encompassing over 2 million slices, paired with their respective radiological reports. Expanding upon the foundational work of our dataset, we craft a retrieval strategy, MedFinder. This approach employs a dual-stream network architecture, harnessing the potential of large language models to advance the field of medical image retrieval beyond existing text-image retrieval solutions. It marks our preliminary step towards developing a system capable of facilitating text-to-image, image-to-text, and keyword-based retrieval tasks.

We present weight normalization: a reparameterization of the weight vectors in a neural network that decouples the length of those weight vectors from their direction. By reparameterizing the weights in this way we improve the conditioning of the optimization problem and we speed up convergence of stochastic gradient descent. Our reparameterization is inspired by batch normalization but does not introduce any dependencies between the examples in a minibatch. This means that our method can also be applied successfully to recurrent models such as LSTMs and to noise-sensitive applications such as deep reinforcement learning or generative models, for which batch normalization is less well suited. Although our method is much simpler, it still provides much of the speed-up of full batch normalization. In addition, the computational overhead of our method is lower, permitting more optimization steps to be taken in the same amount of time. We demonstrate the usefulness of our method on applications in supervised image recognition, generative modelling, and deep reinforcement learning.

A recourse action aims to explain a particular algorithmic decision by showing one specific way in which the instance could be modified to receive an alternate outcome. Existing recourse generation methods often assume that the machine learning model does not change over time. However, this assumption does not always hold in practice because of data distribution shifts, and in this case, the recourse action may become invalid. To redress this shortcoming, we propose the Distributionally Robust Recourse Action (DiRRAc) framework, which generates a recourse action that has a high probability of being valid under a mixture of model shifts. We formulate the robustified recourse setup as a min-max optimization problem, where the max problem is specified by Gelbrich distance over an ambiguity set around the distribution of model parameters. Then we suggest a projected gradient descent algorithm to find a robust recourse according to the min-max objective. We show that our DiRRAc framework can be extended to hedge against the misspecification of the mixture weights. Numerical experiments with both synthetic and three real-world datasets demonstrate the benefits of our proposed framework over state-of-the-art recourse methods.

Deep learning is currently the state-of-the-art for automated detection of referable diabetic retinopathy (DR) from color fundus photographs (CFP). While the general interest is put on improving results through methodological innovations, it is not clear how good these approaches perform compared to standard deep classification models trained with the appropriate settings. In this paper we propose to model a strong baseline for this task based on a simple and standard ResNet-18 architecture. To this end, we built on top of prior art by training the model with a standard preprocessing strategy but using images from several public sources and an empirically calibrated data augmentation setting. To evaluate its performance, we covered multiple clinically relevant perspectives, including image and patient level DR screening, discriminating responses by input quality and DR grade, assessing model uncertainties and analyzing its results in a qualitative manner. With no other methodological innovation than a carefully designed training, our ResNet model achieved an AUC = 0.955 (0.953 - 0.956) on a combined test set of 61007 test images from different public datasets, which is in line or even better than what other more complex deep learning models reported in the literature. Similar AUC values were obtained in 480 images from two separate in-house databases specially prepared for this study, which emphasize its generalization ability. This confirms that standard networks can still be strong baselines for this task if properly trained.

Deep neural networks have enabled improved image quality and fast inference times for various inverse problems, including accelerated magnetic resonance imaging (MRI) reconstruction. However, such models require a large number of fully-sampled ground truth datasets, which are difficult to curate, and are sensitive to distribution drifts. In this work, we propose applying physics-driven data augmentations for consistency training that leverage our domain knowledge of the forward MRI data acquisition process and MRI physics to achieve improved label efficiency and robustness to clinically-relevant distribution drifts. Our approach, termed VORTEX, (1) demonstrates strong improvements over supervised baselines with and without data augmentation in robustness to signal-to-noise ratio change and motion corruption in data-limited regimes; (2) considerably outperforms state-of-the-art purely image-based data augmentation techniques and self-supervised reconstruction methods on both in-distribution and out-of-distribution data; and (3) enables composing heterogeneous image-based and physics-driven data augmentations. Our code is available at https://github.com/ad12/meddlr.

Artificial Intelligence (AI) has demonstrated significant potential in healthcare, particularly in disease diagnosis and treatment planning. Recent progress in Medical Large Vision-Language Models (Med-LVLMs) has opened up new possibilities for interactive diagnostic tools. However, these models often suffer from factual hallucination, which can lead to incorrect diagnoses. Fine-tuning and retrieval-augmented generation (RAG) have emerged as methods to address these issues. However, the amount of high-quality data and distribution shifts between training data and deployment data limit the application of fine-tuning methods. Although RAG is lightweight and effective, existing RAG-based approaches are not sufficiently general to different medical domains and can potentially cause misalignment issues, both between modalities and between the model and the ground truth. In this paper, we propose a versatile multimodal RAG system, MMed-RAG, designed to enhance the factuality of Med-LVLMs. Our approach introduces a domain-aware retrieval mechanism, an adaptive retrieved contexts selection method, and a provable RAG-based preference fine-tuning strategy. These innovations make the RAG process sufficiently general and reliable, significantly improving alignment when introducing retrieved contexts. Experimental results across five medical datasets (involving radiology, ophthalmology, pathology) on medical VQA and report generation demonstrate that MMed-RAG can achieve an average improvement of 43.8% in the factual accuracy of Med-LVLMs. Our data and code are available in https://github.com/richard-peng-xia/MMed-RAG.

This paper presents medBERTde, a pre-trained German BERT model specifically designed for the German medical domain. The model has been trained on a large corpus of 4.7 Million German medical documents and has been shown to achieve new state-of-the-art performance on eight different medical benchmarks covering a wide range of disciplines and medical document types. In addition to evaluating the overall performance of the model, this paper also conducts a more in-depth analysis of its capabilities. We investigate the impact of data deduplication on the model's performance, as well as the potential benefits of using more efficient tokenization methods. Our results indicate that domain-specific models such as medBERTde are particularly useful for longer texts, and that deduplication of training data does not necessarily lead to improved performance. Furthermore, we found that efficient tokenization plays only a minor role in improving model performance, and attribute most of the improved performance to the large amount of training data. To encourage further research, the pre-trained model weights and new benchmarks based on radiological data are made publicly available for use by the scientific community.

Recognition problems in long-tailed data, in which the sample size per class is heavily skewed, have gained importance because the distribution of the sample size per class in a dataset is generally exponential unless the sample size is intentionally adjusted. Various methods have been devised to address these problems. Recently, weight balancing, which combines well-known classical regularization techniques with two-stage training, has been proposed. Despite its simplicity, it is known for its high performance compared with existing methods devised in various ways. However, there is a lack of understanding as to why this method is effective for long-tailed data. In this study, we analyze weight balancing by focusing on neural collapse and the cone effect at each training stage and found that it can be decomposed into an increase in Fisher's discriminant ratio of the feature extractor caused by weight decay and cross entropy loss and implicit logit adjustment caused by weight decay and class-balanced loss. Our analysis enables the training method to be further simplified by reducing the number of training stages to one while increasing accuracy.

Datasets scraped from the internet have been critical to the successes of large-scale machine learning. Yet, this very success puts the utility of future internet-derived datasets at potential risk, as model outputs begin to replace human annotations as a source of supervision. In this work, we first formalize a system where interactions with one model are recorded as history and scraped as training data in the future. We then analyze its stability over time by tracking changes to a test-time bias statistic (e.g. gender bias of model predictions). We find that the degree of bias amplification is closely linked to whether the model's outputs behave like samples from the training distribution, a behavior which we characterize and define as consistent calibration. Experiments in three conditional prediction scenarios - image classification, visual role-labeling, and language generation - demonstrate that models that exhibit a sampling-like behavior are more calibrated and thus more stable. Based on this insight, we propose an intervention to help calibrate and stabilize unstable feedback systems. Code is available at https://github.com/rtaori/data_feedback.

University rankings are increasingly adopted for academic comparison and success quantification, even to establish performance-based criteria for funding assignment. However, rankings are not neutral tools, and their use frequently overlooks disparities in the starting conditions of institutions. In this research, we detect and measure structural biases that affect in inhomogeneous ways the ranking outcomes of universities from diversified territorial and educational contexts. Moreover, we develop a fairer rating system based on a fully data-driven debiasing strategy that returns an equity-oriented redefinition of the achieved scores. The key idea consists in partitioning universities in similarity groups, determined from multifaceted data using complex network analysis, and referring the performance of each institution to an expectation based on its peers. Significant evidence of territorial biases emerges for official rankings concerning both the OECD and Italian university systems, hence debiasing provides relevant insights suggesting the design of fairer strategies for performance-based funding allocations.

Test-time adaptation (TTA) intends to adapt the pretrained model to test distributions with only unlabeled test data streams. Most of the previous TTA methods have achieved great success on simple test data streams such as independently sampled data from single or multiple distributions. However, these attempts may fail in dynamic scenarios of real-world applications like autonomous driving, where the environments gradually change and the test data is sampled correlatively over time. In this work, we explore such practical test data streams to deploy the model on the fly, namely practical test-time adaptation (PTTA). To do so, we elaborate a Robust Test-Time Adaptation (RoTTA) method against the complex data stream in PTTA. More specifically, we present a robust batch normalization scheme to estimate the normalization statistics. Meanwhile, a memory bank is utilized to sample category-balanced data with consideration of timeliness and uncertainty. Further, to stabilize the training procedure, we develop a time-aware reweighting strategy with a teacher-student model. Extensive experiments prove that RoTTA enables continual testtime adaptation on the correlatively sampled data streams. Our method is easy to implement, making it a good choice for rapid deployment. The code is publicly available at https://github.com/BIT-DA/RoTTA

Machine learning models often have uneven performance among subpopulations (a.k.a., groups) in the data distributions. This poses a significant challenge for the models to generalize when the proportions of the groups shift during deployment. To improve robustness to such shifts, existing approaches have developed strategies that train models or perform hyperparameter tuning using the group-labeled data to minimize the worst-case loss over groups. However, a non-trivial amount of high-quality labels is often required to obtain noticeable improvements. Given the costliness of the labels, we propose to adopt a different paradigm to enhance group label efficiency: utilizing the group-labeled data as a target set to optimize the weights of other group-unlabeled data. We introduce Group-robust Sample Reweighting (GSR), a two-stage approach that first learns the representations from group-unlabeled data, and then tinkers the model by iteratively retraining its last layer on the reweighted data using influence functions. Our GSR is theoretically sound, practically lightweight, and effective in improving the robustness to subpopulation shifts. In particular, GSR outperforms the previous state-of-the-art approaches that require the same amount or even more group labels.

Federated Learning (FL) is a rising approach towards collaborative and privacy-preserving machine learning where large-scale medical datasets remain localized to each client. However, the issue of data heterogeneity among clients often compels local models to diverge, leading to suboptimal global models. To mitigate the impact of data heterogeneity on FL performance, we start with analyzing how FL training influence FL performance by decomposing the global loss into three terms: local loss, distribution shift loss and aggregation loss. Remarkably, our loss decomposition reveals that existing local training-based FL methods attempt to reduce the distribution shift loss, while the global aggregation-based FL methods propose better aggregation strategies to reduce the aggregation loss. Nevertheless, a comprehensive joint effort to minimize all three terms is currently limited in the literature, leading to subpar performance when dealing with data heterogeneity challenges. To fill this gap, we propose a novel FL method based on global loss decomposition, called FedLD, to jointly reduce these three loss terms. Our FedLD involves a margin control regularization in local training to reduce the distribution shift loss, and a principal gradient-based server aggregation strategy to reduce the aggregation loss. Notably, under different levels of data heterogeneity, our strategies achieve better and more robust performance on retinal and chest X-ray classification compared to other FL algorithms. Our code is available at https://github.com/Zeng-Shuang/FedLD.

Machine learning has opened up new tools for financial fraud detection. Using a sample of annotated transactions, a machine learning classification algorithm learns to detect frauds. With growing credit card transaction volumes and rising fraud percentages there is growing interest in finding appropriate machine learning classifiers for detection. However, fraud data sets are diverse and exhibit inconsistent characteristics. As a result, a model effective on a given data set is not guaranteed to perform on another. Further, the possibility of temporal drift in data patterns and characteristics over time is high. Additionally, fraud data has massive and varying imbalance. In this work, we evaluate sampling methods as a viable pre-processing mechanism to handle imbalance and propose a data-driven classifier selection strategy for characteristic highly imbalanced fraud detection data sets. The model derived based on our selection strategy surpasses peer models, whilst working in more realistic conditions, establishing the effectiveness of the strategy.

Previous studies have found that PLM-based retrieval models exhibit a preference for LLM-generated content, assigning higher relevance scores to these documents even when their semantic quality is comparable to human-written ones. This phenomenon, known as source bias, threatens the sustainable development of the information access ecosystem. However, the underlying causes of source bias remain unexplored. In this paper, we explain the process of information retrieval with a causal graph and discover that PLM-based retrievers learn perplexity features for relevance estimation, causing source bias by ranking the documents with low perplexity higher. Theoretical analysis further reveals that the phenomenon stems from the positive correlation between the gradients of the loss functions in language modeling task and retrieval task. Based on the analysis, a causal-inspired inference-time debiasing method is proposed, called Causal Diagnosis and Correction (CDC). CDC first diagnoses the bias effect of the perplexity and then separates the bias effect from the overall estimated relevance score. Experimental results across three domains demonstrate the superior debiasing effectiveness of CDC, emphasizing the validity of our proposed explanatory framework. Source codes are available at https://github.com/WhyDwelledOnAi/Perplexity-Trap.

Ensuring the reliability and safety of automated decision-making is crucial. It is well-known that data distribution shifts in machine learning can produce unreliable outcomes. This paper proposes a new approach for measuring the reliability of predictions under distribution shifts. We analyze how the outputs of a trained neural network change using clustering to measure distances between outputs and class centroids. We propose this distance as a metric to evaluate the confidence of predictions under distribution shifts. We assign each prediction to a cluster with centroid representing the mean softmax output for all correct predictions of a given class. We then define a safety threshold for a class as the smallest distance from an incorrect prediction to the given class centroid. We evaluate the approach on the MNIST and CIFAR-10 datasets using a Convolutional Neural Network and a Vision Transformer, respectively. The results show that our approach is consistent across these data sets and network models, and indicate that the proposed metric can offer an efficient way of determining when automated predictions are acceptable and when they should be deferred to human operators given a distribution shift.

Machine learning (ML) holds great potential for accurately forecasting treatment outcomes over time, which could ultimately enable the adoption of more individualized treatment strategies in many practical applications. However, a significant challenge that has been largely overlooked by the ML literature on this topic is the presence of informative sampling in observational data. When instances are observed irregularly over time, sampling times are typically not random, but rather informative -- depending on the instance's characteristics, past outcomes, and administered treatments. In this work, we formalize informative sampling as a covariate shift problem and show that it can prohibit accurate estimation of treatment outcomes if not properly accounted for. To overcome this challenge, we present a general framework for learning treatment outcomes in the presence of informative sampling using inverse intensity-weighting, and propose a novel method, TESAR-CDE, that instantiates this framework using Neural CDEs. Using a simulation environment based on a clinical use case, we demonstrate the effectiveness of our approach in learning under informative sampling.

Unfairness in mortgage lending has created generational inequality among racial and ethnic groups in the US. Many studies address this problem, but most existing work focuses on correlation-based techniques. In our work, we use the framework of counterfactual fairness to train fair machine learning models. We propose a new causal graph for the variables available in the Home Mortgage Disclosure Act (HMDA) data. We use a matching-based approach instead of the latent variable modeling approach, because the former approach does not rely on any modeling assumptions. Furthermore, matching provides us with counterfactual pairs in which the race variable is isolated. We first demonstrate the unfairness in mortgage approval and interest rates between African-American and non-Hispanic White sub-populations. Then, we show that having balanced data using matching does not guarantee perfect counterfactual fairness of the machine learning models.

This paper introduces the Pandemic PACT Advanced Categorisation Engine (PPACE) along with its associated dataset. PPACE is a fine-tuned model developed to automatically classify research abstracts from funded biomedical projects according to WHO-aligned research priorities. This task is crucial for monitoring research trends and identifying gaps in global health preparedness and response. Our approach builds on human-annotated projects, which are allocated one or more categories from a predefined list. A large language model is then used to generate `rationales' explaining the reasoning behind these annotations. This augmented data, comprising expert annotations and rationales, is subsequently used to fine-tune a smaller, more efficient model. Developed as part of the Pandemic PACT project, which aims to track and analyse research funding and clinical evidence for a wide range of diseases with outbreak potential, PPACE supports informed decision-making by research funders, policymakers, and independent researchers. We introduce and release both the trained model and the instruction-based dataset used for its training. Our evaluation shows that PPACE significantly outperforms its baselines. The release of PPACE and its associated dataset offers valuable resources for researchers in multilabel biomedical document classification and supports advancements in aligning biomedical research with key global health priorities.

Cross-validation is the de facto standard for predictive model evaluation and selection. In proper use, it provides an unbiased estimate of a model's predictive performance. However, data sets often undergo various forms of data-dependent preprocessing, such as mean-centering, rescaling, dimensionality reduction, and outlier removal. It is often believed that such preprocessing stages, if done in an unsupervised manner (that does not incorporate the class labels or response values) are generally safe to do prior to cross-validation. In this paper, we study three commonly-practiced preprocessing procedures prior to a regression analysis: (i) variance-based feature selection; (ii) grouping of rare categorical features; and (iii) feature rescaling. We demonstrate that unsupervised preprocessing can, in fact, introduce a substantial bias into cross-validation estimates and potentially hurt model selection. This bias may be either positive or negative and its exact magnitude depends on all the parameters of the problem in an intricate manner. Further research is needed to understand the real-world impact of this bias across different application domains, particularly when dealing with small sample sizes and high-dimensional data.

Experience replay is a key component in reinforcement learning for stabilizing learning and improving sample efficiency. Its typical implementation samples transitions with replacement from a replay buffer. In contrast, in supervised learning with a fixed dataset, it is a common practice to shuffle the dataset every epoch and consume data sequentially, which is called random reshuffling (RR). RR enjoys theoretically better convergence properties and has been shown to outperform with-replacement sampling empirically. To leverage the benefits of RR in reinforcement learning, we propose sampling methods that extend RR to experience replay, both in uniform and prioritized settings. We evaluate our sampling methods on Atari benchmarks, demonstrating their effectiveness in deep reinforcement learning.

Self-Admitted Technical Debt (SATD) refers to circumstances where developers use textual artifacts to explain why the existing implementation is not optimal. Past research in detecting SATD has focused on either identifying SATD (classifying SATD items as SATD or not) or categorizing SATD (labeling instances as SATD that pertain to requirement, design, code, test debt, etc.). However, the performance of these approaches remains suboptimal, particularly for specific types of SATD, such as test and requirement debt, primarily due to extremely imbalanced datasets. To address these challenges, we build on earlier research by utilizing BiLSTM architecture for the binary identification of SATD and BERT architecture for categorizing different types of SATD. Despite their effectiveness, both architectures struggle with imbalanced data. Therefore, we employ a large language model data augmentation strategy to mitigate this issue. Furthermore, we introduce a two-step approach to identify and categorize SATD across various datasets derived from different artifacts. Our contributions include providing a balanced dataset for future SATD researchers and demonstrating that our approach significantly improves SATD identification and categorization performance compared to baseline methods.

Pathology diagnosis based on EEG signals and decoding brain activity holds immense importance in understanding neurological disorders. With the advancement of artificial intelligence methods and machine learning techniques, the potential for accurate data-driven diagnoses and effective treatments has grown significantly. However, applying machine learning algorithms to real-world datasets presents diverse challenges at multiple levels. The scarcity of labelled data, especially in low regime scenarios with limited availability of real patient cohorts due to high costs of recruitment, underscores the vital deployment of scaling and transfer learning techniques. In this study, we explore a real-world pathology classification task to highlight the effectiveness of data and model scaling and cross-dataset knowledge transfer. As such, we observe varying performance improvements through data scaling, indicating the need for careful evaluation and labelling. Additionally, we identify the challenges of possible negative transfer and emphasize the significance of some key components to overcome distribution shifts and potential spurious correlations and achieve positive transfer. We see improvement in the performance of the target model on the target (NMT) datasets by using the knowledge from the source dataset (TUAB) when a low amount of labelled data was available. Our findings indicate a small and generic model (e.g. ShallowNet) performs well on a single dataset, however, a larger model (e.g. TCN) performs better on transfer and learning from a larger and diverse dataset.

In medical imaging, the diffusion models have shown great potential in synthetic image generation tasks. However, these models often struggle with the interpretable connections between the generated and existing images and could create illusions. To address these challenges, our research proposes a novel diffusion-based generative model based on deformation diffusion and recovery. This model, named Deformation-Recovery Diffusion Model (DRDM), diverges from traditional score/intensity and latent feature-based approaches, emphasizing morphological changes through deformation fields rather than direct image synthesis. This is achieved by introducing a topological-preserving deformation field generation method, which randomly samples and integrates a set of multi-scale Deformation Vector Fields (DVF). DRDM is trained to learn to recover unreasonable deformation components, thereby restoring each randomly deformed image to a realistic distribution. These innovations facilitate the generation of diverse and anatomically plausible deformations, enhancing data augmentation and synthesis for further analysis in downstream tasks, such as few-shot learning and image registration. Experimental results in cardiac MRI and pulmonary CT show DRDM is capable of creating diverse, large (over 10\% image size deformation scale), and high-quality (negative rate of the Jacobian matrix's determinant is lower than 1\%) deformation fields. The further experimental results in downstream tasks, 2D image segmentation and 3D image registration, indicate significant improvements resulting from DRDM, showcasing the potential of our model to advance image manipulation and synthesis in medical imaging and beyond. Project page: https://jianqingzheng.github.io/def_diff_rec/

Machine learning models in health care are often deployed in settings where it is important to protect patient privacy. In such settings, methods for differentially private (DP) learning provide a general-purpose approach to learn models with privacy guarantees. Modern methods for DP learning ensure privacy through mechanisms that censor information judged as too unique. The resulting privacy-preserving models, therefore, neglect information from the tails of a data distribution, resulting in a loss of accuracy that can disproportionately affect small groups. In this paper, we study the effects of DP learning in health care. We use state-of-the-art methods for DP learning to train privacy-preserving models in clinical prediction tasks, including x-ray classification of images and mortality prediction in time series data. We use these models to perform a comprehensive empirical investigation of the tradeoffs between privacy, utility, robustness to dataset shift, and fairness. Our results highlight lesser-known limitations of methods for DP learning in health care, models that exhibit steep tradeoffs between privacy and utility, and models whose predictions are disproportionately influenced by large demographic groups in the training data. We discuss the costs and benefits of differentially private learning in health care.

Large-scale data sets on scholarly publications are the basis for a variety of bibliometric analyses and natural language processing (NLP) applications. Especially data sets derived from publication's full-text have recently gained attention. While several such data sets already exist, we see key shortcomings in terms of their domain and time coverage, citation network completeness, and representation of full-text content. To address these points, we propose a new version of the data set unarXive. We base our data processing pipeline and output format on two existing data sets, and improve on each of them. Our resulting data set comprises 1.9 M publications spanning multiple disciplines and 32 years. It furthermore has a more complete citation network than its predecessors and retains a richer representation of document structure as well as non-textual publication content such as mathematical notation. In addition to the data set, we provide ready-to-use training/test data for citation recommendation and IMRaD classification. All data and source code is publicly available at https://github.com/IllDepence/unarXive.

Recent studies suggest that with sufficiently wide models, most SGD solutions can, up to permutation, converge into the same basin. This phenomenon, known as the model re-basin regime, has significant implications for model averaging by ensuring the linear mode connectivity. However, current re-basin strategies are ineffective in many scenarios due to a lack of comprehensive understanding of underlying mechanisms. Addressing this gap, this paper provides novel insights into understanding and improving the standard practice. Firstly, we decompose re-normalization into rescaling and reshift, uncovering that rescaling plays a crucial role in re-normalization while re-basin performance is sensitive to shifts in model activation. The finding calls for a more nuanced handling of the activation shift. Secondly, we identify that the merged model suffers from the issue of activation collapse and magnitude collapse. Varying the learning rate, weight decay, and initialization method can mitigate the issues and improve model performance. Lastly, we propose a new perspective to unify the re-basin and pruning, under which a lightweight yet effective post-pruning technique is derived, which can significantly improve the model performance after pruning. Our implementation is available at https://github.com/XingyuQu/rethink-re-basin.

Medical imaging plays a crucial role in modern healthcare by providing non-invasive visualisation of internal structures and abnormalities, enabling early disease detection, accurate diagnosis, and treatment planning. This study aims to explore the application of deep learning models, particularly focusing on the UNet architecture and its variants, in medical image segmentation. We seek to evaluate the performance of these models across various challenging medical image segmentation tasks, addressing issues such as image normalization, resizing, architecture choices, loss function design, and hyperparameter tuning. The findings reveal that the standard UNet, when extended with a deep network layer, is a proficient medical image segmentation model, while the Res-UNet and Attention Res-UNet architectures demonstrate smoother convergence and superior performance, particularly when handling fine image details. The study also addresses the challenge of high class imbalance through careful preprocessing and loss function definitions. We anticipate that the results of this study will provide useful insights for researchers seeking to apply these models to new medical imaging problems and offer guidance and best practices for their implementation.

This work considers the category distribution heterogeneity in federated learning. This issue is due to biased labeling preferences at multiple clients and is a typical setting of data heterogeneity. To alleviate this issue, most previous works consider either regularizing local models or fine-tuning the global model, while they ignore the adjustment of aggregation weights and simply assign weights based on the dataset size. However, based on our empirical observations and theoretical analysis, we find that the dataset size is not optimal and the discrepancy between local and global category distributions could be a beneficial and complementary indicator for determining aggregation weights. We thus propose a novel aggregation method, Federated Learning with Discrepancy-aware Collaboration (FedDisco), whose aggregation weights not only involve both the dataset size and the discrepancy value, but also contribute to a tighter theoretical upper bound of the optimization error. FedDisco also promotes privacy-preservation, communication and computation efficiency, as well as modularity. Extensive experiments show that our FedDisco outperforms several state-of-the-art methods and can be easily incorporated with many existing methods to further enhance the performance. Our code will be available at https://github.com/MediaBrain-SJTU/FedDisco.

As machine learning tasks continue to evolve, the trend has been to gather larger datasets and train increasingly larger models. While this has led to advancements in accuracy, it has also escalated computational costs to unsustainable levels. Addressing this, our work aims to strike a delicate balance between computational efficiency and model accuracy, a persisting challenge in the field. We introduce a novel method that employs core subset selection for reweighting, effectively optimizing both computational time and model performance. By focusing on a strategically selected coreset, our approach offers a robust representation, as it efficiently minimizes the influence of outliers. The re-calibrated weights are then mapped back to and propagated across the entire dataset. Our experimental results substantiate the effectiveness of this approach, underscoring its potential as a scalable and precise solution for model training.

This paper presents a large publicly available multi-center lumbar spine magnetic resonance imaging (MRI) dataset with reference segmentations of vertebrae, intervertebral discs (IVDs), and spinal canal. The dataset includes 447 sagittal T1 and T2 MRI series from 218 patients with a history of low back pain. It was collected from four different hospitals and was divided into a training (179 patients) and validation (39 patients) set. An iterative data annotation approach was used by training a segmentation algorithm on a small part of the dataset, enabling semi-automatic segmentation of the remaining images. The algorithm provided an initial segmentation, which was subsequently reviewed, manually corrected, and added to the training data. We provide reference performance values for this baseline algorithm and nnU-Net, which performed comparably. We set up a continuous segmentation challenge to allow for a fair comparison of different segmentation algorithms. This study may encourage wider collaboration in the field of spine segmentation, and improve the diagnostic value of lumbar spine MRI.

Chest X-rays (CXR) are the most common medical imaging study and are used to diagnose multiple medical conditions. This study examines the impact of synthetic data supplementation, using diffusion models, on the performance of deep learning (DL) classifiers for CXR analysis. We employed three datasets: CheXpert, MIMIC-CXR, and Emory Chest X-ray, training conditional denoising diffusion probabilistic models (DDPMs) to generate synthetic frontal radiographs. Our approach ensured that synthetic images mirrored the demographic and pathological traits of the original data. Evaluating the classifiers' performance on internal and external datasets revealed that synthetic data supplementation enhances model accuracy, particularly in detecting less prevalent pathologies. Furthermore, models trained on synthetic data alone approached the performance of those trained on real data. This suggests that synthetic data can potentially compensate for real data shortages in training robust DL models. However, despite promising outcomes, the superiority of real data persists.

Many machine learning algorithms are trained and evaluated by splitting data from a single source into training and test sets. While such focus on in-distribution learning scenarios has led to interesting advancement, it has not been able to tell if models are relying on dataset biases as shortcuts for successful prediction (e.g., using snow cues for recognising snowmobiles), resulting in biased models that fail to generalise when the bias shifts to a different class. The cross-bias generalisation problem has been addressed by de-biasing training data through augmentation or re-sampling, which are often prohibitive due to the data collection cost (e.g., collecting images of a snowmobile on a desert) and the difficulty of quantifying or expressing biases in the first place. In this work, we propose a novel framework to train a de-biased representation by encouraging it to be different from a set of representations that are biased by design. This tactic is feasible in many scenarios where it is much easier to define a set of biased representations than to define and quantify bias. We demonstrate the efficacy of our method across a variety of synthetic and real-world biases; our experiments show that the method discourages models from taking bias shortcuts, resulting in improved generalisation. Source code is available at https://github.com/clovaai/rebias.

Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that primarily affects the aging population by impairing cognitive and motor functions. Early detection of AD through accessible methodologies like magnetic resonance imaging (MRI) is vital for developing effective interventions to halt or slow the disease's progression. This study aims to perform a comprehensive analysis of machine learning techniques for selecting MRI-based biomarkers and classifying individuals into healthy controls (HC) and unstable controls (uHC) who later show mild cognitive impairment within five years. The research utilizes MRI data from the Alzheimer's Disease Neuroinformatics Initiative (ADNI) and the Open Access Series of Imaging Studies 3 (OASIS-3), focusing on both HC and uHC participants. The study addresses the challenges of imbalanced data by testing classification methods on balanced and unbalanced datasets, and harmonizes data using polynomial regression to mitigate nuisance variables like age, gender, and intracranial volume. Results indicate that Gaussian Naive Bayes and RusBoost classifiers shows an optimal performance, achieving accuracies of up to 76.46% and 72.48% respectively on the ADNI dataset. For the OASIS-3 dataset, Kernel Naive Bayes and RusBoost yield accuracies ranging from 64.66% to 75.71%, improving further in age-matched datasets. Brain regions like the entorhinal cortex, hippocampus, lateral ventricle, and lateral orbitofrontal cortex are identified as significantly impacted during early cognitive decline. Despite limitations such as small sample sizes, the study's harmonization approach enhances the robustness of biomarker selection, suggesting the potential of this semi-automatic machine learning pipeline for early AD detection using MRI.

Vision-language pre-training for chest X-rays has made significant strides, primarily by utilizing paired radiographs and radiology reports. However, existing approaches often face challenges in encoding medical knowledge effectively. While radiology reports provide insights into the current disease manifestation, medical definitions (as used by contemporary methods) tend to be overly abstract, creating a gap in knowledge. To address this, we propose DeViDe, a novel transformer-based method that leverages radiographic descriptions from the open web. These descriptions outline general visual characteristics of diseases in radiographs, and when combined with abstract definitions and radiology reports, provide a holistic snapshot of knowledge. DeViDe incorporates three key features for knowledge-augmented vision language alignment: First, a large-language model-based augmentation is employed to homogenise medical knowledge from diverse sources. Second, this knowledge is aligned with image information at various levels of granularity. Third, a novel projection layer is proposed to handle the complexity of aligning each image with multiple descriptions arising in a multi-label setting. In zero-shot settings, DeViDe performs comparably to fully supervised models on external datasets and achieves state-of-the-art results on three large-scale datasets. Additionally, fine-tuning DeViDe on four downstream tasks and six segmentation tasks showcases its superior performance across data from diverse distributions.

Enterprise data lakes often suffer from substantial amounts of duplicate and redundant data, with data volumes ranging from terabytes to petabytes. This leads to both increased storage costs and unnecessarily high maintenance costs for these datasets. In this work, we focus on identifying and reducing redundancy in enterprise data lakes by addressing the problem of 'dataset containment'. To the best of our knowledge, this is one of the first works that addresses table-level containment at a large scale. We propose R2D2: a three-step hierarchical pipeline that efficiently identifies almost all instances of containment by progressively reducing the search space in the data lake. It first builds (i) a schema containment graph, followed by (ii) statistical min-max pruning, and finally, (iii) content level pruning. We further propose minimizing the total storage and access costs by optimally identifying redundant datasets that can be deleted (and reconstructed on demand) while respecting latency constraints. We implement our system on Azure Databricks clusters using Apache Spark for enterprise data stored in ADLS Gen2, and on AWS clusters for open-source data. In contrast to existing modified baselines that are inaccurate or take several days to run, our pipeline can process an enterprise customer data lake at the TB scale in approximately 5 hours with high accuracy. We present theoretical results as well as extensive empirical validation on both enterprise (scale of TBs) and open-source datasets (scale of MBs - GBs), which showcase the effectiveness of our pipeline.

Bone density prediction via CT scans to estimate T-scores is crucial, providing a more precise assessment of bone health compared to traditional methods like X-ray bone density tests, which lack spatial resolution and the ability to detect localized changes. However, CT-based prediction faces two major challenges: the high computational complexity of transformer-based architectures, which limits their deployment in portable and clinical settings, and the imbalanced, long-tailed distribution of real-world hospital data that skews predictions. To address these issues, we introduce MedConv, a convolutional model for bone density prediction that outperforms transformer models with lower computational demands. We also adapt Bal-CE loss and post-hoc logit adjustment to improve class balance. Extensive experiments on our AustinSpine dataset shows that our approach achieves up to 21% improvement in accuracy and 20% in ROC AUC over previous state-of-the-art methods.

The race to train language models on vast, diverse, and inconsistently documented datasets has raised pressing concerns about the legal and ethical risks for practitioners. To remedy these practices threatening data transparency and understanding, we convene a multi-disciplinary effort between legal and machine learning experts to systematically audit and trace 1800+ text datasets. We develop tools and standards to trace the lineage of these datasets, from their source, creators, series of license conditions, properties, and subsequent use. Our landscape analysis highlights the sharp divides in composition and focus of commercially open vs closed datasets, with closed datasets monopolizing important categories: lower resource languages, more creative tasks, richer topic variety, newer and more synthetic training data. This points to a deepening divide in the types of data that are made available under different license conditions, and heightened implications for jurisdictional legal interpretations of copyright and fair use. We also observe frequent miscategorization of licenses on widely used dataset hosting sites, with license omission of 72%+ and error rates of 50%+. This points to a crisis in misattribution and informed use of the most popular datasets driving many recent breakthroughs. As a contribution to ongoing improvements in dataset transparency and responsible use, we release our entire audit, with an interactive UI, the Data Provenance Explorer, which allows practitioners to trace and filter on data provenance for the most popular open source finetuning data collections: www.dataprovenance.org.

Machine learning (ML) has the potential to revolutionize various domains, but its adoption is often hindered by the disconnect between the needs of domain experts and translating these needs into robust and valid ML tools. Despite recent advances in LLM-based co-pilots to democratize ML for non-technical domain experts, these systems remain predominantly focused on model-centric aspects while overlooking critical data-centric challenges. This limitation is problematic in complex real-world settings where raw data often contains complex issues, such as missing values, label noise, and domain-specific nuances requiring tailored handling. To address this we introduce CliMB-DC, a human-guided, data-centric framework for LLM co-pilots that combines advanced data-centric tools with LLM-driven reasoning to enable robust, context-aware data processing. At its core, CliMB-DC introduces a novel, multi-agent reasoning system that combines a strategic coordinator for dynamic planning and adaptation with a specialized worker agent for precise execution. Domain expertise is then systematically incorporated to guide the reasoning process using a human-in-the-loop approach. To guide development, we formalize a taxonomy of key data-centric challenges that co-pilots must address. Thereafter, to address the dimensions of the taxonomy, we integrate state-of-the-art data-centric tools into an extensible, open-source architecture, facilitating the addition of new tools from the research community. Empirically, using real-world healthcare datasets we demonstrate CliMB-DC's ability to transform uncurated datasets into ML-ready formats, significantly outperforming existing co-pilot baselines for handling data-centric challenges. CliMB-DC promises to empower domain experts from diverse domains -- healthcare, finance, social sciences and more -- to actively participate in driving real-world impact using ML.

Datasets are central to training machine learning (ML) models. The ML community has recently made significant improvements to data stewardship and documentation practices across the model development life cycle. However, the act of deprecating, or deleting, datasets has been largely overlooked, and there are currently no standardized approaches for structuring this stage of the dataset life cycle. In this paper, we study the practice of dataset deprecation in ML, identify several cases of datasets that continued to circulate despite having been deprecated, and describe the different technical, legal, ethical, and organizational issues raised by such continuations. We then propose a Dataset Deprecation Framework that includes considerations of risk, mitigation of impact, appeal mechanisms, timeline, post-deprecation protocols, and publication checks that can be adapted and implemented by the ML community. Finally, we propose creating a centralized, sustainable repository system for archiving datasets, tracking dataset modifications or deprecations, and facilitating practices of care and stewardship that can be integrated into research and publication processes.