Taha Kass-Hout

Pengcheng Jiang, Cao Xiao, Tianfan Fu et al.

Molecular representation learning is vital for various downstream applications, including the analysis and prediction of molecular properties and side effects. While Graph Neural Networks (GNNs) have been a popular framework for modeling molecular data, they often struggle to capture the full complexity of molecular representations. In this paper, we introduce a novel method called GODE, which accounts for the dual-level structure inherent in molecules. Molecules possess an intrinsic graph structure and simultaneously function as nodes within a broader molecular knowledge graph. GODE integrates individual molecular graph representations with multi-domain biochemical data from knowledge graphs. By pre-training two GNNs on different graph structures and employing contrastive learning, GODE effectively fuses molecular structures with their corresponding knowledge graph substructures. This fusion yields a more robust and informative representation, enhancing molecular property predictions by leveraging both chemical and biological information. When fine-tuned across 11 chemical property tasks, our model significantly outperforms existing benchmarks, achieving an average ROC-AUC improvement of 12.7% for classification tasks and an average RMSE/MAE improvement of 34.4% for regression tasks. Notably, GODE surpasses the current leading model in property prediction, with advancements of 2.2% in classification and 7.2% in regression tasks.

Deepa Anand, Gurunath Reddy M, Vanika Singhal et al.

Recent advances in Vision Transformers (ViT) and Stable Diffusion (SD) models with their ability to capture rich semantic features of the image have been used for image correspondence tasks on natural images. In this paper, we examine the ability of a variety of pre-trained ViT (DINO, DINOv2, SAM, CLIP) and SD models, trained exclusively on natural images, for solving the correspondence problems on medical images. While many works have made a case for in-domain training, we show that the models trained on natural images can offer good performance on medical images across different modalities (CT,MR,Ultrasound) sourced from various manufacturers, over multiple anatomical regions (brain, thorax, abdomen, extremities), and on wide variety of tasks. Further, we leverage the correspondence with respect to a template image to prompt a Segment Anything (SAM) model to arrive at single shot segmentation, achieving dice range of 62%-90% across tasks, using just one image as reference. We also show that our single-shot method outperforms the recently proposed few-shot segmentation method - UniverSeg (Dice range 47%-80%) on most of the semantic segmentation tasks(six out of seven) across medical imaging modalities.

Alex Boyd, Andrew Warrington, Taha Kass-Hout et al.

Foundational marked temporal point process (MTPP) models, such as the Hawkes process, often use inexpressive model families in order to offer interpretable parameterizations of event data. On the other hand, neural MTPPs models forego this interpretability in favor of absolute predictive performance. In this work, we present a new family MTPP models: the hyper Hawkes process (HHP), which aims to be as flexible and performant as neural MTPPs, while retaining interpretable aspects. To achieve this, the HHP extends the classical Hawkes process to increase its expressivity by first expanding the dimension of the process into a latent space, and then introducing a hypernetwork to allow time- and data-dependent dynamics. These extensions define a highly performant MTPP family, achieving state-of-the-art performance across a range of benchmark tasks and metrics. Furthermore, by retaining the linearity of the recurrence, albeit now piecewise and conditionally linear, the HHP also retains much of the structure of the original Hawkes process, which we exploit to create direct probes into how the model creates predictions. HHP models therefore offer both state-of-the-art predictions, while also providing an opportunity to ``open the box'' and inspect how predictions were generated.

Aishik Konwer, Zhijian Yang, Erhan Bas et al.

Foundational models such as the Segment Anything Model (SAM) are gaining traction in medical imaging segmentation, supporting multiple downstream tasks. However, such models are supervised in nature, still relying on large annotated datasets or prompts supplied by experts. Conventional techniques such as active learning to alleviate such limitations are limited in scope and still necessitate continuous human involvement and complex domain knowledge for label refinement or establishing reward ground truth. To address these challenges, we propose an enhanced Segment Anything Model (SAM) framework that utilizes annotation-efficient prompts generated in a fully unsupervised fashion, while still capturing essential semantic, location, and shape information through contrastive language-image pretraining and visual question answering. We adopt the direct preference optimization technique to design an optimal policy that enables the model to generate high-fidelity segmentations with simple ratings or rankings provided by a virtual annotator simulating the human annotation process. State-of-the-art performance of our framework in tasks such as lung segmentation, breast tumor segmentation, and organ segmentation across various modalities, including X-ray, ultrasound, and abdominal CT, justifies its effectiveness in low-annotation data scenarios.

Aofei Chang, Le Huang, Parminder Bhatia et al.

Large Vision Language Models (LVLMs) are becoming increasingly important in the medical domain, yet Medical LVLMs (Med-LVLMs) frequently generate hallucinations due to limited expertise and the complexity of medical applications. Existing benchmarks fail to effectively evaluate hallucinations based on their underlying causes and lack assessments of mitigation strategies. To address this gap, we introduce MedHEval, a novel benchmark that systematically evaluates hallucinations and mitigation strategies in Med-LVLMs by categorizing them into three underlying causes: visual misinterpretation, knowledge deficiency, and context misalignment. We construct a diverse set of close- and open-ended medical VQA datasets with comprehensive evaluation metrics to assess these hallucination types. We conduct extensive experiments across 11 popular (Med)-LVLMs and evaluate 7 state-of-the-art hallucination mitigation techniques. Results reveal that Med-LVLMs struggle with hallucinations arising from different causes while existing mitigation methods show limited effectiveness, especially for knowledge- and context-based errors. These findings underscore the need for improved alignment training and specialized mitigation strategies to enhance Med-LVLMs' reliability. MedHEval establishes a standardized framework for evaluating and mitigating medical hallucinations, guiding the development of more trustworthy Med-LVLMs.

Shuyang Yu, Runxue Bao, Parminder Bhatia et al.

Large language models (LLMs) can learn vast amounts of knowledge from diverse domains during pre-training. However, long-tail knowledge from specialized domains is often scarce and underrepresented, rarely appearing in the models' memorization. Prior work has shown that in-context learning (ICL) with retriever augmentation can help LLMs better capture long-tail knowledge, reducing their reliance on pre-trained data. Despite these advances, we observe that LLM predictions for long-tail questions remain uncertain to variations in retrieved samples. To take advantage of the uncertainty in ICL for guiding LLM predictions toward correct answers on long-tail samples, we propose a reinforcement learning-based dynamic uncertainty ranking method for ICL that accounts for the varying impact of each retrieved sample on LLM predictions. Our approach prioritizes more informative and stable samples while demoting misleading ones, updating rankings based on the feedback from the LLM w.r.t. each retrieved sample. To enhance training efficiency and reduce query costs, we introduce a learnable dynamic ranking threshold, adjusted when the model encounters negative prediction shifts. Experimental results on various question-answering datasets from different domains show that our method outperforms the best baseline by $2.76\%$, with a notable $5.96\%$ boost in accuracy on long-tail questions that elude zero-shot inference.

Yuxin Chang, Alex Boyd, Cao Xiao et al.

Marked temporal point processes (MTPPs) model sequences of events occurring at irregular time intervals, with wide-ranging applications in fields such as healthcare, finance and social networks. We propose the state-space point process (S2P2) model, a novel and performant model that leverages techniques derived for modern deep state-space models (SSMs) to overcome limitations of existing MTPP models, while simultaneously imbuing strong inductive biases for continuous-time event sequences that other discrete sequence models (i.e., RNNs, transformers) do not capture. Inspired by the classical linear Hawkes processes, we propose an architecture that interleaves stochastic jump differential equations with nonlinearities to create a highly expressive intensity-based MTPP model, without the need for restrictive parametric assumptions for the intensity. Our approach enables efficient training and inference with a parallel scan, bringing linear complexity and sublinear scaling while retaining expressivity to MTPPs. Empirically, S2P2 achieves state-of-the-art predictive likelihoods across eight real-world datasets, delivering an average improvement of 33% over the best existing approaches.

Aofei Chang, Le Huang, Alex James Boyd et al.

Medical Large Vision-Language Models (Med-LVLMs) often exhibit suboptimal attention distribution on visual inputs, leading to hallucinated or inaccurate outputs. Existing mitigation methods primarily rely on inference-time interventions, which are limited in attention adaptation or require additional supervision. To address this, we propose A$^3$Tune, a novel fine-tuning framework for Automatic Attention Alignment Tuning. A$^3$Tune leverages zero-shot weak labels from SAM, refines them into prompt-aware labels using BioMedCLIP, and then selectively modifies visually-critical attention heads to improve alignment while minimizing interference. Additionally, we introduce a A$^3$MoE module, enabling adaptive parameter selection for attention tuning across diverse prompts and images. Extensive experiments on medical VQA and report generation benchmarks show that A$^3$Tune outperforms state-of-the-art baselines, achieving enhanced attention distributions and performance in Med-LVLMs.

Haoyan Yang, Runxue Bao, Cao Xiao et al.

LLM-as-a-Judge has emerged as a promising tool for automatically evaluating generated outputs, but its reliability is often undermined by potential biases in judgment. Existing efforts to mitigate these biases face key limitations: in-context learning-based methods fail to address rooted biases due to the evaluator's limited capacity for self-reflection, whereas fine-tuning is not applicable to all evaluator types, especially closed-source models. To address this challenge, we introduce the Reasoning-based Bias Detector (RBD), which is a plug-in module that identifies biased evaluations and generates structured reasoning to guide evaluator self-correction. Rather than modifying the evaluator itself, RBD operates externally and engages in an iterative process of bias detection and feedback-driven revision. To support its development, we design a complete pipeline consisting of biased dataset construction, supervision collection, distilled reasoning-based fine-tuning of RBD, and integration with LLM evaluators. We fine-tune four sizes of RBD models, ranging from 1.5B to 14B, and observe consistent performance improvements across all scales. Experimental results on 4 bias types--verbosity, position, bandwagon, and sentiment--evaluated using 8 LLM evaluators demonstrate RBD's strong effectiveness. For example, the RBD-8B model improves evaluation accuracy by an average of 18.5% and consistency by 10.9%, and surpasses prompting-based baselines and fine-tuned judges by 12.8% and 17.2%, respectively. These results highlight RBD's effectiveness and scalability. Additional experiments further demonstrate its strong generalization across biases and domains, as well as its efficiency.

Chenliang Li, Adel Elmahdy, Alex Boyd et al.

Reinforcement learning (RL) algorithms such as PPO and GRPO are widely used to train large language models (LLMs) for multi-turn agentic tasks. However, in off-policy training pipelines, these methods often exhibit unstable optimization dynamics and are prone to performance collapse. Through empirical analysis, we identify two fundamental sources of instability in this setting: (1)~a granularity mismatch between token-level policy optimization and turn-structured interactions, and (2) high-variance and unreliable gradient updates induced by off-policy importance sampling and inaccurate advantage estimation. To address these challenges, we propose SORL, \underline{S}tabilizing \underline{O}ff-Policy \underline{R}einforcement \underline{L}earning for Long-Horizon Agent Training. SORL introduces principled mechanisms that align policy optimization with the structure of multi-turn interactions and adaptively suppress unreliable off-policy updates, yielding more conservative and robust learning dynamics. Within this framework, we instantiate two stabilized algorithms: SO-PPO and SO-GRPO. Both algorithms are designed to mitigate gradient variance and prevent optimization collapse without requiring careful early stopping or heuristic tuning. We evaluate SO-PPO and SO-GRPO on a range of multi-turn search benchmarks, including general question answering, multi-hop question answering, and medical multiple-choice QA tasks. Experimental results show that both methods consistently prevent training instabilities and performance collapses observed in standard PPO and GRPO, maintain lower clipping ratios and more stable optimization trajectories, and achieve superior or comparable task performance. These results demonstrate that the proposed algorithm provides a practical, scalable, and general framework for stabilizing reinforcement learning in multi-turn LLM agent training.

Sicheng Zhou, Lei Wu, Cao Xiao et al.

Self-supervised learning (SSL) has transformed vision encoder training in general domains but remains underutilized in medical imaging due to limited data and domain specific biases. We present MammoDINO, a novel SSL framework for mammography, pretrained on 1.4 million mammographic images. To capture clinically meaningful features, we introduce a breast tissue aware data augmentation sampler for both image-level and patch-level supervision and a cross-slice contrastive learning objective that leverages 3D digital breast tomosynthesis (DBT) structure into 2D pretraining. MammoDINO achieves state-of-the-art performance on multiple breast cancer screening tasks and generalizes well across five benchmark datasets. It offers a scalable, annotation-free foundation for multipurpose computer-aided diagnosis (CAD) tools for mammogram, helping reduce radiologists' workload and improve diagnostic efficiency in breast cancer screening.

Zhijian Yang, Noel DSouza, Istvan Megyeri et al.

Magnetic Resonance Imaging (MRI) is a critical medical imaging modality in clinical diagnosis and research, yet its complexity and heterogeneity pose challenges for automated analysis, particularly in scalable and generalizable machine learning applications. While foundation models have revolutionized natural language and vision tasks, their application to MRI remains limited due to data scarcity and narrow anatomical focus. In this work, we present Decipher-MR, a 3D MRI-specific vision-language foundation model trained on a large-scale dataset comprising 200,000 MRI series from over 22,000 studies spanning diverse anatomical regions, sequences, and pathologies. Decipher-MR integrates self-supervised vision learning with report-guided text supervision to build robust, generalizable representations, enabling effective adaptation across broad applications. To enable robust and diverse clinical tasks with minimal computational overhead, Decipher-MR supports a modular design that enables tuning of lightweight, task-specific decoders attached to a frozen pretrained encoder. Following this setting, we evaluate Decipher-MR across diverse benchmarks including disease classification, demographic prediction, anatomical localization, and cross-modal retrieval, demonstrating consistent performance gains over existing foundation models and task-specific approaches. Our results establish Decipher-MR as a scalable and versatile foundation for MRI-based AI, facilitating efficient development across clinical and research domains.

Fred Qin, Vivek Madan, Ujjwal Ratan et al.

Sepsis is a life-threatening disease with high morbidity, mortality and healthcare costs. The early prediction and administration of antibiotics and intravenous fluids is considered crucial for the treatment of sepsis and can save potentially millions of lives and billions in health care costs. Professional clinical care practitioners have proposed clinical criterion which aid in early detection of sepsis; however, performance of these criterion is often limited. Clinical text provides essential information to estimate the severity of the sepsis in addition to structured clinical data. In this study, we explore how clinical text can complement structured data towards early sepsis prediction task. In this paper, we propose multi modal model which incorporates both structured data in the form of patient measurements as well as textual notes on the patient. We employ state-of-the-art NLP models such as BERT and a highly specialized NLP model in Amazon Comprehend Medical to represent the text. On the MIMIC-III dataset containing records of ICU admissions, we show that by using these notes, one achieves an improvement of 6.07 points in a standard utility score for Sepsis prediction and 2.89% in AUROC score. Our methods significantly outperforms a clinical criteria suggested by experts, qSOFA, as well as the winning model of the PhysioNet Computing in Cardiology Challenge for predicting Sepsis.

Parminder Bhatia, Lan Liu, Kristjan Arumae et al.

Coronavirus disease (COVID-19) has been declared as a pandemic by WHO with thousands of cases being reported each day. Numerous scientific articles are being published on the disease raising the need for a service which can organize, and query them in a reliable fashion. To support this cause we present AWS CORD-19 Search (ACS), a public, COVID-19 specific, neural search engine that is powered by several machine learning systems to support natural language based searches. ACS with capabilities such as document ranking, passage ranking, question answering and topic classification provides a scalable solution to COVID-19 researchers and policy makers in their search and discovery for answers to high priority scientific questions. We present a quantitative evaluation and qualitative analysis of the system against other leading COVID-19 search platforms. ACS is top performing across these systems yielding quality results which we detail with relevant examples in this work.

Mengqi Jin, Mohammad Taha Bahadori, Aaron Colak et al.

Clinical text provides essential information to estimate the acuity of a patient during hospital stays in addition to structured clinical data. In this study, we explore how clinical text can complement a clinical predictive learning task. We leverage an internal medical natural language processing service to perform named entity extraction and negation detection on clinical notes and compose selected entities into a new text corpus to train document representations. We then propose a multimodal neural network to jointly train time series signals and unstructured clinical text representations to predict the in-hospital mortality risk for ICU patients. Our model outperforms the benchmark by 2% AUC.