arXiv subjects

Jimeng Sun

Publications and source records attributed to Jimeng Sun.

At least 37 records · Page 2Linked to original sources

arXiv2026

KMM-CP: Practical Conformal Prediction under Covariate Shift via Selective Kernel Mean Matching

Uncertainty quantification is essential for deploying machine learning models in high-stakes domains such as scientific discovery and healthcare. Conformal Prediction (CP) provides finite-sample coverage guarantees under exchangeability, an assumption often violated in practice due to distribution shift. Under covariate shift, restoring validity requires importance weighting, yet accurate density-ratio estimation becomes unstable when training and test distributions exhibit limited support overlap. We propose KMM-CP, a conformal prediction framework based on Kernel Mean Matching (KMM) for covariate-shift correction. We show that KMM directly controls the bias-variance components governing conformal coverage error by minimizing RKHS moment discrepancy under explicit weight constraints, and establish asymptotic coverage guarantees under mild conditions. We then introduce a selective extension that identifies regions of reliable support overlap and restricts conformal correction to this subset, further improving stability in low-overlap regimes. Experiments on molecular property prediction benchmarks with realistic distribution shifts show that KMM-CP reduces coverage gap by over 50% compared to existing approaches. The code is available at https://github.com/siddharthal/KMM-CP.

cs.LG↗

arXiv2026

A Practical Guide Towards Interpreting Time-Series Deep Clinical Predictive Models: A Reproducibility Study

Clinical decisions are high-stakes and require explicit justification, making model interpretability essential for auditing deep clinical models prior to deployment. As the ecosystem of model architectures and explainability methods expands, critical questions remain: Do architectural features like attention improve explainability? Do interpretability approaches generalize across clinical tasks? While prior benchmarking efforts exist, they often lack extensibility and reproducibility, and critically, fail to systematically examine how interpretability varies across the interplay of clinical tasks and model architectures. To address these gaps, we present a comprehensive benchmark evaluating interpretability methods across diverse clinical prediction tasks and model architectures. Our analysis reveals that: (1) attention when leveraged properly is a highly efficient approach for faithfully interpreting model predictions; (2) black-box interpreters like KernelSHAP and LIME are computationally infeasible for time-series clinical prediction tasks; and (3) several interpretability approaches are too unreliable to be trustworthy. From our findings, we discuss several guidelines on improving interpretability within clinical predictive pipelines. To support reproducibility and extensibility, we provide our implementations via PyHealth, a well-documented open-source framework: https://github.com/sunlabuiuc/PyHealth.

cs.LG↗

arXiv2026

Adaptation of Agentic AI: A Survey of Post-Training, Memory, and Skills

Large language model (LLM) agents are moving beyond prompting alone. ChatGPT marked the rise of general-purpose LLM assistants, DeepSeek showed that on-policy reinforcement learning with verifiable rewards can improve reasoning and tool use, and OpenClaw highlights a newer direction in which agents accumulate persistent memory and reusable skills. Yet the research landscape remains fragmented across post-training, retrieval, memory, and skill systems. This survey studies these developments under a single notion of \emph{adaptation}: improving an agent, its tools, or their interaction after pretraining. We organize the field with a four-paradigm framework spanning agent adaptation and tool adaptation. On the agent side, A1 (tool-execution-signaled) and A2 (agent-output-signaled) improve the agent itself through supervised fine-tuning, preference optimization, and reinforcement learning with verifiable rewards. On the tool side, T1 (agent-agnostic) provides reusable pre-trained modules any agent can call, while T2 (agent-supervised) uses the agent's outputs to train memory systems, skill libraries, or lightweight subagents. Using this framework, we review post-training methods, adaptive memory architectures, and agent skills; compare their trade-offs in cost, flexibility, and generalization; and summarize evaluation practices across deep research, software development, computer use, and drug discovery. We conclude by outlining open problems in agent-tool co-adaptation, continual learning, safety, and efficient deployment.

cs.AI↗

arXiv2026

How Well Do Multimodal Models Reason on ECG Signals?

While multimodal large language models offer a promising solution to the "black box" nature of health AI by generating interpretable reasoning traces, verifying the validity of these traces remains a critical challenge. Existing evaluation methods are either unscalable, relying on manual clinician review, or superficial, utilizing proxy metrics (e.g. QA) that fail to capture the semantic correctness of clinical logic. In this work, we introduce a reproducible framework for evaluating reasoning in ECG signals. We propose decomposing reasoning into two distinct, components: (i) Perception, the accurate identification of patterns within the raw signal, and (ii) Deduction, the logical application of domain knowledge to those patterns. To evaluate Perception, we employ an agentic framework that generates code to empirically verify the temporal structures described in the reasoning trace. To evaluate Deduction, we measure the alignment of the model's logic against a structured database of established clinical criteria in a retrieval-based approach. This dual-verification method enables the scalable assessment of "true" reasoning capabilities.

cs.AI↗

arXiv2026

ConfHit: Conformal Generative Design with Oracle Free Guarantees

The success of deep generative models in scientific discovery requires not only the ability to generate novel candidates but also reliable guarantees that these candidates indeed satisfy desired properties. Recent conformal-prediction methods offer a path to such guarantees, but its application to generative modeling in drug discovery is limited by budget constraints, lack of oracle access, and distribution shift. To this end, we introduce ConfHit, a distribution-free framework that provides validity guarantees under these conditions. ConfHit formalizes two central questions: (i) Certification: whether a generated batch can be guaranteed to contain at least one hit with a user-specified confidence level, and (ii) Design: whether the generation can be refined to a compact set without weakening this guarantee. ConfHit leverages weighted exchangeability between historical and generated samples to eliminate the need for an experimental oracle, constructs multiple-sample density-ratio weighted conformal p-value to quantify statistical confidence in hits, and proposes a nested testing procedure to certify and refine candidate sets of multiple generated samples while maintaining statistical guarantees. Across representative generative molecule design tasks and a broad range of methods, ConfHit consistently delivers valid coverage guarantees at multiple confidence levels while maintaining compact certified sets, establishing a principled and reliable framework for generative modeling.

cs.LG↗

arXiv2026

Bridging the Reproducibility Divide: Open Source Software's Role in Standardizing Healthcare AI

Our analysis of recent AI4H publications reveals that, despite a trend toward utilizing open datasets and sharing modeling code, 74% of AI4H papers still rely on private datasets or do not share their code. This is especially concerning in healthcare applications, where trust is essential. Furthermore, inconsistent and poorly documented data preprocessing pipelines result in variable model performance reports, even for identical tasks and datasets, making it challenging to evaluate the true effectiveness of AI models. Despite the challenges posed by the reproducibility crisis, addressing these issues through open practices offers substantial benefits. For instance, while the reproducibility mandate adds extra effort to research and publication, it significantly enhances the impact of the work. Our analysis shows that papers that used both public datasets and shared code received, on average, 110% more citations than those that do neither--more than doubling the citation count. Given the clear benefits of enhancing reproducibility, it is imperative for the AI4H community to take concrete steps to overcome existing barriers. The community should promote open science practices, establish standardized guidelines for data preprocessing, and develop robust benchmarks. Tackling these challenges through open-source development can improve reproducibility, which is essential for ensuring that AI models are safe, effective, and beneficial for patient care. This approach will help build more trustworthy AI systems that can be integrated into healthcare settings, ultimately contributing to better patient outcomes and advancing the field of medicine.

cs.CY↗

arXiv2026

ODEBrain: Continuous-Time EEG Graph for Modeling Dynamic Brain Networks

Modeling neural population dynamics is crucial for foundational neuroscientific research and various clinical applications. Conventional latent variable methods typically model continuous brain dynamics through discretizing time with recurrent architecture, which necessarily results in compounded cumulative prediction errors and failure of capturing instantaneous, nonlinear characteristics of EEGs. We propose ODEBRAIN, a Neural ODE latent dynamic forecasting framework to overcome these challenges by integrating spatio-temporal-frequency features into spectral graph nodes, followed by a Neural ODE modeling the continuous latent dynamics. Our design ensures that latent representations can capture stochastic variations of complex brain states at any given time point. Extensive experiments verify that ODEBRAIN can improve significantly over existing methods in forecasting EEG dynamics with enhanced robustness and generalization capabilities.

cs.AI↗

arXiv2026

AdNanny: One Reasoning LLM for All Offline Ads Recommendation Tasks

Large Language Models (LLMs) have shown strong capabilities in Natural Language Understanding and Generation, but deploying them directly in online advertising systems is often impractical due to strict millisecond-level latency constraints. This has motivated the use of LLMs offline to improve retrieval, ranking, and recommendation models. Existing solutions typically fine-tune separate LLMs for individual tasks such as query-ad relevance labeling, keyword-based query generation, and user profiling. This results in redundant models, high maintenance cost, and limited performance gains despite substantial overlap in domain knowledge and reasoning patterns. We introduce AdNanny, a unified reasoning-centric LLM that serves as a shared backbone for offline advertising tasks. AdNanny is obtained by fine-tuning a public 671B-parameter DeepSeek-R1 checkpoint using a scalable training system that supports hybrid dense-MoE parallelism. We construct reasoning-augmented corpora that pair structured supervision with step-by-step natural language explanations. A multi-task supervised fine-tuning stage with adaptive reweighting enables AdNanny to handle diverse labeling and generation tasks in a consistent reasoning format. This is followed by reinforcement learning using downstream advertising metrics to align model behavior with online retrieval and ranking objectives. AdNanny is deployed in production within Bing Ads, where it significantly reduces manual labeling effort and improves accuracy across multiple offline tasks. By consolidating many task-specific models into a single reasoning-centric foundation model, AdNanny provides a scalable and cost-effective solution for large-scale advertising systems.

cs.SE↗

arXiv2026

RAS: Retrieval-And-Structuring for Knowledge-Intensive LLM Generation

Large language models (LLMs) have achieved impressive performance on knowledge-intensive tasks, yet they often struggle with multi-step reasoning due to the unstructured nature of retrieved context. While retrieval-augmented generation (RAG) methods provide external information, the lack of explicit organization among retrieved passages limits their effectiveness, leading to brittle reasoning pathways. Recent interpretability studies highlighting the importance of structured intermediate reasoning further align with this perspective. We propose Retrieval-And-Structuring (RAS), a framework that dynamically constructs question-specific knowledge graphs through iterative retrieval and structured knowledge building. RAS interleaves targeted retrieval planning with incremental graph construction, enabling models to assemble and reason over evolving knowledge structures tailored to each query. On seven knowledge-intensive benchmarks, RAS consistently outperforms strong baselines, achieving up to 8.7\% and 7.0\% gains with proprietary and open-source LLMs, respectively. Our results demonstrate that dynamic, question-specific knowledge structuring offers a robust path to improving reasoning accuracy and robustness in language model generation.

cs.CL↗

arXiv2025

DeepEvidence: Empowering Biomedical Discovery with Deep Knowledge Graph Research

Biomedical knowledge graphs (KGs) encode vast, heterogeneous information spanning literature, genes, pathways, drugs, diseases, and clinical trials, but leveraging them collectively for scientific discovery remains difficult. Their structural differences, continual evolution, and limited cross-resource alignment require substantial manual integration, limiting the depth and scale of knowledge exploration. We introduce DeepEvidence, an AI-agent framework designed to perform Deep Research across various heterogeneous biomedical KGs. Unlike generic Deep Research systems that rely primarily on internet-scale text, DeepEvidence incorporates specialized knowledge-graph tooling and coordinated exploration strategies to systematically bridge heterogeneous resources. At its core is an orchestrator that directs two complementary agents: Breadth-First ReSearch (BFRS) for broad, multi-graph entity search, and Depth-First ReSearch (DFRS) for multi-hop, evidence-focused reasoning. An internal, incrementally built evidence graph provides a structured record of retrieved entities, relations, and supporting evidence. To operate at scale, DeepEvidence includes unified interfaces for querying diverse biomedical APIs and an execution sandbox that enables programmatic data retrieval, extraction, and analysis. Across established deep-reasoning benchmarks and four key stages of the biomedical discovery lifecycle: drug discovery, pre-clinical experimentation, clinical trial development, and evidence-based medicine, DeepEvidence demonstrates substantial gains in systematic exploration and evidence synthesis. These results highlight the potential of knowledge-graph-driven Deep Research to accelerate biomedical discovery.

cs.IR↗

arXiv2025

MIMIC-RD: Can LLMs differentially diagnose rare diseases in real-world clinical settings?

Despite rare diseases affecting 1 in 10 Americans, their differential diagnosis remains challenging. Due to their impressive recall abilities, large language models (LLMs) have been recently explored for differential diagnosis. Existing approaches to evaluating LLM-based rare disease diagnosis suffer from two critical limitations: they rely on idealized clinical case studies that fail to capture real-world clinical complexity, or they use ICD codes as disease labels, which significantly undercounts rare diseases since many lack direct mappings to comprehensive rare disease databases like Orphanet. To address these limitations, we explore MIMIC-RD, a rare disease differential diagnosis benchmark constructed by directly mapping clinical text entities to Orphanet. Our methodology involved an initial LLM-based mining process followed by validation from four medical annotators to confirm identified entities were genuine rare diseases. We evaluated various models on our dataset of 145 patients and found that current state-of-the-art LLMs perform poorly on rare disease differential diagnosis, highlighting the substantial gap between existing capabilities and clinical needs. From our findings, we outline several future steps towards improving differential diagnosis of rare diseases.

cs.AI↗

arXiv2025

Developing Large Language Models for Clinical Research Using One Million Clinical Trials

Developing artificial intelligence (AI) for clinical research requires a comprehensive data foundation that supports model training and rigorous evaluation. Here, we introduce TrialPanorama, a large-scale structured resource that aggregates 1.6M clinical trial records from fifteen global registries and links them with biomedical ontologies and associated literature. To demonstrate its utility, we build a pipeline that constructs 152K training and testing samples for eight key clinical research tasks. Three tasks support systematic review workflows, including study search, study screening, and evidence summarization. Five tasks focus on trial design and optimization, including arm design, eligibility criteria design, endpoint selection, sample size estimation, and trial completion assessment and rationalization. Benchmarking cutting-edge large language models (LLMs) reveals that generic LLMs have limited capability in clinical reasoning. In contrast, an 8B LLM we developed on TrialPanorama using supervised finetuning and reinforcement learning wins over the 70B generic counterparts in all eight tasks, with a relative improvement of 73.7%, 67.6%, 38.4%, 37.8%, 26.5%, 20.7%, 20.0%, 18.1%, and 5.2%, respectively. We envision that TrialPanorama provides a solid foundation for future scaling of AI for clinical research.

cs.AI↗

arXiv2025

Social Determinants of Health Prediction for ICD-9 Code with Reasoning Models

Social Determinants of Health correlate with patient outcomes but are rarely captured in structured data. Recent attention has been given to automatically extracting these markers from clinical text to supplement diagnostic systems with knowledge of patients' social circumstances. Large language models demonstrate strong performance in identifying Social Determinants of Health labels from sentences. However, prediction in large admissions or longitudinal notes is challenging given long distance dependencies. In this paper, we explore hospital admission multi-label Social Determinants of Health ICD-9 code classification on the MIMIC-III dataset using reasoning models and traditional large language models. We exploit existing ICD-9 codes for prediction on admissions, which achieved an 89% F1. Our contributions include our findings, missing SDoH codes in 139 admissions, and code to reproduce the results.

cs.LG↗

arXiv2025

Prostate-VarBench: A Benchmark with Interpretable TabNet Framework for Prostate Cancer Variant Classification

Variants of Uncertain Significance (VUS) limit the clinical utility of prostate cancer genomics by delaying diagnosis and therapy when evidence for pathogenicity or benignity is incomplete. Progress is further limited by inconsistent annotations across sources and the absence of a prostate-specific benchmark for fair comparison. We introduce Prostate-VarBench, a curated pipeline for creating prostate-specific benchmarks that integrates COSMIC (somatic cancer mutations), ClinVar (expert-curated clinical variants), and TCGA-PRAD (prostate tumor genomics from The Cancer Genome Atlas) into a harmonized dataset of 193,278 variants supporting patient- or gene-aware splits to prevent data leakage. To ensure data integrity, we corrected a Variant Effect Predictor (VEP) issue that merged multiple transcript records, introducing ambiguity in clinical significance fields. We then standardized 56 interpretable features across eight clinically relevant tiers, including population frequency, variant type, and clinical context. AlphaMissense pathogenicity scores were incorporated to enhance missense variant classification and reduce VUS uncertainty. Building on this resource, we trained an interpretable TabNet model to classify variant pathogenicity, whose step-wise sparse masks provide per-case rationales consistent with molecular tumor board review practices. On the held-out test set, the model achieved 89.9% accuracy with balanced class metrics, and the VEP correction yields an 6.5% absolute reduction in VUS.

q-bio.QM↗

arXiv2025

s3: You Don't Need That Much Data to Train a Search Agent via RL

Retrieval-augmented generation (RAG) systems empower large language models (LLMs) to access external knowledge during inference. Recent advances have enabled LLMs to act as search agents via reinforcement learning (RL), improving information acquisition through multi-turn interactions with retrieval engines. However, existing approaches either optimize retrieval using search-only metrics (e.g., NDCG) that ignore downstream utility or fine-tune the entire LLM to jointly reason and retrieve-entangling retrieval with generation and limiting the real search utility and compatibility with frozen or proprietary models. In this work, we propose s3, a lightweight, model-agnostic framework that decouples the searcher from the generator and trains the searcher using a Gain Beyond RAG reward: the improvement in generation accuracy over naive RAG. s3 requires only 2.4k training samples to outperform baselines trained on over 70x more data, consistently delivering stronger downstream performance across six general QA and five medical QA benchmarks.

cs.AI↗

arXiv2025

Hulu-Med: A Transparent Generalist Model towards Holistic Medical Vision-Language Understanding

Real-world clinical decision-making requires integrating heterogeneous data, including medical text, 2D images, 3D volumes, and videos, while existing AI systems fail to unify all these signals, limiting their utility. In this paper, we introduce Hulu-Med, a transparent, generalist medical Vision-Language Model (VLM) designed to unify language-only, 2D/3D vision-language, and video understanding within a single architecture. Hulu-Med is trained on a curated corpus of 16.7 million samples, comprising exclusively public or synthetic data, spanning 12 major anatomical systems and 14 medical imaging modalities. Hulu-Med employs a medical-aware token-reduction strategy that prunes redundant visual tokens, achieving up to a 55% reduction for 3D and video inputs, improving cross-modal efficiency, and enabling training at 7B-32B parameter scales in approximately 4,000-40,000 GPU hours. Across 30 public in-domain and out-of-domain medical benchmarks-covering text reasoning, visual question answering, report generation, multilingual dialogue, video understanding, and rare disease diagnosis-Hulu-Med surpasses existing open-source models on 27 of 30 benchmarks and outperforms proprietary systems such as GPT-4o on 16 benchmarks. Despite being a VLM, Hulu-Med outperforms GPT-4o and matches GPT-o1 on the text-only HealthBench. For the first time in the community, we provide a fully transparent, reproducible and cost-effective pipeline for holistic medical vision-language understanding by releasing our end-to-end data curation, training procedures, and model parameters. Code and models are available at https://github.com/ZJUI-AI4H/Hulu-Med.

cs.CV↗

arXiv2025

Reinforcement Learning for Out-of-Distribution Reasoning in LLMs: An Empirical Study on Diagnosis-Related Group Coding

Diagnosis-Related Group (DRG) codes are essential for hospital reimbursement and operations but require labor-intensive assignment. Large Language Models (LLMs) struggle with DRG coding due to the out-of-distribution (OOD) nature of the task: pretraining corpora rarely contain private clinical or billing data. We introduce DRG-Sapphire, which uses large-scale reinforcement learning (RL) for automated DRG coding from clinical notes. Built on Qwen2.5-7B and trained with Group Relative Policy Optimization (GRPO) using rule-based rewards, DRG-Sapphire introduces a series of RL enhancements to address domain-specific challenges not seen in previous mathematical tasks. Our model achieves state-of-the-art accuracy on the MIMIC-IV benchmark and generates physician-validated reasoning for DRG assignments, significantly enhancing explainability. Our study further sheds light on broader challenges of applying RL to knowledge-intensive, OOD tasks. We observe that RL performance scales approximately linearly with the logarithm of the number of supervised fine-tuning (SFT) examples, suggesting that RL effectiveness is fundamentally constrained by the domain knowledge encoded in the base model. For OOD tasks like DRG coding, strong RL performance requires sufficient knowledge infusion prior to RL. Consequently, scaling SFT may be more effective and computationally efficient than scaling RL alone for such tasks.

cs.LG↗

arXiv2025

DentVLM: A Multimodal Vision-Language Model for Comprehensive Dental Diagnosis and Enhanced Clinical Practice

Diagnosing and managing oral diseases necessitate advanced visual interpretation across diverse imaging modalities and integrated information synthesis. While current AI models excel at isolated tasks, they often fall short in addressing the complex, multimodal requirements of comprehensive clinical dental practice. Here we introduce DentVLM, a multimodal vision-language model engineered for expert-level oral disease diagnosis. DentVLM was developed using a comprehensive, large-scale, bilingual dataset of 110,447 images and 2.46 million visual question-answering (VQA) pairs. The model is capable of interpreting seven 2D oral imaging modalities across 36 diagnostic tasks, significantly outperforming leading proprietary and open-source models by 19.6% higher accuracy for oral diseases and 27.9% for malocclusions. In a clinical study involving 25 dentists, evaluating 1,946 patients and encompassing 3,105 QA pairs, DentVLM surpassed the diagnostic performance of 13 junior dentists on 21 of 36 tasks and exceeded that of 12 senior dentists on 12 of 36 tasks. When integrated into a collaborative workflow, DentVLM elevated junior dentists' performance to senior levels and reduced diagnostic time for all practitioners by 15-22%. Furthermore, DentVLM exhibited promising performance across three practical utility scenarios, including home-based dental health management, hospital-based intelligent diagnosis and multi-agent collaborative interaction. These findings establish DentVLM as a robust clinical decision support tool, poised to enhance primary dental care, mitigate provider-patient imbalances, and democratize access to specialized medical expertise within the field of dentistry.

cs.CV↗