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Jiazhen Pan

Publications and source records attributed to Jiazhen Pan.

At least 19 recordsLinked to original sources
arXiv2026

Glyph: An Interpretability Engine for AI-Driven Scientific Discovery in Clinical Data

Automated scientific discovery has the potential to advance understanding of disease mechanisms and accelerate identification of early disease markers. Manual data annotation is infeasible at population scale, motivating methods that automatically extract pre-defined phenotypes in multimodal and unstructured clinical data. Such pre-defined feature sets determine and limit which associations these approaches can discover. This limitation extends to agentic AI systems that use these tools to query population-scale data. In contrast, foundation models (FMs) trained on large volumes of clinical data can perform tasks beyond their training objectives. This suggests their latent embeddings may represent novel or unexplored features that could yield insights into disease mechanisms, yet such latent features remain difficult to interpret. To address this challenge, we introduce Glyph, an automated multistage framework that extracts features from multimodal and unstructured clinical data using FMs and sparse autoencoders, interprets them as coded clinical concepts, and evaluates their value for clinical scientific discovery. We applied Glyph to abdominal CT volumes, CT radiology reports and laboratory measurements from 41,628 patients across different institutions. We identified 397 predictive concepts supported by 4,463 Bonferroni-significant associations. Moreover, a majority of discovered associations were automatically reproducible in held-out cohorts across different sites. Glyph concepts provided complementary associations to literature-derived markers, leading to gains in predictive power. We envision that interpretability can extend beyond a mechanistic understanding of neural networks to connecting implicitly learned features with clinical knowledge and establishing their significance for patient outcomes. We release Glyph at https://github.com/StanfordMIMI/Glyph.

cs.AI↗
arXiv2026

Unified-protocol voxel-level pulmonary embolism annotations for three public CT angiography datasets

Reliable clot-volume quantification and subsequent risk assessment in pulmonary embolism depend on precise segmentation of emboli on computed tomography pulmonary angiography. Deep learning models for this task must be trained on accurate voxel-level labels. The three public datasets that provide such labels were annotated under different protocols, and some of their studies contain unlabeled emboli or labels that are discontinuous across slices. This Data Descriptor presents voxel-level pulmonary embolism annotations for 149 of the 166 studies in these datasets. A primary rater drew all annotations under a single protocol. A thoracic radiologist with more than 20 years of experience reviewed and revised them. Three raters at three different centers independently annotated a subset of 15 studies. The subset was selected by source dataset and embolus location. Technical validation quantifies volumetric agreement with the source annotations, changes in within-mask attenuation, and inter-rater agreement on the subset. The dataset is intended to allow segmentation models to be developed and compared under a common reference standard.

eess.IV↗
arXiv2026

LabFactory: Building and Evaluating Executable AI Labs

Scientific tasks specify a desired capability, but realizing it often requires building a computational system tailored to the task---acquiring data, designing representations, training models, implementing tools, and deciding how they are used at inference. We present, a framework in which an AI builder turns a scientific brief into an executable AI lab: a task-specific solver that integrates models, knowledge resources, tools, and a controller behind a fixed interface. The builder develops and packages the lab in a metered workspace; a separate host then executes the delivered artifact on held-out inputs, with reference labels kept outside the solver's input interface, and scores its outputs under the task's protocol. This makes the delivered system, rather than the builder's account of its progress, the object of evaluation. We document 10 selected constructions across six scientific task categories---from molecular and genomic prediction to medical imaging, clinical decision support, and biomedical text---whose delivered labs exceeded their configured reference values on all 12 subtests under host-side execution. Four contain predictive models fitted during construction; the others assemble executable analysis environments, knowledge resources, and tool-driven workflows around a fixed platform LLM. Together they show that an AI agent can carry a scientific brief all the way to a working lab that can still be invoked, inspected, and checked after construction ends.

cs.LG↗
arXiv2026

What Makes a Good Medical Image Tokenizer? Rethinking Reconstruction and Generation in Medical Image Tokenization

Latent diffusion models now dominate medical image generation, and every such pipeline rests on a \emph{tokenizer} that compresses images into the latent codes for image generation to operate on. Thereby, the tokenizer choice bounds every downstream task from reconstruction fidelity and generation quality to the representations available for downstream analysis. Yet, medical imaging pipelines routinely utilize tokenizers from natural imaging on the hypothesis that their behavior carries over. However, this is an assumption never tested in the medical imaging regime, where datasets are orders of magnitude smaller and images exhibit far lower inter-sample variance. We present a systematic evaluation of medical image tokenizers evaluating thirty configurations across ten model families on twelve datasets at three compression factors, spanning reconstruction, generation, latent geometry, downstream classification, and memorization. We find that (1) performance on image reconstruction and generation strongly correlate, unlike prior reports on natural images; (2) modern tokenizers use nearly all of their codebook entries, but still leave most of the latent space unused; (3) training-set memorization is mild and is further suppressed by stronger latent space compression; and (4) discrete quantization can largely preserve downstream classification, with lookup-free schemes being the main exception.

cs.CV↗
arXiv2026

MedRSI: Recursive Self-Improvement for Medical Agents via Clinically Aligned Self-Evolution

Medical agents increasingly combine general reasoning models with specialized clinical tools, yet their capabilities remain largely fixed by what clinicians and engineers design before deployment. Recursive self-improvement (RSI) offers a different paradigm in which agents learn from their own failures and autonomously expand their capabilities, but directly applying RSI to medicine introduces fundamental safety challenges. We introduce MedRSI, the first recursive self-improvement framework for medicine, which continuously transforms diagnostic failures into new clinical capabilities through tool composition and task-specific model training. Inspired by clinical practice, MedRSI introduces two mechanisms for clinically aligned self-evolution. Clinical-cost-aware failure prioritization directs improvement toward errors according to their potential clinical consequences rather than frequency alone. Fast discovery with slow registration separates rapid capability invention from conservative adoption, allowing new tools to enter the persistent agent only after demonstrating sustained benefit across subsequent patient cohorts. Across public glaucoma and heart disease benchmarks and two private clinical tasks, MedRSI progressively develops segmentation, measurement, prediction, multimodal reasoning, and generative capabilities, surpasses manually engineered medical agents, and autonomously discovers solutions to clinical problems not anticipated by its original designers. Our results show that medical agents need not remain constrained by capabilities specified before deployment: with clinically grounded mechanisms governing what to improve and what to retain, they can continuously construct, validate, and accumulate new capabilities from diagnostic experience. Code is available at https://github.com/ImprintLab/MedRSI.

cs.AI↗
arXiv2026

Agentic Large Language Models for Training-Free Neuro-Radiological Image Analysis

State-of-the-art large language models (LLMs) show high performance in general visual question answering. However, a fundamental limitation remains: current architectures lack the native 3D spatial reasoning required to directly analyze volumetric medical imaging, such as CT or MRI. Emerging agentic AI offers a new solution, eliminating the need for intrinsic 3D processing by enabling LLMs to orchestrate and leverage specialized external tools. Yet, the feasibility of such agentic frameworks in complex, multi-step radiological workflows remains underexplored. In this work, we present a training-free agentic pipeline for automated brain MRI analysis. Validating our methodology on several LLMs (GPT-5.4, Gemini 3.1 Pro, Claude Sonnet 4.6) with off-the-shelf domain-specific tools, our system autonomously executes complex end-to-end workflows, including preprocessing (skull stripping, registration), pathology segmentation (glioma, meningioma, metastases), and volumetric reasoning. We evaluate our framework across increasingly complex radiological tasks, from single-scan tumor and anatomy analysis to longitudinal response assessment requiring multi-timepoint comparisons. We analyze the impact of architectural design by comparing single-agent models against multi-agent "domain-expert" collaborations. To support rigorous evaluation of future agentic systems, we release a benchmark dataset of image-prompt-answer tuples derived from public data. Our results demonstrate that agentic AI can solve highly neuro-radiological image analysis tasks through tool use without the need for training or fine-tuning.

cs.CV↗
arXiv2026

Are LLMs Ready to Assist Physicians? PhysAssistBench for Interactive Doctor-Patient-EHR Assistance

The most plausible near-term role of medical LLMs is to assist rather than replace physicians, yet current evaluations often test isolated capabilities: clinical knowledge, EHR system interaction, or patient communication. Physician assistance instead requires coordinating these capabilities within the same interaction, where physicians issue underspecified requests, patients describe symptoms ambiguously, and EHR systems demand precise tool use. We introduce PhysAssistBench, a benchmark for interactive doctor-patient-EHR assistance. Built from real MIMIC-IV cases, PhysAssistBench uses a scalable pipeline to construct agentic patients: interactive, record-grounded agents that turn static EHR records into multi-turn clinical scenarios while preserving clinical factuality. PhysAssistBench provides a curated bilingual evaluation set of 1,296 manually reviewed and physician-validated turns. Experiments with leading LLMs show that current models remain unreliable in this setting, which exposes a key bottleneck for clinical LLMs: reliable assistance requires coordination across knowledge, communication, and systems, not isolated gains in any of them.

cs.CL↗
arXiv2026

AI Can Be Easily Persuaded in Clinical Decision Making

As AI becomes increasingly integrated into clinical practice, it is playing a growing role in medical decision making. Medicine, however, is a high stakes and evidence based field, where decisions can directly affect patients' lives. It is therefore important to understand whether AI can maintain objective judgment when others try to persuade it. In this paper, we study how easily AI can be persuaded through controlled experiments. We find that professional authority, national background, institutional affiliation, claimed past performance, multiple physicians, supported clinician views, and repeated pressure can all affect AI decisions. Surprisingly, the same persuasive input changes about 10% more cases when it comes from a senior clinician than from a medical student. Simply claiming a better performance history consistently makes the physician more persuasive. More strikingly, a plausible clinician view can persuade AI away from a correct decision even when it is fabricated to support an incorrect answer. This indicates that AI can be strongly influenced by convincing support without reliably determining whether this view from the clinician is correct. Together, these findings suggest that AI can be easily persuaded by what people say, who says it, and how the opinion is presented. Therefore, it is essential for AI to maintain sound judgment under persuasion, enabling its safe and reliable use in high stakes medical decision making.

cs.CL↗
arXiv2026

GRASP: Gated Regression-Aware Skill Proposer for Self-Improving LLM Agents

LLM agents acting in structured environments fail in operational rather than conversational ways, and reliability depends on procedural knowledge of the environment. Prior self-improvement methods accumulate natural-language guidance without checking that each new item preserves previously correct behavior, so a note that fixes one trajectory can silently regress another. We introduce GRASP (Gated Regression-Aware Skill Proposer), which treats agent improvement as a sequence of edits to a bounded skill library, admitting each candidate only if it produces a net improvement on a balanced held-out probe under a hard regression budget. We evaluate GRASP across five base models on two FHIR-based clinical benchmarks, which score procedural reliability against FHIR state rather than clinical correctness or patient outcomes. On MedAgentBench, GRASP lifts gpt-oss-120b from 40.6% to 88.8%, exceeds the strongest of five self-improvement baselines by 21.0 points, and improves every other base model by 17.2 to 40.3 points. Ablations attribute the gain to comparative proposal generation, the acceptance gate, and the hard regression budget rather than to skill writing itself, which without validation is no better than using no skills. Granting the same acceptance gate to all five baselines lifts each of them in-domain and none of them out of distribution, isolating the gain to the gate applied to a bounded, editable library rather than to held-out validation itself. The mechanism helps in non-clinical environments where tasks recur with verifiable structure and is flat where the action space is open-ended. Frozen libraries transfer across models and across benchmarks that share a tool-calling convention and degrade under interface mismatch.

cs.AI↗
arXiv2026

Git Context Controller: Manage the Context of LLM-based Agents like Git

Large language model (LLM) agents have demonstrated strong capabilities in long-horizon tasks by interleaving reasoning with tool use. However, as these agents scale to complex workflows such as software engineering and open-ended research, context management becomes a fundamental bottleneck: interaction histories grow unbounded, become costly to maintain, and are difficult to reuse across sessions and agents. We introduce \textbf{Git-Context-Controller (GCC)}, a structured context management framework inspired by software version control systems. GCC elevates agent context from a transient token stream to a persistent, navigable memory workspace with explicit operations -- \texttt{COMMIT}, \texttt{BRANCH}, \texttt{MERGE}, and \texttt{CONTEXT}, that enable milestone-based checkpointing, isolated exploration of alternative reasoning paths, and hierarchical retrieval of historical context. By organizing agent memory as a versioned file system, GCC allows agents to manage long-term goals, recover and transfer reasoning across sessions, and coordinate multi-trajectory problem solving in a principled manner. Empirically, agents equipped with GCC achieve state-of-the-art performance on both SWE-Bench and BrowseComp benchmarks. On SWE-Bench Verified, GCC improves task resolution by over 13\% relative to strong long-context baselines and outperforms 26 existing open and commercial systems, reaching over 80\% success rate. The project will be open-sourced for the research community. https://github.com/ImprintLab/git-context-controller

cs.SE↗
arXiv2026

Latent Interpolation Learning Using Diffusion Models for Cardiac Volume Reconstruction

Cardiac Magnetic Resonance (CMR) imaging is a critical tool for diagnosing and managing cardiovascular disease, yet its utility is often limited by the sparse acquisition of 2D short-axis slices, resulting in incomplete volumetric information. Accurate 3D reconstruction from these sparse slices is essential for comprehensive cardiac assessment, but existing methods face challenges, including reliance on predefined interpolation schemes (e.g., linear or spherical), computational inefficiency, and dependence on additional semantic inputs such as segmentation labels or motion data. To address these limitations, we propose a novel Cardiac Latent Interpolation Diffusion (CaLID) framework that introduces three key innovations. First, we present a data-driven interpolation scheme based on diffusion models, which can capture complex, non-linear relationships between sparse slices and improves reconstruction accuracy. Second, we design a computationally efficient method that operates in the latent space and speeds up 3D whole-heart upsampling time by a factor of 24, reducing computational overhead compared to previous methods. Third, with only sparse 2D CMR images as input, our method achieves SOTA performance against baseline methods, eliminating the need for auxiliary input such as morphological guidance, thus simplifying workflows. We further extend our method to 2D+T data, enabling the effective modeling of spatiotemporal dynamics and ensuring temporal coherence. Extensive volumetric evaluations and downstream segmentation tasks demonstrate that CaLID achieves superior reconstruction quality and efficiency. By addressing the fundamental limitations of existing approaches, our framework advances the state of the art for spatio and spatiotemporal whole-heart reconstruction, offering a robust and clinically practical solution for cardiovascular imaging.

eess.IV↗
arXiv2026

J-CoT: Chain-of-Thought in J-Space

Chain-of-thought prompting improves language-model reasoning by carrying intermediate states across successive computation steps. However, relying on natural language as the only recurrent interface is overly restrictive, since many transient computations do not need to be fully verbalized. Existing latent-reasoning methods remove this constraint by recurrently propagating continuous hidden states. However, these methods pass a dense hidden vector as a whole, without an explicit mechanism for selecting and organizing the information needed by the next reasoning step. This motivates an intermediate interface that remains linguistically grounded without requiring a decoded sentence. We introduce \textbf{J-CoT}, a recurrent reasoning framework built on \emph{J-space}, a vocabulary-indexed coordinate system within the model's hidden representations. Within each cycle, the model computes in its full hidden space. At the cycle boundary, J-CoT expresses the intermediate state as vocabulary-indexed coefficients, carries these coefficients forward as a \emph{J-thought}, and maps them back into the model's hidden representation for the next cycle. J-CoT therefore requires neither a fluent intermediate rationale nor recurrence over the complete hidden state. Under matched backbone and inference settings, J-CoT-Zero matches or exceeds the strongest evaluated latent-reasoning baseline on every benchmark, while J-CoT-Train obtains the highest score across the evaluated mathematical, scientific, coding, and structured path-reasoning tasks.

cs.CL↗
arXiv2026

Addressing Benchmarking Gaps in Large Language Models for Health and Medicine with Dynamic Red-Teaming

Large language models (LLMs) are increasingly used to answer health-related questions and support healthcare workflows, yet evidence for their safety still relies heavily on static benchmarks that can rapidly become obsolete or be optimized against. Here we introduce a Dynamic, Automatic, and Systematic (DAS) red-teaming audit framework that continuously stress-tests LLMs for health across four safety-critical axes: robustness, privacy, bias/fairness, and hallucination/factual inaccuracies. Validated against board-certified clinicians with high concordance, a suite of adversarial agents autonomously mutates health-related test cases to uncover vulnerabilities in real time. Applying DAS to 15 proprietary and open-source LLMs revealed a profound gap between high static benchmark performance and low dynamic reliability--the "Benchmarking Gap". Despite median MedQA accuracy exceeding 80\%, 94\% of previously correct answers failed under dynamic robustness testing. This brittleness generalized to the realistic, open-ended HealthBench dataset, where top-tier models exhibited failure rates exceeding 70\% and sharp shifts in model rankings across evaluations, suggesting that high scores on established static benchmarks may reflect superficial memorization. We observed similarly high failure rates across other domains: privacy leaks were elicited in 86\% of scenarios, cognitive-bias priming altered recommendations in 81\% of fairness tests, and hallucination rates exceeded 74\% in widely used models. By converting LLM safety evaluation for health from a static checklist into a living adversarial audit, DAS provides a scalable framework for surfacing latent risks before such systems are deployed in consumer-facing health assistants, clinician-facing tools, and broader healthcare workflows. Code is available at https://github.com/JZPeterPan/DAS-Medical-Red-Teaming-Agents.

cs.LG↗
arXiv2026

BioMedArena: An Open-source Toolkit for Building and Evaluating Biomedical Deep Research Agents

Reproducing and comparing deep research agents today is hard: the same backbone evaluated on the same benchmark can report different accuracies across papers because the harness and tool registry differ, and integrating a new model into a comparable evaluation surface costs weeks of model-specific engineering. These are symptoms of a broader reproducibility problem in deep research agent research. Here, we introduce BioMedArena, an open-source toolkit that addresses this reproducibility gap and provides an arena for comparing deep research agents under a shared evaluation environment. BioMedArena decouples six layers of biomedical agent evaluation -- benchmark loading, tool exposure, tool selection, harness mode, context management, and scoring -- and exposes 166 biomedical benchmarks and 75 biomedical tools across 9 functional families. Adding a new model, benchmark, or tool can be accomplished with a few-line provider adapter. Beyond evaluation infrastructure, BioMedArena ships a library of high-quality reference components: 6 agent harnesses (including our proposed Mutual-Evolve) and 6 context-management strategies, any of which can be equipped on any backbone. Equipping these components substantially improves all 12 backbones; on each of 8 representative biomedical benchmarks, the best equipped backbone surpasses prior state-of-the-art (SOTA), by 15.01 percentage points on average. The toolkit, configurations, and per-task traces are available at https://github.com/AI-in-Health/BioMedArena.

cs.AI↗
arXiv2026

DDX-TRACE: A Benchmark for Medical Diagnostic Trajectories in VLMs

Medical diagnosis is not a single prediction from a fully specified vignette. It is a sequential workup: clinicians decide what evidence to obtain, revise a differential diagnosis, and stop when the diagnosis is sufficiently supported. Most medical AI benchmarks instead reveal the relevant context upfront and score only the final answer, making unsupported correct guesses, premature closure, inefficient workups, and poor uncertainty updating invisible. We introduce DDX-TRACE, a physician-adjudicated benchmark for multimodal neuroradiology that evaluates diagnostic trajectories under hidden evidence over 211 challenging cases. Each case begins with limited clinical history; models request imaging studies in free form, receive matched image bundles when available, update a probabilistic differential diagnosis after each turn, and stop with a localized final diagnosis. Evaluating state-of-the-art VLMs, we find that final diagnosis scores can substantially misrepresent workup quality: models may guess plausible diagnoses without essential evidence, request useful studies but misinterpret raw images, or acquire evidence inefficiently while updating uncertainty poorly. Controlled evidence variants isolate bottlenecks in planning, visual evidence extraction, and downstream differential reasoning. DDX-TRACE shifts medical AI evaluation from final answers to evidence-supported diagnostic trajectories.

cs.CV↗
arXiv2026

From Failure to Feedback: Group Revision Unlocks Hard Cases in Object-Level Grounding

Finetuning Large Vision-Language Models with reinforcement learning has emerged as a promising approach to enhance their capability in object-level grounding. However, existing methods, mainly based on GRPO, assign rewards at the response level. Such sparse reward, often criterion-induced, leads to minimal learning signals when all candidate responses fail in challenging scenarios. In this work, we propose a group-revision optimisation paradigm that enhances learning on hard cases. It begins with a sampled initial response and generates a set of revised candidates to explore improved grounding outcomes. Inspired by reward shaping, we introduce a consolidation process that quantifies each candidate's improvement over the initial attempt and converts it into informative shaping signals. These signals are used to both refine the reward and modulate the advantage, amplifying the influence of high-quality revisions. Our method achieves consistent gains across referring and reasoning segmentation, REC, and counting benchmarks compared with prior GRPO-based models. Our code is available at https://github.com/yyliu01/GroupRevision.

cs.CV↗
arXiv2026

MedOpenClaw and MedFlowBench: Auditing Medical Agents in Full-Study Workflows

Medical imaging benchmarks often evaluate VLMs on pre-selected 2D images, slices, crops, or patches, making evaluation closer to visual recognition. Real clinical workflows impose a different burden: readers must search through complete studies, operate imaging software, navigate across slices and magnifications, and document visual evidence that can be audited. We argue that this evidence-producing workflow is a critical missing evaluation axis for medical imaging agents. To study it, we introduce MedFlowBench, a full-study benchmark for VLM agents, together with MedOpenClaw, a controlled and replayable runtime in which agents operate medical imaging viewers such as 3D Slicer and QuPath. In each episode, an agent inspects a complete radiology study or whole-slide pathology image, returns a task answer, and submits structured evidence, including key slices, coordinates, regions of interest, or lesion-state fields. This evidence is automatically checked against withheld masks, annotations, and labels. Across evaluated models, final answer-only scoring gives an overly optimistic picture: when answers must also be supported by correct evidence, performance drops substantially on complex workflows. We further find that adding image-analysis tools does not by itself solve the problem. Tools help when they make a complex procedure simple and reliable, but agents still struggle when they must choose inputs, manage viewer state, and verify intermediate outputs over multiple steps. MedFlowBench exposes whether medical imaging agents can produce auditable evidence from complete studies, rather than plausible answers from selected images.

cs.CV↗
arXiv2026

RealICU: Do LLM Agents Understand Long-Context ICU Data? A Benchmark Beyond Behavior Imitation

Intensive care units (ICU) generate long, dense and evolving streams of clinical information, where physicians must repeatedly reassess patient states under time pressure, underscoring a clear need for reliable AI decision support. Existing ICU benchmarks typically treat historical clinician actions as ground truth. However, these actions are made under incomplete information and limited temporal context of the underlying patient state, and may therefore be suboptimal, making it difficult to assess the true reasoning capabilities of AI systems. We introduce RealICU, a hindsight-annotated benchmark for evaluating large language models (LLMs) under realistic ICU conditions, where labels are created after senior physicians review the full patient trajectory. We formulate four physician-motivated tasks: assess Patient Status, Acute Problems, Recommended Actions, and Red Flag actions that risk unsafe outcomes. We partition each trajectory with 30-min windows and release two datasets: RealICU-Gold with 930-window annotations from 94 MIMIC-IV patients, and RealICU-Scale with 11,862 windows extended by Oracle, a physician-validated LLM hindsight labeler. Existing LLMs including memory-augmented ones performed poorly on RealICU, exposing two failure modes: a recall-safety tradeoff for clinical recommendations, and an anchoring bias to early interpretations of the patient. We further introduce ICU-Evo to study structured-memory agents that improves long-horizon reasoning but does not fully eliminate safety failures. Together, RealICU provides a clinically grounded testbed for measuring and improving AI sequential decision-support in high-stakes care. Project page: https://chengzhi-leo.github.io/RealICU-Bench/

cs.AI↗