arXiv subjects

Pengcheng Qiu

Publications and source records attributed to Pengcheng Qiu.

12 recordsLinked to original sources

arXiv2026

A Vision-language Framework for Comparative Reasoning in Radiology

Medical imaging artificial intelligence has achieved strong performance in isolated image interpretation, but remains poorly aligned with radiological practice, where diagnosis and follow-up rely on comparison across prior studies and analogous reference cases. Here we formulate radiological comparison as an entity-aware cross-image reasoning problem and introduce a framework that supports both reference-case retrieval and temporal comparative interpretation. We construct MedReCo-DB, a large-scale comparative imaging resource derived from routine image-report pairs, comprising more than 690,000 images from over 160,000 patients across eight institutions, four countries and seven imaging modalities. Reports are decomposed into anatomical structures, abnormal findings and pathological conditions to provide supervision for entity-conditioned retrieval and comparative visual question answering. Using this resource, we develop MedReCo, an entity-aware visual encoder for controllable retrieval of clinically analogous cases, and MedReCo-VLM, a vision--language extension for generative interpretation of interval change. Across internal, external and cross-center evaluations, MedReCo achieved the highest Recall@1 in all 12 internal retrieval settings and improved external retrieval by a mean of 6.0 percentage points. In clinically confusable differential groups, it consistently outperformed the strongest baselines. MedReCo-VLM achieved the best performance across all comparative generation evaluations and improved longitudinal follow-up accuracy by 14.5-46.5 percentage points on chest radiographs and 13.0-27.9 percentage points on CT. These findings suggest that entity-aware comparative reasoning can be learned from routine clinical data at scale and may provide a more clinically aligned foundation for medical imaging AI.

cs.CV↗

arXiv2026

Evaluating Large Language Models in Dynamic Clinical Decision-Making with Standardized Patient Cases

Large language models (LLMs) are increasingly proposed as clinical agents, yet static, single-turn benchmarks cannot capture how a model dynamically delivers care across an encounter: gathering information, planning treatment, and adapting longitudinal management across successive patient states. Medical education has long addressed an analogous challenge through standardized patients (SPs): trained actors who consistently portray clinical cases, enabling realistic practice and objective, scripted assessment. Here we introduce MedSP1000, an SP-derived interactive benchmark for clinical-agent evaluation, including 1,638 SP cases with 24,602 trajectory-level peer-reviewed rubrics. MedSP1000 converts peer-reviewed SP teaching cases into executable scenarios with defined SP case scripts, clinical environment contexts, and human-validated structured rubric. In each simulation evaluation run, a clinical agent interacts in closed loop with a patient agent and an environment controller, and its behaviour is scored throughout the encounter against expert criteria specified in the original materials. Applying MedSP1000 to a range of general-purpose and medically specialized LLMs, we find that performance on static benchmarks does not reliably translate to such educational scenarios. The best-performing model, GPT-5.5, completes only 60.4% of expert-defined rubric items, whereas the strongest medically specialized model reaches 40.0%; increasing test-time compute produces no measurable gain. These results suggest that current LLMs, including agentic systems tuned for medicine, are not yet reliable enough to be safely integrated into actual clinical practice. More broadly, MedSP1000 shows how process-level, SP-style evaluation can reveal clinically relevant failure modes that single-turn benchmarks miss.

cs.CL↗

arXiv2025

EHR-R1: A Reasoning-Enhanced Foundational Language Model for Electronic Health Record Analysis

Electronic Health Records (EHRs) contain rich yet complex information, and their automated analysis is critical for clinical decision-making. Despite recent advances of large language models (LLMs) in clinical workflows, their ability to analyze EHRs remains limited due to narrow task coverage and lack of EHR-oriented reasoning capabilities. This paper aims to bridge the gap, specifically, we present EHR-Ins, a large-scale, comprehensive EHR reasoning instruction dataset, comprising 300k high-quality reasoning cases and 4M non-reasoning cases across 42 distinct EHR tasks. Its core innovation is a thinking-graph-driven framework that enables to generate high-quality reasoning data at scale. Based on it, we develop EHR-R1, a series of reasoning-enhanced LLMs with up to 72B parameters tailored for EHR analysis. Through a multi-stage training paradigm, including domain adaptation, reasoning enhancement, and reinforcement learning, EHR-R1 systematically acquires domain knowledge and diverse reasoning capabilities, enabling accurate and robust EHR analysis. Lastly, we introduce EHR-Bench, a new benchmark curated from MIMIC-IV, spanning 42 tasks, to comprehensively assess reasoning and prediction across EHR scenarios. In experiments, we show that the resulting EHR-R1 consistently outperforms state-of-the-art commercial and open-source LLMs (including DeepSeek-V3 and GPT-4o), surpassing GPT-4o by over 30 points on MIMIC-Bench and achieving a 10\% higher zero-shot AUROC on EHRSHOT. Collectively, EHR-Ins, EHR-R1, and EHR-Bench have significantly advanced the development for more reliable and clinically relevant EHR analysis.

cs.CL↗

arXiv2025

Evolving Interactive Diagnostic Agents in a Virtual Clinical Environment

We present a framework for training large language models (LLMs) as diagnostic agents with reinforcement learning, enabling them to manage multi-turn interactive diagnostic processes, adaptively select examinations, and commit to final diagnoses. Unlike instruction-tuned models trained on static data, our method acquires diagnostic strategies through dynamic exploration and outcome-based feedback, mapping evolving patient states to the next optimal examination and subsequent diagnosis. Our contributions include: (i) DiagGym, a diagnostics world model trained with electronic health records, serving as a virtual clinical environment to support closed-loop in-silico training and evaluation for interactive diagnosis; (ii) DiagAgent, trained via end-to-end multi-turn RL to learn dynamic diagnostic policies that optimize both interactive effectiveness and final accuracy; (iii) DiagBench, a multi-center diagnostic benchmark designed to evaluate multi-turn diagnostic interaction trajectories. The benchmark comprises 2.2K physician-validated cases sourced from 4 distinct distributions, alongside 3.3K physician-written rubrics for granular process-oriented evaluation. (iv) Extensive evaluations demonstrate DiagAgent's superior performance across both in-domain and out-of-domain (OOD) settings. DiagAgent significantly outperforms 11 SOTA LLMs and 2 prompt-engineered agents. In the end-to-end setting, it delivers a 11.20% increase in diagnostic accuracy and a 17.58% boost in examination recommendation F1 score, while consistently maintaining SOTA performance across all three external centers. Furthermore, in rubric-based evaluations, it surpasses the next-best model by 7.1% in weighted rubric score. These findings indicate that learning policies in interactive clinical environments confers long-term diagnostic management abilities unattainable through passive training.

cs.CL↗

arXiv2025

End-to-End Agentic RAG System Training for Traceable Diagnostic Reasoning

The integration of Large Language Models (LLMs) into healthcare is constrained by knowledge limitations, hallucinations, and a disconnect from Evidence-Based Medicine (EBM). While Retrieval-Augmented Generation (RAG) offers a solution, current systems often rely on static workflows that miss the iterative, hypothetico-deductive reasoning of clinicians. To address this, we introduce Deep-DxSearch, an agentic RAG system trained end-to-end via reinforcement learning (RL) for traceable diagnostic reasoning. Deep-DxSearch acts as an active investigator, treating the LLM as an agent within an environment of 16,000+ guideline-derived disease profiles, 150,000+ patient records for case-based reasoning, and over 27 million biomedical documents. Using soft verifiable rewards that co-optimize retrieval and reasoning, the model learns to formulate queries, evaluate evidence, and refine searches to close diagnostic gaps. Experiments show our end-to-end RL framework consistently outperforms prompt-engineering and training-free RAG methods. On in-distribution (ID) and out-of-distribution (OOD) benchmarks for common and rare diseases, Deep-DxSearch surpasses strong baselines-including GPT-4o, DeepSeek-R1, and medical-specific frameworks-achieving an average accuracy gain of 22.7% over the second-best model. In validation with 150 real-world cases, Deep-DxSearch boosts physicians' average diagnostic accuracy from 45.6% to 69.1%. These results indicate that evolving agentic systems to leverage statistical regularities in large-scale healthcare data is key for trustworthy diagnostic assistants. All data, code, and checkpoints are available at https://qiaoyu-zheng.github.io/Deep-DxSearch.

cs.CL↗

arXiv2025

An Agentic System for Rare Disease Diagnosis with Traceable Reasoning

Rare diseases affect over 300 million individuals worldwide, yet timely and accurate diagnosis remains an urgent challenge. Patients often endure a prolonged diagnostic odyssey exceeding five years, marked by repeated referrals, misdiagnoses, and unnecessary interventions, leading to delayed treatment and substantial emotional and economic burdens. Here we present DeepRare, a multi-agent system for rare disease differential diagnosis decision support powered by large language models, integrating over 40 specialized tools and up-to-date knowledge sources. DeepRare processes heterogeneous clinical inputs, including free-text descriptions, structured Human Phenotype Ontology terms, and genetic testing results, to generate ranked diagnostic hypotheses with transparent reasoning linked to verifiable medical evidence. Evaluated across nine datasets from literature, case reports and clinical centres across Asia, North America and Europe spanning 14 medical specialties, DeepRare demonstrates exceptional performance on 3,134 diseases. In human-phenotype-ontology-based tasks, it achieves an average Recall@1 of 57.18%, outperforming the next-best method by 23.79%; in multi-modal tests, it reaches 69.1% compared with Exomiser's 55.9% on 168 cases. Expert review achieved 95.4% agreement on its reasoning chains, confirming their validity and traceability. Our work not only advances rare disease diagnosis but also demonstrates how the latest powerful large-language-model-driven agentic systems can reshape current clinical workflows.

cs.CL↗

arXiv2025

Quantifying the Reasoning Abilities of LLMs on Real-world Clinical Cases

Recent advancements in reasoning-enhanced large language models (LLMs), such as DeepSeek-R1 and OpenAI-o3, have demonstrated significant progress. However, their application in professional medical contexts remains underexplored, particularly in evaluating the quality of their reasoning processes alongside final outputs. Here, we introduce MedR-Bench, a benchmarking dataset of 1,453 structured patient cases, annotated with reasoning references derived from clinical case reports. Spanning 13 body systems and 10 specialties, it includes both common and rare diseases. To comprehensively evaluate LLM performance, we propose a framework encompassing three critical examination recommendation, diagnostic decision-making, and treatment planning, simulating the entire patient care journey. To assess reasoning quality, we present the Reasoning Evaluator, a novel automated system that objectively scores free-text reasoning responses based on efficiency, actuality, and completeness using dynamic cross-referencing and evidence checks. Using this benchmark, we evaluate five state-of-the-art reasoning LLMs, including DeepSeek-R1, OpenAI-o3-mini, and Gemini-2.0-Flash Thinking, etc. Our results show that current LLMs achieve over 85% accuracy in relatively simple diagnostic tasks when provided with sufficient examination results. However, performance declines in more complex tasks, such as examination recommendation and treatment planning. While reasoning outputs are generally reliable, with factuality scores exceeding 90%, critical reasoning steps are frequently missed. These findings underscore both the progress and limitations of clinical LLMs. Notably, open-source models like DeepSeek-R1 are narrowing the gap with proprietary systems, highlighting their potential to drive accessible and equitable advancements in healthcare.

cs.CL↗

arXiv2024

How Well Can Modern LLMs Act as Agent Cores in Radiology Environments?

Radiology, with its heterogeneous modalities, anatomies, and evolving protocols, is a natural yet high-stakes testbed for agentic AI. As LLMs grow more capable and tool ecosystems such as MCP and Agent Skills more complex, their capability boundaries in radiology remain unclear. We introduce RadA-BenchPlat, a two-layer benchmark spanning idealized reasoning and real-world execution: a synthetic layer with 2.2k clinician-verified records, 24.2k QA pairs, and 10 tool categories under diverse availability settings; and a real-environment layer pairing 165 2D/3D cases with executable tools for grounding, diagnosis, and report generation. We find that high completion rates under idealized settings do not carry over to real environments, where the best agents trail their upper bound by approximately 15% and drop to 0.327 on long-chain tasks. Prompting strategies (few-shot exemplars, multi-agent coordination) and AutoTB (on-the-fly synthesis of missing tools) mitigate execution drift and breakdowns in difficult scenarios, lifting execution success to 94.5%, yet remain not fully reliable. Overall, our findings suggest that radiology agents are no longer limited to conceptual demonstrations, but are beginning to show potential for real-world applications. Project repository: https://github.com/MAGIC-AI4Med/RadABench

cs.CV↗

arXiv2024

Towards Evaluating and Building Versatile Large Language Models for Medicine

In this study, we present MedS-Bench, a comprehensive benchmark designed to evaluate the performance of large language models (LLMs) in clinical contexts. Unlike existing benchmarks that focus on multiple-choice question answering, MedS-Bench spans 11 high-level clinical tasks, including clinical report summarization, treatment recommendations, diagnosis, named entity recognition, and medical concept explanation, among others. We evaluated six leading LLMs, e.g., MEDITRON, Mistral, InternLM 2, Llama 3, GPT-4, and Claude-3.5 using few-shot prompting, and found that even the most sophisticated models struggle with these complex tasks. To address these limitations, we developed MedS-Ins, a large-scale instruction tuning dataset for medicine. MedS-Ins comprises 58 medically oriented language corpora, totaling 13.5 million samples across 122 tasks. To demonstrate the dataset's utility, we conducted a proof-of-concept experiment by performing instruction tuning on a lightweight, open-source medical language model. The resulting model, MMedIns-Llama 3, significantly outperformed existing models across nearly all clinical tasks. To promote further advancements in the application of LLMs to clinical challenges, we have made the MedS-Ins dataset fully accessible and invite the research community to contribute to its expansion.Additionally, we have launched a dynamic leaderboard for MedS-Bench, which we plan to regularly update the test set to track progress and enhance the adaptation of general LLMs to the medical domain. Leaderboard: https://henrychur.github.io/MedS-Bench/. Github: https://github.com/MAGIC-AI4Med/MedS-Ins.

cs.CL↗

arXiv2024

Towards Building Multilingual Language Model for Medicine

The development of open-source, multilingual medical language models can benefit a wide, linguistically diverse audience from different regions. To promote this domain, we present contributions from the following: First, we construct a multilingual medical corpus, containing approximately 25.5B tokens encompassing 6 main languages, termed as MMedC, enabling auto-regressive domain adaptation for general LLMs; Second, to monitor the development of multilingual medical LLMs, we propose a multilingual medical multi-choice question-answering benchmark with rationale, termed as MMedBench; Third, we have assessed a number of open-source large language models (LLMs) on our benchmark, along with those further auto-regressive trained on MMedC. Our final model, MMed-Llama 3, with only 8B parameters, achieves superior performance compared to all other open-source models on both MMedBench and English benchmarks, even rivaling GPT-4. In conclusion, in this work, we present a large-scale corpus, a benchmark and a series of models to support the development of multilingual medical LLMs.

cs.CL↗

arXiv2018

A Flip-Syndrome-List Polar Decoder Architecture for Ultra-Low-Latency Communications

We consider practical hardware implementation of Polar decoders. To reduce latency due to the serial nature of successive cancellation (SC), existing optimizations improve parallelism with two approaches, i.e., multi-bit decision or reduced path splitting. In this paper, we combine the two procedures into one with an error-pattern-based architecture. It simultaneously generates a set of candidate paths for multiple bits with pre-stored patterns. For rate-1 (R1) or single parity-check (SPC) nodes, we prove that a small number of deterministic patterns are required to guarantee performance preservation. For general nodes, low-weight error patterns are indexed by syndrome in a look-up table and retrieved in O(1) time. The proposed flip-syndrome-list (FSL) decoder fully parallelizes all constituent code blocks without sacrificing performance, thus is suitable for ultra-low-latency applications. Meanwhile, two code construction optimizations are presented to further reduce complexity and improve performance, respectively.

cs.IT↗

arXiv2018

A 5.16Gbps decoder ASIC for Polar Code in 16nm FinFET

Polar codes has been selected as 5G standard. However, only a couple of ASIC featuring decoders are fabricated,and none of them support list size L > 4 and code length N > 1024. This paper presents an ASIC implementation of three decoders for polar code: successive cancellation (SC) decoder, flexible decoder and ultra-reliable decoder. These decoders are all SC based decoder, supporting list size up to 1,8,32 and code length up to 2^15,2^14,2^11 respectively. This chip is fabricated in a 16nm TSMC FinFET technology, and can be clocked at 1 Ghz. Optimization techniques are proposed and employed to increase throughput. Experiment result shows that the throughput can achieve up to 5.16Gbps. Compared with fabricated AISC decoder and synthesized decoder in literature, the flexible decoder achieves higher area efficiency.

cs.IT↗