arXiv subjects

Qingyu Chen

Publications and source records attributed to Qingyu Chen.

At least 55 records · Page 3Linked to original sources

arXiv2025

Med-PRM: Medical Reasoning Models with Stepwise, Guideline-verified Process Rewards

Large language models have shown promise in clinical decision making, but current approaches struggle to localize and correct errors at specific steps of the reasoning process. This limitation is critical in medicine, where identifying and addressing reasoning errors is essential for accurate diagnosis and effective patient care. We introduce Med-PRM, a process reward modeling framework that leverages retrieval-augmented generation to verify each reasoning step against established medical knowledge bases. By verifying intermediate reasoning steps with evidence retrieved from clinical guidelines and literature, our model can precisely assess the reasoning quality in a fine-grained manner. Evaluations on five medical QA benchmarks and two open-ended diagnostic tasks demonstrate that Med-PRM achieves state-of-the-art performance, with improving the performance of base models by up to 13.50% using Med-PRM. Moreover, we demonstrate the generality of Med-PRM by integrating it in a plug-and-play fashion with strong policy models such as Meerkat, achieving over 80\% accuracy on MedQA for the first time using small-scale models of 8 billion parameters. Our code and data are available at: https://med-prm.github.io/

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arXiv2025

Is an Ultra Large Natural Image-Based Foundation Model Superior to a Retina-Specific Model for Detecting Ocular and Systemic Diseases?

The advent of foundation models (FMs) is transforming medical domain. In ophthalmology, RETFound, a retina-specific FM pre-trained sequentially on 1.4 million natural images and 1.6 million retinal images, has demonstrated high adaptability across clinical applications. Conversely, DINOv2, a general-purpose vision FM pre-trained on 142 million natural images, has shown promise in non-medical domains. However, its applicability to clinical tasks remains underexplored. To address this, we conducted head-to-head evaluations by fine-tuning RETFound and three DINOv2 models (large, base, small) for ocular disease detection and systemic disease prediction tasks, across eight standardized open-source ocular datasets, as well as the Moorfields AlzEye and the UK Biobank datasets. DINOv2-large model outperformed RETFound in detecting diabetic retinopathy (AUROC=0.850-0.952 vs 0.823-0.944, across three datasets, all P<=0.007) and multi-class eye diseases (AUROC=0.892 vs. 0.846, P<0.001). In glaucoma, DINOv2-base model outperformed RETFound (AUROC=0.958 vs 0.940, P<0.001). Conversely, RETFound achieved superior performance over all DINOv2 models in predicting heart failure, myocardial infarction, and ischaemic stroke (AUROC=0.732-0.796 vs 0.663-0.771, all P<0.001). These trends persisted even with 10% of the fine-tuning data. These findings showcase the distinct scenarios where general-purpose and domain-specific FMs excel, highlighting the importance of aligning FM selection with task-specific requirements to optimise clinical performance.

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arXiv2025

Performance of GPT-5 Frontier Models in Ophthalmology Question Answering

Large language models (LLMs) such as GPT-5 integrate advanced reasoning capabilities that may improve performance on complex medical question-answering tasks. For this latest generation of reasoning models, the configurations that maximize both accuracy and cost-efficiency have yet to be established. We evaluated 12 configurations of OpenAI's GPT-5 series (three model tiers across four reasoning effort settings) alongside o1-high, o3-high, and GPT-4o, using 260 closed-access multiple-choice questions from the American Academy of Ophthalmology Basic Clinical Science Course (BCSC) dataset. The primary outcome was multiple-choice accuracy; secondary outcomes included head-to-head ranking via a Bradley-Terry model, rationale quality assessment using a reference-anchored, pairwise LLM-as-a-judge framework, and analysis of accuracy-cost trade-offs using token-based cost estimates. GPT-5-high achieved the highest accuracy (0.965; 95% CI, 0.942-0.985), outperforming all GPT-5-nano variants (P < .001), o1-high (P = .04), and GPT-4o (P < .001), but not o3-high (0.958; 95% CI, 0.931-0.981). GPT-5-high ranked first in both accuracy (1.66x stronger than o3-high) and rationale quality (1.11x stronger than o3-high). Cost-accuracy analysis identified several GPT-5 configurations on the Pareto frontier, with GPT-5-mini-low offering the most favorable low-cost, high-performance balance. These results benchmark GPT-5 on a high-quality ophthalmology dataset, demonstrate the influence of reasoning effort on accuracy, and introduce an autograder framework for scalable evaluation of LLM-generated answers against reference standards in ophthalmology.

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arXiv2025

AMD-Mamba: A Phenotype-Aware Multi-Modal Framework for Robust AMD Prognosis

Age-related macular degeneration (AMD) is a leading cause of irreversible vision loss, making effective prognosis crucial for timely intervention. In this work, we propose AMD-Mamba, a novel multi-modal framework for AMD prognosis, and further develop a new AMD biomarker. This framework integrates color fundus images with genetic variants and socio-demographic variables. At its core, AMD-Mamba introduces an innovative metric learning strategy that leverages AMD severity scale score as prior knowledge. This strategy allows the model to learn richer feature representations by aligning learned features with clinical phenotypes, thereby improving the capability of conventional prognosis methods in capturing disease progression patterns. In addition, unlike existing models that use traditional CNN backbones and focus primarily on local information, such as the presence of drusen, AMD-Mamba applies Vision Mamba and simultaneously fuses local and long-range global information, such as vascular changes. Furthermore, we enhance prediction performance through multi-scale fusion, combining image information with clinical variables at different resolutions. We evaluate AMD-Mamba on the AREDS dataset, which includes 45,818 color fundus photographs, 52 genetic variants, and 3 socio-demographic variables from 2,741 subjects. Our experimental results demonstrate that our proposed biomarker is one of the most significant biomarkers for the progression of AMD. Notably, combining this biomarker with other existing variables yields promising improvements in detecting high-risk AMD patients at early stages. These findings highlight the potential of our multi-modal framework to facilitate more precise and proactive management of AMD.

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arXiv2025

AI Workflow, External Validation, and Development in Eye Disease Diagnosis

Timely disease diagnosis is challenging due to increasing disease burdens and limited clinician availability. AI shows promise in diagnosis accuracy but faces real-world application issues due to insufficient validation in clinical workflows and diverse populations. This study addresses gaps in medical AI downstream accountability through a case study on age-related macular degeneration (AMD) diagnosis and severity classification. We designed and implemented an AI-assisted diagnostic workflow for AMD, comparing diagnostic performance with and without AI assistance among 24 clinicians from 12 institutions with real patient data sampled from the Age-Related Eye Disease Study (AREDS). Additionally, we demonstrated continual enhancement of an existing AI model by incorporating approximately 40,000 additional medical images (named AREDS2 dataset). The improved model was then systematically evaluated using both AREDS and AREDS2 test sets, as well as an external test set from Singapore. AI assistance markedly enhanced diagnostic accuracy and classification for 23 out of 24 clinicians, with the average F1-score increasing by 20% from 37.71 (Manual) to 45.52 (Manual + AI) (P-value < 0.0001), achieving an improvement of over 50% in some cases. In terms of efficiency, AI assistance reduced diagnostic times for 17 out of the 19 clinicians tracked, with time savings of up to 40%. Furthermore, a model equipped with continual learning showed robust performance across three independent datasets, recording a 29% increase in accuracy, and elevating the F1-score from 42 to 54 in the Singapore population.

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arXiv2025

BEnchmarking LLMs for Ophthalmology (BELO) for Ophthalmological Knowledge and Reasoning

Current benchmarks evaluating large language models (LLMs) in ophthalmology are limited in scope and disproportionately prioritise accuracy. We introduce BELO (BEnchmarking LLMs for Ophthalmology), a standardized and comprehensive evaluation benchmark developed through multiple rounds of expert checking by 13 ophthalmologists. BELO assesses ophthalmology-related clinical accuracy and reasoning quality. Using keyword matching and a fine-tuned PubMedBERT model, we curated ophthalmology-specific multiple-choice-questions (MCQs) from diverse medical datasets (BCSC, MedMCQA, MedQA, BioASQ, and PubMedQA). The dataset underwent multiple rounds of expert checking. Duplicate and substandard questions were systematically removed. Ten ophthalmologists refined the explanations of each MCQ's correct answer. This was further adjudicated by three senior ophthalmologists. To illustrate BELO's utility, we evaluated six LLMs (OpenAI o1, o3-mini, GPT-4o, DeepSeek-R1, Llama-3-8B, and Gemini 1.5 Pro) using accuracy, macro-F1, and five text-generation metrics (ROUGE-L, BERTScore, BARTScore, METEOR, and AlignScore). In a further evaluation involving human experts, two ophthalmologists qualitatively reviewed 50 randomly selected outputs for accuracy, comprehensiveness, and completeness. BELO consists of 900 high-quality, expert-reviewed questions aggregated from five sources: BCSC (260), BioASQ (10), MedMCQA (572), MedQA (40), and PubMedQA (18). A public leaderboard has been established to promote transparent evaluation and reporting. Importantly, the BELO dataset will remain a hold-out, evaluation-only benchmark to ensure fair and reproducible comparisons of future models.

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arXiv2025

Vidi: Large Multimodal Models for Video Understanding and Editing

Humans naturally share information with those they are connected to, and video has become one of the dominant mediums for communication and expression on the Internet. To support the creation of high-quality large-scale video content, a modern pipeline requires a comprehensive understanding of both the raw input materials (e.g., the unedited footage captured by cameras) and the editing components (e.g., visual effects). In video editing scenarios, models must process multiple modalities (e.g., vision, audio, text) with strong background knowledge and handle flexible input lengths (e.g., hour-long raw videos), which poses significant challenges for traditional models. In this report, we introduce Vidi, a family of Large Multimodal Models (LMMs) for a wide range of video understand editing scenarios. The first release focuses on temporal retrieval, i.e., identifying the time ranges within the input videos corresponding to a given text query, which plays a critical role in intelligent editing. The model is capable of processing hour-long videos with strong temporal understanding capability, e.g., retrieve time ranges for certain queries. To support a comprehensive evaluation in real-world scenarios, we also present the VUE-TR benchmark, which introduces five key advancements. 1) Video duration: significantly longer than videos of existing temporal retrival datasets, 2) Audio support: includes audio-based queries, 3) Query format: diverse query lengths/formats, 4) Annotation quality: ground-truth time ranges are manually annotated. 5) Evaluation metric: a refined IoU metric to support evaluation over multiple time ranges. Remarkably, Vidi significantly outperforms leading proprietary models, e.g., GPT-4o and Gemini, on the temporal retrieval task, indicating its superiority in video editing scenarios.

cs.CV↗

arXiv2025

GraphCheck: Breaking Long-Term Text Barriers with Extracted Knowledge Graph-Powered Fact-Checking

Large language models (LLMs) are widely used, but they often generate subtle factual errors, especially in long-form text. These errors are fatal in some specialized domains such as medicine. Existing fact-checking with grounding documents methods face two main challenges: (1) they struggle to understand complex multihop relations in long documents, often overlooking subtle factual errors; (2) most specialized methods rely on pairwise comparisons, requiring multiple model calls, leading to high resource and computational costs. To address these challenges, we propose GraphCheck, a fact-checking framework that uses extracted knowledge graphs to enhance text representation. Graph Neural Networks further process these graphs as a soft prompt, enabling LLMs to incorporate structured knowledge more effectively. Enhanced with graph-based reasoning, GraphCheck captures multihop reasoning chains that are often overlooked by existing methods, enabling precise and efficient fact-checking in a single inference call. Experimental results on seven benchmarks spanning both general and medical domains demonstrate up to a 7.1% overall improvement over baseline models. Notably, GraphCheck outperforms existing specialized fact-checkers and achieves comparable performance with state-of-the-art LLMs, such as DeepSeek-V3 and OpenAI-o1, with significantly fewer parameters.

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arXiv2025

MMLU-ProX: A Multilingual Benchmark for Advanced Large Language Model Evaluation

Existing large language model (LLM) evaluation benchmarks primarily focus on English, while current multilingual tasks lack parallel questions that specifically assess cross-linguistic reasoning abilities. This dual limitation makes it challenging to comprehensively assess LLMs' performance in the multilingual setting. To fill this gap, we introduce MMLU-ProX, a comprehensive benchmark covering 29 languages, built on an English benchmark. Each language version consists of 11,829 identical questions, enabling direct cross-linguistic comparisons. Additionally, to meet efficient evaluation needs, we provide a lite version containing 658 questions per language. To ensure the high quality of MMLU-ProX, we employ a rigorous development process that involves multiple powerful LLMs for translation, followed by expert review to ensure accurate expression, consistent terminology, and cultural relevance. Building on this, we systematically evaluate 36 state-of-the-art LLMs, including reasoning-enhanced and multilingual-optimized LLMs. The results reveal significant disparities in the multilingual capabilities of LLMs: While they perform well in high-resource languages, their performance declines markedly in low-resource languages, with gaps of up to 24.3%. Through MMLU-ProX, we aim to advance the development of more inclusive AI systems and promote equitable access to technology across global contexts.

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arXiv2025

Benchmarking large language models for biomedical natural language processing applications and recommendations

The rapid growth of biomedical literature poses challenges for manual knowledge curation and synthesis. Biomedical Natural Language Processing (BioNLP) automates the process. While Large Language Models (LLMs) have shown promise in general domains, their effectiveness in BioNLP tasks remains unclear due to limited benchmarks and practical guidelines. We perform a systematic evaluation of four LLMs, GPT and LLaMA representatives on 12 BioNLP benchmarks across six applications. We compare their zero-shot, few-shot, and fine-tuning performance with traditional fine-tuning of BERT or BART models. We examine inconsistencies, missing information, hallucinations, and perform cost analysis. Here we show that traditional fine-tuning outperforms zero or few shot LLMs in most tasks. However, closed-source LLMs like GPT-4 excel in reasoning-related tasks such as medical question answering. Open source LLMs still require fine-tuning to close performance gaps. We find issues like missing information and hallucinations in LLM outputs. These results offer practical insights for applying LLMs in BioNLP.

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arXiv2025

Benchmarking Next-Generation Reasoning-Focused Large Language Models in Ophthalmology: A Head-to-Head Evaluation on 5,888 Items

Recent advances in reasoning-focused large language models (LLMs) mark a shift from general LLMs toward models designed for complex decision-making, a crucial aspect in medicine. However, their performance in specialized domains like ophthalmology remains underexplored. This study comprehensively evaluated and compared the accuracy and reasoning capabilities of four newly developed reasoning-focused LLMs, namely DeepSeek-R1, OpenAI o1, o3-mini, and Gemini 2.0 Flash-Thinking. Each model was assessed using 5,888 multiple-choice ophthalmology exam questions from the MedMCQA dataset in zero-shot setting. Quantitative evaluation included accuracy, Macro-F1, and five text-generation metrics (ROUGE-L, METEOR, BERTScore, BARTScore, and AlignScore), computed against ground-truth reasonings. Average inference time was recorded for a subset of 100 randomly selected questions. Additionally, two board-certified ophthalmologists qualitatively assessed clarity, completeness, and reasoning structure of responses to differential diagnosis questions.O1 (0.902) and DeepSeek-R1 (0.888) achieved the highest accuracy, with o1 also leading in Macro-F1 (0.900). The performance of models across the text-generation metrics varied: O3-mini excelled in ROUGE-L (0.151), o1 in METEOR (0.232), DeepSeek-R1 and o3-mini tied for BERTScore (0.673), DeepSeek-R1 (-4.105) and Gemini 2.0 Flash-Thinking (-4.127) performed best in BARTScore, while o3-mini (0.181) and o1 (0.176) led AlignScore. Inference time across the models varied, with DeepSeek-R1 being slowest (40.4 seconds) and Gemini 2.0 Flash-Thinking fastest (6.7 seconds). Qualitative evaluation revealed that DeepSeek-R1 and Gemini 2.0 Flash-Thinking tended to provide detailed and comprehensive intermediate reasoning, whereas o1 and o3-mini displayed concise and summarized justifications.

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arXiv2025

Mixture-of-Shape-Experts (MoSE): End-to-End Shape Dictionary Framework to Prompt SAM for Generalizable Medical Segmentation

Single domain generalization (SDG) has recently attracted growing attention in medical image segmentation. One promising strategy for SDG is to leverage consistent semantic shape priors across different imaging protocols, scanner vendors, and clinical sites. However, existing dictionary learning methods that encode shape priors often suffer from limited representational power with a small set of offline computed shape elements, or overfitting when the dictionary size grows. Moreover, they are not readily compatible with large foundation models such as the Segment Anything Model (SAM). In this paper, we propose a novel Mixture-of-Shape-Experts (MoSE) framework that seamlessly integrates the idea of mixture-of-experts (MoE) training into dictionary learning to efficiently capture diverse and robust shape priors. Our method conceptualizes each dictionary atom as a shape expert, which specializes in encoding distinct semantic shape information. A gating network dynamically fuses these shape experts into a robust shape map, with sparse activation guided by SAM encoding to prevent overfitting. We further provide this shape map as a prompt to SAM, utilizing the powerful generalization capability of SAM through bidirectional integration. All modules, including the shape dictionary, are trained in an end-to-end manner. Extensive experiments on multiple public datasets demonstrate its effectiveness.

cs.CV↗

arXiv2025

Humans and Large Language Models in Clinical Decision Support: A Study with Medical Calculators

Although large language models (LLMs) have been assessed for general medical knowledge using licensing exams, their ability to support clinical decision-making, such as selecting medical calculators, remains uncertain. We assessed nine LLMs, including open-source, proprietary, and domain-specific models, with 1,009 multiple-choice question-answer pairs across 35 clinical calculators and compared LLMs to humans on a subset of questions. While the highest-performing LLM, OpenAI o1, provided an answer accuracy of 66.0% (CI: 56.7-75.3%) on the subset of 100 questions, two human annotators nominally outperformed LLMs with an average answer accuracy of 79.5% (CI: 73.5-85.0%). Ultimately, we evaluated medical trainees and LLMs in recommending medical calculators across clinical scenarios like risk stratification and diagnosis. With error analysis showing that the highest-performing LLMs continue to make mistakes in comprehension (49.3% of errors) and calculator knowledge (7.1% of errors), our findings highlight that LLMs are not superior to humans in calculator recommendation.

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arXiv2025

LMOD: A Large Multimodal Ophthalmology Dataset and Benchmark for Large Vision-Language Models

The prevalence of vision-threatening eye diseases is a significant global burden, with many cases remaining undiagnosed or diagnosed too late for effective treatment. Large vision-language models (LVLMs) have the potential to assist in understanding anatomical information, diagnosing eye diseases, and drafting interpretations and follow-up plans, thereby reducing the burden on clinicians and improving access to eye care. However, limited benchmarks are available to assess LVLMs' performance in ophthalmology-specific applications. In this study, we introduce LMOD, a large-scale multimodal ophthalmology benchmark consisting of 21,993 instances across (1) five ophthalmic imaging modalities: optical coherence tomography, color fundus photographs, scanning laser ophthalmoscopy, lens photographs, and surgical scenes; (2) free-text, demographic, and disease biomarker information; and (3) primary ophthalmology-specific applications such as anatomical information understanding, disease diagnosis, and subgroup analysis. In addition, we benchmarked 13 state-of-the-art LVLM representatives from closed-source, open-source, and medical domains. The results demonstrate a significant performance drop for LVLMs in ophthalmology compared to other domains. Systematic error analysis further identified six major failure modes: misclassification, failure to abstain, inconsistent reasoning, hallucination, assertions without justification, and lack of domain-specific knowledge. In contrast, supervised neural networks specifically trained on these tasks as baselines demonstrated high accuracy. These findings underscore the pressing need for benchmarks in the development and validation of ophthalmology-specific LVLMs.

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arXiv2025

Can OpenAI o1 Reason Well in Ophthalmology? A 6,990-Question Head-to-Head Evaluation Study

Question: What is the performance and reasoning ability of OpenAI o1 compared to other large language models in addressing ophthalmology-specific questions? Findings: This study evaluated OpenAI o1 and five LLMs using 6,990 ophthalmological questions from MedMCQA. O1 achieved the highest accuracy (0.88) and macro-F1 score but ranked third in reasoning capabilities based on text-generation metrics. Across subtopics, o1 ranked first in ``Lens'' and ``Glaucoma'' but second to GPT-4o in ``Corneal and External Diseases'', ``Vitreous and Retina'' and ``Oculoplastic and Orbital Diseases''. Subgroup analyses showed o1 performed better on queries with longer ground truth explanations. Meaning: O1's reasoning enhancements may not fully extend to ophthalmology, underscoring the need for domain-specific refinements to optimize performance in specialized fields like ophthalmology.

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arXiv2025

Enhancing Patient-Centric Communication: Leveraging LLMs to Simulate Patient Perspectives

Large Language Models (LLMs) have demonstrated impressive capabilities in role-playing scenarios, particularly in simulating domain-specific experts using tailored prompts. This ability enables LLMs to adopt the persona of individuals with specific backgrounds, offering a cost-effective and efficient alternative to traditional, resource-intensive user studies. By mimicking human behavior, LLMs can anticipate responses based on concrete demographic or professional profiles. In this paper, we evaluate the effectiveness of LLMs in simulating individuals with diverse backgrounds and analyze the consistency of these simulated behaviors compared to real-world outcomes. In particular, we explore the potential of LLMs to interpret and respond to discharge summaries provided to patients leaving the Intensive Care Unit (ICU). We evaluate and compare with human responses the comprehensibility of discharge summaries among individuals with varying educational backgrounds, using this analysis to assess the strengths and limitations of LLM-driven simulations. Notably, when LLMs are primed with educational background information, they deliver accurate and actionable medical guidance 88% of the time. However, when other information is provided, performance significantly drops, falling below random chance levels. This preliminary study shows the potential benefits and pitfalls of automatically generating patient-specific health information from diverse populations. While LLMs show promise in simulating health personas, our results highlight critical gaps that must be addressed before they can be reliably used in clinical settings. Our findings suggest that a straightforward query-response model could outperform a more tailored approach in delivering health information. This is a crucial first step in understanding how LLMs can be optimized for personalized health communication while maintaining accuracy.

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arXiv2025

Fair Text to Medical Image Diffusion Model with Subgroup Distribution Aligned Tuning

The text to medical image (T2MedI) with latent diffusion model has great potential to alleviate the scarcity of medical imaging data and explore the underlying appearance distribution of lesions in a specific patient status description. However, as the text to nature image models, we show that the T2MedI model can also bias to some subgroups to overlook the minority ones in the training set. In this work, we first build a T2MedI model based on the pre-trained Imagen model, which has the fixed contrastive language-image pre-training (CLIP) text encoder, while its decoder has been fine-tuned on medical images from the Radiology Objects in COntext (ROCO) dataset. Its gender bias is analyzed qualitatively and quantitatively. Toward this issue, we propose to fine-tune the T2MedI toward the target application dataset to align their sensitive subgroups distribution probability. Specifically, the alignment loss for fine-tuning is guided by an off-the-shelf sensitivity-subgroup classifier to match the classification probability between the generated images and the expected target dataset. In addition, the image quality is maintained by a CLIP-consistency regularization term following a knowledge distillation scheme. For evaluation, we set the target dataset to be enhanced as the BraST18 dataset, and trained a brain magnetic resonance (MR) slice-based gender classifier from it. With our method, the generated MR image can markedly reduce the inconsistency with the gender proportion in the BraTS18 dataset.

cs.CV↗

arXiv2025

Information Extraction from Clinical Notes: Are We Ready to Switch to Large Language Models?

Backgrounds: Information extraction (IE) is critical in clinical natural language processing (NLP). While large language models (LLMs) excel on generative tasks, their performance on extractive tasks remains debated. Methods: We investigated Named Entity Recognition (NER) and Relation Extraction (RE) using 1,588 clinical notes from four sources (UT Physicians, MTSamples, MIMIC-III, and i2b2). We developed an annotated corpus covering 4 clinical entities and 16 modifiers, and compared instruction-tuned LLaMA-2 and LLaMA-3 against BERT in terms of performance, generalizability, computational resources, and throughput to BERT. Results: LLaMA models outperformed BERT across datasets. With sufficient training data, LLaMA showed modest improvements (1% on NER, 1.5-3.7% on RE); improvements were larger with limited training data. On unseen i2b2 data, LLaMA-3-70B outperformed BERT by 7% (F1) on NER and 4% on RE. However, LLaMA models required more computing resources and ran up to 28 times slower. We implemented "Kiwi," a clinical IE package featuring both models, available at https://kiwi.clinicalnlp.org/. Conclusion: This study is among the first to develop and evaluate a comprehensive clinical IE system using open-source LLMs. Results indicate that LLaMA models outperform BERT for clinical NER and RE but with higher computational costs and lower throughputs. These findings highlight that choosing between LLMs and traditional deep learning methods for clinical IE applications should remain task-specific, taking into account both performance metrics and practical considerations such as available computing resources and the intended use case scenarios.

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