arXiv subjects

Yifan Peng

Publications and source records attributed to Yifan Peng.

At least 55 records · Page 3Linked to original sources

arXiv2026

Overview of the CXR-LT 2026 Challenge: Multi-Center Long-Tailed and Zero Shot Chest X-ray Classification

Chest X-ray (CXR) interpretation is hindered by the long-tailed distribution of pathologies and the open-world nature of clinical environments. Existing benchmarks often rely on closed-set classes from single institutions, failing to capture the prevalence of rare diseases or the appearance of novel findings. To address this, we present the CXR-LT 2026 challenge. This third iteration of the benchmark introduces a multi-center dataset comprising over 145,000 images from PadChest and NIH Chest X-ray datasets. The challenge defines two core tasks: (1) Robust Multi-Label Classification on 30 known classes and (2) Open-World Generalization to 6 unseen (out-of-distribution) rare disease classes. We report the results of the top-performing teams, evaluating them via mean Average Precision (mAP), AUROC, and F1-score. The winning solutions achieved an mAP of 0.5854 on Task 1 and 0.4315 on Task 2, demonstrating that large-scale vision-language pre-training significantly mitigates the performance drop typically associated with zero-shot diagnosis.

cs.CV↗

arXiv2026

PhyGaP: Physically-Grounded Gaussians with Polarization Cues

Recent advances in 3D Gaussian Splatting (3DGS) have demonstrated great success in modeling reflective 3D objects and their interaction with the environment via deferred rendering (DR). However, existing methods often struggle with correctly reconstructing physical attributes such as albedo and reflectance, and therefore they do not support high-fidelity relighting. Observing that this limitation stems from the lack of shape and material information in RGB images, we present PhyGaP, a physically-grounded 3DGS method that leverages polarization cues to facilitate precise reflection decomposition and visually consistent relighting of reconstructed objects. Specifically, we design a polarimetric deferred rendering (PolarDR) process to model polarization by reflection, and a self-occlusion-aware environment map building technique (GridMap) to resolve indirect lighting of non-convex objects. We validate on multiple synthetic and real-world scenes, including those featuring only partial polarization cues, that PhyGaP not only excels in reconstructing the appearance and surface normal of reflective 3D objects (~2 dB in PSNR and 45.7% in Cosine Distance better than existing RGB-based methods on average), but also achieves state-of-the-art inverse rendering and relighting capability. Our code will be released soon.

cs.CV↗

arXiv2026

SAP: Segment Any 4K Panorama

Promptable instance segmentation is widely adopted in embodied and AR systems, yet the performance of foundation models trained on perspective imagery often degrades on 360° panoramas. In this paper, we introduce Segment Any 4K Panorama (SAP), a foundation model for 4K high-resolution panoramic instance-level segmentation. We reformulate panoramic segmentation as fixed-trajectory perspective video segmentation, decomposing a panorama into overlapping perspective patches sampled along a continuous spherical traversal. This memory-aligned reformulation preserves native 4K resolution while restoring the smooth viewpoint transitions required for stable cross-view propagation. To enable large-scale supervision, we synthesize 183,440 4K-resolution panoramic images with instance segmentation labels using the InfiniGen engine. Trained under this trajectory-aligned paradigm, SAP generalizes effectively to real-world 360° images, achieving +17.2 zero-shot mIoU gain over vanilla SAM2 of different sizes on real-world 4K panorama benchmark.

cs.CV↗

arXiv2026

Thinking in Uncertainty: Mitigating Hallucinations in MLRMs with Latent Entropy-Aware Decoding

Recent advancements in multimodal large reasoning models (MLRMs) have significantly improved performance in visual question answering. However, we observe that transition words (e.g., because, however, and wait) are closely associated with hallucinations and tend to exhibit high-entropy states. We argue that adequate contextual reasoning information can be directly extracted from the token probability distribution. Inspired by superposed representation theory, we propose leveraging latent superposed reasoning to integrate multiple candidate semantics and maintain latent reasoning trajectories. The hypothesis is that reliance on discrete textual inputs may drive the model toward sequential explicit reasoning, underutilizing dense contextual cues during high-entropy reasoning stages. Therefore, we propose constructing rich semantic representations from the token probability distributions to enhance in-context reasoning. With this goal, we present Latent Entropy-Aware Decoding (LEAD), an efficient plug-and-play decoding strategy that leverages semantic context to achieve reliable reasoning. The heart of our method lies in entropy-aware reasoning mode switching. The model employs probability-weighted continuous embeddings under high-entropy states and transitions back to discrete token embeddings as entropy decreases. Moreover, we propose a prior-guided visual anchor injection strategy that encourages the model to focus on visual information. Extensive experiments show that LEAD effectively mitigates hallucinations across various MLRMs on multiple benchmarks.

cs.CV↗

arXiv2026

A General Model for Retinal Segmentation and Quantification

Retinal imaging is fast, non-invasive, and widely available, offering quantifiable structural and vascular signals for ophthalmic and systemic health assessment. This accessibility creates an opportunity to study how quantitative retinal phenotypes relate to ocular and systemic diseases. However, such analyses remain difficult at scale due to the limited availability of public multi-label datasets and the lack of a unified segmentation-to-quantification pipeline. We present RetSAM, a general retinal segmentation and quantification framework for fundus imaging. It delivers robust multi-target segmentation and standardized biomarker extraction, supporting downstream ophthalmologic studies and oculomics correlation analyses. Trained on over 200,000 fundus images, RetSAM supports three task categories and segments five anatomical structures, four retinal phenotypic patterns, and more than 20 distinct lesion types. It converts these segmentation results into over 30 standardized biomarkers that capture structural morphology, vascular geometry, and degenerative changes. Trained with a multi-stage strategy using both private and public fundus data, RetSAM achieves superior segmentation performance on 17 public datasets. It improves on prior best methods by 3.9 percentage points in DSC on average, with up to 15 percentage points on challenging multi-task benchmarks, and generalizes well across diverse populations, imaging devices, and clinical settings. The resulting biomarkers enable systematic correlation analyses across major ophthalmic diseases, including diabetic retinopathy, age-related macular degeneration, glaucoma, and pathologic myopia. Together, RetSAM transforms fundus images into standardized, interpretable quantitative phenotypes, enabling large-scale ophthalmic research and translation.

cs.CV↗

arXiv2026

Establishing dermatopathology encyclopedia DermpathNet with Artificial Intelligence-Based Workflow

Accessing high-quality, open-access dermatopathology image datasets for learning and cross-referencing is a common challenge for clinicians and dermatopathology trainees. To establish a comprehensive open-access dermatopathology dataset for educational, cross-referencing, and machine-learning purposes, we employed a hybrid workflow to curate and categorize images from the PubMed Central (PMC) repository. We used specific keywords to extract relevant images, and classified them using a novel hybrid method that combined deep learning-based image modality classification with figure caption analyses. Validation on 651 manually annotated images demonstrated the robustness of our workflow, with an F-score of 89.6% for the deep learning approach, 61.0% for the keyword-based retrieval method, and 90.4% for the hybrid approach. We retrieved over 7,772 images across 166 diagnoses and released this fully annotated dataset, reviewed by board-certified dermatopathologists. Using our dataset as a challenging task, we found the current image analysis algorithm from OpenAI inadequate for analyzing dermatopathology images. In conclusion, we have developed a large, peer-reviewed, open-access dermatopathology image dataset, DermpathNet, which features a semi-automated curation workflow.

cs.CV↗

arXiv2026

Scaling Medical Reasoning Verification via Tool-Integrated Reinforcement Learning

Large language models have achieved strong performance on medical reasoning benchmarks, yet their deployment in clinical settings demands rigorous verification to ensure factual accuracy. While reward models offer a scalable approach for reasoning trace verification, existing methods face two limitations: they produce only scalar reward values without explicit justification, and they rely on single-pass retrieval that precludes adaptive knowledge access as verification unfolds. We introduce $\method$, an agentic framework that addresses these limitations by training medical reasoning verifiers to iteratively query external medical corpora during evaluation. Our approach combines tool-augmented verification with an iterative reinforcement learning paradigm that requires only trace-level supervision, alongside an adaptive curriculum mechanism that dynamically adjusts training data distribution. Across four medical reasoning benchmarks, $\method$ achieves substantial gains over existing methods, improving MedQA accuracy by 23.5% and MedXpertQA by 32.0% relative to the base generator in particular. Crucially, $\method$ demonstrates an $\mathbf{8\times}$ reduction in sampling budget requirement compared to prior reward model baselines. These findings establish that grounding verification in dynamically retrieved evidence offers a principled path toward more reliable medical reasoning systems.

cs.AI↗

arXiv2026

RSNA Large Language Model Benchmark Dataset for Chest Radiographs of Cardiothoracic Disease: Radiologist Evaluation and Validation Enhanced by AI Labels (REVEAL-CXR)

Multimodal large language models have demonstrated comparable performance to that of radiology trainees on multiple-choice board-style exams. However, to develop clinically useful multimodal LLM tools, high-quality benchmarks curated by domain experts are essential. To curate released and holdout datasets of 100 chest radiographic studies each and propose an artificial intelligence (AI)-assisted expert labeling procedure to allow radiologists to label studies more efficiently. A total of 13,735 deidentified chest radiographs and their corresponding reports from the MIDRC were used. GPT-4o extracted abnormal findings from the reports, which were then mapped to 12 benchmark labels with a locally hosted LLM (Phi-4-Reasoning). From these studies, 1,000 were sampled on the basis of the AI-suggested benchmark labels for expert review; the sampling algorithm ensured that the selected studies were clinically relevant and captured a range of difficulty levels. Seventeen chest radiologists participated, and they marked "Agree all", "Agree mostly" or "Disagree" to indicate their assessment of the correctness of the LLM suggested labels. Each chest radiograph was evaluated by three experts. Of these, at least two radiologists selected "Agree All" for 381 radiographs. From this set, 200 were selected, prioritizing those with less common or multiple finding labels, and divided into 100 released radiographs and 100 reserved as the holdout dataset. The holdout dataset is used exclusively by RSNA to independently evaluate different models. A benchmark of 200 chest radiographic studies with 12 benchmark labels was created and made publicly available https://imaging.rsna.org, with each chest radiograph verified by three radiologists. In addition, an AI-assisted labeling procedure was developed to help radiologists label at scale, minimize unnecessary omissions, and support a semicollaborative environment.

cs.CL↗

arXiv2026

Generative Modeling via Hierarchical Tensor Sketching

We propose a hierarchical tensor-network approach for approximating high-dimensional probability density via empirical distribution. This leverages randomized singular value decomposition (SVD) techniques and involves solving linear equations for tensor cores in this tensor network. The complexity of the resulting algorithm scales linearly in the dimension of the high-dimensional density. An analysis of estimation error demonstrates the effectiveness of this method through several numerical experiments.

math.NA↗

arXiv2026

CPGPrompt: Translating Clinical Guidelines into LLM-Executable Decision Support

Clinical practice guidelines (CPGs) provide evidence-based recommendations for patient care; however, integrating them into Artificial Intelligence (AI) remains challenging. Previous approaches, such as rule-based systems, face significant limitations, including poor interpretability, inconsistent adherence to guidelines, and narrow domain applicability. To address this, we develop and validate CPGPrompt, an auto-prompting system that converts narrative clinical guidelines into large language models (LLMs). Our framework translates CPGs into structured decision trees and utilizes an LLM to dynamically navigate them for patient case evaluation. Synthetic vignettes were generated across three domains (headache, lower back pain, and prostate cancer) and distributed into four categories to test different decision scenarios. System performance was assessed on both binary specialty-referral decisions and fine-grained pathway-classification tasks. The binary specialty referral classification achieved consistently strong performance across all domains (F1: 0.85-1.00), with high recall (1.00 $\pm$ 0.00). In contrast, multi-class pathway assignment showed reduced performance, with domain-specific variations: headache (F1: 0.47), lower back pain (F1: 0.72), and prostate cancer (F1: 0.77). Domain-specific performance differences reflected the structure of each guideline. The headache guideline highlighted challenges with negation handling. The lower back pain guideline required temporal reasoning. In contrast, prostate cancer pathways benefited from quantifiable laboratory tests, resulting in more reliable decision-making.

cs.AI↗

arXiv2026

Toward Global Large Language Models in Medicine

Despite continuous advances in medical technology, the global distribution of health care resources remains uneven. The development of large language models (LLMs) has transformed the landscape of medicine and holds promise for improving health care quality and expanding access to medical information globally. However, existing LLMs are primarily trained on high-resource languages, limiting their applicability in global medical scenarios. To address this gap, we constructed GlobMed, a large multilingual medical dataset, containing over 500,000 entries spanning 12 languages, including four low-resource languages. Building on this, we established GlobMed-Bench, which systematically assesses 56 state-of-the-art proprietary and open-weight LLMs across multiple multilingual medical tasks, revealing significant performance disparities across languages, particularly for low-resource languages. Additionally, we introduced GlobMed-LLMs, a suite of multilingual medical LLMs trained on GlobMed, with parameters ranging from 1.7B to 8B. GlobMed-LLMs achieved an average performance improvement of over 40% relative to baseline models, with a more than threefold increase in performance on low-resource languages. Together, these resources provide an important foundation for advancing the equitable development and application of LLMs globally, enabling broader language communities to benefit from technological advances.

cs.CL↗

arXiv2026

Scalable Scientific Interest Profiling Using Large Language Models

Research profiles highlight scientists' research focus, enabling talent discovery and collaborations, but are often outdated. Automated, scalable methods are urgently needed to keep profiles current. We design and evaluate two Large Language Models (LLMs)-based methods to generate scientific interest profiles--one summarizing PubMed abstracts and the other using Medical Subject Headings (MeSH) terms--comparing them with researchers' self-summarized interests. We collected titles, MeSH terms, and abstracts of PubMed publications for 595 faculty at Columbia University Irving Medical Center, obtaining human-written profiles for 167. GPT-4o-mini was prompted to summarize each researcher's interests. Manual and automated evaluations characterized similarities between machine-generated and self-written profiles. The similarity study showed low ROUGE-L, BLEU, and METEOR scores, reflecting little terminological overlap. BERTScore analysis revealed moderate semantic similarity (F1: 0.542 for MeSH-based, 0.555 for abstract-based), despite low lexical overlap. In validation, paraphrased summaries achieved a higher F1 of 0.851. Comparing original and manually paraphrased summaries indicated limitations of such metrics. Kullback-Leibler (KL) Divergence of TF-IDF values (8.56 for MeSH-based, 8.58 for abstract-based) suggests machine summaries employ different keywords than human-written ones. Manual reviews showed 77.78% rated MeSH-based profiling "good" or "excellent," with readability rated favorably in 93.44% of cases, though granularity and accuracy varied. Panel reviews favored 67.86% of MeSH-derived profiles over abstract-derived ones. LLMs promise to automate scientific interest profiling at scale. MeSH-derived profiles have better readability than abstract-derived ones. Machine-generated summaries differ from human-written ones in concept choice, with the latter initiating more novel ideas.

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

Supervisory Measurement-Guided Noise Covariance Estimation

Reliable state estimation hinges on accurate specification of sensor noise covariances, which weigh heterogeneous measurements. In practice, these covariances are difficult to identify due to environmental variability, front-end preprocessing, and other reasons. We address this by formulating noise covariance estimation as a bilevel optimization that, from a Bayesian perspective, factorizes the joint likelihood of so-called odometry and supervisory measurements, thereby balancing information utilization with computational efficiency. The factorization converts the nested Bayesian dependency into a chain structure, enabling efficient parallel computation: at the lower level, an invariant extended Kalman filter with state augmentation estimates trajectories, while a derivative filter computes analytical gradients in parallel for upper-level gradient updates. The upper level refines the covariance to guide the lower-level estimation. Experiments on synthetic and real-world datasets show that our method achieves higher efficiency over existing baselines.

cs.RO↗

arXiv2025

UniBiomed: A Universal Foundation Model for Grounded Biomedical Image Interpretation

The integration of AI-assisted biomedical image analysis into clinical practice demands AI-generated findings that are not only accurate but also interpretable to clinicians. However, existing biomedical AI models generally lack the ability to simultaneously generate diagnostic findings and localize corresponding biomedical objects. This limitation makes it challenging for clinicians to correlate AI-generated findings with visual evidence (e.g., tiny lesions) in images and interpret the results of AI models. To address this challenge, we introduce UniBiomed, the first universal foundation model for grounded biomedical image interpretation, which is capable of generating accurate diagnostic findings and simultaneously segmenting the corresponding biomedical targets. UniBiomed is based on a novel integration of Multi-modal Large Language Model and Segment Anything Model, which can effectively unify diverse biomedical tasks in universal training for advancing grounded interpretation. To develop UniBiomed, we curate a large-scale dataset comprising over 27 million triplets of images, region annotations, and text descriptions across ten biomedical imaging modalities. Extensive validation on 70 internal and 14 external datasets demonstrated the state-of-the-art performance of UniBiomed in diverse biomedical tasks, including image segmentation, disease recognition, region-aware diagnosis, vision question answering, and report generation. In summary, UniBiomed is a powerful and versatile biomedical foundation model, unlocking the untapped grounded interpretation capability for optimizing AI-assisted biomedical image analysis.

cs.CV↗

arXiv2025

Orchestrator Multi-Agent Clinical Decision Support System for Secondary Headache Diagnosis in Primary Care

Unlike most primary headaches, secondary headaches need specialized care and can have devastating consequences if not treated promptly. Clinical guidelines highlight several 'red flag' features, such as thunderclap onset, meningismus, papilledema, focal neurologic deficits, signs of temporal arteritis, systemic illness, and the 'worst headache of their life' presentation. Despite these guidelines, determining which patients require urgent evaluation remains challenging in primary care settings. Clinicians often work with limited time, incomplete information, and diverse symptom presentations, which can lead to under-recognition and inappropriate care. We present a large language model (LLM)-based multi-agent clinical decision support system built on an orchestrator-specialist architecture, designed to perform explicit and interpretable secondary headache diagnosis from free-text clinical vignettes. The multi-agent system decomposes diagnosis into seven domain-specialized agents, each producing a structured and evidence-grounded rationale, while a central orchestrator performs task decomposition and coordinates agent routing. We evaluated the multi-agent system using 90 expert-validated secondary headache cases and compared its performance with a single-LLM baseline across two prompting strategies: question-based prompting (QPrompt) and clinical practice guideline-based prompting (GPrompt). We tested five open-source LLMs (Qwen-30B, GPT-OSS-20B, Qwen-14B, Qwen-8B, and Llama-3.1-8B), and found that the orchestrated multi-agent system with GPrompt consistently achieved the highest F1 scores, with larger gains in smaller models. These findings demonstrate that structured multi-agent reasoning improves accuracy beyond prompt engineering alone and offers a transparent, clinically aligned approach for explainable decision support in secondary headache diagnosis.

cs.AI↗

arXiv2025

Supervisory Measurement-Guided Noise Covariance Estimation: Discussing Forward and Reverse Differentiation

Reliable state estimation depends on accurately modeled noise covariances, which are difficult to determine in practice. This paper formulates the noise covariance estimation as a bilevel optimization problem that factorizes the joint likelihood of primary and supervisory measurements to reconcile information exploitation with computational tractability. The factorization converts the nested Bayesian dependency into a Markov-chain structure, allowing efficient computation. At the lower level, a Kalman filter with state augmentation performs such computation. Meanwhile, closed-form forward and reverse differentiation provide efficient gradients for the upper-level updates, and we compare the two models' space and time complexities to inform their practical selection. The upper level subsequently refines the noise covariances to guide the lower-level estimation. Taken together, the proposed algorithms offer a systematic and computationally efficient approach to noise covariance estimation in linear Gaussian systems.

eess.SY↗

arXiv2025

A Disease-Aware Dual-Stage Framework for Chest X-ray Report Generation

Radiology report generation from chest X-rays is an important task in artificial intelligence with the potential to greatly reduce radiologists' workload and shorten patient wait times. Despite recent advances, existing approaches often lack sufficient disease-awareness in visual representations and adequate vision-language alignment to meet the specialized requirements of medical image analysis. As a result, these models usually overlook critical pathological features on chest X-rays and struggle to generate clinically accurate reports. To address these limitations, we propose a novel dual-stage disease-aware framework for chest X-ray report generation. In Stage~1, our model learns Disease-Aware Semantic Tokens (DASTs) corresponding to specific pathology categories through cross-attention mechanisms and multi-label classification, while simultaneously aligning vision and language representations via contrastive learning. In Stage~2, we introduce a Disease-Visual Attention Fusion (DVAF) module to integrate disease-aware representations with visual features, along with a Dual-Modal Similarity Retrieval (DMSR) mechanism that combines visual and disease-specific similarities to retrieve relevant exemplars, providing contextual guidance during report generation. Extensive experiments on benchmark datasets (i.e., CheXpert Plus, IU X-ray, and MIMIC-CXR) demonstrate that our disease-aware framework achieves state-of-the-art performance in chest X-ray report generation, with significant improvements in clinical accuracy and linguistic quality.

cs.CV↗