arXiv subjects

Junlin Hou

Publications and source records attributed to Junlin Hou.

At least 19 recordsLinked to original sources

arXiv2026

Paired Uterine Whole-Slide Images and Pathology Reports for Multimodal Computational Pathology

Uterine diseases represent an important category of gynecologic pathology and require accurate histopathological assessment for diagnosis and treatment planning. Whole-slide images (WSI) have enabled the digital transformation of pathology workflows and provided new opportunities for artificial intelligence (AI) in computational pathology. In particular, multimodal models that jointly analyze histopathology images and pathology reports have shown promising potential for automated pathology report generation and AI-assisted diagnosis. However, the development of such systems remains limited by the scarcity of datasets that pair whole-slide images with clinically meaningful pathology reports. Instead, existing pathology datasets focus on patch- or slide-level annotations of a single endpoint (e.g., disease class), which do not fully capture the rich information in full clinical diagnostic workflow reports. Here, we introduce TUM-Uteria, a uterine pathology dataset comprising WSIs paired with diagnostic pathology reports at both the case and slide levels, collected from a tertiary medical center. The dataset contains 216 clinical cases, comprising 455 slide-level WSI-report pairs. The dataset underwent a structured multi-stage validation procedure involving board-certified pathologists to ensure reliable annotations. TUM-Uteria supports research in computational pathology, including whole-slide image analysis, multimodal learning, and automated pathology report generation.

cs.CV↗

arXiv2026

Democratizing and accelerating AI-driven pathology research through agentic intelligence

Computational pathology has advanced rapidly with the emergence of foundation models, yet widespread adoption remains limited by substantial technical complexity and programming requirements. Here we present PathLab, an autonomous agentic framework that translates natural-language research objectives into executable and validated computational pathology workflows through the structured composition of domain-specific skills and tools. By organizing workflow generation around reusable methodological modules, including data preprocessing, model development, evaluation and interpretation, PathLab enables studies to be specified at the level of scientific intent rather than implementation details. We evaluated PathLab across 12 public datasets spanning four representative task families: region-of-interest classification, whole-slide image classification, segmentation and survival prediction. Across all task categories, PathLab achieved non-inferior performance relative to expert implementations, while consistently enforcing semantic validity of user prompts and proactively rejecting incompatible workflow specifications prior to execution. In controlled user studies, PathLab substantially reduced the time required to generate executable analytical pipelines and enabled domain experts without programming experience to independently design, execute and evaluate computational pathology studies. Together, these results establish PathLab as a reliable interface between biomedical intent and computational execution, enabling computational pathology studies to be designed at the level of scientific questions rather than programming expertise. By lowering technical barriers to advanced AI methodologies, PathLab provides a foundation for the broader democratization of computational pathology.

cs.AI↗

arXiv2026

A Multimodal Agentic Pathology Co-pilot via Evidence Grounded Reasoning

Pathology is the cornerstone of modern medicine, where accurate decision-making relies heavily on evidence-based practices. While artificial intelligence (AI) has the potential to transform clinical workflows, the intersection of AI and evidence-based medicine remains under-explored, with primitive attempts restricted to text-only general medicine. In this work, we present PathPocket, a multimodal AI agentic co-pilot designed specifically for evidence grounded pathology. We construct the most comprehensive pathology evidence corpus to date, encompassing approximately 110,472 public and authorized documents structured across a rigorous hierarchy of evidence from clinical guideline to expert opinion. From this meticulously graded foundation, we build a large-scale multimodal pathology hypergraph containing over 4.55 million entities and 7.10 million relations. Serving as a robust knowledge engine, this hypergraph provides traceable evidence for a collaborative multi-agent reasoning framework integrating input understanding, evidence retrieval, filtering, and diagnosis generation. This enables PathPocket to seamlessly resolve a wide spectrum of clinical tasks, ranging from text-only queries to complex multimodal diagnostics involving region-of-interest (ROI) and gigapixel whole-slide images (WSIs). We rigorously evaluate the system on a multidimensional benchmark of over 200,000 real-world cases, where it significantly outperforms existing state-of-the-arts. Crucially, extensive user studies demonstrate that PathPocket substantially improves the diagnostic accuracy and confidence of pathologists. By directly grounding pathology interpretations in verifiable literature, PathPocket offers a practical and scalable solution for the future of evidence grounded computational pathology.

cs.AI↗

arXiv2026

A Clinically Validated Foundation Model for Comprehensive Lung Pathology Interpretation

Pathological assessment guides lung cancer diagnosis, treatment selection, and prognostic evaluation, yet current CPath approaches rely on task-specific models for isolated objectives. Although pan-cancer foundation models offer versatility, they lack subspecialty-level depth and have not been evaluated across clinical workflows or prospectively validated in real-world settings. We introduce PulmoFoundation, a multi-center, prospectively validated, randomized controlled trial (RCT)-evaluated foundation model for comprehensive lung pathology assessment across pre-operative, intra-operative, and post-operative care. Built upon Virchow2 via subspecialty-specific pretraining using ~40,000 diagnostic H&E-stained whole-slide images (WSIs), PulmoFoundation was systematically evaluated on ~26,000 WSIs across 32 clinically relevant tasks. In addition to accurately predicting molecular markers and patient survival, our model achieves clinical-grade performance in core diagnostic tasks across biopsy, frozen section, and surgical resection slides. In a registered prospective study of 1,357 patients across 11 diagnostic tasks, our model achieved an average AUC of 92.3%. Using pre-specified triage thresholds, PulmoFoundation could reduce additional second-review burden for 68.8% of biopsies and 83.0% of frozen sections, and defer 44.5% of IHC stain orders, with PPVs of 1.000, 0.991, and 0.966. Beyond prospective validation, we conducted a crossover RCT with eight pathologists, in which AI assistance improved diagnostic accuracy across 5,264 case-reader pairs (91.7% w/ AI vs. 83.2% w/o AI). AI assistance also reduced median diagnostic time by 18.3%, increased diagnostic confidence by 9.0%, and improved inter-rater agreement from moderate (kappa = 0.55) to substantial (kappa = 0.76). Together, these evaluations support PulmoFoundation as a clinically validated decision-support system for lung pathology.

eess.IV↗

arXiv2026

Clinical Priors Guided Lung Disease Detection in 3D CT Scans

Accurate classification of lung diseases from chest CT scans plays an important role in computer-aided diagnosis systems. However, medical imaging datasets often suffer from severe class imbalance, which may significantly degrade the performance of deep learning models, especially for minority disease categories. To address this issue, we propose a gender-aware two-stage lung disease classification framework. The proposed approach explicitly incorporates gender information into the disease recognition pipeline. In the first stage, a gender classifier is trained to predict the patient's gender from CT scans. In the second stage, the input CT image is routed to a corresponding gender-specific disease classifier to perform final disease prediction. This design enables the model to better capture gender-related imaging characteristics and alleviate the influence of imbalanced data distribution. Experimental results demonstrate that the proposed method improves the recognition performance for minority disease categories, particularly squamous cell carcinoma, while maintaining competitive performance on other classes.

eess.IV↗

arXiv2026

Vision-Language Model Based Multi-Expert Fusion for CT Image Classification

Robust detection of COVID-19 from chest CT remains challenging in multi-institutional settings due to substantial source shift, source imbalance, and hidden test-source identities. In this work, we propose a three-stage source-aware multi-expert framework for multi-source COVID-19 CT classification. First, we build a lung-aware 3D expert by combining original CT volumes and lung-extracted CT volumes for volumetric classification. Second, we develop two MedSigLIP-based experts: a slice-wise representation and probability learning module, and a Transformer-based inter-slice context modeling module for capturing cross-slice dependency. Third, we train a source classifier to predict the latent source identity of each test scan. By leveraging the predicted source information, we perform model fusion and voting based on different experts. On the validation set covering all four sources, the Stage 1 model achieves the best macro-F1 of 0.9711, ACC of 0.9712, and AUC of 0.9791. Stage~2a and Stage~2b achieve the best AUC scores of 0.9864 and 0.9854, respectively. Stage~3 source classifier reaches 0.9107 ACC and 0.9114 F1. These results demonstrate that source-aware expert modeling and hierarchical voting provide an effective solution for robust COVID-19 CT classification under heterogeneous multi-source conditions.

eess.IV↗

arXiv2026

Free Lunch in Medical Image Foundation Model Pre-training via Randomized Synthesis and Disentanglement

Medical image foundation models (MIFMs) have demonstrated remarkable potential for a wide range of clinical tasks, yet their development is constrained by the scarcity, heterogeneity, and high cost of large-scale annotated datasets. Here, we propose RaSD (Randomized Synthesis and Disentanglement), a scalable framework for pre-training MIFMs entirely on synthetic data. By modeling anatomical structures and appearance variations with randomized Gaussian distributions, RaSD exposes models to sufficient multi-scale structural and appearance perturbations, forcing them to rely on invariant and task-relevant anatomical cues rather than dataset-specific textures, thereby enabling robust and transferable representation learning. We pre-trained RaSD on 1.2 million 3D volumes and 9.6 million 2D images, and extensively evaluated the resulting models across 6 imaging modalities, 48 datasets, and 56 downstream tasks. Across all evaluated downstream tasks, RaSD consistently outperforms training-from-scratch models, achieves the best performance on 17 tasks, and remains comparable to models pre-trained on large real datasets in most others. These results demonstrate that the capacity of synthetic data alone to drive robust representation learning. Our findings establish a paradigm shift in medical AI, demonstrating that synthetic data can serve as a "free lunch" for scalable, privacy-preserving, and clinically generalizable foundation models.

q-bio.QM↗

arXiv2025

Benchmarking Real-World Medical Image Classification with Noisy Labels: Challenges, Practice, and Outlook

Learning from noisy labels remains a major challenge in medical image analysis, where annotation demands expert knowledge and substantial inter-observer variability often leads to inconsistent or erroneous labels. Despite extensive research on learning with noisy labels (LNL), the robustness of existing methods in medical imaging has not been systematically assessed. To address this gap, we introduce LNMBench, a comprehensive benchmark for Label Noise in Medical imaging. LNMBench encompasses \textbf{10} representative methods evaluated across 7 datasets, 6 imaging modalities, and 3 noise patterns, establishing a unified and reproducible framework for robustness evaluation under realistic conditions. Comprehensive experiments reveal that the performance of existing LNL methods degrades substantially under high and real-world noise, highlighting the persistent challenges of class imbalance and domain variability in medical data. Motivated by these findings, we further propose a simple yet effective improvement to enhance model robustness under such conditions. The LNMBench codebase is publicly released to facilitate standardized evaluation, promote reproducible research, and provide practical insights for developing noise-resilient algorithms in both research and real-world medical applications.The codebase is publicly available on https://github.com/myyy777/LNMBench.

cs.CV↗

arXiv2025

A Versatile Foundation Model for AI-enabled Mammogram Interpretation

Breast cancer is the most commonly diagnosed cancer and the leading cause of cancer-related mortality in women globally. Mammography is essential for the early detection and diagnosis of breast lesions. Despite recent progress in foundation models (FMs) for mammogram analysis, their clinical translation remains constrained by several fundamental limitations, including insufficient diversity in training data, limited model generalizability, and a lack of comprehensive evaluation across clinically relevant tasks. Here, we introduce VersaMammo, a versatile foundation model for mammograms, designed to overcome these limitations. We curated the largest multi-institutional mammogram dataset to date, comprising 706,239 images from 21 sources. To improve generalization, we propose a two-stage pre-training strategy to develop VersaMammo, a mammogram foundation model. First, a teacher model is trained via self-supervised learning to extract transferable features from unlabeled mammograms. Then, supervised learning combined with knowledge distillation transfers both features and clinical knowledge into VersaMammo. To ensure a comprehensive evaluation, we established a benchmark comprising 92 specific tasks, including 68 internal tasks and 24 external validation tasks, spanning 5 major clinical task categories: lesion detection, segmentation, classification, image retrieval, and visual question answering. VersaMammo achieves state-of-the-art performance, ranking first in 50 out of 68 specific internal tasks and 20 out of 24 external validation tasks, with average ranks of 1.5 and 1.2, respectively. These results demonstrate its superior generalization and clinical utility, offering a substantial advancement toward reliable and scalable breast cancer screening and diagnosis.

cs.CV↗

arXiv2025

A Unified Low-level Foundation Model for Enhancing Pathology Image Quality

Foundation models have revolutionized computational pathology by achieving remarkable success in high-level diagnostic tasks, yet the critical challenge of low-level image enhancement remains largely unaddressed. Real-world pathology images frequently suffer from degradations such as noise, blur, and low resolution due to slide preparation artifacts, staining variability, and imaging constraints, while the reliance on physical staining introduces significant costs, delays, and inconsistency. Although existing methods target individual problems like denoising or super-resolution, their task-specific designs lack the versatility to handle the diverse low-level vision challenges encountered in practice. To bridge this gap, we propose the first unified Low-level Pathology Foundation Model (LPFM), capable of enhancing image quality in restoration tasks, including super-resolution, deblurring, and denoising, as well as facilitating image translation tasks like virtual staining (H&E and special stains), all through a single adaptable architecture. Our approach introduces a contrastive pre-trained encoder that learns transferable, stain-invariant feature representations from 190 million unlabeled pathology images, enabling robust identification of degradation patterns. A unified conditional diffusion process dynamically adapts to specific tasks via textual prompts, ensuring precise control over output quality. Trained on a curated dataset of 87,810 whole slied images (WSIs) across 34 tissue types and 5 staining protocols, LPFM demonstrates statistically significant improvements (p<0.01) over state-of-the-art methods in most tasks (56/66), achieving Peak Signal-to-Noise Ratio (PSNR) gains of 10-15% for image restoration and Structural Similarity Index Measure (SSIM) improvements of 12-18% for virtual staining.

cs.CV↗

arXiv2025

Solutions for Mitotic Figure Detection and Atypical Classification in MIDOG 2025

Deep learning has driven significant advances in mitotic figure analysis within computational pathology. In this paper, we present our approach to the Mitosis Domain Generalization (MIDOG) 2025 Challenge, which consists of two distinct tasks, i.e., mitotic figure detection and atypical mitosis classification. For the mitotic figure detection task, we propose a two-stage detection-classification framework that first localizes candidate mitotic figures and subsequently refines the predictions using a dedicated classification module. For the atypical mitosis classification task, we employ an ensemble strategy that integrates predictions from multiple state-of-the-art deep learning architectures to improve robustness and accuracy. Extensive experiments demonstrate the effectiveness of our proposed methods across both tasks.

eess.IV↗

arXiv2025

A Versatile Pathology Co-pilot via Reasoning Enhanced Multimodal Large Language Model

Multimodal large language models (MLLMs) have emerged as powerful tools for computational pathology, offering unprecedented opportunities to integrate pathological images with language context for comprehensive diagnostic analysis. These models hold particular promise for automating complex tasks that traditionally require expert interpretation of pathologists. However, current MLLM approaches in pathology demonstrate significantly constrained reasoning capabilities, primarily due to their reliance on expensive chain-of-thought annotations. Additionally, existing methods remain limited to simplex application of visual question answering (VQA) at the region-of-interest (ROI) level, failing to address the full spectrum of diagnostic needs such as ROI classification, detection, segmentation, whole-slide-image (WSI) classification and VQA in clinical practice. In this study, we present SmartPath-R1, a versatile MLLM capable of simultaneously addressing both ROI-level and WSI-level tasks while demonstrating robust pathological reasoning capability. Our framework combines scale-dependent supervised fine-tuning and task-aware reinforcement fine-tuning, which circumvents the requirement for chain-of-thought supervision by leveraging the intrinsic knowledge within MLLM. Furthermore, SmartPath-R1 integrates multiscale and multitask analysis through a mixture-of-experts mechanism, enabling dynamic processing for diverse tasks. We curate a large-scale dataset comprising 2.3M ROI samples and 188K WSI samples for training and evaluation. Extensive experiments across 72 tasks validate the effectiveness and superiority of the proposed approach. This work represents a significant step toward developing versatile, reasoning-enhanced AI systems for precision pathology.

eess.IV↗

arXiv2025

Advancing Lung Disease Diagnosis in 3D CT Scans

To enable more accurate diagnosis of lung disease in chest CT scans, we propose a straightforward yet effective model. Firstly, we analyze the characteristics of 3D CT scans and remove non-lung regions, which helps the model focus on lesion-related areas and reduces computational cost. We adopt ResNeSt50 as a strong feature extractor, and use a weighted cross-entropy loss to mitigate class imbalance, especially for the underrepresented squamous cell carcinoma category. Our model achieves a Macro F1 Score of 0.80 on the validation set of the Fair Disease Diagnosis Challenge, demonstrating its strong performance in distinguishing between different lung conditions.

eess.IV↗

arXiv2025

Multi-Source COVID-19 Detection via Variance Risk Extrapolation

We present our solution for the Multi-Source COVID-19 Detection Challenge, which aims to classify chest CT scans into COVID and Non-COVID categories across data collected from four distinct hospitals and medical centers. A major challenge in this task lies in the domain shift caused by variations in imaging protocols, scanners, and patient populations across institutions. To enhance the cross-domain generalization of our model, we incorporate Variance Risk Extrapolation (VREx) into the training process. VREx encourages the model to maintain consistent performance across multiple source domains by explicitly minimizing the variance of empirical risks across environments. This regularization strategy reduces overfitting to center-specific features and promotes learning of domain-invariant representations. We further apply Mixup data augmentation to improve generalization and robustness. Mixup interpolates both the inputs and labels of randomly selected pairs of training samples, encouraging the model to behave linearly between examples and enhancing its resilience to noise and limited data. Our method achieves an average macro F1 score of 0.96 across the four sources on the validation set, demonstrating strong generalization.

eess.IV↗

arXiv2025

Segment Anything in Pathology Images with Natural Language

Pathology image segmentation is crucial in computational pathology for analyzing histological features relevant to cancer diagnosis and prognosis. However, current methods face major challenges in clinical applications due to limited annotated data and restricted category definitions. To address these limitations, we propose PathSegmentor, the first text-prompted segmentation foundation model designed specifically for pathology images. We also introduce PathSeg, the largest and most comprehensive dataset for pathology segmentation, built from 21 public sources and containing 275k image-mask-label triples across 160 diverse categories. With PathSegmentor, users can perform semantic segmentation using natural language prompts, eliminating the need for laborious spatial inputs such as points or boxes. Extensive experiments demonstrate that PathSegmentor outperforms specialized models with higher accuracy and broader applicability, while maintaining a compact architecture. It significantly surpasses existing spatial- and text-prompted models by 0.145 and 0.429 in overall Dice scores, respectively, showing strong robustness in segmenting complex structures and generalizing to external datasets. Moreover, PathSegmentor's outputs enhance the interpretability of diagnostic models through feature importance estimation and imaging biomarker discovery, offering pathologists evidence-based support for clinical decision-making. This work advances the development of explainable AI in precision oncology.

cs.CV↗

arXiv2025

EgoExo-Gen: Ego-centric Video Prediction by Watching Exo-centric Videos

Generating videos in the first-person perspective has broad application prospects in the field of augmented reality and embodied intelligence. In this work, we explore the cross-view video prediction task, where given an exo-centric video, the first frame of the corresponding ego-centric video, and textual instructions, the goal is to generate futur frames of the ego-centric video. Inspired by the notion that hand-object interactions (HOI) in ego-centric videos represent the primary intentions and actions of the current actor, we present EgoExo-Gen that explicitly models the hand-object dynamics for cross-view video prediction. EgoExo-Gen consists of two stages. First, we design a cross-view HOI mask prediction model that anticipates the HOI masks in future ego-frames by modeling the spatio-temporal ego-exo correspondence. Next, we employ a video diffusion model to predict future ego-frames using the first ego-frame and textual instructions, while incorporating the HOI masks as structural guidance to enhance prediction quality. To facilitate training, we develop an automated pipeline to generate pseudo HOI masks for both ego- and exo-videos by exploiting vision foundation models. Extensive experiments demonstrate that our proposed EgoExo-Gen achieves better prediction performance compared to previous video prediction models on the Ego-Exo4D and H2O benchmark datasets, with the HOI masks significantly improving the generation of hands and interactive objects in the ego-centric videos.

cs.CV↗

arXiv2024

Cross-Fundus Transformer for Multi-modal Diabetic Retinopathy Grading with Cataract

Diabetic retinopathy (DR) is a leading cause of blindness worldwide and a common complication of diabetes. As two different imaging tools for DR grading, color fundus photography (CFP) and infrared fundus photography (IFP) are highly-correlated and complementary in clinical applications. To the best of our knowledge, this is the first study that explores a novel multi-modal deep learning framework to fuse the information from CFP and IFP towards more accurate DR grading. Specifically, we construct a dual-stream architecture Cross-Fundus Transformer (CFT) to fuse the ViT-based features of two fundus image modalities. In particular, a meticulously engineered Cross-Fundus Attention (CFA) module is introduced to capture the correspondence between CFP and IFP images. Moreover, we adopt both the single-modality and multi-modality supervisions to maximize the overall performance for DR grading. Extensive experiments on a clinical dataset consisting of 1,713 pairs of multi-modal fundus images demonstrate the superiority of our proposed method. Our code will be released for public access.

eess.IV↗

arXiv2024

Concept Complement Bottleneck Model for Interpretable Medical Image Diagnosis

Models based on human-understandable concepts have received extensive attention to improve model interpretability for trustworthy artificial intelligence in the field of medical image analysis. These methods can provide convincing explanations for model decisions but heavily rely on the detailed annotation of pre-defined concepts. Consequently, they may not be effective in cases where concepts or annotations are incomplete or low-quality. Although some methods automatically discover effective and new visual concepts rather than using pre-defined concepts or could find some human-understandable concepts via large Language models, they are prone to veering away from medical diagnostic evidence and are challenging to understand. In this paper, we propose a concept complement bottleneck model for interpretable medical image diagnosis with the aim of complementing the existing concept set and finding new concepts bridging the gap between explainable models. Specifically, we propose to use concept adapters for specific concepts to mine the concept differences and score concepts in their own attention channels to support almost fairly concept learning. Then, we devise a concept complement strategy to learn new concepts while jointly using known concepts to improve model performance. Comprehensive experiments on medical datasets demonstrate that our model outperforms the state-of-the-art competitors in concept detection and disease diagnosis tasks while providing diverse explanations to ensure model interpretability effectively.

cs.CV↗