Minxi Ouyang

Xitong Ling, Minxi Ouyang, Yizhi Wang et al. · tsinghua

Histopathology analysis is the gold standard for medical diagnosis. Accurate classification of whole slide images (WSIs) and region-of-interests (ROIs) localization can assist pathologists in diagnosis. The gigapixel resolution of WSI and the absence of fine-grained annotations make direct classification and analysis challenging. In weakly supervised learning, multiple instance learning (MIL) presents a promising approach for WSI classification. The prevailing strategy is to use attention mechanisms to measure instance importance for classification. However, attention mechanisms fail to capture inter-instance information, and self-attention causes quadratic computational complexity. To address these challenges, we propose AMD-MIL, an agent aggregator with a mask denoise mechanism. The agent token acts as an intermediate variable between the query and key for computing instance importance. Mask and denoising matrices, mapped from agents-aggregated value, dynamically mask low-contribution representations and eliminate noise. AMD-MIL achieves better attention allocation by adjusting feature representations, capturing micro-metastases in cancer, and improving interpretability. Extensive experiments on CAMELYON-16, CAMELYON-17, TCGA-KIDNEY, and TCGA-LUNG show AMD-MIL's superiority over state-of-the-art methods.

Minxi Ouyang, Lianghui Zhu, Yaqing Bao et al.

Multimodal large models have shown great potential in automating pathology image analysis. However, current multimodal models for gastrointestinal pathology are constrained by both data quality and reasoning transparency: pervasive noise and incomplete annotations in public datasets predispose vision language models to factual hallucinations when generating diagnostic text, while the absence of explicit intermediate reasoning chains renders the outputs difficult to audit and thus less trustworthy in clinical practice. To address these issues, we construct a large scale gastrointestinal pathology dataset containing both microscopic descriptions and diagnostic conclusions, and propose a prompt argumentation strategy that incorporates lesion classification and anatomical site information. This design guides the model to better capture image specific features and maintain semantic consistency in generation. Furthermore, we employ a post training pipeline that combines supervised fine tuning with Group Relative Policy Optimization (GRPO) to improve reasoning quality and output structure. Experimental results on real world pathology report generation tasks demonstrate that our approach significantly outperforms state of the art open source and proprietary baselines in terms of generation quality, structural completeness, and clinical relevance. Our solution outperforms state of the art models with 18.7% higher clinical relevance, 32.4% improved structural completeness, and 41.2% fewer diagnostic errors, demonstrating superior accuracy and clinical utility compared to existing solutions.

Xinyi Guo, Mingyi He, Haobin Ding et al.

Implicit neural representations (INRs) encode images as neural-network weights, making image classification a problem of weight-space classifiability. A natural geometric hypothesis is that classifier feedback should make image-specific weights cluster by class in the shared-anchor coordinate. We test this hypothesis in the SIREN-based Meta Weight Transformer (MWT) regime, where end-to-end training meta-learns a shared initialization and inner-loop update schedule for fitting image-specific SIRENs. We find that this prediction fails. Exposed weight-space geometry and supervised clustering pressure do not reliably track trained-reader accuracy; clustering can even make local neighborhoods more class-consistent while making the trained reader worse. Crucially, the reader constructs rather than inherits class-aligned geometry: token-flow diagnostics show that class-aligned neighborhoods become strongly predictive of trained-reader accuracy only after late reader interactions, not in the input coordinate. We further identify the native SIREN bias column in the augmented weight token as a low-dimensional, sample-dependent causal readout route for the trained reader; targeted controls rule out generic scalar-column and marginal-distribution artifacts. The diagnosis motivates interventions that strengthen reader routing, add an explicit bias route, or use denser inner-loop fitting; under the lane-specific training conventions used here, route-directed variants often outperform the shared-anchor baseline but interact non-additively. Task-induced INR weights are classifiable not because they form raw geometric clusters, but because their class signal is routed through the reader.

Weiming Chen, Xitong Ling, Xidong Wang et al.

Pathology foundation models (PFMs) have rapidly advanced and are becoming a common backbone for downstream clinical tasks, offering strong transferability across tissues and institutions. However, for dense prediction (e.g., segmentation), practical deployment still lacks a clear, reproducible understanding of how different PFMs behave across datasets and how adaptation choices affect performance and stability. We present PFM-DenseBench, a large-scale benchmark for dense pathology prediction, evaluating 17 PFMs across 18 public segmentation datasets. Under a unified protocol, we systematically assess PFMs with multiple adaptation and fine-tuning strategies, and derive insightful, practice-oriented findings on when and why different PFMs and tuning choices succeed or fail across heterogeneous datasets. We release containers, configs, and dataset cards to enable reproducible evaluation and informed PFM selection for real-world dense pathology tasks. Project Website: https://m4a1tastegood.github.io/PFM-DenseBench

Lianghui Zhu, Xitong Ling, Minxi Ouyang et al.

Gastrointestinal (GI) diseases represent a clinically significant burden, necessitating precise diagnostic approaches to optimize patient outcomes. Conventional histopathological diagnosis suffers from limited reproducibility and diagnostic variability. To overcome these limitations, we develop Digepath, a specialized foundation model for GI pathology. Our framework introduces a dual-phase iterative optimization strategy combining pretraining with fine-screening, specifically designed to address the detection of sparsely distributed lesion areas in whole-slide images. Digepath is pretrained on over 353 million multi-scale images from 210,043 H&E-stained slides of GI diseases. It attains state-of-the-art performance on 33 out of 34 tasks related to GI pathology, including pathological diagnosis, protein expression status prediction, gene mutation prediction, and prognosis evaluation. We further translate the intelligent screening module for early GI cancer and achieve near-perfect 99.70% sensitivity across nine independent medical institutions. This work not only advances AI-driven precision pathology for GI diseases but also bridge critical gaps in histopathological practice.

Xitong Ling, Yifeng Ping, Jiawen Li et al.

Multiple Instance Learning (MIL) plays a significant role in computational pathology, enabling weakly supervised analysis of Whole Slide Image (WSI) datasets. The field of WSI analysis is confronted with a severe long-tailed distribution problem, which significantly impacts the performance of classifiers. Long-tailed distributions lead to class imbalance, where some classes have sparse samples while others are abundant, making it difficult for classifiers to accurately identify minority class samples. To address this issue, we propose an ensemble learning method based on MIL, which employs expert decoders with shared aggregators and consistency constraints to learn diverse distributions and reduce the impact of class imbalance on classifier performance. Moreover, we introduce a multimodal distillation framework that leverages text encoders pre-trained on pathology-text pairs to distill knowledge and guide the MIL aggregator in capturing stronger semantic features relevant to class information. To ensure flexibility, we use learnable prompts to guide the distillation process of the pre-trained text encoder, avoiding limitations imposed by specific prompts. Our method, MDE-MIL, integrates multiple expert branches focusing on specific data distributions to address long-tailed issues. Consistency control ensures generalization across classes. Multimodal distillation enhances feature extraction. Experiments on Camelyon+-LT and PANDA-LT datasets show it outperforms state-of-the-art methods.

Jiawen Li, Jiali Hu, Qiehe Sun et al. · tsinghua

The emergence of foundation models in computational pathology has transformed histopathological image analysis, with whole slide imaging (WSI) diagnosis being a core application. Traditionally, weakly supervised fine-tuning via multiple instance learning (MIL) has been the primary method for adapting foundation models to WSIs. However, in this work we present a key experimental finding: a simple nonlinear mapping strategy combining mean pooling and a multilayer perceptron, called SiMLP, can effectively adapt patch-level foundation models to slide-level tasks without complex MIL-based learning. Through extensive experiments across diverse downstream tasks, we demonstrate the superior performance of SiMLP with state-of-the-art methods. For instance, on a large-scale pan-cancer classification task, SiMLP surpasses popular MIL-based methods by 3.52%. Furthermore, SiMLP shows strong learning ability in few-shot classification and remaining highly competitive with slide-level foundation models pretrained on tens of thousands of slides. Finally, SiMLP exhibits remarkable robustness and transferability in lung cancer subtyping. Overall, our findings challenge the conventional MIL-based fine-tuning paradigm, demonstrating that a task-agnostic representation strategy alone can effectively adapt foundation models to WSI analysis. These insights offer a unique and meaningful perspective for future research in digital pathology, paving the way for more efficient and broadly applicable methodologies.