Hongxiao Wang

Ye Zhang, Yu Zhou, Jingwen Qi et al.

Deep learning based automated pathological diagnosis has markedly improved diagnostic efficiency and reduced variability between observers, yet its clinical adoption remains limited by opaque model decisions and a lack of traceable rationale. To address this, recent multimodal visual reasoning architectures provide a unified framework that generates segmentation masks at the pixel level alongside semantically aligned textual explanations. By localizing lesion regions and producing expert style diagnostic narratives, these models deliver the transparent and interpretable insights necessary for dependable AI assisted pathology. Building on these advancements, we propose PathMR, a cell-level Multimodal visual Reasoning framework for Pathological image analysis. Given a pathological image and a textual query, PathMR generates expert-level diagnostic explanations while simultaneously predicting cell distribution patterns. To benchmark its performance, we evaluated our approach on the publicly available PathGen dataset as well as on our newly developed GADVR dataset. Extensive experiments on these two datasets demonstrate that PathMR consistently outperforms state-of-the-art visual reasoning methods in text generation quality, segmentation accuracy, and cross-modal alignment. These results highlight the potential of PathMR for improving interpretability in AI-driven pathological diagnosis. The code will be publicly available in https://github.com/zhangye-zoe/PathMR.

Kewen Cao, Jianxu Chen, Yongbing Zhang et al.

Automated pathology image analysis is central to clinical diagnosis, but clinicians still ask which slide features drive a model's decision and why. Vision-language models can produce natural language explanations, but these are often correlational and lack verifiable evidence. In this paper, we introduce an SQL-centered agentic framework that enables both feature measurement and reasoning to be auditable. Specifically, after extracting human-interpretable cellular features, Feature Reasoning Agents compose and execute SQL queries over feature tables to aggregate visual evidence into quantitative findings. A Knowledge Comparison Agent then evaluates these findings against established pathological knowledge, mirroring how pathologists justify diagnoses from measurable observations. Extensive experiments evaluated on two pathology visual question answering datasets demonstrate our method improves interpretability and decision traceability while producing executable SQL traces that link cellular measurements to diagnostic conclusions.

Pengfei Gu, Hongxiao Wang, Yejia Zhang et al.

Topological structures in image data, such as connected components and loops, play a crucial role in understanding image content (e.g., biomedical objects). % Despite remarkable successes of numerous image processing methods that rely on appearance information, these methods often lack sensitivity to topological structures when used in general deep learning (DL) frameworks. % In this paper, we introduce a new general approach, called TopoImages (for Topology Images), which computes a new representation of input images by encoding local topology of patches. % In TopoImages, we leverage persistent homology (PH) to encode geometric and topological features inherent in image patches. % Our main objective is to capture topological information in local patches of an input image into a vectorized form. % Specifically, we first compute persistence diagrams (PDs) of the patches, % and then vectorize and arrange these PDs into long vectors for pixels of the patches. % The resulting multi-channel image-form representation is called a TopoImage. % TopoImages offers a new perspective for data analysis. % To garner diverse and significant topological features in image data and ensure a more comprehensive and enriched representation, we further generate multiple TopoImages of the input image using various filtration functions, which we call multi-view TopoImages. % The multi-view TopoImages are fused with the input image for DL-based classification, with considerable improvement. % Our TopoImages approach is highly versatile and can be seamlessly integrated into common DL frameworks. Experiments on three public medical image classification datasets demonstrate noticeably improved accuracy over state-of-the-art methods.

Kaiyue Zhou, Zelong Tan, Hongxiao Wang et al.

Recovering point clouds involves the sequential process of sampling and restoration, yet existing methods struggle to effectively leverage both topological and geometric attributes. To address this, we propose an end-to-end architecture named \textbf{TopGeoFormer}, which maintains these critical properties throughout the sampling and restoration phases. First, we revisit traditional feature extraction techniques to yield topological embedding using a continuous mapping of relative relationships between neighboring points, and integrate it in both phases for preserving the structure of the original space. Second, we propose the \textbf{InterTwining Attention} to fully merge topological and geometric embeddings, which queries shape with local awareness in both phases to form a learnable 3D shape context facilitated with point-wise, point-shape-wise, and intra-shape features. Third, we introduce a full geometry loss and a topological constraint loss to optimize the embeddings in both Euclidean and topological spaces. The geometry loss uses inconsistent matching between coarse-to-fine generations and targets for reconstructing better geometric details, and the constraint loss limits embedding variances for better approximation of the topological space. In experiments, we comprehensively analyze the circumstances using the conventional and learning-based sampling/upsampling/recovery algorithms. The quantitative and qualitative results demonstrate that our method significantly outperforms existing sampling and recovery methods.

Xiuzhen Guo, Lianyuan Yu, Ji Shi et al.

Semi-supervised learning utilizes insights from unlabeled data to improve model generalization, thereby reducing reliance on large labeled datasets. Most existing studies focus on limited samples and fail to capture the overall data distribution. We contend that combining distributional information with detailed information is crucial for achieving more robust and accurate segmentation results. On the one hand, with its robust generative capabilities, diffusion models (DM) learn data distribution effectively. However, it struggles with fine detail capture, leading to generated images with misleading details. Combining DM with convolutional neural networks (CNNs) enables the former to learn data distribution while the latter corrects fine details. While capturing complete high-frequency details by CNNs requires substantial computational resources and is susceptible to local noise. On the other hand, given that both labeled and unlabeled data come from the same distribution, we believe that regions in unlabeled data similar to overall class semantics to labeled data are likely to belong to the same class, while regions with minimal similarity are less likely to. This work introduces a semi-supervised medical image segmentation framework from the distribution perspective (Diff-CL). Firstly, we propose a cross-pseudo-supervision learning mechanism between diffusion and convolution segmentation networks. Secondly, we design a high-frequency mamba module to capture boundary and detail information globally. Finally, we apply contrastive learning for label propagation from labeled to unlabeled data. Our method achieves state-of-the-art (SOTA) performance across three datasets, including left atrium, brain tumor, and NIH pancreas datasets.

Lianyuan Yu, Xiuzhen Guo, Ji Shi et al.

Semi-supervised learning enhances medical image segmentation by leveraging unlabeled data, reducing reliance on extensive labeled datasets. On the one hand, the distribution discrepancy between limited labeled data and abundant unlabeled data can hinder model generalization. Most existing methods rely on local similarity matching, which may introduce bias. In contrast, Mamba effectively models global context with linear complexity, learning more comprehensive data representations. On the other hand, medical images usually exhibit consistent anatomical structures defined by geometric features. Most existing methods fail to fully utilize global geometric priors, such as volumes, moments etc. In this work, we introduce a global information interaction and geometric priors focus framework (GIGP). Firstly, we present a Global Information Interaction Mamba module to reduce distribution discrepancy between labeled and unlabeled data. Secondly, we propose a Geometric Moment Attention Mechanism to extract richer global geometric features. Finally, we propose Global Geometric Perturbation Consistency to simulate organ dynamics and geometric variations, enhancing the ability of the model to learn generalized features. The superior performance on the NIH Pancreas and Left Atrium datasets demonstrates the effectiveness of our approach.

Pengfei Gu, Zihan Zhao, Hongxiao Wang et al.

The Segment Anything Model (SAM) exhibits impressive capabilities in zero-shot segmentation for natural images. Recently, SAM has gained a great deal of attention for its applications in medical image segmentation. However, to our best knowledge, no studies have shown how to harness the power of SAM for medical image classification. To fill this gap and make SAM a true ``foundation model'' for medical image analysis, it is highly desirable to customize SAM specifically for medical image classification. In this paper, we introduce SAMAug-C, an innovative augmentation method based on SAM for augmenting classification datasets by generating variants of the original images. The augmented datasets can be used to train a deep learning classification model, thereby boosting the classification performance. Furthermore, we propose a novel framework that simultaneously processes raw and SAMAug-C augmented image input, capitalizing on the complementary information that is offered by both. Experiments on three public datasets validate the effectiveness of our new approach.

Hongxiao Wang, Hao Zheng, Jianxu Chen et al.

Automatic histopathology image segmentation is crucial to disease analysis. Limited available labeled data hinders the generalizability of trained models under the fully supervised setting. Semi-supervised learning (SSL) based on generative methods has been proven to be effective in utilizing diverse image characteristics. However, it has not been well explored what kinds of generated images would be more useful for model training and how to use such images. In this paper, we propose a new data guided generative method for histopathology image segmentation by leveraging the unlabeled data distributions. First, we design an image generation module. Image content and style are disentangled and embedded in a clustering-friendly space to utilize their distributions. New images are synthesized by sampling and cross-combining contents and styles. Second, we devise an effective data selection policy for judiciously sampling the generated images: (1) to make the generated training set better cover the dataset, the clusters that are underrepresented in the original training set are covered more; (2) to make the training process more effective, we identify and oversample the images of "hard cases" in the data for which annotated training data may be scarce. Our method is evaluated on glands and nuclei datasets. We show that under both the inductive and transductive settings, our SSL method consistently boosts the performance of common segmentation models and attains state-of-the-art results.