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Publications

Research across pathology foundation models, image analysis and clinical applications.

Selected venues: Nature Machine Intelligence · IEEE TMI · NeurIPS · CVPR · ICLR

Selected team research and external clinical references.

Featured Research

Highlighted Publications

Selected peer-reviewed research from our team and collaborators.

Clinical research using D-PathAI

Two peer-reviewed breast cancer studies: what was assessed, how the software was used, and where the findings apply.

Journal article Westlake coauthored

HER2-LADDER: response prediction in HER2-positive breast cancer

Wu et al. · Signal Transduction and Targeted Therapy 11, 241 (2026)

Published 19 June 2026

Pretreatment H&E and HER2 IHC biopsy slides plus clinical variables informed a research score for pathological complete response after neoadjuvant dual HER2-targeted therapy.

Study design & Limitations
Study design
Model development in 276 cases at Fudan University Shanghai Cancer Center, with temporal (82), trial-based (85), and Chongqing external (40) validation cohorts.
D-PathAI’s role
A customized D-PathAI pipeline characterized tumor-cell HER2 membrane staining intensity and completeness. HoVer-Net analyzed H&E images; a separate research framework combined the features.
Limitations
Retrospective analyses may introduce selection bias. The authors call for prospective validation and staining/scanning standardization before wider clinical use.
Journal article External clinical research

HER2 scoring: reader agreement and remaining limits

Dong et al. · npj Breast Cancer 12, 9 (2026)

First published 9 December 2025; version of record 12 January 2026

HER2 IHC sections and score assignments were assessed for staining reproducibility and agreement between readers and consensus scores.

Study design & Limitations
Study design
Three components: 1,455 retrospective cases at the First Affiliated Hospital of China Medical University; a 45-laboratory staining assessment; and a separate 209-slide manual/AI comparison.
D-PathAI’s role
D-PathAI assisted HER2 IHC interpretation in the 209-slide comparison; AI-assisted readings showed higher agreement in that dataset.
Limitations
Cell-detection errors and nonspecific staining persisted. Ultralow/null separation remained unreliable in this study, and manual verification was still required.

These summaries describe the published research workflows. They do not establish performance for every current module, scanner, or deployment; product configuration and intended use require a separate evaluation.

Publication library

Browse the collection by topic, or search by title, author and venue.

Foundation Models

Large multimodal and generative pathology models that unify patch, report, and whole-slide understanding.

NeurIPS

CPathAgent: An Agent-based Foundation Model for Interpretable High-Resolution Pathology Image Analysis Mimicking Pathologists' Diagnostic Logic

Conference paper Westlake coauthored

Sun, Y., Si, Y., Zhu, C., Zhang, K., Shui, Z., Ding, B., Lin, T., Yang, L. · NeurIPS 2025 · 2025

NeurIPS

PathVQ: Reforming Computational Pathology Foundation Model for Whole Slide Image Analysis via Vector Quantization

Conference paper Westlake coauthored

Li, H., Shui, Z., Zhang, Y., Zhu, C., Yang, L. · NeurIPS 2025 · 2025

TMI

ToPoFM: Topology-Guided Pathology Foundation Model for High-Resolution Pathology Image Synthesis with Cellular-Level Control

Li, J., Zhu, C., Zheng, S., Chen, P., Sun, Y., Li, H., Yang, L. · IEEE Trans. Medical Imaging · 2025

CVPR

CPath-Omni: A Unified Multimodal Foundation Model for Patch and Whole Slide Image Analysis in Computational Pathology

Sun, Y., Si, Y., Zhu, C., Gong, X., Zhang, K., Chen, P., Zhang, Y., Shui, Z., Lin, T., Yang, L. · CVPR 2025 (CCF-A) · 2025

ICLR

PathGen-1.6M: 1.6 Million Pathology Image-text Pairs Generation through Multi-agent Collaboration

Sun, Y., Zhang, Y., Si, Y., Zhu, C., Zhang, K., Shui, Z., Li, J., Gong, X., Lyu, X., Lin, T., Yang, L. · ICLR 2025 (Oral) · 2025

AAAI

PathAsst: A Generative Foundation AI Assistant towards Artificial General Intelligence of Pathology

Sun, Y., Zhu, C., Zheng, S., Zhang, K., Sun, L., Shui, Z., Zhang, Y., Li, H., Yang, L. · AAAI 2024 (CCF-A, Oral) · 2024

ECCV

WSI-VQA: Interpreting Whole Slide Images by Generative Visual Question Answering

Chen, P., Zhu, C., Zheng, S., Li, H., Yang, L. · ECCV 2024 (CCF-A) · 2024

ACM MM

PathUp: Patch-wise Timestep Tracking for Multi-class Large Pathology Image Synthesising Diffusion Model

Li, J., Zheng, S., Zhu, C., Sun, Y., Chen, P., Shui, Z., Zhang, Y., Li, H., Yang, L. · ACM MM 2024 (CCF-A, Oral) · 2024

MICCAI

WSICaption: Multiple Instance Generation of Pathology Reports for Gigapixel Whole-Slide Images

Chen, P., Li, H., Zhu, C., Zheng, S., Shui, Z., Yang, L. · MICCAI 2024 (CCF-B, Oral) · 2024

Applications

Task-specific pathology AI methods, team collaborations, and selected external clinical references.

STTT

Spatially interpretable artificial intelligence framework to tailored neoadjuvant dual HER2 blockade in HER2-positive breast cancer

Journal article Westlake coauthored Clinical Focus HER2 D-PathAI Neoadjuvant

Wu, X.-R., Lv, H., Zhao, S., Zeng, X.-H., Dai, L.-J., Xu, Y.-Z., Li, Y.-W., Qiu, Z.-Y., Huang, J.-T., Zhang, N.-N., Chen, L., He, M., Zhao, Y.-Z., Yang, L., Zhou, T., Li, J.-J., Wu, J., Jiang, Y.-Z., Yang, W.-T., Di, G.-H., Shao, Z.-M., Ma, D. · Signal Transduction and Targeted Therapy · 2026

npj Breast

HER2-low and ultralow expression of invasive breast carcinoma: clinicopathological features and immunohistochemical consistency analysis

Journal article External clinical research Uses D-PathAI Clinical Focus HER2 IHC AI-Assisted Scoring

Dong, Y.-h., Xu, Y.-t., Jiang, X.-z., Xu, L., Yu, R.-j., Wang, R., Zhang, Q.-f. · npj Breast Cancer · 2026

USCAP

Differentiation Between HER2 Ultra-Low and HER2 Null Breast Cancers Using an AI Support Tool: A Multi-Site Study

Conference abstract External clinical reference Clinical Focus HER2-Ultralow IHC Multi-Site Study

Grinwald, M., Schnitt, S., Vincent-Salomon, A., et al. · USCAP 2025 · Abstract 156 · 2025

USCAP

Artificial Intelligence Assisted Assessment of HER2-ultralow and HER2-low Immunohistochemical Scoring in Breast Cancer Core Needle Biopsy Specimens

Conference abstract External clinical reference Clinical Focus HER2 IHC Core Needle Biopsy

Li, M., Cai, M., Lv, H., Zhou, S., Lin, M., Shui, R., Yang, W. · USCAP 2024 · Abstract 178 · 2024

SABCS

The Advantage of Artificial-Intelligence in HER2 IHC 0 and 1+ Scoring in Breast Cancer

Poster abstract Westlake coauthored Clinical Focus HER2 IHC AI Scoring

Li, M., Lv, H., Zhao, Y., Zhu, C., Li, H., Lin, M., Yang, W. · SABCS 2023 · Cancer Research 84(9 Suppl.), PO4-26-09 · 2024

AAAI

Towards Effective and Efficient Context-aware Nucleus Detection in Histopathology Whole Slide Images

Conference paper Westlake coauthored

Shui, Z., Li, H., Zhang, Y., Sun, Y., Ye, Y., Chen, P., Guo, R., Cui, L., Zhu, C., Yang, L. · AAAI 2026 · 2026

PLOS One

Weakly supervised deep multi-instance learning for classification of endometrial lesions on hematoxylin and eosin-stained whole-slide images

Journal article Westlake coauthored

Zhou, Z., Guo, J., Du, X., Li, H., Xie, N., Liu, C., He, H., Yang, L., Cui, L., Fu, C. · PLOS One · 2026

MICCAI

AEM: Attention Entropy Maximization for Multiple Instance Learning based Whole Slide Image Classification

Conference paper Westlake coauthored

Zhang, Y., Li, H., Sun, Y., Shui, Z., Li, J., Zhu, C., Yang, L. · MICCAI 2025 · 2025

Allergy

Artificial Intelligence-Based Pathological Subtype Diagnosis of Nasal Polyps: A Multidimensional and Micro-Visualization Study

Clinical Focus Nasal Polyp

Luo, X., Li, H., Chen, J., Zhou, Z., Zhou, L., Luo, R., ..., Cui, L., Yang, L., Yang, Q. · Allergy · 2026

ICASSP

Stable Test-Time Training for Semantic Segmentation with Output Contrastive Loss

Zhang, Y., Shui, Z., Li, H., Sun, Y., Zhu, C., Yang, L. · ICASSP 2025 (CCF-B) · 2025

Cancer Cell

Spatial determinants of antibody-drug conjugate SHR-A1811 efficacy in neoadjuvant treatment for HER2-positive breast cancer

Clinical Focus HER2 Neoadjuvant

Ma, D., Dai, L.-J., Wu, X.-R., Liu, C.-L., Zhao, S., Zhang, H., Chen, L., Xiao, Y., Li, M., Zhao, Y.-Z., ... · Cancer Cell · 2025

ECCV

Attention-Challenging Multiple Instance Learning for Whole Slide Image Classification

Zhang, Y., Li, H., Sun, Y., Zheng, S., Zhu, C., Yang, L. · ECCV 2024 (CCF-A) · 2024

ECCV

Unleashing the Power of Prompt-Driven Nucleus Instance Segmentation

Shui, Z., Zhang, Y., Yao, K., Zhu, C., Zheng, S., Li, J., Li, H., Sun, Y., Guo, R., Yang, L. · ECCV 2024 (CCF-A) · 2024

NeurIPS

Rethinking Transformer for Long Contextual Histopathology Whole Slide Image Analysis

Li, H., Zhang, Y., Chen, P., Shui, Z., Zhu, C., Yang, L. · NeurIPS 2024 (CCF-A) · 2024

AAAI

DPA-P2PNet: Deformable Proposal-Aware P2PNet for Accurate Point-Based Cell Detection

Shui, Z., Zheng, S., Zhu, C., Zhang, S., Yu, X., Li, H., Li, J., Chen, P., Yang, L. · AAAI 2024 (CCF-A) · 2024

Neural Net.

Gradient-Aware Learning for Joint Biases: Label Noise and Class Imbalance

Zhang, S., Zhu, C., Li, H., Cai, J., Yang, L. · Neural Networks · 2024

CSBJ

Performance of a HER2 Testing Algorithm Tailored for Urothelial Bladder Cancer: A Bi-centre Study

Clinical Focus HER2 IHC

Huang, A., Zhao, Y., Guan, F., Zhang, H., ... · Computational and Structural Biotechnology Journal · 2024

ICME

Context-Aware Text-Assisted Multimodal Framework for Cervical Cytology Cell Diagnosis and Chatting

Clinical Focus TCT Cervical Cytology

Sun, Y., Zhu, C., Zheng, S., Zhang, Y., Li, H., Yang, L. · ICME 2024 (CCF-B) · 2024

ICASSP

HLS-FGVC: Hierarchical Label Semantics Enhanced Fine-Grained Visual Classification

Zhang, S., Zheng, S., Shui, Z., Yang, L. · ICASSP 2024 (CCF-B) · 2024

BIBM

Multi-modal Learning with Missing Modality in Predicting Axillary Lymph Node Metastasis

Zhang, S., Zheng, S., Shui, Z., Li, H., Yang, L. · BIBM 2023 (CCF-B) · 2023

CVPR

Task-specific Fine-tuning via Variational Information Bottleneck for Weakly-supervised Pathology WSI Classification

Li, H., Zhu, C., Zhang, Y., Sun, Y., Shui, Z., Kuang, W., Zheng, S., Yang, L. · CVPR 2023 (CCF-A) · 2023

MICCAI

Segment Membranes and Nuclei from Histopathological Images via Nuclei Point-Level Supervision

Clinical Focus IHC Membrane Segmentation

Li, H., Xu, Z., Zhou, M., Shi, X., Kang, Y., Bu, Q., Lv, H., Li, M., Lin, M., Cui, L., Feng, J., Yang, W., Yang, L. · MICCAI 2023 (CCF-B) · 2023

TMI

Masked Conditional Variational Autoencoders for Chromosome Straightening

Li, J., Zheng, S., Shui, Z., Zhang, S., Yang, L., Sun, Y., Zhang, Y., Li, H., ... · IEEE Trans. Medical Imaging · 2023

MICCAI

Exploring Unsupervised Cell Recognition with Prior Self-Activation Maps

Chen, P., Zhu, C., Shui, Z., Cai, J., Zheng, S., Zhang, S., Yang, L. · MICCAI 2023 (CCF-B) · 2023

MICCAI

End-to-End Cell Recognition by Point Annotation

Shui, Z., Zhang, S., Zhu, C., Wang, B., Chen, P., Zheng, S., Yang, L. · MICCAI 2022 (CCF-B) · 2022

MICCAI

ChrsNet: Chromosome Straightening Using Self-Attention Guided Networks

Zheng, S., Li, J., Shui, Z., Zhu, C., Zhang, Y., Chen, P., Yang, L. · MICCAI 2022 (CCF-B) · 2022

ISBI

Weakly Supervised Learning for Cell Recognition in Immunohistochemical Cytoplasm Staining Images

Clinical Focus IHC

Zhang, S., Zhu, C., Li, H., Cai, J., Yang, L. · ISBI 2022 · 2022

ISBI

Category Separation For Weakly Supervised Multi-Class Cell Counting

Cai, J., Zhu, C., Chen, P., Zhang, S., Li, H., Sun, Y., Yang, L. · ISBI 2022 · 2022

ISBI

Weakly Supervised Classification Using Multi-Level Instance-Aware Optimization on Cervical Cytologic Image

Clinical Focus TCT

Zhu, C., Sun, Y., Li, H., Cui, C., Zhang, S., Cai, J., Ling, Y. · ISBI 2022 · 2022

MICCAI

Generalizing Nucleus Recognition Model in Multi-Source Ki67 Immunohistochemistry Stained Images via Domain-Specific Pruning

Clinical Focus IHC Ki67

Cai, J., Zhu, C., Cui, C., Li, H., Wu, T., Zhang, S., Yang, L. · MICCAI 2021 (CCF-B) · 2021

J. Transl. Med.

Automated Tumor Proportion Scoring for PD-L1 Expression Based on Multistage Ensemble Strategy in NSCLC

Clinical Focus PD-L1 IHC

Pan, B., Kang, Y., Jin, Y., Yang, L., Zheng, Y., Cui, L., Sun, J., Feng, J., Li, Y., Guo, L., Liang, Z. · J. Translational Medicine · 2021

AI Med.

Rule-based automatic diagnosis of thyroid nodules from intraoperative frozen sections using deep learning

Clinical Focus Frozen Section Thyroid

Li, Y., Chen, P., Li, Z., Su, H., Yang, L., Zhong, D. · Artificial Intelligence in Medicine · 2020

Nature Mach. Intell.

Pathologist-level Interpretable Whole-slide Cancer Diagnosis with Deep Learning

Zhang, Z., Chen, P., McGough, M., ..., Cui, L., ..., Yang, L. · Nature Machine Intelligence · 2019

Benchmark

Evaluation suites and robustness studies that measure pathology AI performance across patch and whole-slide settings.

TMI

PathBench: Advancing the Benchmark of Large Multimodal Models for Pathology Image Understanding at Patch and Whole Slide Level

Sun, Y., Wu, H., Zhu, C., Si, Y., Chen, Q., Zhang, Y., Zhang, K., Li, J., Cai, J., Wang, Y., ... · IEEE Trans. Medical Imaging · 2025

ECCV

PathMMU: A Massive Multimodal Expert-Level Benchmark for Understanding and Reasoning in Pathology

Sun, Y., Wu, H., Zhu, C., Zheng, S., Chen, Q., Zhang, K., Zhang, Y., Wan, D., Lan, X., ... · ECCV 2024 (CCF-A, Oral) · 2024

JIIM

Benchmarking PathCLIP for Pathology Image Analysis

Zheng, S., Cui, X., Sun, Y., Li, J., Li, H., Zhang, Y., Chen, P., Jing, X., Ye, Z., Yang, L. · J. Imaging Informatics in Medicine · 2024

ICASSP

Assessing the Robustness of Deep Learning-Assisted Pathological Image Analysis Under Practical Variables of Imaging System

Sun, Y., Zhu, C., Zhang, Y., Li, H., Chen, P., Yang, L. · ICASSP 2023 (CCF-B) · 2023

MICCAI

Benchmarking the Robustness of Deep Neural Networks to Common Corruptions in Digital Pathology

Zhang, Y., Sun, Y., Li, H., Zheng, S., Zhu, C., Yang, L. · MICCAI 2022 (CCF-B) · 2022

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