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Kunming Tang

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JBHI Journal 2025 Journal Article

Partial-Label Contrastive Representation Learning for Fine-Grained Biomarkers Prediction From Histopathology Whole Slide Images

  • Yushan Zheng
  • Kun Wu
  • Jun Li
  • Kunming Tang
  • Jun Shi
  • Haibo Wu
  • Zhiguo Jiang
  • Wei Wang

In the domain of histopathology analysis, existing representation learning methods for biomarkers prediction from whole slide images (WSIs) face challenges due to the complexity of tissue subtypes and label noise problems. This paper proposed a novel partial-label contrastive representation learning approach to enhance the discrimination of histopathology image representations for fine-grained biomarkers prediction. We designed a partial-label contrastive clustering (PLCC) module for partial-label disambiguation and a dynamic clustering algorithm to sample the most representative features of each category to the clustering queue during the contrastive learning process. We conducted comprehensive experiments on three gene mutation prediction datasets, including USTC-EGFR, BRCA-HER2, and TCGA-EGFR. The results show that our method outperforms 9 existing methods in terms of Accuracy, AUC, and F1 Score. Specifically, our method achieved an AUC of 0. 950 in EGFR mutation subtyping of TCGA-EGFR and an AUC of 0. 853 in HER2 0/1+/2+/3+ grading of BRCA-HER2, which demonstrates its superiority in fine-grained biomarkers prediction from histopathology whole slide images.

AAAI Conference 2025 Conference Paper

Promptable Representation Distribution Learning and Data Augmentation for Gigapixel Histopathology WSI Analysis

  • Kunming Tang
  • Zhiguo Jiang
  • Jun Shi
  • Wei Wang
  • Haibo Wu
  • Yushan Zheng

Gigapixel image analysis, particularly for whole slide images (WSIs), often relies on multiple instance learning (MIL). Under the paradigm of MIL, patch image representations are extracted and then fixed during the training of the MIL classifiers for efficiency consideration. However, the invariance of representations makes it difficult to perform data augmentation for WSI-level model training, which significantly limits the performance of the downstream WSI analysis. The current data augmentation methods for gigapixel images either introduce additional computational costs or result in a loss of semantic information, which is hard to meet the requirements for efficiency and stability needed for WSI model training. In this paper, we propose a Promptable Representation Distribution Learning framework (PRDL) for both patch-level representation learning and WSI-level data augmentation. Meanwhile, we explore the use of prompts to guide data augmentation in feature space, which achieves promptable data augmentation for training robust WSI-level models. The experimental results have demonstrated that the proposed method stably outperforms state-of-the-art methods.