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Hao Bian

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3 papers

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JBHI Journal 2023 Journal Article

dMIL-Transformer: Multiple Instance Learning Via Integrating Morphological and Spatial Information for Lymph Node Metastasis Classification

Yang Chen
Zhuchen Shao
Hao Bian
Zijie Fang
Yifeng Wang
Yuanhao Cai
Haoqian Wang
Guojun Liu

Automated classification of lymph node metastasis (LNM) plays an important role in the diagnosis and prognosis. However, it is very challenging to achieve satisfactory performance in LNM classification, because both the morphology and spatial distribution of tumor regions should be taken into account. To address this problem, this article proposes a two-stage dMIL-Transformer framework, which integrates both the morphological and spatial information of the tumor regions based on the theory of multiple instance learning (MIL). In the first stage, a double Max-Min MIL (dMIL) strategy is devised to select the suspected top-K positive instances from each input histopathology image, which contains tens of thousands of patches (primarily negative). The dMIL strategy enables a better decision boundary for selecting the critical instances compared with other methods. In the second stage, a Transformer-based MIL aggregator is designed to integrate all the morphological and spatial information of the selected instances from the first stage. The self-attention mechanism is further employed to characterize the correlation between different instances and learn the bag-level representation for predicting the LNM category. The proposed dMIL-Transformer can effectively deal with the thorny classification in LNM with great visualization and interpretability. We conduct various experiments over three LNM datasets, and achieve 1. 79%-7. 50% performance improvement compared with other state-of-the-art methods.

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AAAI Conference 2023 Conference Paper

HVTSurv: Hierarchical Vision Transformer for Patient-Level Survival Prediction from Whole Slide Image

Zhuchen Shao
Yang Chen
Hao Bian
Jian Zhang
Guojun Liu
Yongbing Zhang

Survival prediction based on whole slide images (WSIs) is a challenging task for patient-level multiple instance learning (MIL). Due to the vast amount of data for a patient (one or multiple gigapixels WSIs) and the irregularly shaped property of WSI, it is difficult to fully explore spatial, contextual, and hierarchical interaction in the patient-level bag. Many studies adopt random sampling pre-processing strategy and WSI-level aggregation models, which inevitably lose critical prognostic information in the patient-level bag. In this work, we propose a hierarchical vision Transformer framework named HVTSurv, which can encode the local-level relative spatial information, strengthen WSI-level context-aware communication, and establish patient-level hierarchical interaction. Firstly, we design a feature pre-processing strategy, including feature rearrangement and random window masking. Then, we devise three layers to progressively obtain patient-level representation, including a local-level interaction layer adopting Manhattan distance, a WSI-level interaction layer employing spatial shuffle, and a patient-level interaction layer using attention pooling. Moreover, the design of hierarchical network helps the model become more computationally efficient. Finally, we validate HVTSurv with 3,104 patients and 3,752 WSIs across 6 cancer types from The Cancer Genome Atlas (TCGA). The average C-Index is 2.50-11.30% higher than all the prior weakly supervised methods over 6 TCGA datasets. Ablation study and attention visualization further verify the superiority of the proposed HVTSurv. Implementation is available at: https://github.com/szc19990412/HVTSurv.

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NeurIPS Conference 2021 Conference Paper

TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification

Zhuchen Shao
Hao Bian
Yang Chen
Yifeng Wang
Jian Zhang
Xiangyang Ji
Yongbing Zhang

Multiple instance learning (MIL) is a powerful tool to solve the weakly supervised classification in whole slide image (WSI) based pathology diagnosis. However, the current MIL methods are usually based on independent and identical distribution hypothesis, thus neglect the correlation among different instances. To address this problem, we proposed a new framework, called correlated MIL, and provided a proof for convergence. Based on this framework, we devised a Transformer based MIL (TransMIL), which explored both morphological and spatial information. The proposed TransMIL can effectively deal with unbalanced/balanced and binary/multiple classification with great visualization and interpretability. We conducted various experiments for three different computational pathology problems and achieved better performance and faster convergence compared with state-of-the-art methods. The test AUC for the binary tumor classification can be up to 93. 09% over CAMELYON16 dataset. And the AUC over the cancer subtypes classification can be up to 96. 03% and 98. 82% over TCGA-NSCLC dataset and TCGA-RCC dataset, respectively. Implementation is available at: https: //github. com/szc19990412/TransMIL.

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