Self-supervised learning-based Multi-Scale feature Fusion Network for survival analysis from whole slide images. (February 2023)

• Record Type: Journal Article
• Authors: Li, Le; Liang, Yong; Shao, Mingwen; Lu, Shanghui; liao, Shuilin; Ouyang, Dong
• Is Part Of: Computers in biology and medicine. Volume 153(2023)
• Publication Date: 2023-02
• Subjects: Whole slide images -- Survival analysis -- Self-supervised learning -- Sampling strategy -- Multi-scale representation; Medicine -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; 610.285
• DOI: 10.1016/j.compbiomed.2022.106482
• Languages: English
• ISSNs: 0010-4825

Abstract

Abstract: Understanding prognosis and mortality is critical for evaluating the treatment plan of patients. Advances in digital pathology and deep learning techniques have made it practical to perform survival analysis in whole slide images (WSIs). Current methods are usually based on a multi-stage framework which includes patch sampling, feature extraction and prediction. However, the random patch sampling strategy is highly unstable and prone to sampling non-ROI. Feature extraction typically relies on hand-crafted features or convolutional neural networks (CNNs) pre-trained on ImageNet, while the artificial error or domain gaps may affect the survival prediction performance. Besides, the limited information representation of local sampling patches will create a bottleneck limitation on the effectiveness of prediction. To address the above challenges, we propose a novel patch sampling strategy based on image information entropy and construct a Multi-Scale feature Fusion Network (MSFN) based on self-supervised feature extractor. Specifically, we adopt image information entropy as a criterion to select representative sampling patches, thereby avoiding the noise interference caused by random to blank regions. Meanwhile, we pretrain the feature extractor utilizing self-supervised learning mechanism to improve the efficiency of feature extraction. Furthermore, a global–local feature fusion prediction network based on the attention mechanism is constructed to improve the survival prediction effect of WSIs with comprehensive multi-scale information representation. The proposed method is validated by adequate experiments and achieves competitive results on both of the most popular WSIs survival analysis datasets, TCGA-GBM and TCGA-LUSC. Code and trained models are made available at: https://github.com/Mercuriiio/MSFN . Highlights: Self-supervised feature extraction is able to improve model applicability. Multi-scale pathological image fusion can improve the accuracy of survival analysis. Patch sampling strategy based on image entropy avoids noise influence. The c-index of 0.691 and 0.701 was obtained on TCGA-GBM and TCGA-LUSC.