Vision transformer-based weakly supervised histopathological image analysis of primary brain tumors

Li，Zhongxiao1,2; Cong，Yuwei3; Chen，Xin4; Qi，Jiping3; Sun，Jingxian4; Yan，Tao4; Yang，He4; Liu，Junsi4; Lu，Enzhou4; Wang，Lixiang4; Li，Jiafeng4; Hu，Hong4; Zhang，Cheng5; Yang，Quan4; Yao，Jiawei4; Yao，Penglei4; Jiang，Qiuyi4; Liu，Wenwu4; Song，Jiangning6,7; Carin，Lawrence1; Chen，Yupeng8; Zhao，Shiguang4,9; Gao，Xin1,2

2023-01-20

10.1016/j.isci.2022.105872

iScience   Impact Factor & Quartile

2589-0042

Diagnosis of primary brain tumors relies heavily on histopathology. Although various computational pathology methods have been developed for automated diagnosis of primary brain tumors, they usually require neuropathologists’ annotation of region of interests or selection of image patches on whole-slide images (WSI). We developed an end-to-end Vision Transformer (ViT) – based deep learning architecture for brain tumor WSI analysis, yielding a highly interpretable deep-learning model, ViT-WSI. Based on the principle of weakly supervised machine learning, ViT-WSI accomplishes the task of major primary brain tumor type and subtype classification. Using a systematic gradient-based attribution analysis procedure, ViT-WSI can discover diagnostic histopathological features for primary brain tumors. Furthermore, we demonstrated that ViT-WSI has high predictive power of inferring the status of three diagnostic glioma molecular markers, IDH1 mutation, p53 mutation, and MGMT methylation, directly from H&E-stained histopathological images, with patient level AUC scores of 0.960, 0.874, and 0.845, respectively.

Cancer Machine learning Pathology

English

Corresponding

2-s2.0-85146042593

Scopus

1.Computer Science Program,Computer,Electrical and Mathematical Sciences and Engineering (CEMSE) Division,King Abdullah University of Science and Technology (KAUST),Thuwal,23955-6900,Saudi Arabia
2.KAUST Computational Bioscience Research Center (CBRC),King Abdullah University of Science and Technology (KAUST),Thuwal,23955-6900,Saudi Arabia
3.Department of Pathology,The First Affiliated Hospital of Harbin Medical University,Nangang District,23 Youzheng Street, Harbin,150001,China
4.Department of Neurosurgery,The First Affiliated Hospital of Harbin Medical University,Harbin,Heilongjiang Province,150001,China
5.Suffolk University,Boston,United States
6.Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology,Monash University,Melbourne,3800,Australia
7.Monash Data Futures Institute,Monash University,Melbourne,3800,Australia
8.School of Microelectronics,Southern University of Science and Technology,Shenzhen,518055,China
9.Department of Neurosurgery,Shenzhen University General Hospital,Shenzhen,Guangdong Province,518100,China

Li，Zhongxiao,Cong，Yuwei,Chen，Xin,et al. Vision transformer-based weakly supervised histopathological image analysis of primary brain tumors[J]. iScience,2023,26(1).

Li，Zhongxiao.,Cong，Yuwei.,Chen，Xin.,Qi，Jiping.,Sun，Jingxian.,...&Gao，Xin.(2023).Vision transformer-based weakly supervised histopathological image analysis of primary brain tumors.iScience,26(1).

Li，Zhongxiao,et al."Vision transformer-based weakly supervised histopathological image analysis of primary brain tumors".iScience 26.1(2023).