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

Publication ,  Journal Article
Li, Z; Cong, Y; Chen, X; Qi, J; Sun, J; Yan, T; Yang, H; Liu, J; Lu, E; Wang, L; Li, J; Hu, H; Zhang, C; Yang, Q; Yao, J; Yao, P; Liu, W ...
Published in: iScience
January 20, 2023

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.

Duke Scholars

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Published In

iScience

DOI

EISSN

2589-0042

Publication Date

January 20, 2023

Volume

26

Issue

1
 

Citation

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Li, Z., Cong, Y., Chen, X., Qi, J., Sun, J., Yan, T., … Gao, X. (2023). Vision transformer-based weakly supervised histopathological image analysis of primary brain tumors. IScience, 26(1). https://doi.org/10.1016/j.isci.2022.105872
Li, Z., Y. Cong, X. Chen, J. Qi, J. Sun, T. Yan, H. Yang, et al. “Vision transformer-based weakly supervised histopathological image analysis of primary brain tumors.” IScience 26, no. 1 (January 20, 2023). https://doi.org/10.1016/j.isci.2022.105872.
Li Z, Cong Y, Chen X, Qi J, Sun J, Yan T, et al. Vision transformer-based weakly supervised histopathological image analysis of primary brain tumors. iScience. 2023 Jan 20;26(1).
Li, Z., et al. “Vision transformer-based weakly supervised histopathological image analysis of primary brain tumors.” IScience, vol. 26, no. 1, Jan. 2023. Scopus, doi:10.1016/j.isci.2022.105872.
Li Z, Cong Y, Chen X, Qi J, Sun J, Yan T, Yang H, Liu J, Lu E, Wang L, Li J, Hu H, Zhang C, Yang Q, Yao J, Yao P, Jiang Q, Liu W, Song J, Carin L, Chen Y, Zhao S, Gao X. Vision transformer-based weakly supervised histopathological image analysis of primary brain tumors. iScience. 2023 Jan 20;26(1).
Journal cover image

Published In

iScience

DOI

EISSN

2589-0042

Publication Date

January 20, 2023

Volume

26

Issue

1