Meirelles AL, Kurc T, Saltz J, Teodoro G. Effective active learning in digital pathology: A case study in tumor infiltrating lymphocytes.
Comput Methods Programs Biomed 2022;
220:106828. [PMID:
35500506 DOI:
10.1016/j.cmpb.2022.106828]
[Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/09/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND OBJECTIVE
Deep learning methods have demonstrated remarkable performance in pathology image analysis, but they require a large amount of annotated training data from expert pathologists. The aim of this study is to minimize the data annotation need in these analyses.
METHODS
Active learning (AL) is an iterative approach to training deep learning models. It was used in our context with a Tumor Infiltrating Lymphocytes (TIL) classification task to minimize annotation. State-of-the-art AL methods were evaluated with the TIL application and we have proposed and evaluated a more efficient and effective AL acquisition method. The proposed method uses data grouping based on imaging features and model prediction uncertainty to select meaningful training samples (image patches).
RESULTS
An experimental evaluation with a collection of cancer tissue images shows that: (i) Our approach reduces the number of patches required to attain a given AUC as compared to other approaches, and (ii) our optimization (subpooling) leads to AL execution time improvement of about 2.12×.
CONCLUSIONS
This strategy enabled TIL based deep learning analyses using smaller annotation demand. We expect this approach may be used to build other analyses in digital pathology with fewer training samples.
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