Deep learning for detection and segmentation of artefact and disease instances in gastrointestinal endoscopy

Ali, Sharib, Dmitrieva, Mariia, Ghatwary, Noha, Bano, Sophia, Polat, Gorkem, Temizel, Alptekin, Krenzer, Adrian, Hekalo, Amar, Guo, Yun Bo, Matuszewski, Bogdan, Gridach, Mourad, Voiculescu, Irina, Yoganand, Vishnusai, Chavan, Arnav, Raj, Aryan, Nguyen, Nhan T., Tran, Dat Q., Huynh, Le Duy, Boutry, Nicolas, Rezvy, Shahadate ORCID: https://orcid.org/0000-0002-2684-7117, Chen, Haijian, Choi, Yoon Ho, Subramanian, Anand, Balasubramanian, Velmurugan, Gao, Xiaohong W. ORCID: https://orcid.org/0000-0002-8103-6624, Hu, Hongyu, Liao, Yusheng, Stoyanov, Danail, Daul, Christian, Realdon, Stefano, Cannizzaro, Renato, Lamarque, Dominique, Tran-Nguyen, Terry, Bailey, Adam, Braden, Barbara, East, James E. and Rittscher, Jens (2021) Deep learning for detection and segmentation of artefact and disease instances in gastrointestinal endoscopy. Medical Image Analysis, 70 , 102002. ISSN 1361-8415 [Article] (doi:10.1016/j.media.2021.102002)

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Abstract

The Endoscopy Computer Vision Challenge (EndoCV) is a crowd-sourcing initiative to address eminent problems in developing
reliable computer aided detection and diagnosis endoscopy systems and suggest a pathway for clinical translation
of technologies. Whilst endoscopy is a widely used diagnostic and treatment tool for hollow-organs, there are several core
challenges often faced by endoscopists, mainly: 1) presence of multi-class artefacts that hinder their visual interpretation, and
2) difficulty in identifying subtle precancerous precursors and cancer abnormalities. Artefacts often affect the robustness of
deep learning methods applied to the gastrointestinal tract organs as they can be confused with tissue of interest. EndoCV2020
challenges are designed to address research questions in these remits. In this paper, we present a summary of methods
developed by the top 17 teams and provide an objective comparison of state-of-the-art methods and methods designed by
the participants for two sub-challenges: i) artefact detection and segmentation (EAD2020), and ii) disease detection and
segmentation (EDD2020). Multi-center, multi-organ, multi-class, and multi-modal clinical endoscopy datasets were compiled
for both EAD2020 and EDD2020 sub-challenges. The out-of-sample generalization ability of detection algorithms was also
evaluated. Whilst most teams focused on accuracy improvements, only a few methods hold credibility for clinical usability. The
best performing teams provided solutions to tackle class imbalance, and variabilities in size, origin, modality and occurrences
by exploring data augmentation, data fusion, and optimal class thresholding techniques.

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