Open this publication in new window or tab >>2024 (English)In: 2024 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), IEEE, 2024Conference paper, Published paper (Refereed)
Abstract [en]
Making breast cancer prognosis from gene expression profiles of the primary tumor has become a promising application of deep learning. Yet, to be relevant to real world applications in the clinic and for knowledge discovery, these models must be robust to common distribution shifts. In this study, we evaluate recently proposed methods for improving domain and subgroup shifts. We test the in-distribution and out-of-distribution generalization of multiple episode learning, stochastic weight averaging, group distributionally robust optimization, and a subsampling scheme on one training and four external breast cancer prognosis datasets. The evaluation found that the methods can, to various degrees, improve generalization across domains, although there remain, partially high, generalization gaps. Additionally, in-distribution and out-of-distribution generalization differs between clinical subtypes of breast cancer. Thus, we conclude that further research into methods specifically addressing challenges in breast cancer prognosis from gene expression data are warranted.
Place, publisher, year, edition, pages
IEEE, 2024
Series
IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), ISSN 2994-9351, E-ISSN 2994-9408
Keywords
breast cancer, domain generalization, gene expression, subgroup shift, survival analysis, Contrastive Learning, Diseases, Lung cancer, Stochastic systems, Breast cancer prognosis, Gene expression profiles, Generalisation, Genes expression, Learning models, Real-world
National Category
Cancer and Oncology Bioinformatics and Computational Biology Other Computer and Information Science
Research subject
Bioinformatics; Skövde Artificial Intelligence Lab (SAIL)
Identifiers
urn:nbn:se:his:diva-24659 (URN)10.1109/CIBCB58642.2024.10702166 (DOI)001546450400010 ()2-s2.0-85207504799 (Scopus ID)979-8-3503-5663-2 (ISBN)979-8-3503-5664-9 (ISBN)
Conference
21st IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2024, 27-29 August 2024, Natal, Brazil
Funder
Knowledge Foundation, 20170302Knowledge Foundation, 20200014Swedish Research Council, 2022-06725
Note
© 2024 IEEE
Correspondence Address: S.R. Stahlschmidt; University of Skövde, Systems Biology Research Center, Skövde, Sweden; email: soren.richard.stahlschmidt@his.se
This work was supported by the University of Skövde, Sweden under grants from the Knowledge Foundation (20170302, 20200014). The computations were enabled by resources provided by Chalmers e-Commons at Chalmers and the National Academic Infrastructure for Supercomputing in Sweden (NAISS), partially funded by the Swedish Research Council through grant agreement no. 2022-06725.
2024-11-072024-11-072025-10-17Bibliographically approved