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Schneider, M. ; Wang, L. ; Marr, C.

Evaluation of domain adaptation approaches for robust classification of heterogeneous biological data sets.

Lect. Notes Comput. Sc. 11728 LNCS, 673-686 (2019)
Postprint DOI
Open Access Green
Most machine learning algorithms require that training data are identically distributed to ensure effective learning. In biological studies, however, even small variations in the experimental setup can lead to substantial deviations. Domain adaptation offers tools to deal with this problem. It is particularly useful for cases where only a small amount of training data is available in the domain of interest, while a large amount of training data is available in a different, but relevant domain. We investigated to what extent domain adaptation was able to improve prediction accuracy for complex biological data. To that end, we used simulated data and time-lapse movies of differentiating blood stem cells in different cell cycle stages from multiple experiments and compared three commonly used domain adaptation approaches. EasyAdapt, a simple technique of structured pooling of related data sets, was able to improve accuracy when classifying the simulated data and cell cycle stages from microscopic images. Meanwhile, the technique proved robust to the potential negative impact on the classification accuracy that is common in other techniques that build models with heterogeneous data. Despite its implementation simplicity, EasyAdapt consistently produced more accurate predictions compared to conventional techniques. Domain adaptation is therefore able to substantially reduce the amount of work required to create a large amount of annotated training data in the domain of interest necessary whenever the domain changes even a little, which is common not only in biological experiments, but universally exists in almost all data collection routines.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Batch Effect ; Domain Adaptation ; Easyadapt ; Transfer Learning
ISSN (print) / ISBN 0302-9743
e-ISSN 1611-3349
Journal Lecture Notes in Computer Science
Quellenangaben Volume: 11728 LNCS, Issue: , Pages: 673-686 Article Number: , Supplement: ,
Publisher Springer
Publishing Place Berlin [u.a.]
Non-patent literature Publications
Institute(s) Institute of Computational Biology (ICB)
Institute of Radiation Biology (ISB)