Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report
File(s)Immunoinformatics_2023.pdf (934.02 KB)
Published version
Author(s)
Type
Journal Article
Abstract
Many different solutions to predicting the cognate epitope target of a T-cell receptor (TCR) have been proposed. However several questions on the advantages and disadvantages of these different approaches remain unresolved, as most methods have only been evaluated within the context of their initial publications and data sets. Here, we report the findings of the first public TCR-epitope prediction benchmark performed on 23 prediction models in the context of the ImmRep 2022 TCR-epitope specificity workshop. This benchmark revealed that the use of paired-chain alpha-beta, as well as CDR1/2 or V/J information, when available, improves classification obtained with CDR3 data, independent of the underlying approach. In addition, we found that straight-forward distance-based approaches can achieve a respectable performance when compared to more complex machine-learning models. Finally, we highlight the need for a truly independent follow-up benchmark and provide recommendations for the design of such a next benchmark.
Date Issued
2023-03
Date Acceptance
2023-01-31
Citation
ImmunoInformatics, 2023, 9, pp.1-8
ISSN
2667-1190
Publisher
Elsevier BV
Start Page
1
End Page
8
Journal / Book Title
ImmunoInformatics
Volume
9
Copyright Statement
© 2023 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
License URL
Identifier
https://www.sciencedirect.com/science/article/pii/S2667119023000046
Publication Status
Published
Article Number
100024
Date Publish Online
2023-02-03