MultiRBP: Multi-task neural network for protein-RNA binding prediction

Jonathan Karin, Hagai Michel, Yaron Orenstein

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

3 Scopus citations

Abstract

Protein-RNA binding plays vital roles in post-transcriptional gene regulation. High-throughput in vitro binding measurements were generated for more than 200 RNA-binding proteins, enabling the development of computational methods to predict binding to any RNA transcript of interest. In recent years, deep learning-based methods have been developed to predict RNA binding in vitro achieving state-of-the-art results. However, all methods train a single model per protein, under-utilizing the similarities in binding preferences shared by multiple RNA-binding proteins. In this work, we developed MultiRBP, a deep learning-based method to predict RNA binding of hundreds of proteins to a given RNA sequence. The innovation of MultiRBP is in its multi-task nature, i.e., predicting binding for hundreds of proteins at the same time. We trained MultiRBP on the RNAcompete dataset, the most comprehensive dataset of in vitro binding measurements. Our method outperformed extant methods in both in vitro and in vivo RNA-binding prediction. Our method achieved an average Pearson correlation of 0.692±0.17 for in vitro binding prediction, and a median AUROC of 0.668±0.09 for in vivo binding prediction. Moreover, by visualizing the learned binding preferences, MultiRBP provided more interpretable visualization than a single-task model. The code is publicly available at github.com/OrensteinLab/MultiRBP.

Original languageEnglish
Title of host publicationProceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2021
PublisherAssociation for Computing Machinery, Inc
ISBN (Electronic)9781450384506
DOIs
StatePublished - 18 Jan 2021
Externally publishedYes
Event12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2021 - Virtual, Online, United States
Duration: 1 Aug 20214 Aug 2021

Publication series

NameProceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2021

Conference

Conference12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2021
Country/TerritoryUnited States
CityVirtual, Online
Period1/08/214/08/21

Bibliographical note

Publisher Copyright:
© 2021 Owner/Author.

Keywords

  • RNA-binding proteins
  • RNAcompete
  • deep learning
  • eCLIP
  • multi-task learning
  • neural networks
  • protein-RNA binding

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