RNA SECONDARY STRUCTURE PREDICTION BY LEARNING UNROLLED ALGORITHMS

Xinshi Chen, Yu Li, Ramzan Umarov, Xin Gao, Le Song

Research output: Chapter in Book/Report/Conference proceedingConference contribution

38 Scopus citations

Abstract

In this paper, we propose an end-to-end deep learning model, called E2Efold, for RNA secondary structure prediction which can effectively take into account the inherent constraints in the problem. The key idea of E2Efold is to directly predict the RNA base-pairing matrix, and use an unrolled algorithm for constrained programming as the template for deep architectures to enforce constraints. With comprehensive experiments on benchmark datasets, we demonstrate the superior performance of E2Efold: it predicts significantly better structures compared to previous SOTA (especially for pseudoknotted structures), while being as efficient as the fastest algorithms in terms of inference time.
Original languageEnglish (US)
Title of host publication8th International Conference on Learning Representations, ICLR 2020
PublisherInternational Conference on Learning Representations, ICLR
StatePublished - 2020

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