Towards Optimal Grammars for RNA Structures
Data Structures and Algorithms
2024-01-31 v1 Information Theory
math.IT
Abstract
In past work (Onokpasa, Wild, Wong, DCC 2023), we showed that (a) for joint compression of RNA sequence and structure, stochastic context-free grammars are the best known compressors and (b) that grammars which have better compression ability also show better performance in ab initio structure prediction. Previous grammars were manually curated by human experts. In this work, we develop a framework for automatic and systematic search algorithms for stochastic grammars with better compression (and prediction) ability for RNA. We perform an exhaustive search of small grammars and identify grammars that surpass the performance of human-expert grammars.
Keywords
Cite
@article{arxiv.2401.16623,
title = {Towards Optimal Grammars for RNA Structures},
author = {Evarista Onokpasa and Sebastian Wild and Prudence W. H. Wong},
journal= {arXiv preprint arXiv:2401.16623},
year = {2024}
}
Comments
to be presented at DCC 2024