Towards Optimal Grammars for RNA Structures
Fuente:
arXiv
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| Autori principali: | , , |
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| _version_ | 1866913215174148096 |
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| author | Onokpasa, Evarista Wild, Sebastian Wong, Prudence W. H. |
| author_facet | Onokpasa, Evarista Wild, Sebastian Wong, Prudence W. H. |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2401_16623 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Towards Optimal Grammars for RNA Structures Onokpasa, Evarista Wild, Sebastian Wong, Prudence W. H. Data Structures and Algorithms Information Theory 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. |
| title | Towards Optimal Grammars for RNA Structures |
| topic | Data Structures and Algorithms Information Theory |
| url | https://arxiv.org/abs/2401.16623 |