Recognition and parsing of context-free languages in time n3
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The standard RNA secondary structure prediction problem can be cast as a parsing problem and solved by the CKY algorithm.
“Thus, the standard RNA secondary structure prediction problem can be cast as a parsing problem: given the above SCFG and an input RNA sequence, find the minimum-weight derivation in that can generate the sequence. This can be solved by the classical CKY algorithm from computational linguistics41–43.”
From Algorithm for optimized mRNA design improves stability and immunogenicity (2023) · cites this paper as [42]
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Algorithm for optimized mRNA design improves stability and immunogenicity
Zhang, H., Zhang, L., Lin, A., Xu, C., Li, Z., Liu, K., Liu, B., Ma, X., Zhao, F., Jiang, H., et al. (2023) · Nature · doi:10.1038/s41586-023-06127-z · Cited by 498 · see citing works
LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search
Huang, L., Zhang, H., Deng, D., Zhao, K., Liu, K., Hendrix, D. A., & Mathews, D. H. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz375 · Cited by 207 · see citing works
“1965; Younger, 1967), has a running time of O ( n 3 ) that scales cubically with the sequence length n , which is too slow for long RNA sequences (Lange et al. , 2012).”
BackgroundThe four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective
Rivas, E. (2013) · RNA Biology · doi:10.4161/rna.24971 · Cited by 57 · see citing works
- Authors
- Younger, D. H.
- Affiliations
- General Electric (United States) (US)
- Corresponding author
- Younger, Daniel H.
- Venue
- Information and Control
- Publisher
- Elsevier BV
- Published
- 1967-02
- Volume
- 10
- Issue
- 2
- Pages
- 189-208
- ISSN
- 0019-9958 (ISSN-L)
- OpenAlex
- W1970961429
- Cited by
- 935
- References
- 11
- Citations by year
- 2026: 3 · 2025: 13 · 2024: 11 · 2023: 17 · 2022: 19 · 2021: 37 · 2020: 35 · 2019: 32 · 2018: 26 · 2017: 28 · 2016: 37 · 2015: 28 · 2014: 21 · 2013: 36 · 2012: 35
- FWCI
- 10.29
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Information and Control (publishedVersion)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › semigroups and automata theory
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Social Sciences › Arts and Humanities › Language and Linguistics › Syntax, Semantics, Linguistic Variation
- Keywords
- context-free languages, string recognition, syntactic analysis, cubic time algorithm, syntactic ambiguity, Turing machine simulation, computational complexity, grammatical analysis
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