Given a context-free grammar (CFG) and a finite-state automaton (FA), we tackle the problem of computing the most similar pair of strings from two languages. We in particular consider three different gap cost models, linear, affine and concave models, that are crucial for finding a proper alignment between two bio sequences. We design efficient algorithms for computing the edit-distance between a CFG and an FA under these gap cost models. The time complexity of our algorithm for computing the linear or affine gap distance is polynomial and the time complexity for the concave gap distance is exponential.
|Title of host publication||Implementation and Application of Automata - 18th International Conference, CIAA 2013, Proceedings|
|Number of pages||12|
|Publication status||Published - 2013|
|Event||18th International Conference on Implementation and Application of Automata, CIAA 2013 - Halifax, NS, Canada|
Duration: 2013 Jul 16 → 2013 Jul 19
|Name||Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|
|Other||18th International Conference on Implementation and Application of Automata, CIAA 2013|
|Period||13/7/16 → 13/7/19|
Bibliographical noteFunding Information:
Ko and Han were supported by the Basic Science Research Program through NRF funded by MEST ( 2015R1D1A1A01060097 ), the Yonsei University Future-leading Research Initiative of 2015 and the International Cooperation Program managed by NRF of Korea ( 2014K2A1A2048512 ), and Salomaa was supported by the Natural Sciences and Engineering Research Council of Canada Grant OGP0147224 .
All Science Journal Classification (ASJC) codes
- Theoretical Computer Science
- Computer Science(all)