English

Streaming $k$-edit approximate pattern matching via string decomposition

Data Structures and Algorithms 2023-05-02 v1

Abstract

In this paper we give an algorithm for streaming kk-edit approximate pattern matching which uses space O~(k2)\widetilde{O}(k^2) and time O~(k2)\widetilde{O}(k^2) per arriving symbol. This improves substantially on the recent algorithm of Kociumaka, Porat and Starikovskaya (2022) which uses space O~(k5)\widetilde{O}(k^5) and time O~(k8)\widetilde{O}(k^8) per arriving symbol. In the kk-edit approximate pattern matching problem we get a pattern PP and text TT and we want to identify all substrings of the text TT that are at edit distance at most kk from PP. In the streaming version of this problem both the pattern and the text arrive in a streaming fashion symbol by symbol and after each symbol of the text we need to report whether there is a current suffix of the text with edit distance at most kk from PP. We measure the total space needed by the algorithm and time needed per arriving symbol.

Keywords

Cite

@article{arxiv.2305.00615,
  title  = {Streaming $k$-edit approximate pattern matching via string decomposition},
  author = {Sudatta Bhattacharya and Michal Koucký},
  journal= {arXiv preprint arXiv:2305.00615},
  year   = {2023}
}