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An Invertible Transform for Efficient String Matching in Labeled Digraphs

Authors Abhinav Nellore , Austin Nguyen , Reid F. Thompson

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Abhinav Nellore
  • Oregon Health & Science University, Portland, Oregon 97239, USA
Austin Nguyen
  • Oregon Health & Science University, Portland, Oregon 97239, USA
Reid F. Thompson
  • Oregon Health & Science University, Portland, Oregon 97239, USA
  • VA Portland Healthcare System, Portland, Oregon 97239, USA

Acknowledgements

We thank Rachel Ward, Ben Langmead, Chris Wilks, and the anonymous reviewers for the 32nd Annual Symposium on Combinatorial Pattern Matching, all of whose feedback improved this paper considerably.

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Abhinav Nellore, Austin Nguyen, and Reid F. Thompson. An Invertible Transform for Efficient String Matching in Labeled Digraphs. In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 20:1-20:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021) https://doi.org/10.4230/LIPIcs.CPM.2021.20

Abstract

Let G = (V, E) be a digraph where each vertex is unlabeled, each edge is labeled by a character in some alphabet Ω, and any two edges with both the same head and the same tail have different labels. The powerset construction gives a transform of G into a weakly connected digraph G' = (V', E') that enables solving the decision problem of whether there is a walk in G matching an arbitrarily long query string q in time linear in |q| and independent of |E| and |V|. We show G is uniquely determined by G' when for every v_𝓁 ∈ V, there is some distinct string s_𝓁 on Ω such that v_𝓁 is the origin of a closed walk in G matching s_𝓁, and no other walk in G matches s_𝓁 unless it starts and ends at v_𝓁. We then exploit this invertibility condition to strategically alter any G so its transform G' enables retrieval of all t terminal vertices of walks in the unaltered G matching q in O(|q| + t log |V|) time. We conclude by proposing two defining properties of a class of transforms that includes the Burrows-Wheeler transform and the transform presented here.

Subject Classification

ACM Subject Classification
  • Mathematics of computing → Graph algorithms
  • Mathematics of computing → Combinatorics on words
Keywords
  • pattern matching
  • string matching
  • Burrows-Wheeler transform
  • labeled graphs

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