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Approximate Similarity Search Under Edit Distance Using Locality-Sensitive Hashing

Author Samuel McCauley

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Subject Classification

ACM Subject Classification
  • Information systems → Nearest-neighbor search
  • Theory of computation → Pattern matching
Keywords
  • edit distance
  • approximate pattern matching
  • approximate nearest neighbor
  • similarity search
  • locality-sensitive hashing

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Abstract

Edit distance similarity search, also called approximate pattern matching, is a fundamental problem with widespread database applications. The goal of the problem is to preprocess n strings of length d, to quickly answer queries q of the form: if there is a database string within edit distance r of q, return a database string within edit distance cr of q. 
Previous approaches to this problem either rely on very large (superconstant) approximation ratios c, or very small search radii r. Outside of a narrow parameter range, these solutions are not competitive with trivially searching through all n strings.
In this work we give a simple and easy-to-implement hash function that can quickly answer queries for a wide range of parameters. Specifically, our strategy can answer queries in time Õ(d3^rn^{1/c}). The best known practical results require c ≫ r to achieve any correctness guarantee; meanwhile, the best known theoretical results are very involved and difficult to implement, and require query time that can be loosely bounded below by 24^r. Our results significantly broaden the range of parameters for which there exist nontrivial theoretical bounds, while retaining the practicality of a locality-sensitive hash function.

Cite As Get BibTex

Samuel McCauley. Approximate Similarity Search Under Edit Distance Using Locality-Sensitive Hashing. In 24th International Conference on Database Theory (ICDT 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 186, pp. 21:1-21:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021) https://doi.org/10.4230/LIPIcs.ICDT.2021.21

Author Details

Samuel McCauley
  • Williams College, Williamstown, MA, USA

Funding

This research was supported in part by the European ResearchCouncil under the European Union’s 7th Framework Programme (FP7/2007-2013) / ERC grant agreement no. 61433, by the VILLUM Foundation grant 16582, and by a Zuckerman STEM Postdoctoral Fellowship.

Acknowledgements

I would like to thank Thomas Ahle, Martin Aumüller, Tobias Christiani, Tsvi Kopelowitz, Rasmus Pagh, Ely Porat, Francesco Silvestri, and Shikha Singh for many helpful comments and discussions.

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