Leuvenshtein: Efficient FHE-based Edit Distance Computation with Single
  Bootstrap per Cell
Authors: name: Wouter Legiest; name: Jan-Pieter D'Anvers; name: Bojan Spasic; name: Nam-Luc Tran; name: Ingrid Verbauwhede
Published: 2025-08-20 09:40:06

Abstract: This paper presents a novel approach to calculating the Levenshtein (edit)
distance within the framework of Fully Homomorphic Encryption (FHE),
specifically targeting third-generation schemes like TFHE. Edit distance
computations are essential in applications across finance and genomics, such as
DNA sequence alignment. We introduce an optimised algorithm that significantly
reduces the cost of edit distance calculations called Leuvenshtein. This
algorithm specifically reduces the number of programmable bootstraps (PBS)
needed per cell of the calculation, lowering it from approximately 94
operations -- required by the conventional Wagner-Fisher algorithm -- to just
1. Additionally, we propose an efficient method for performing equality checks
on characters, reducing ASCII character comparisons to only 2 PBS operations.
Finally, we explore the potential for further performance improvements by
utilising preprocessing when one of the input strings is unencrypted. Our
Leuvenshtein achieves up to 278times faster performance compared to the best
available TFHE implementation and up to 39times faster than an optimised
implementation of the Wagner-Fisher algorithm. Moreover, when offline
preprocessing is possible due to the presence of one unencrypted input on the
server side, an additional 3times speedup can be achieved.