A bit catastrophe, loosely defined, is when a change in just one character of a string causes a significant change in the size of the compressed string. We study this phenomenon for the Burrows-Wheeler Transform (BWT), a string transform at the heart of several of the most popular compressors and aligners today. The parameter determining the size of the compressed data is the number of equal-letter runs of the BWT, commonly denoted r. We exhibit infinite families of strings in which insertion, deletion, resp. substitution of one character increases r from constant to Θ(log n), where n is the length of the string. These strings can be interpreted both as ex- amples for an increase by a multiplicative or an additive Θ(log n)-factor. As regards multiplicative factor, they attain the upper bound given by Akagi, Funakoshi, and Inenaga [Inf & Comput. 2023] of O(lognlogr), since here r = O(1). We then give examples of strings in which insertion, deletion, resp. sub- stitution of a character increases r by a Θ(√n) additive factor. These strings significantly improve the best known lower bound for an additive factor of Ω(log n) [Giuliani et al., SOFSEM 2021].

Bit Catastrophes for the Burrows-Wheeler Transform

Sara Giuliani;Zsuzsanna Liptak;
2023-01-01

Abstract

A bit catastrophe, loosely defined, is when a change in just one character of a string causes a significant change in the size of the compressed string. We study this phenomenon for the Burrows-Wheeler Transform (BWT), a string transform at the heart of several of the most popular compressors and aligners today. The parameter determining the size of the compressed data is the number of equal-letter runs of the BWT, commonly denoted r. We exhibit infinite families of strings in which insertion, deletion, resp. substitution of one character increases r from constant to Θ(log n), where n is the length of the string. These strings can be interpreted both as ex- amples for an increase by a multiplicative or an additive Θ(log n)-factor. As regards multiplicative factor, they attain the upper bound given by Akagi, Funakoshi, and Inenaga [Inf & Comput. 2023] of O(lognlogr), since here r = O(1). We then give examples of strings in which insertion, deletion, resp. sub- stitution of a character increases r by a Θ(√n) additive factor. These strings significantly improve the best known lower bound for an additive factor of Ω(log n) [Giuliani et al., SOFSEM 2021].
2023
978-3-031-33263-0
Burrows-Wheeler transform, Equal-letter run, Repetitiveness measure, Sensitivity
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11562/1091847
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