Bit Catastrophes for the Burrows-Wheeler Transform

被引:2
|
作者
Giuliani, Sara [1 ]
Inenaga, Shunsuke [2 ]
Liptak, Zsuzsanna [1 ]
Romana, Giuseppe [3 ]
Sciortino, Marinella [3 ]
Urbina, Cristian [4 ]
机构
[1] Univ Verona, Verona, Italy
[2] Kyushu Univ, Fukuoka, Japan
[3] Univ Palermo, Palermo, Italy
[4] Univ Chile, Santiago, Chile
来源
关键词
Burrows-Wheeler transform; Equal-letter run; Repetitiveness measure; Sensitivity;
D O I
10.1007/978-3-031-33264-7_8
中图分类号
TP39 [计算机的应用];
学科分类号
081203 ; 0835 ;
摘要
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 Theta(log n), where n is the length of the string. These strings can be interpreted both as examples for an increase by a multiplicative or an additive Theta(log n)-factor. As regards multiplicative factor, they attain the upper bound given by Akagi, Funakoshi, and Inenaga [Inf & Comput. 2023] of O( log n log r), since here r = O(1). We then give examples of strings in which insertion, deletion, resp. substitution of a character increases r by a Theta(root n) additive factor. These strings significantly improve the best known lower bound for an additive factor of Omega(log n) [Giuliani et al., SOFSEM 2021].
引用
收藏
页码:86 / 99
页数:14
相关论文
共 50 条
  • [1] An analysis of the Burrows-Wheeler Transform
    Manzini, G
    JOURNAL OF THE ACM, 2001, 48 (03) : 407 - 430
  • [2] Burrows-Wheeler transform for terabases
    Siren, Jouni
    2016 DATA COMPRESSION CONFERENCE (DCC), 2016, : 211 - 220
  • [3] Dynamic Burrows-Wheeler Transform
    Salson, Mikael
    Lecroq, Thierry
    Leonard, Martine
    Mouchard, Laurent
    PROCEEDINGS OF THE PRAGUE STRINGOLOGY CONFERENCE 2008, 2008, : 13 - 25
  • [4] Inverting the Burrows-Wheeler Transform
    Bird, RS
    Mu, SC
    JOURNAL OF FUNCTIONAL PROGRAMMING, 2004, 14 : 603 - 612
  • [5] An extension of the Burrows-Wheeler transform
    Mantaci, S.
    Restivo, A.
    Rosone, G.
    Sciortino, M.
    THEORETICAL COMPUTER SCIENCE, 2007, 387 (03) : 298 - 312
  • [6] An analysis of the Burrows-Wheeler Transform
    Manzini, G
    PROCEEDINGS OF THE TENTH ANNUAL ACM-SIAM SYMPOSIUM ON DISCRETE ALGORITHMS, 1999, : 669 - 677
  • [7] Attacking Scrambled Burrows-Wheeler Transform
    Stanek, Martin
    INFOCOMMUNICATIONS JOURNAL, 2012, 4 (04): : 24 - 27
  • [8] The Burrows-Wheeler similarity distribution between biological sequences based on Burrows-Wheeler transform
    Yang, Lianping
    Zhang, Xiangde
    Wang, Tianming
    JOURNAL OF THEORETICAL BIOLOGY, 2010, 262 (04) : 742 - 749
  • [9] Burrows-Wheeler transform and Sturmian words
    Mantaci, S
    Restivo, A
    Sciortino, M
    INFORMATION PROCESSING LETTERS, 2003, 86 (05) : 241 - 246
  • [10] Resolution of the Burrows-Wheeler Transform Conjecture
    Kempa, Dominik
    Kociumaka, Tomasz
    2020 IEEE 61ST ANNUAL SYMPOSIUM ON FOUNDATIONS OF COMPUTER SCIENCE (FOCS 2020), 2020, : 1002 - 1013