CompressedSuffixArraysbasedonRunLengthEncoding.pptVIP

20.6.2005 Compressed suffix arrays based on run-length encoding Compressed Suffix Arrays based on Run-Length Encoding Veli M?kinen Bielefeld University Abstract We introduce a new full-text index that occupies O(Hk|T|) bits and supports counting queries in O(|P|) time.- optimal space / search time on constant alphabet- works on any alphabet size s, adding log s to the space/time bounds. Introduction We consider exact string matching on static text. The task is to construct an index for the text such that the occurrences of a given pattern can be found efficiently. Well known optimal solution exists: build a suffix tree over the text. Introduction... The suffix-tree-based solution takes O(|T| log |T|) bits of space. Text itself can be represented in O(|T| log s) bits.- or even less space if text is compressible. In many applications the space usage is the real bottleneck, not the search efficiency. Introduction... During the last 15 years, many practical / theoretical solutions with reduced space complexities have been proposed. The work can roughly be divided into three categories:(1) Reducing constant factors(2) Concrete optimization(3) Abstract optimization Reducing constant factors Suffix arrays (Manber Myers 1990) Suffix cactuses (K?rkk?inen 1995) Sparse suffix trees (K?rkk?inen Ukkonen 1996) Space-efficient suffix trees (Kurtz 1998) Enhanced suffix arrays (Abouelhoda Ohlebusch Kurtz 2002) Concrete optimization “? Minimizing automata” DAWGS (Blumer Blumer Haussler McConnel Ehrenfeucht 1983) Compact DAWGS (Crochemore Vérin 1997) Compact suffix arrays (M?kinen 2000) Abstract optimization Objective: Use as few space as possible to support the functionality of a given abstract definition of a data structure. Space is measured in bits and usually given proportional to the entropy of the text. Abstract optimization: Example A full text index for a given text T supports the following operations:- Exists(P): is P a substring of T? - Count(P): h