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1 Fundamenta Informaticae

1 2004

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Efficient String Matching in Huffman Compressed Texts

Fredriksson K., Tarhio J.

Fundamenta Informaticae

2004

Vol. 63, nr 1

1--16

We present an efficient algorithm for scanning Huffman compressed texts. The algorithm parses the compressed text in O(n[(log2σ)/ b]) time, where n is the size of the compressed text in bytes, s is the size of the alphabet, and b is a user specified parameter. The method uses a variable size super-alphabet, with an average size of O([b/( H log2σ)]) characters, where H is the entropy of the text. Each super-character is processed in O(1) time. The algorithm uses O(2b) space and O(b2b) preprocessing time. The method can be easily augmented by auxiliary functions, which can e.g. decompress the text or perform pattern matching in the compressed text. We give three example functions: decoding the text in average time O(n [(log2σ)/ Hω]), where w is the number of bits in a machine word; an Aho-Corasick dictionary matching algorithm, which works in time O(n[(log2 s)/ b]+t), where t is the number of occurrences reported; and a shift-or string matching algorithm that works in time O(n [(log2σ)/ b] é (m+s-1)/ω] u`+t), where m is the length of the pattern and s depends on the encoding. The Aho-Corasick algorithm uses an automaton with variable length moves, i.e. it processes variable number of states at each step. The shift-or algorithm makes variable length shifts, effectively also processing variable number of states at each step. The number of states processed in O(1) time is O([b/( H log2σ)]). The method can be applied to several other algorithms as well. Finally, we apply the methods to natural language taking the words (vocabulary) as the alphabet. This improves the compression ratio and allows more complex search problems to be solved efficiently. We conclude with some experimental results.