Increased Bit-Parallelism for Approximate String Matching

Abstract. Bit-parallelism permits executing several operations simultaneously over a set of bits or numbers stored in a single computer word. This technique permits searching for the approximate occurrences of a pattern of length m in a text of length n in time O(⌈m/w⌉n), where w is the number of bits in the computer word. Although this is asymptotically the optimal speedup over the basic O(mn) time algorithm, it wastes bitparallelism’s power in the common case where m is much smaller than w, since w − m bits in the computer words get unused. In this paper we explore different ways to increase the bit-parallelism when the search pattern is short. First, we show how multiple patterns can be packed in a single computer word so as to search for multiple patterns simultaneously. Instead of paying O(rn) time to search for r patterns of length m < w, we obtain O(⌈r/⌊w/m⌋⌉n) time. Second, we show how the mechanism permits boosting the search for a single pattern of length ...

• Type: Conference
• Year: 2004
• Where: WEA
• Authors: Heikki Hyyrö, Kimmo Fredriksson, Gonzalo Navarro
• Keywords: Algorithms, Approximate Occurrences, Computer Word, Multiple Patterns, WEA 2004