A faster and more accurate heuristic for cyclic edit distance computation

• Published in: Pattern recognition letters Vol. 88; pp. 81 - 87
• Main Authors: Ayad, Lorraine A.K., Barton, Carl, Pissis, Solon P.
• Format: Journal Article
• Language: English
• Published: Amsterdam Elsevier B.V 01-03-2017; Elsevier Science Ltd
• Subjects: Algorithms; Chain code; Circular DNA; Circular sequences; Circularity; Computation; Cyclic edit distance; Cyclic strings; Deoxyribonucleic acid; DNA; Gene sequencing; Heuristic; Microprocessors; Nucleotide sequence; Pattern recognition; Problem solving; q-gram distance; Visibility; Chain code; Circular sequences; Cyclic strings; q-gram distance; 41A10; 65D05; 65D17; Cyclic edit distance; 41A05
• ISSN: 0167-8655; 1872-7344
• DOI: 10.1016/j.patrec.2017.01.018

•This letter describes a new heuristic algorithm to compute the cyclic edit distance.•We extend an existing algorithm which compares circular sequences using q-grams.•Theoretical insight to support the suitability of the algorithm is provided.•Experiments show the heuristic is more accurate compared to existing heuristics.•Experiments show the heuristic is faster compared to existing heuristics.
Sequence comparison is the core computation of many applications involving textual representations of data. Edit distance is the most widely used measure to quantify the similarity of two sequences. Edit distance can be defined as the minimal total cost of a sequence of edit operations to transform one sequence into the other; for a sequence x of length m and a sequence y of length n, it can be computed in time O(mn). In many applications, it is common to consider sequences with circular structure: for instance, the orientation of two images or the leftmost position of two linearised circular DNA sequences may be irrelevant. To this end, an algorithm to compute the cyclic edit distance in time O(mnlogm) was proposed (Maes, 2003 [18]) and several heuristics have been proposed to speed up this computation. Recently, a new algorithm based on q-grams was proposed for circular sequence comparison (Grossi et al., 2016 [13]). We extend this algorithm for cyclic edit distance computation and show that this new heuristic is faster and more accurate than the state of the art. The aim of this letter is to give visibility to this idea in the pattern recognition community.