title: Efficient edit distance with duplications and contractions.
abstract: : We propose three algorithms for string edit distance with duplications and contractions. These include an efficient general algorithm and two improvements which apply under certain constraints on the cost function. The new algorithms solve a more general problem variant and obtain better time complexities with respect to previous algorithms. Our general algorithm is based on min-plus multiplication of square matrices and has time and space complexities of O (|Σ|MP (n)) and O (|Σ|n2), respectively, where |Σ| is the alphabet size, n is the length of the strings, and MP (n) is the time bound for the computation of min-plus matrix multiplication of two n × n matrices (currently, MP(n)=On3log3lognlog2n due to an algorithm by Chan).For integer cost functions, the running time is further improved to O|Σ|n3log2n. In addition, this variant of the algorithm is online, in the sense that the input strings may be given letter by letter, and its time complexity bounds the processing time of the first n given letters. This acceleration is based on our efficient matrix-vector min-plus multiplication algorithm, intended for matrices and vectors for which differences between adjacent entries are from a finite integer interval D. Choosing a constant 1log|D|n<λ<1, the algorithm preprocesses an n × n matrix in On2+λ|D| time and On2+λ|D|λ2log|D|2n space. Then, it may multiply the matrix with any given n-length vector in On2λ2log|D|2n time. Under some discreteness assumptions, this matrix-vector min-plus multiplication algorithm applies to several problems from the domains of context-free grammar parsing and RNA folding and, in particular, implies the asymptotically fastest On3log2n time algorithm for single-strand RNA folding with discrete cost functions.Finally, assuming a different constraint on the cost function, we present another version of the algorithm that exploits the run-length encoding of the strings and runs in O|Σ|nMP(ñ)ñ time and O(|Σ|nñ) space, where ñ is the length of the run-length encoding of the strings.
authors.affiliation: Department of Computer Science, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
authors.forename: Tamar
authors.initials: T
authors.lastname: Pinhas
authors.affiliation: Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA.
authors.forename: Shay
authors.initials: S
authors.lastname: Zakov
authors.affiliation: Department of Computer Science, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
authors.forename: Dekel
authors.initials: D
authors.lastname: Tsur
authors.affiliation: Department of Computer Science, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
authors.forename: Michal
authors.initials: M
authors.lastname: Ziv-Ukelson