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Title: Time Warps, String Edits and Macromolecules
Written By: Joseph Kruskal
David Sankoff
Description:

Time Warps, String Edits and Macromolecules is a young classic in computational science, scientific analysis from a computational perspective, reissued with a foreword by John Nerbonne. The computational perspective is that of sequence processing, in particular the problem of recognizing related sequences. The book is the first, and still best compilation of papers explaining how to measure distance between sequences, and how to compute that measure effectively. This is called string distance, Levenshtein distance, or edit distance. The book contains lucid explanations of the basic techniques; well-annotated examples of applications; mathematical analysis of its computational (algorithmic) complexity; and extensive discussion of the variants needed for weighted measures, timed sequences (songs), applications to continuous data, comparison of multiple sequences and extensions to tree-structures. In molecular biology the sequences compared are the macromolecules DNA and RNA. Sequence distance allows the recognition of homologies (correspondences) between related molecules. One may interpret the distance between molecular sequences in terms of the mutations necessary for one molecule to evolve into another. A further application explores methods of predicting the secondary structure (chemical bonding) of RNA sequences. In speech recognition speech input must be compared to stored patterns to find the most likely interpretation (e.g., syllable). Because speech varies in tempo, part of the comparison allows for temporal variation, and is known as "time-warping". In dialectology Levenshtein distance allows analysis of the learned variation in pronunication, its cultural component. Levenshtein distance introduces a metric which allows more sophisticated analysis than traditional dialectology's focus on classes of alternative pronunciations. A similar application is the study of bird song, where degrees of distance in song are seen to correspond to the divergence of bird populations. A final application area is software, where Levenshtein distance is employed to located differing parts of different versions of computer files, and to perform error correction.

Publication Year: 2000
Publisher: CSLI Publications
Review: Not available for review. If you would like to review a book on The LINGUIST List, please login to view the AFR list.
BibTex: View BibTex record
Linguistic Field(s): Computational Linguistics
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Versions:
Format: Paperback
ISBN: 1575862174
ISBN-13: N/A
Pages: 408 p