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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Bulletin of mathematical biology 46 (1984), S. 327-332 
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract Levenshtein dissimilarity measures are used to compare sequences in application areas including coding theory, computer science and macromolecular biology. In general, they measure sequence dissimilarity by the length of a shortest weighted sequence of insertions, deletions and substitutions required, to transform one sequence into another. Those Levenshtein dissimilarity measures based on insertions and deletions are analyzed by a model involving valuations on a partially ordered set. The model reveals structural relationships among poset, valuation and dissimilarity measure. As a consequence, certain Levenshtein dissimilarity measures are shown to be metrics characterized by betweenness properties and computable in terms of well-known measures of sequence similarity.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Journal of classification 1 (1984), S. 7-24 
    ISSN: 1432-1343
    Keywords: Algorithm complexity ; Algorithm design ; Centroid clustering method ; Geometric model ; SAHN clustering method
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract Whenevern objects are characterized by a matrix of pairwise dissimilarities, they may be clustered by any of a number of sequential, agglomerative, hierarchical, nonoverlapping (SAHN) clustering methods. These SAHN clustering methods are defined by a paradigmatic algorithm that usually requires 0(n 3) time, in the worst case, to cluster the objects. An improved algorithm (Anderberg 1973), while still requiring 0(n 3) worst-case time, can reasonably be expected to exhibit 0(n 2) expected behavior. By contrast, we describe a SAHN clustering algorithm that requires 0(n 2 logn) time in the worst case. When SAHN clustering methods exhibit reasonable space distortion properties, further improvements are possible. We adapt a SAHN clustering algorithm, based on the efficient construction of nearest neighbor chains, to obtain a reasonably general SAHN clustering algorithm that requires in the worst case 0(n 2) time and space. Whenevern objects are characterized byk-tuples of real numbers, they may be clustered by any of a family of centroid SAHN clustering methods. These methods are based on a geometric model in which clusters are represented by points ink-dimensional real space and points being agglomerated are replaced by a single (centroid) point. For this model, we have solved a class of special packing problems involving point-symmetric convex objects and have exploited it to design an efficient centroid clustering algorithm. Specifically, we describe a centroid SAHN clustering algorithm that requires 0(n 2) time, in the worst case, for fixedk and for a family of dissimilarity measures including the Manhattan, Euclidean, Chebychev and all other Minkowski metrics.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of classification 1 (1984), S. 93-124 
    ISSN: 1432-1343
    Keywords: Algorithm complexity ; Algorithm design ; Binary tree ; Crossover metric ; Dissimilarity measure ; Distance measure ; Hierarchical classification ; nni metric
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract The nearest neighbor interchange (nni) metric is a distance measure providing a quantitative measure of dissimilarity between two unrooted binary trees with labeled leaves. The metric has a transparent definition in terms of a simple transformation of binary trees, but its use in nontrivial problems is usually prevented by the absence of a computationally efficient algorithm. Since recent attempts to discover such an algorithm continue to be unsuccessful, we address the complementary problem of designing an approximation to the nni metric. Such an approximation should be well-defined, efficient to compute, comprehensible to users, relevant to applications, and a close fit to the nni metric; the challenge, of course, is to compromise these objectives in such a way that the final design is acceptable to users with practical and theoretical orientations. We describe an approximation algorithm that appears to satisfy adequately these objectives. The algorithm requires O(n) space to compute dissimilarity between binary trees withn labeled leaves; it requires O(n logn) time for rooted trees and O(n 2 logn) time for unrooted trees. To help the user interpret the dissimilarity measures based on this algorithm, we describe empirical distributions of dissimilarities between pairs of randomly selected trees for both rooted and unrooted cases.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Journal of classification 1 (1984), S. 271-288 
    ISSN: 1432-1343
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Type of Medium: Electronic Resource
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  • 5
    Publication Date: 1983-08-01
    Print ISSN: 0022-5193
    Electronic ISSN: 1095-8541
    Topics: Biology
    Published by Elsevier
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  • 6
    Publication Date: 1983-03-01
    Print ISSN: 0022-5193
    Electronic ISSN: 1095-8541
    Topics: Biology
    Published by Elsevier
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