An Optimal Algorithm To Recognize Robinsonian Dissimilarities

A dissimilarity D on a finite set S is said to be Robinsonian if S can be totally ordered in such a way that, for every i < j < k, D (i, j) ≤ D (i, k) and D (j, k) ≤ D (i, k). Intuitively, D is Robinsonian if S can be represented by points on a line. Recognizing Robinsonian dissimilarities has many applications in seriation and classification. In this paper, we present an optimal O (n2) algorithm to recognize Robinsonian dissimilarities, where n is the cardinal of S. Our result improves the already known algorithms.

[1]  Alain Guénoche,et al.  Trees and proximity representations , 1991, Wiley-Interscience series in discrete mathematics and optimization.

[2]  Volker Heun Analysis of a modification of Gusfield's recursive algorithm for reconstructing ultrametric trees , 2008, Inf. Process. Lett..

[3]  Kellogg S. Booth PQ-tree algorithms. , 1975 .

[4]  Gilles Caraux,et al.  PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order , 2005, Bioinform..

[5]  Hans-Hermann Bock,et al.  Classification and Related Methods of Data Analysis , 1988 .

[6]  Laurent Viennot,et al.  Lex-BFS and partition refinement, with applications to transitive orientation, interval graph recognition and consecutive ones testing , 2000, Theor. Comput. Sci..

[7]  D. R. Fulkerson,et al.  Incidence matrices and interval graphs , 1965 .

[8]  David Halperin Musical chronology by seriation , 1994, Comput. Humanit..

[9]  Sergey N. Rodin,et al.  Graphs and Genes , 1984 .

[10]  Kellogg S. Booth,et al.  Testing for the Consecutive Ones Property, Interval Graphs, and Graph Planarity Using PQ-Tree Algorithms , 1976, J. Comput. Syst. Sci..

[11]  Lawrence Hubert,et al.  SOME APPLICATIONS OF GRAPH THEORY AND RELATED NON‐METRIC TECHNIQUES TO PROBLEMS OF APPROXIMATE SERIATION: THE CASE OF SYMMETRIC PROXIMITY MEASURES , 1974 .

[12]  M. Golummc Algorithmic graph theory and perfect graphs , 1980 .

[13]  Robert E. Tarjan,et al.  Three Partition Refinement Algorithms , 1987, SIAM J. Comput..

[14]  W. S. Robinson A Method for Chronologically Ordering Archaeological Deposits , 1951, American Antiquity.

[15]  Anna Lubiw,et al.  Doubly lexical orderings of matrices , 1985, STOC '85.

[16]  Victor Chepoi,et al.  Recognition of Robinsonian dissimilarities , 1997 .

[17]  Edwin Diday,et al.  Orders and overlapping clusters by pyramids , 1987 .

[18]  Jeremy P. Spinrad,et al.  Doubly Lexical Ordering of Dense 0 - 1 Matrices , 1993, Inf. Process. Lett..

[19]  M. Golumbic Algorithmic Graph Theory and Perfect Graphs (Annals of Discrete Mathematics, Vol 57) , 2004 .

[20]  Morgan Seston Dissimilarités de Robinson : algorithmes de reconnaissance et d'approximation , 2008 .

[21]  M. Brusco A branch-and-bound algorithm for fitting anti-robinson structures to symmetric dissimilarity matrices , 2002 .

[22]  S. Benzer The fine structure of the gene. , 1962, Scientific American.

[23]  Joydeep Ghosh,et al.  Relationship-Based Clustering and Visualization for High-Dimensional Data Mining , 2003, INFORMS J. Comput..

[24]  Prabhakar Raghavan,et al.  Sparse matrix reordering schemes for browsing hypertext , 1996 .

[25]  János Podani,et al.  REARRANGEMENT OF ECOLOGICAL DATA MATRICES VIA MARKOV CHAIN MONTE CARLO SIMULATION , 2005 .

[26]  K. Okuda,et al.  [The fine structure of the retina]. , 1965, Nihon ganka kiyo.

[27]  Frank Critchley,et al.  The partial order by inclusion of the principal classes of dissimilarity on a finite set, and some of their basic properties , 1994 .

[28]  Victor Chepoi,et al.  Seriation in the Presence of Errors: A Factor 16 Approximation Algorithm for l∞-Fitting Robinson Structures to Distances , 2011, Algorithmica.

[29]  R. Möhring Algorithmic graph theory and perfect graphs , 1986 .

[30]  L. Boneva Seriation with applications in philology , 1980 .

[31]  P. Gilmore,et al.  A Characterization of Comparability Graphs and of Interval Graphs , 1964, Canadian Journal of Mathematics.

[32]  Jean-Pierre Barthélemy,et al.  NP-hard Approximation Problems in Overlapping Clustering , 2001, J. Classif..

[33]  Victor Chepoi,et al.  Seriation in the Presence of Errors: NP-Hardness of l∞ -Fitting Robinson Structures to Dissimilarity Matrices , 2009, J. Classif..

[34]  D. Kendall Incidence matrices, interval graphs and seriation in archeology. , 1969 .

[35]  Chun-Houh Chen,et al.  Matrix Visualization and Information Mining , 2004 .

[36]  W. M. Flinders Petrie,et al.  Sequences in Prehistoric Remains , 1899 .