Combinatorial algorithms for the seriation problem

In this thesis we study the seriation problem, a combinatorial problem arising in data analysis, which asks to sequence a set of objects in such a way that similar objects are ordered close to each other. We focus on the combinatorial structure and properties of Robinsonian matrices, a special class of structured matrices which best achieve the seriation goal. Our contribution is both theoretical and practical, with a particular emphasis on algorithms. In Chapter 2 we introduce basic concepts about graphs, permutations and proximity matrices used throughout the thesis. In Chapter 3 we present Robinsonian matrices, discussing their characterizations and recognition algorithms existing in the literature. In Chapter 4 we discuss Lexicographic Breadth-First search (Lex-BFS), a special graph traversal algorithm used in multisweep algorithms for the recognition of several classes of graphs. In Chapter 5 we introduce a new Lex-BFS based algorithm to recognize Robinsonian matrices, which is derived from a new characterization of Robinsonian matrices in terms of straight enumerations of unit interval graphs. In Chapter 6 we introduce the novel Similarity-First Search algorithm (SFS), a weighted version of Lex-BFS which we use in a multisweep algorithm for the recognition of Robinsonian matrices. In Chapter 7 we model the seriation problem as an instance of Quadratic Assignment Problem (QAP) and we show that if the data has a Robinsonian structure, then one can find an optimal solution for QAP using a Robinsonian recognition algorithm. In Chapter 8 we discuss how to solve the seriation problem when the data does not have a Robinsonian structure, by finding a Robinsonian approximation of the original data. Finally, in Chapter 9 we discuss some experiments which we have carried out in order to compare the performance of the algorithms introduced in the thesis.

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