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

Graph classes and forbidden patterns on three vertices

This paper deals with graph classes characterization and recognition. A popular way to characterize a graph class is to list a minimal set of forbidden induced subgraphs. Unfortunately this strategy usually does not lead to an efficient recognition algorithm. On the other hand, many graph classes can be efficiently recognized by techniques based on some interesting orderings of the nodes, such as the ones given by traversals. We study specifically graph classes that have an ordering avoiding some ordered structures. More precisely, we consider what we call patterns on three nodes, and the recognition complexity of the associated classes. In this domain, there are two key previous works. Damashke started the study of the classes defined by forbidden patterns, a set that contains interval, chordal and bipartite graphs among others. On the algorithmic side, Hell, Mohar and Rafiey proved that any class defined by a set of forbidden patterns can be recognized in polynomial time. We improve on these two works, by characterizing systematically all the classes defined sets of forbidden patterns (on three nodes), and proving that among the 23 different classes (up to complementation) that we find, 21 can actually be recognized in linear time. Beyond this result, we consider that this type of characterization is very useful, leads to a rich structure of classes, and generates a lot of open questions worth investigating.Comment: Third version version. 38 page

Perfect Elimination Orderings for Symmetric Matrices

We introduce a new class of structured symmetric matrices by extending the notion of perfect elimination ordering from graphs to weighted graphs or matrices. This offers a common framework capturing common vertex elimination orderings of monotone families of chordal graphs, Robinsonian matrices and ultrametrics. We give a structural characterization for matrices that admit perfect elimination orderings in terms of forbidden substructures generalizing chordless cycles in graphs.Comment: 16 pages, 3 figure

Graph Searches and Their End Vertices

Graph search, the process of visiting vertices in a graph in a specific order, has demonstrated magical powers in many important algorithms. But a systematic study was only initiated by Corneil et al.~a decade ago, and only by then we started to realize how little we understand it. Even the apparently na\"{i}ve question "which vertex can be the last visited by a graph search algorithm," known as the end vertex problem, turns out to be quite elusive. We give a full picture of all maximum cardinality searches on chordal graphs, which implies a polynomial-time algorithm for the end vertex problem of maximum cardinality search. It is complemented by a proof of NP-completeness of the same problem on weakly chordal graphs. We also show linear-time algorithms for deciding end vertices of breadth-first searches on interval graphs, and end vertices of lexicographic depth-first searches on chordal graphs. Finally, we present $2^n\cdot n^{O(1)}$-time algorithms for deciding the end vertices of breadth-first searches, depth-first searches, maximum cardinality searches, and maximum neighborhood searches on general graphs