On the Enumeration of all Minimal Triangulations

We present an algorithm that enumerates all the minimal triangulations of a graph in incremental polynomial time. Consequently, we get an algorithm for enumerating all the proper tree decompositions, in incremental polynomial time, where "proper" means that the tree decomposition cannot be improved by removing or splitting a bag

On the Enumeration of Minimal Dominating Sets and Related Notions

A dominating set $D$ in a graph is a subset of its vertex set such that each vertex is either in $D$ or has a neighbour in $D$. In this paper, we are interested in the enumeration of (inclusion-wise) minimal dominating sets in graphs, called the Dom-Enum problem. It is well known that this problem can be polynomially reduced to the Trans-Enum problem in hypergraphs, i.e., the problem of enumerating all minimal transversals in a hypergraph. Firstly we show that the Trans-Enum problem can be polynomially reduced to the Dom-Enum problem. As a consequence there exists an output-polynomial time algorithm for the Trans-Enum problem if and only if there exists one for the Dom-Enum problem. Secondly, we study the Dom-Enum problem in some graph classes. We give an output-polynomial time algorithm for the Dom-Enum problem in split graphs, and introduce the completion of a graph to obtain an output-polynomial time algorithm for the Dom-Enum problem in $P_6$-free chordal graphs, a proper superclass of split graphs. Finally, we investigate the complexity of the enumeration of (inclusion-wise) minimal connected dominating sets and minimal total dominating sets of graphs. We show that there exists an output-polynomial time algorithm for the Dom-Enum problem (or equivalently Trans-Enum problem) if and only if there exists one for the following enumeration problems: minimal total dominating sets, minimal total dominating sets in split graphs, minimal connected dominating sets in split graphs, minimal dominating sets in co-bipartite graphs.Comment: 15 pages, 3 figures, In revisio

Finding Optimal Tree Decompositions

The task of organizing a given graph into a structure called a tree decomposition is relevant in multiple areas of computer science. In particular, many NP-hard problems can be solved in polynomial time if a suitable tree decomposition of a graph describing the problem instance is given as a part of the input. This motivates the task of finding as good tree decompositions as possible, or ideally, optimal tree decompositions. This thesis is about finding optimal tree decompositions of graphs with respect to several notions of optimality. Each of the considered notions measures the quality of a tree decomposition in the context of an application. In particular, we consider a total of seven problems that are formulated as finding optimal tree decompositions: treewidth, minimum fill-in, generalized and fractional hypertreewidth, total table size, phylogenetic character compatibility, and treelength. For each of these problems we consider the BT algorithm of Bouchitté and Todinca as the method of finding optimal tree decompositions. The BT algorithm is well-known on the theoretical side, but to our knowledge the first time it was implemented was only recently for the 2nd Parameterized Algorithms and Computational Experiments Challenge (PACE 2017). The author’s implementation of the BT algorithm took the second place in the minimum fill-in track of PACE 2017. In this thesis we review and extend the BT algorithm and our implementation. In particular, we improve the eciency of the algorithm in terms of both theory and practice. We also implement the algorithm for each of the seven problems considered, introducing a novel adaptation of the algorithm for the maximum compatibility problem of phylogenetic characters. Our implementation outperforms alternative state-of-the-art approaches in terms of numbers of test instances solved on well-known benchmarks on minimum fill-in, generalized hypertreewidth, fractional hypertreewidth, total table size, and the maximum compatibility problem of phylogenetic characters. Furthermore, to our understanding the implementation is the first exact approach for the treelength problem

Finding Optimal Triangulations Parameterized by Edge Clique Cover

Peer reviewe

Finding Optimal Triangulations Parameterized by Edge Clique Cover

Publisher Copyright: © 2022, The Author(s).We consider problems that can be formulated as a task of finding an optimal triangulation of a graph w.r.t. some notion of optimality. We present algorithms parameterized by the size of a minimum edge clique cover (cc) to such problems. This parameterization occurs naturally in many problems in this setting, e.g., in the perfect phylogeny problem cc is at most the number of taxa, in fractional hypertreewidth cc is at most the number of hyperedges, and in treewidth of Bayesian networks cc is at most the number of non-root nodes. We show that the number of minimal separators of graphs is at most 2 cc, the number of potential maximal cliques is at most 3 cc, and these objects can be listed in times O∗(2 cc) and O∗(3 cc) , respectively, even when no edge clique cover is given as input; the O∗(·) notation omits factors polynomial in the input size. These enumeration algorithms imply O∗(3 cc) time algorithms for problems such as treewidth, weighted minimum fill-in, and feedback vertex set. For generalized and fractional hypertreewidth we give O∗(4 m) time and O∗(3 m) time algorithms, respectively, where m is the number of hyperedges. When an edge clique cover of size cc′ is given as a part of the input we give O∗(2cc′) time algorithms for treewidth, minimum fill-in, and chordal sandwich. This implies an O∗(2 n) time algorithm for perfect phylogeny, where n is the number of taxa. We also give polynomial space algorithms with time complexities O∗(9cc′) and O∗(9cc+O(log2cc)) for problems in this framework.Peer reviewe

Enumerating Minimal Connected Dominating Sets in Graphs of Bounded Chordality

Listing, generating or enumerating objects of specified type is one of the principal tasks in algorithmics. In graph algorithms one often enumerates vertex subsets satisfying a certain property. We study the enumeration of all minimal connected dominating sets of an input graph from various graph classes of bounded chordality. We establish enumeration algorithms as well as lower and upper bounds for the maximum number of minimal connected dominating sets in such graphs. In particular, we present algorithms to enumerate all minimal connected dominating sets of chordal graphs in time O(1.7159^n), of split graphs in time O(1.3803^n), and of AT-free, strongly chordal, and distance-hereditary graphs in time O^*(3^{n/3}), where n is the number of vertices of the input graph. Our algorithms imply corresponding upper bounds for the number of minimal connected dominating sets for these graph classes

Solving Graph Problems via Potential Maximal Cliques : An Experimental Evaluation of the Bouchitté-Todinca Algorithm

Peer reviewe

Polynomial-time algorithm for Maximum Weight Independent Set on P6P_6-free graphs

In the classic Maximum Weight Independent Set problem we are given a graph $G$ with a nonnegative weight function on vertices, and the goal is to find an independent set in $G$ of maximum possible weight. While the problem is NP-hard in general, we give a polynomial-time algorithm working on any $P_6$-free graph, that is, a graph that has no path on $6$ vertices as an induced subgraph. This improves the polynomial-time algorithm on $P_5$-free graphs of Lokshtanov et al. (SODA 2014), and the quasipolynomial-time algorithm on $P_6$-free graphs of Lokshtanov et al (SODA 2016). The main technical contribution leading to our main result is enumeration of a polynomial-size family $\mathcal{F}$ of vertex subsets with the following property: for every maximal independent set $I$ in the graph, $\mathcal{F}$ contains all maximal cliques of some minimal chordal completion of $G$ that does not add any edge incident to a vertex of $I$