Incremental complexity of a bi-objective hypergraph transversal problem

The hypergraph transversal problem has been intensively studied, from both a theoretical and a practical point of view. In particular , its incremental complexity is known to be quasi-polynomial in general and polynomial for bounded hypergraphs. Recent applications in computational biology however require to solve a generalization of this problem, that we call bi-objective transversal problem. The instance is in this case composed of a pair of hypergraphs (A, B), and the aim is to find minimal sets which hit all the hyperedges of A while intersecting a minimal set of hyperedges of B. In this paper, we formalize this problem, link it to a problem on monotone boolean $\land$ -- $\lor$ formulae of depth 3 and study its incremental complexity

Polynomial Delay Algorithm for Listing Minimal Edge Dominating sets in Graphs

The Transversal problem, i.e, the enumeration of all the minimal transversals of a hypergraph in output-polynomial time, i.e, in time polynomial in its size and the cumulated size of all its minimal transversals, is a fifty years old open problem, and up to now there are few examples of hypergraph classes where the problem is solved. A minimal dominating set in a graph is a subset of its vertex set that has a non empty intersection with the closed neighborhood of every vertex. It is proved in [M. M. Kant\'e, V. Limouzy, A. Mary, L. Nourine, On the Enumeration of Minimal Dominating Sets and Related Notions, In Revision 2014] that the enumeration of minimal dominating sets in graphs and the enumeration of minimal transversals in hypergraphs are two equivalent problems. Hoping this equivalence can help to get new insights in the Transversal problem, it is natural to look inside graph classes. It is proved independently and with different techniques in [Golovach et al. - ICALP 2013] and [Kant\'e et al. - ISAAC 2012] that minimal edge dominating sets in graphs (i.e, minimal dominating sets in line graphs) can be enumerated in incremental output-polynomial time. We provide the first polynomial delay and polynomial space algorithm that lists all the minimal edge dominating sets in graphs, answering an open problem of [Golovach et al. - ICALP 2013]. Besides the result, we hope the used techniques that are a mix of a modification of the well-known Berge's algorithm and a strong use of the structure of line graphs, are of great interest and could be used to get new output-polynomial time algorithms.Comment: proofs simplified from previous version, 12 pages, 2 figure

The Bases of Association Rules of High Confidence

We develop a new approach for distributed computing of the association rules of high confidence in a binary table. It is derived from the D-basis algorithm in K. Adaricheva and J.B. Nation (TCS 2017), which is performed on multiple sub-tables of a table given by removing several rows at a time. The set of rules is then aggregated using the same approach as the D-basis is retrieved from a larger set of implications. This allows to obtain a basis of association rules of high confidence, which can be used for ranking all attributes of the table with respect to a given fixed attribute using the relevance parameter introduced in K. Adaricheva et al. (Proceedings of ICFCA-2015). This paper focuses on the technical implementation of the new algorithm. Some testing results are performed on transaction data and medical data.Comment: Presented at DTMN, Sydney, Australia, July 28, 201

Computing knock out strategies in metabolic networks

Given a metabolic network in terms of its metabolites and reactions, our goal is to efficiently compute the minimal knock out sets of reactions required to block a given behaviour. We describe an algorithm which improves the computation of these knock out sets when the elementary modes (minimal functional subsystems) of the network are given. We also describe an algorithm which computes both the knock out sets and the elementary modes containing the blocked reactions directly from the description of the network and whose worst-case computational complexity is better than the algorithms currently in use for these problems. Computational results are included.Comment: 12 page

Enumerating all minimal hitting sets in polynomial total time

Consider a hypergraph (=set system) $\mathbb{H}$ whose $h$ hyperedges are subsets of a set with w elements. We show that the $R$ minimal hitting sets of $\mathbb{H}$ can be enumerated in polynomial total time $O(Rh^2 w^2)$.Comment: 8 page

Discovery of the D-basis in binary tables based on hypergraph dualization

Discovery of (strong) association rules, or implications, is an important task in data management, and it nds application in arti cial intelligence, data mining and the semantic web. We introduce a novel approach for the discovery of a speci c set of implications, called the D-basis, that provides a representation for a reduced binary table, based on the structure of its Galois lattice. At the core of the method are the D-relation de ned in the lattice theory framework, and the hypergraph dualization algorithm that allows us to e ectively produce the set of transversals for a given Sperner hypergraph. The latter algorithm, rst developed by specialists from Rutgers Center for Operations Research, has already found numerous applications in solving optimization problems in data base theory, arti cial intelligence and game theory. One application of the method is for analysis of gene expression data related to a particular phenotypic variable, and some initial testing is done for the data provided by the University of Hawaii Cancer Cente

Discovery of the D-basis in binary tables based on hypergraph dualization

Discovery of (strong) association rules, or implications, is an important task in data management, and it nds application in arti cial intelligence, data mining and the semantic web. We introduce a novel approach for the discovery of a speci c set of implications, called the D-basis, that provides a representation for a reduced binary table, based on the structure of its Galois lattice. At the core of the method are the D-relation de ned in the lattice theory framework, and the hypergraph dualization algorithm that allows us to e ectively produce the set of transversals for a given Sperner hypergraph. The latter algorithm, rst developed by specialists from Rutgers Center for Operations Research, has already found numerous applications in solving optimization problems in data base theory, arti cial intelligence and game theory. One application of the method is for analysis of gene expression data related to a particular phenotypic variable, and some initial testing is done for the data provided by the University of Hawaii Cancer Cente