Graph Modification Problems: A Modern Perspective

We give an overview of recent results and techniques in parameterized algorithms for graph modification problems.

sgen1: A generator of small but difficult satisfiability benchmarks

The satisfiability problem is known to be NP-Complete; therefore, there should be relatively small problem instances that take a very long time to solve. However, most of the smaller benchmarks that were once thought challenging, especially the satisfiable ones, can be processed quickly by modern SAT-solvers. We describe and make available a generator that produces both unsatisfiable and, more significantly, satisfiable formulae that take longer to solve than any others known. At the two most recent international SAT Competitions, the smallest unsolved benchmarks were created by this generator. We analyze the results of all solvers in the most recent competition when applied to these benchmarks and also present our own more focused experiments.

Weakening Cardinality Constraints Creates Harder Satisfiability Benchmarks

For some time, the satisfiability formulae that have been the most difficult to solve for their size have been crafted to be unsatisfiable by the use of cardinality constraints. Recent solvers have introduced explicit checking of such constraints, rendering previously difficult formulae trivial to solve. A family of unsatisfiable formulae is described that is derived from the sgen4 family but cannot be solved using cardinality constraints detection and reasoning alone. These formulae were found to be the most difficult during the SAT2014 competition by a significant margin and include the shortest unsolved benchmark in the competition, sgen6-1200-5-1.cnf.

Évolution de familles de gènes par duplications et pertes : algorithmes pour la correction d’arbres bruités

Les gènes sont les parties du génome qui codent pour les protéines. Les gènes d’une ou plusieurs espèces peuvent être regroupés en "familles", en fonction de leur similarité de séquence. Cependant, pour connaître les relations fonctionnelles entre ces copies de gènes, la similarité de séquence ne suffit pas. Pour cela, il est important d’étudier l’évolution d’une famille par duplications et pertes afin de pouvoir distinguer entre gènes orthologues, des copies ayant évolué par spéciation et susceptibles d’avoir conservé une fonction commune, et gènes paralogues, des copies ayant évolué par duplication qui ont probablement développé des nouvelles fonctions. Étant donnée une famille de gènes présents dans n espèces différentes, un arbre de gènes (obtenu par une méthode phylogénétique classique), et un arbre phylogénétique pour les n espèces, la "réconciliation" est l’approche la plus courante permettant d’inférer une histoire d’évolution de cette famille par duplications, spéciations et pertes. Le degré de confiance accordé à l’histoire inférée est directement relié au degré de confiance accordé à l’arbre de gènes lui-même. Il est donc important de disposer d’une méthode préliminaire de correction d’arbres de gènes. Ce travail introduit une méthodologie permettant de "corriger" un arbre de gènes : supprimer le minimum de feuilles "mal placées" afin d’obtenir un arbre dont les sommets de duplications (inférés par la réconciliation) sont tous des sommets de "duplications apparentes" et obtenir ainsi un arbre de gènes en "accord" avec la phylogénie des espèces. J’introduis un algorithme exact pour des arbres d’une certaine classe, et une heuristique pour le cas général.

Essays on decision sciences: exploring cognition, information processing, and complexity

This thesis provides three original contributions to the field of Decision Sciences. The first contribution explores the field of heuristics and biases. New variations of the Cognitive Reflection Test (CRT--a test to measure "the ability or disposition to resist reporting the response that first comes to mind"), are provided. The original CRT (S. Frederick [2005] Journal of Economic Perspectives, v. 19:4, pp.24-42) has items in which the response is immediate--and erroneous. It is shown that by merely varying the numerical parameters of the problems, large deviations in response are found. Not only the final results are affected by the proposed variations, but so is processing fluency. It seems that numbers' magnitudes serve as a cue to activate system-2 type reasoning. The second contribution explores Managerial Algorithmics Theory (M. Moldoveanu [2009] Strategic Management Journal, v. 30, pp. 737-763); an ambitious research program that states that managers display cognitive choices with a "preference towards solving problems of low computational complexity". An empirical test of this hypothesis is conducted, with results showing that this premise is not supported. A number of problems are designed with the intent of testing the predictions from managerial algorithmics against the predictions of cognitive psychology. The results demonstrate (once again) that framing effects profoundly affect choice, and (an original insight) that managers are unable to distinguish computational complexity problem classes. The third contribution explores a new approach to a computationally complex problem in marketing: the shelf space allocation problem (M-H Yang [2001] European Journal of Operational Research, v. 131, pp.107--118). A new representation for a genetic algorithm is developed, and computational experiments demonstrate its feasibility as a practical solution method. These studies lie at the interface of psychology and economics (with bounded rationality and the heuristics and biases programme), psychology, strategy, and computational complexity, and heuristics for computationally hard problems in management science.

A general-purpose tunable landscape generator

The research literature on metalieuristic and evolutionary computation has proposed a large number of algorithms for the solution of challenging real-world optimization problems. It is often not possible to study theoretically the performance of these algorithms unless significant assumptions are made on either the algorithm itself or the problems to which it is applied, or both. As a consequence, metalieuristics are typically evaluated empirically using a set of test problems. Unfortunately, relatively little attention has been given to the development of methodologies and tools for the large-scale empirical evaluation and/or comparison of metaheuristics. In this paper, we propose a landscape (test-problem) generator that can be used to generate optimization problem instances for continuous, bound-constrained optimization problems. The landscape generator is parameterized by a small number of parameters, and the values of these parameters have a direct and intuitive interpretation in terms of the geometric features of the landscapes that they produce. An experimental space is defined over algorithms and problems, via a tuple of parameters for any specified algorithm and problem class (here determined by the landscape generator). An experiment is then clearly specified as a point in this space, in a way that is analogous to other areas of experimental algorithmics, and more generally in experimental design. Experimental results are presented, demonstrating the use of the landscape generator. In particular, we analyze some simple, continuous estimation of distribution algorithms, and gain new insights into the behavior of these algorithms using the landscape generator.