A Computational Algebra Approach to the Reverse Engineering of Gene Regulatory Networks

This paper proposes a new method to reverse engineer gene regulatory networks from experimental data. The modeling framework used is time-discrete deterministic dynamical systems, with a finite set of states for each of the variables. The simplest examples of such models are Boolean networks, in which variables have only two possible states. The use of a larger number of possible states allows a finer discretization of experimental data and more than one possible mode of action for the variables, depending on threshold values. Furthermore, with a suitable choice of state set, one can employ powerful tools from computational algebra, that underlie the reverse-engineering algorithm, avoiding costly enumeration strategies. To perform well, the algorithm requires wildtype together with perturbation time courses. This makes it suitable for small to meso-scale networks rather than networks on a genome-wide scale. The complexity of the algorithm is quadratic in the number of variables and cubic in the number of time points. The algorithm is validated on a recently published Boolean network model of segment polarity development in Drosophila melanogaster.Comment: 28 pages, 5 EPS figures, uses elsart.cl

Consensus theories: an oriented survey

This article surveys seven directions of consensus theories: Arrowian results, federation consensus rules, metric consensus rules, tournament solutions, restricted domains, abstract consensus theories, algorithmic and complexity issues. This survey is oriented in the sense that it is mainly – but not exclusively – concentrated on the most significant results obtained, sometimes with other searchers, by a team of French searchers who are or were full or associate members of the Centre d'Analyse et de Mathématique Sociale (CAMS).Consensus theories ; Arrowian results ; aggregation rules ; metric consensus rules ; median ; tournament solutions ; restricted domains ; lower valuations ; median semilattice ; complexity

On the Use of Dynamic GP Fitness Cases in Static and Dynamic Optimisation Problems

In Genetic Programming (GP), the fitness of individuals is normally computed by using a set of fitness cases (FCs). Research on the use of FCs in GP has primarily focused on how to reduce the size of these sets. However, often, only a small set of FCs is available and there is no need to reduce it. In this work, we are interested in using the whole FCs set, but rather than adopting the commonly used GP approach of presenting the entire set of FCs to the system from the beginning of the search, referred as static FCs, we allow the GP system to build it by aggregation over time, named as dynamic FCs, with the hope to make the search more amenable. Moreover, there is no study on the use of FCs in Dynamic Optimisation Problems (DOPs). To this end, we also use the Kendall Tau Distance (KTD) approach, which quantifies pairwise dissimilarities among two lists of fitness values. KTD aims to capture the degree of a change in DOPs and we use this to promote structural diversity. Results on eight symbolic regression functions indicate that both approaches are highly beneficial in GP

Learning with Latent Language

The named concepts and compositional operators present in natural language provide a rich source of information about the kinds of abstractions humans use to navigate the world. Can this linguistic background knowledge improve the generality and efficiency of learned classifiers and control policies? This paper aims to show that using the space of natural language strings as a parameter space is an effective way to capture natural task structure. In a pretraining phase, we learn a language interpretation model that transforms inputs (e.g. images) into outputs (e.g. labels) given natural language descriptions. To learn a new concept (e.g. a classifier), we search directly in the space of descriptions to minimize the interpreter's loss on training examples. Crucially, our models do not require language data to learn these concepts: language is used only in pretraining to impose structure on subsequent learning. Results on image classification, text editing, and reinforcement learning show that, in all settings, models with a linguistic parameterization outperform those without

Consensus theories: an oriented survey

URL des Documents de travail : http://ces.univ-paris1.fr/cesdp/cesdp2010.htmlDocuments de travail du Centre d'Economie de la Sorbonne 2010.57 - ISSN : 1955-611XThis article surveys seven directions of consensus theories: Arrowian results, federation consensus rules, metric consensus rules, tournament solutions, restricted domains, abstract consensus theories, algorithmic and complexity issues. This survey is oriented in the sense that it is mainly – but not exclusively – concentrated on the most significant results obtained, sometimes with other searchers, by a team of French searchers who are or were full or associate members of the Centre d'Analyse et de Mathématique Sociale (CAMS).Cet article présente une vue d'ensemble de sept directions de recherche en théorie du consensus : résultats arrowiens, règles d'agrégation définies au moyen de fédérations, règles définies au moyen de distances, solutions de tournoi, domaines restreints, théories abstraites du consensus, questions de complexité et d'algorithmique. Ce panorama est orienté dans la mesure où il présente principalement – mais non exclusivement – les travaux les plus significatifs obtenus – quelquefois avec d'autres chercheurs – par une équipe de chercheurs français qui sont – ou ont été – membres pléniers ou associés du Centre d'Analyse et de Mathématique Sociale (CAMS)

A review on Estimation of Distribution Algorithms in Permutation-based Combinatorial Optimization Problems

Estimation of Distribution Algorithms (EDAs) are a set of algorithms that belong to the field of Evolutionary Computation. Characterized by the use of probabilistic models to represent the solutions and the dependencies between the variables of the problem, these algorithms have been applied to a wide set of academic and real-world optimization problems, achieving competitive results in most scenarios. Nevertheless, there are some optimization problems, whose solutions can be naturally represented as permutations, for which EDAs have not been extensively developed. Although some work has been carried out in this direction, most of the approaches are adaptations of EDAs designed for problems based on integer or real domains, and only a few algorithms have been specifically designed to deal with permutation-based problems. In order to set the basis for a development of EDAs in permutation-based problems similar to that which occurred in other optimization fields (integer and real-value problems), in this paper we carry out a thorough review of state-of-the-art EDAs applied to permutation-based problems. Furthermore, we provide some ideas on probabilistic modeling over permutation spaces that could inspire the researchers of EDAs to design new approaches for these kinds of problems

Prototype definition through consensus analysis between fuzzy c-means and archetypal analysis

The general aim of cluster analysis is to build prototypes, or typologies of units that present similar characteristics. In this paper we propose an alternative approach based on consensus analysis of two different clustering methods to suitably obtain prototypes. The clustering methods used are fuzzy c-means (centre approach) and archetypal analysis (extreme approach). The consensus clustering is used to assess the correspondence between the clustering solutions obtained

PROTOTYPE DEFINITION THROUGH CONSENSUS ANALYSIS BETWEEN FUZZY C-MEANS AND ARCHETYPAL ANALYSIS

The general aim of cluster analysis is to build prototypes, or typologies of units that present similar characteristics. In this paper we propose an alternative approach based on consensus analysis of two different clustering methods to suitably obtain proto- types. The clustering methods used are fuzzy c-means (centre approach) and archetypal analysis (extreme approach). The consensus clustering is used to assess the correspon- dence between the clustering solutions obtained