Contributions à l’élaboration de connaissances qualitatives en bio-informatique

This habilitation thesis gathers several works in the field of formal methods for biology. In our works, we tackled the challenge of modeling and analyzing the dynamics of large-scale biological regulatory networks. To address this issue, we identified some relevant class of formal models on which it is possible to perform effective analysis of its dynamics. After discussing the different modeling criteria to be taken into account in biology, we introduce the Process Hitting framework. We then present the methods that we designed to analyze such models, and their respective merits and limitats. Finally, we give an overview of recent research aiming to build a fruitful link between machine learning, logic programming, model-checking and bioinformatics. This allows us to bring out a new set of scientific questions.Cette synthèse pour l’HDR est un recueil de plusieurs travaux dans le domaine des méthodes formelles pour la biologie. Devant l’enjeu que représente la modélisation et l’analyse de la dynamique de réseaux de régulation biologiques à grande échelle, nous avons identifié une classe pertinente de modèles formels sur laquelle il est possible de mener des analyses efficaces de la dynamique. Après avoir discuté les différents critères de modélisation à prendre en compte en biologie, nous introduisons ainsi le formalisme des Frappes de Processus. Nous présentons ensuite les méthodes d’analyse conçues pour ce paradigme, leurs mérites et leurs limites. Enfin, nous revenons sur des résultats plus récents, consécutifs à l’établissement de liens fructueux entre l’apprentissage automatique, la programmation logique, le model-checking et la bio-informatique, ce qui nous permet de faire émerger un ensemble de nouvelles questions scientifiques

Exhaustive analysis of dynamical properties of Biological Regulatory Networks with Answer Set Programming

International audienceThe combination of numerous simple influences between the components of a Biological Regulatory Network (BRN) often leads to behaviors that cannot be grasped intuitively. They thus call for the development of proper mathematical methods to delineate their dynamical properties. As a consequence , formal methods and computer tools for the modeling and simulation of BRNs become essential. Our recently introduced discrete formalism called the Process Hitting (PH), a restriction of synchronous automata networks, is notably suitable to such study. In this paper, we propose a new logical approach to perform model-checking of dynamical properties of BRNs modeled in PH. Our work here focuses on state reachability properties on the one hand, and on the identification of fixed points on the other hand. The originality of our model-checking approach relies in the exhaustive enumeration of all possible simulations verifying the dynamical properties thanks to the use of Answer Set Programming

Abducing Biological Regulatory Networks from Process Hitting models

International audienceThe Process Hitting (PH) is a recently introduced framework to model concurrent processes. It is notably suitable to model Biological Regulatory Networks (BRNs) with partial knowledge of cooperations by defining the most permissive dynamics. On the other hand, the qualitative modeling of BRNs has been widely addressed using René Thomas' formalism. Given a PH model of a BRN, we first tackle the inference of the underlying Interaction Graph between components. Then the inference of corresponding Thomas' models is provided by inferring some parameters and abducing the compatible parametrizations

ITyPA, un premier MOOC francophone et connectiviste

International audienceITyPA, première expérience francophone de MOOC (Massive Open Online Course) au travers d'un cours portant sur l'apprendre avec Internet, a permis de prouver la faisabilité d'une telle approche et de développer une nouvelle communauté de pratique autour de cette thématique. Cet article présente un premier bilan, et les caractéristiques principales de ce dispositif

Identification of Biological Regulatory Networks from Process Hitting models

International audienceQualitative formalisms offer a well-established alternative to the more tradi-tionally used differential equation models of Biological Regulatory Networks (BRNs). These formalisms led to numerous theoretical works and practical tools to understand emerging behaviors. The analysis of the dynamics of very large models is however a rather hard problem, which led us to previously in-troduce the Process Hitting framework (PH), which is a particular class of non-deterministic asynchronous automata network (or safe Petri nets). Its major advantage lies in the efficiency of several static analyses recently designed to assess dynamical properties, making it possible to tackle very large models. In this paper, we address the formal identification of qualitative models of BRNs from PH models. First, the inference of the Interaction Graph from a PH model summarizes the signed influences between the components that are effective for the dynamics. Second, we provide the inference of all René-Thomas models of BRNs that are compatible with a given PH. As the PH allows the specification of nondeterministic interactions between components, our inference emphasizes the ability of PH to deal with large BRNs with incomplete knowledge on interactions, where Thomas's approach fails because of the combinatorics of parameters. The inference of corresponding Thomas models is implemented using An-swer Set Programming, which allows in particular an efficient enumeration of (possibly numerous) compatible parametrizations

Peeling the Paint off the Walls: Kelli Morgan on Black Performance and Racial Justice in Western Institutions

In this conversation with editors Hanna B. Hölling, Jules Pelta Feldman, and Emilie Magnin, Kelli Morgan—critical race scholar, curator, educator, and social justice activist—discusses the challenges related to Western conceptions of institutions and their underpinning values. Addressing the colonialist roots of modern museums, Morgan talks about the challenges she has faced as a Black woman in several U.S. American museums; emphasizes the importance of creating change in museum collections (rather than only in temporary exhibitions); considers alternative practices for conserving art and knowledge; and explains her efforts to address these problems in her pedagogy

Peeling the Paint off the Walls: Kelli Morgan on Black performance and racial justice in Western institutions—A conversation with Hanna B. Hölling, Jules Pelta Feldman and Emilie Magnin

In conversation with editors Hanna B. Hölling, Jules Pelta Feldman and Emilie Magnin, Kelli Morgan—critical race scholar, curator, educator and social justice activist—discusses challenges relating to Western conceptions of institutions and their underpinning values. Addressing the colonialist roots of modern museums, Morgan talks about the challenges she has faced as a Black woman in several US American museums; emphasizes the importance of creating change in museum collections (rather than only in temporary exhibitions); considers alternative practices for conserving art and knowledge; and explains her efforts to address these problems in her pedagogy

Le numérique : une bibliothèque universelle pour la création scientifique ?

La réflexion qui suit trouve sa source dans l’expérience personnelle des auteurs et dans la pratique de leurs collègues français. Elle est propre aux sciences « exactes », mais certains constats, évolutions ou perspectives concernent certainement aussi d’autres secteurs disciplinaires. L’objet de ce propos est d’identifier le rôle et l’emploi de la documentation dans le processus d’élaboration cognitif qui mène le chercheur à la découverte, puis de cerner l’usage de la numérisation qui s’impo..

Un MOOC et ses partenaires - Remettre l'humain dans le massif

International audienceCes derniers mois, les MOOC ont attiré l'attention des professionnels de l'enseignement et la formation. Alors que la croissance des MOOC est phénoménale, des nombreuses critiques surgissent à propos des modèles économiques, l'ingénierie pédagogique insuffisante ou les taux d'abandon élevés. Du 10 octobre au 12 décembre 2013, la deuxième saison d'ITyPA a réuni quelques 2.600 participants. En collaboration avec une quarantaine de partenaires français et internationaux, des rencontres physiques et virtuelles étaient proposées afin de permettre aux inscrits de mieux appréhender les différents aspects du cours, de rythmer leur participation et de maintenir leur niveau de motivation. Du simple meet-up au programme de formation parallèle, les partenaires ont permis une plus grande personnalisation de l'expérience de l'apprenant dans le MOOC, un renforcement de l'ingénierie pédagogique et l'émergence de nouveaux modèles économiques