Publications

2019

• Avis en réponse à la saisine HCB - dossier EFSA-GMO-NL-2018-153. Paris, le 24 mai 2019
  
  • Comité Scientifique Du Haut Conseil Des Biotechnologies .
  • Angevin Frédérique
  • Bagnis Claude
  • Bar-Hen Avner
  • Barny Marie-Anne
  • Boireau Pascal
  • Brévault Thierry
  • Chauvel Bruno B.
  • Collonnier Cécile
  • Couvet Denis
  • Dassa Elie
  • de Verneuil Hubert
  • Demeneix Barbara
  • Franche Claudine
  • Guerche Philippe
  • Guillemain Joël
  • Hernandez Raquet Guillermina
  • Khalife Jamal
  • Klonjkowski Bernard
  • Lavielle Marc
  • Le Corre Valérie
  • Lefèvre François
  • Lemaire Olivier
  • Lereclus Didier D.
  • Maximilien Rémy
  • Meurs Eliane
  • Naffakh Nadia
  • Négre Didier
  • Noyer Jean-Louis
  • Ochatt Sergio
  • Pages Jean-Christophe
  • Raynaud Xavier
  • Regnault-Roger Catherine
  • Renard Michel M.
  • Renault Tristan
  • Saindrenan Patrick
  • Simonet Pascal
  • Troadec Marie-Bérengère
  • Vaissière Bernard
  • Vilotte Jean-Luc
  , 2019.
• Stability Properties of Systems of Linear Stochastic Differential Equations with Random Coefficients
  
  • Bishop Adrian N
  • del Moral Pierre
  SIAM Journal on Control and Optimization, Society for Industrial and Applied Mathematics, 2019, 57 (2), pp.1023-1042. This work is concerned with the stability properties of linear stochastic differential equationswith random (drift and diffusion) coefficient matrices, and the stability of a corresponding ran-dom transition matrix (or exponential semigroup). We consider a class of random matrix driftcoefficients that involves random perturbations of an exponentially stable flow of deterministic(time-varying) drift matrices. In contrast with more conventional studies, our analysis is notbased on the existence of Lyapunov functions, and it does notrely on any ergodic properties.These approaches are often difficult to apply in practice whenthe drift/diffusion coefficients arerandom. We present rather weak and easily checked perturbation-type conditions for the asymp-totic stability of time-varying and random linear stochastic differential equations. We providenew log-Lyapunov estimates and exponential contraction inequalities on any time horizon assoon as the fluctuation parameter is sufficiently small. Theseseem to be the first results of thistype for this class of linear stochastic differential equations with random coefficient matrices. (10.1137/18M1182759)
  DOI : 10.1137/18M1182759
• Inheritance and variability of kinetic gene expression parameters in microbial cells: modeling and inference from lineage tree data
  
  • Marguet Aline
  • Lavielle Marc
  • Cinquemani Eugenio
  Bioinformatics, Oxford University Press (OUP), 2019, 35 (14), pp.i586-i595. Motivation: Modern experimental technologies enable monitoring of gene expression dynamics in individual cells and quantification of its variability in isogenic microbial populations. Among the sources of this variability is the randomness that affects inheritance of gene expression factors at cell division. Known parental relationships among individually observed cells provide invaluable information for the characterization of this extrinsic source of gene expression noise. Despite this fact, most existing methods to infer stochastic gene expression models from single-cell data dedicate little attention to the reconstruction of mother-daughter inheritance dynamics. Results: Starting from a transcription and translation model of gene expression, we propose a sto-chastic model for the evolution of gene expression dynamics in a population of dividing cells. Based on this model, we develop a method for the direct quantification of inheritance and variability of kinetic gene expression parameters from single-cell gene expression and lineage data. We demonstrate that our approach provides unbiased estimates of mother-daughter inheritance parameters, whereas indirect approaches using lineage information only in the post-processing of individual-cell parameters underestimate inheritance. Finally, we show on yeast osmotic shock response data that daughter cell parameters are largely determined by the mother, thus confirming the relevance of our method for the correct assessment of the onset of gene expression variability and the study of the transmission of regulatory factors. Availability and implementation: Software code is available at https://github.com/almarguet/IdentificationWithARME. Lineage tree data is available upon request. (10.1093/bioinformatics/btz378)
  DOI : 10.1093/bioinformatics/btz378
• Scaling of Sub-Ballistic 1D Random Walks Among Biased Random Conductances
  
  • Berger Quentin
  • Salvi Michele
  Markov Processes And Related Fields, Polymat Publishing Company, 2019, 25 (1), pp.171-187. We consider two models of one-dimensional random walks among biased i.i.d.\ random conductances: the first is the classical exponential tilt of the conductances, while the second comes from the effect of adding an external field to a random walk on a point process (the bias depending on the distance between points). We study the case when the walk is transient to the right but sub-ballistic, and identify the correct scaling of the random walk: we find Undefined control sequence \ga such that Undefined control sequence \ga. Interestingly, Undefined control sequence \ga does not depend on the intensity of the bias in the first case, but it does in the second case. %Moreover, with additional information on the distribution of the conductances, we are able to identify more sharply the correct scaling, and the limiting distribution for the rescaled Xn.
• Bayesian Estimation of Population Size Changes by Sampling Tajima's Trees
  
  • Palacios Julia
  • Véber Amandine
  • Cappello Lorenzo
  • Wang Zhangyuan
  • Wakeley John
  • Ramachandran Sohini
  Genetics, Oxford University Press, 2019. The large state space of gene genealogies is a major hurdle for inference methods based on Kingman's coalescent. Here, we present a new Bayesian approach for inferring past population sizes which relies on a lower resolution coalescent process we refer to as "Tajima's coalescent". Tajima's coalescent has a drastically smaller state space, and hence it is a computationally more efficient model, than the standard Kingman coalescent. We provide a new algorithm for efficient and exact likelihood calculations for data without recombination, which exploits a directed acyclic graph and a correspondingly tailored Markov Chain Monte Carlo method. We compare the performance of our Bayesian Estimation of population size changes by Sampling Tajima's Trees (BESTT) with a popular implementation of coalescent-based inference in BEAST using simulated data and human data. We empirically demonstrate that BESTT can accurately infer effective population sizes, and it further provides an efficient alternative to the Kingman's coalescent. The algorithms described here are implemented in the R package phylodyn, which is available for download at https://github.com/JuliaPalacios/phylodyn.
• Stochastic Approximation Schemes for Economic Capital and Risk Margin Computations
  
  • Barrera David
  • Crépey Stéphane
  • Diallo Babacar
  • Fort Gersende
  • Gobet Emmanuel
  • Stazhynski Uladzislau
  ESAIM: Proceedings and Surveys, EDP Sciences, 2019, 65, pp.182-218. We consider the problem of the numerical computation of its economic capital by an insurance or a bank, in the form of a value-at-risk or expected shortfall of its loss over a given time horizon. This loss includes the appreciation of the mark-to-model of the liabilities of the firm, which we account for by nested Monte Carlo à la Gordy and Juneja (2010) or by regression à la Broadie, Du, and Moallemi (2015). Using a stochastic approximation point of view on value-at-risk and expected shortfall, we establish the convergence of the resulting economic capital simulation schemes, under mild assumptions that only bear on the theoretical limiting problem at hand, as opposed to assumptions on the approximating problems in Gordy-Juneja (2010) and Broadie-Du-Moallemi (2015). Our economic capital estimates can then be made conditional in a Markov framework and integrated in an outer Monte Carlo simulation to yield the risk margin of the firm, corresponding to a market value margin (MVM) in insurance or to a capital valuation adjustment (KVA) in banking par- lance. This is illustrated numerically by a KVA case study implemented on GPUs. (10.1051/proc/201965182)
  DOI : 10.1051/proc/201965182
• Reflected stochastic differential equations driven by $G$-Brownian motion in non-convex domains
  
  • Lin Yiqing
  • Soumana-Hima Abdoulaye
  Stochastics and Dynamics, World Scientific Publishing, 2019, 19 (3), pp.n°1950025. In this paper, we first review the penalization method for solving deterministic Skorokhod problems in non-convex domains and establish estimates for problems with $\alpha$-H\"older continuous functions. With the help of these results obtained previously for deterministic problems, we pathwisely define the reflected $G$-Brownian motion and prove its existence and uniqueness in a Banach space. Finally, multi-dimensional reflected stochastic differential equations driven by $G$-Brownian motion are investigated via a fixed-point argument. (10.1142/S0219493719500254)
  DOI : 10.1142/S0219493719500254
• A policy iteration algorithm for non-zero sum stochastic impulse games
  
  • Aïd René
  • Bernal Francisco
  • Mnif Mohamed
  • Zabaljauregui Diego
  • Zubelli Jorge P.
  ESAIM: Proceedings and Surveys, EDP Sciences, 2019, 65 (CEMRACS 2017). This work presents a novel policy iteration algorithm to tackle nonzero-sum stochastic impulse games arising naturally in many applications. Despite the obvious impact of solving such problems, there are no suitable numerical methods available, to the best of our knowledge. Our method relies on the recently introduced characterisation of the value functions and Nash equilibrium via a system of quasi-variational inequalities. While our algorithm is heuristic and we do not provide a convergence analysis, numerical tests show that it performs convincingly in a wide range of situations, including the only analytically solvable example available in the literature at the time of writing. (10.1051/proc/201965027)
  DOI : 10.1051/proc/201965027
• Copula-like Variational Inference
  
  • Hirt Marcel
  • Dellaportas Petros
  • Durmus Alain
  , 2019. This paper considers a new family of variational distributions motivated by Sklar's theorem. This family is based on new copula-like densities on the hypercube with non-uniform marginals which can be sampled efficiently, i.e. with a complexity linear in the dimension of state space. Then, the proposed variational densities that we suggest can be seen as arising from these copula-like densities used as base distributions on the hypercube with Gaussian quantile functions and sparse rotation matrices as normalizing flows. The latter correspond to a rotation of the marginals with complexity $\mathcal{O}(d \log d)$. We provide some empirical evidence that such a variational family can also approximate non-Gaussian posteriors and can be beneficial compared to Gaussian approximations. Our method performs largely comparably to state-of-the-art variational approximations on standard regression and classification benchmarks for Bayesian Neural Networks.
• Climatic niche change of fish is faster at high latitude and in marine environments
  
  • Bourgeaud Luana
  • Rolland Jonathan
  • Carvajal-Quintero Juan David
  • Jézéquel Céline
  • Tedesco Pablo
  • Murienne Jérôme
  • Grenouillet Gaël
  , 2019. Change in species’ climatic niches is a key mechanism influencing species distribution patterns. The question of which factors impact niche change remains a highly debated topic in evolutionary biology. Previous studies have proposed that rates of climatic niche change might be correlated with climatic oscillations at high latitude or adaptation to new environmental conditions. Yet, very few studies have asked if those factors are also predominant in aquatic environments. Here, we reconstruct the climatic niche changes of fish species on a new phylogeny encompassing 12,616 species. We first confirm that the rate of niche change is faster at high latitude and show that this association is steeper for freshwater than for marine species. We also show that freshwater species have slower rates of niche change than marine species. These results may be explained by the fact that freshwater species have larger climatic niche breadth and thermal safety margin than marine species at high latitude. Overall, our study sheds a new light on the environmental conditions and species features impacting rates of climatic niche change in aquatic habitats. (10.1101/853374)
  DOI : 10.1101/853374
• Non-abelian Radon transform and its applications
  
  • Novikov Roman G
  , 2019, pp.115–128. Considerations of the non-abelian Radon transform were started in [Manakov, Zakharov, 1981] in the framework of the theory of solitons in dimension 2+1. On the other hand, the problem of inversion of transforms of such a type arises in different tomographies, including emission tomographies, polarization tomographies, and vector field tomography. In this article we give a short review of old and recent results on this subject. This article is an extended version of the talk given at the conference "100 Years of the Radon Transform", Linz, 27-31 March 2017.
• Commentaires sur le rapport de surveillance de culture du MON 810 en 2017. Paris, le 23 décembre 2019
  
  • Comité Scientifique Du Haut Conseil Des Biotechnologies .
  • Angevin Frédérique
  • Bagnis Claude
  • Bar-Hen Avner
  • Barny Marie-Anne
  • Boireau Pascal
  • Brévault Thierry
  • Chauvel Bruno B.
  • Collonnier Cécile
  • Couvet Denis
  • Dassa Elie
  • Demeneix Barbara
  • Franche Claudine
  • Guerche Philippe
  • Guillemain Joël
  • Hernandez Raquet Guillermina
  • Khalife Jamal
  • Klonjkowski Bernard
  • Lavielle Marc
  • Le Corre Valérie
  • Lefèvre François
  • Lemaire Olivier
  • Lereclus Didier D.
  • Maximilien Rémy
  • Meurs Eliane
  • Naffakh Nadia
  • Négre Didier
  • Noyer Jean-Louis
  • Ochatt Sergio
  • Pages Jean-Christophe
  • Raynaud Xavier
  • Regnault-Roger Catherine
  • Renard Michel M.
  • Renault Tristan
  • Saindrenan Patrick
  • Simonet Pascal
  • Troadec Marie-Bérengère
  • Vaissière Bernard
  • de Verneuil Hubert
  • Vilotte Jean-Luc
  , 2019, pp.41 p.. Les analyses contenues dans le rapport de surveillance de Monsanto ne font apparaître aucun problème majeur associé à la culture de maïs MON 810 en 2017. Cependant, le Comité scientifique (CS) du Haut Conseil des biotechnologies (HCB) a identifié une erreur significative d’analyse statistique remettant en question l’analyse du suivi de la sensibilité des sésamies à la toxine Cry1Ab, et suggérant un possible développement de résistance dans les populations du nord-est de la péninsule Ibérique. Par ailleurs, le CS du HCB identifie encore certaines faiblesses et limites méthodologiques concernant la surveillance de la résistance et la mise en oeuvre des zones refuges. Le HCB estime notamment que l’utilisation d’une dose diagnostic présente certaines limites pour la détection précoce de l’évolution de la résistance, et recommande une méthode alternative de type F2 screen permettant de déterminer la fréquence des allèles de résistance au sein d’une population de ravageurs cibles. Enfin, le HCB demande à obtenir les données brutes des différents essais biologiques pour évaluer la qualité des données et de leur analyse. Concernant la surveillance générale, le CS du HCB relève un problème de pertinence méthodologique quant aux questions étudiées, avec des règles de décision arbitraires, des conclusions incorrectement justifiées et un possible biais associé au format d’enquête auprès d’une sélection d’agriculteurs. Enfin, le CS du HCB recommande que le rapport de surveillance considère la présence de téosinte dans des zones de culture du maïs MON 810 en Espagne et les risques potentiels associés à une éventuelle introgression de gènes de maïs MON 810 chez le téosinte.