{"id":112,"date":"2023-09-28T15:13:56","date_gmt":"2023-09-28T13:13:56","guid":{"rendered":"https:\/\/project.inria.fr\/gdtmathbio\/?page_id=112"},"modified":"2026-03-26T09:01:32","modified_gmt":"2026-03-26T08:01:32","slug":"rencontres-passees","status":"publish","type":"page","link":"https:\/\/project.inria.fr\/gdtmathbio\/rencontres-passees\/","title":{"rendered":"Rencontres pass\u00e9es"},"content":{"rendered":"<p class=\"has-medium-font-size\"> <strong>Journ\u00e9e 2 \u00e0 Lyon (UMPA) le 20 mars 2026 (10h30 -16h) <\/strong><\/p>\n<ul>\n<li> 10h30 : Charles Elbar : <em>Including surface tension for tumor growth modeling with the Cahn-Hilliard equation<\/em> <\/li>\n<p class=\"has-small-font-size\"> We are motivated by invasive cancer. A common approach is to use Hele-Shaw models with surface tension, these are models where the tumor is decribed by a set, moving with pressure effects. The surface tension models the cell-to-cell adhesive forces on the boundary of the tumor. However these models may be hard to study \/ compute numerically, and we can use instead the Cahn-Hilliard equation. <\/p>\n<\/li>\n<li> 11h30 :Maxime Colomb : <em>ICI: Simulations \u00e9pid\u00e9miologiques utilisant un jumeau num\u00e9rique du territoire et de sa population<\/em> <\/li>\n<li> 14h : C\u00e9line Bonnet : <em> Data-driven mathematical modeling differentiates between cytotoxic and cytostatic effects of nutritive environments<\/em>\n<p class=\"has-small-font-size\"> I will present a method to analysis longitudinal flow cytometry and population growth biological data using Bellman Harris stochastic processes (or age-structured Birth and Death processes).  <\/p>\n<\/li>\n<li> 15h : Franck Picard : <em> PCA for Point Processes<\/em>\n<p class=\"has-small-font-size\"> We introduce a novel statistical framework for the analysis of replicated point processes that allows for the study of point pattern variability at a population level. By treating point process realizations as random measures, we adopt a functional analysis perspective and propose a form of functional Principal Component Analysis (fPCA) for point processes. The originality of our method is to base our analysis on the cumulative mass functions of the random measures which gives us a direct and interpretable analysis. Key theoretical contributions include establishing a Karhunen-Lo\u00e8ve expansion for the random measures and a Mercer Theorem for covariance measures. We establish convergence in a strong sense, and introduce the concept of principal measures, which can be seen as latent processes governing the dynamics of the observed point patterns. We propose an easy-to-implement estimation strategy of eigenelements for which parametric rates are achieved. We fully characterize the solutions of our approach to Poisson and Hawkes processes and validate our methodology via simulations and diverse applications in seismology, single-cell biology and neurosiences, demonstrating its versatility and effectiveness. Our method is implemented in the pppca R-package.  <\/p>\n<\/li>\n<\/ul>\n<p class=\"has-medium-font-size\"> <strong>29 janvier, \u00e0 l&rsquo;Institut Fourier, Grenoble.<\/strong><\/p>\n<ul>\n<li>Olivier Ali (INRIA et ENS Lyon): <em>Geometry hidden in plain stress &#8211; Exploring the relationship between pressure-induced stresses and geometry in plant tissues.<\/em>\n<p class=\"has-small-font-size\"> Mechanical stresses play a central role during the morphogenesis of multicellular structures. Not only do they generate tissue deformations but they also provide cells with signals triggering differentiation and pacing development. This is especially true in growing plant epthelia where turgidity generates tremendous stresses within cell walls.<br \/>\nFrom a systematic perspective, one can wonder what kind of signaling cues, turgor-induced stresses can provide growing cells with?<br \/>\nIn this presentation, we will see how such stresses can be related to a specific kind of geometrical descriptors of surfaces: Killing and \u00ab\u00a0pseudo\u00a0\u00bb-Killing vectors fields.<\/p>\n<\/li>\n<li>Sylvain Billiard (Universit\u00e9 de Lille): <em> Stochastic interactions in ecology: microscopic models, macroscopic approximations and inference.<br \/>\n<\/em><\/p>\n<p class=\"has-small-font-size\"> How rapidly do individuals interact in ecological systems? What mechanisms drive variation in interaction rates? These questions are central to population biology, as interaction rates determine the birth and death processes of prey and predators and, consequently, their population dynamics. Interaction rates also influence, among many others, the intensity of competition, infection success, and the fluxes of matter and energy within ecosystems.<br \/>\nI will present two stochastic process frameworks used to derive approximations of interaction rates from individual behavior and traits, with a particular focus on predator\u2013prey interactions. Within each framework, I will then develop inferential tools based on these approximations. Finally, I will apply these tools to experimental data to identify and quantify the different sources of variation in interaction rates, including measurement error, inter-individual variability, and endogenous stochasticity.<\/p>\n<\/li>\n<\/ul>\n<p class=\"has-medium-font-size\"> <strong>Journ\u00e9e 1 \u00e0 Marseille le 5 d\u00e9cembre 2025 (10h30 -16h).<\/strong><\/p>\n<ul>\n<li>Fran\u00e7ois d&rsquo;Alayer de Costemore d&rsquo;Arc (INRAE BioSP)<\/li>\n<li> Loup Rimbaud (INRAE PV),<\/li>\n<li> Daniel Pasquel (INRAE EMMAH),<\/li>\n<li> Th\u00e9o Garcia (I2M, ALEA). <\/li>\n<\/ul>\n<p class=\"has-medium-font-size\"> <strong>9 octobre 2025 \u00e0 l&rsquo;UMPA, ENS de Lyon.<\/strong><\/p>\n<ul>\n<li>Vitaly Volpert, (CNRS, University Lyon 1): <em>Mathematical modelling of inflammation and inflammatory diseases<\/em>\n<p class=\"has-small-font-size\"> Inflammation is a fundamental biological response to injury or infection, but its dysregulation underlies numerous chronic diseases. This lecture explores the mathematical modelling of inflammation and inflammatory diseases, integrating biological mechanisms at local and systemic levels. We begin with a biological background, highlighting key cellular and molecular players and their roles in initiating, amplifying, and resolving inflammation. We examine the amplification and resolution phases of inflammation, emphasizing feedback loops, thresholds, and bifurcations that govern transitions between acute and chronic states. Applications to atherosclerosis, Alzheimer\u2019s disease and other inflammatory disorders are discussed illustrating how models predict disease progression and treatment.<\/p>\n<\/li>\n<li>Peter Vermeiren, (Charg\u00e9 de Recherche, RiverLy Unit, INRAE Lyon-Grenoble Auvergne-Rh\u00f4ne-Alpes)<em> Modelling bioaccumulation of environmental pollutants using scarce wildlife biomonitoring data.<br \/>\n<\/em><\/p>\n<p class=\"has-small-font-size\"> With 1000s of chemicals interacting with 1000s of species in our environment, understanding and predicting the risks of environmental pollutants to biodiversity structure and functioning is of critical importance to species conservation and environmental management. Nevertheless, data regarding concentrations of pollutants within wildlife species are scarce, with data collection limited by financial, labour and ethical restrictions, as well as technical difficulties to measure small trace amounts for a large number of environmental pollutants. In this presentation, I will use a case study of the maternal transfer of organic pollutants between reptile mothers and their eggs, to illustrate some of the challenges and approaches toward quantifying pollution bioaccumulation across generations.<br \/>\nSpecifically, we developed a large database through the systematic review and extraction of data from the published literature. In parallel, we set up a Bayesian error-in-variable (EIV) regression model to quantitatively link observed variables (e.g. pollutant concentrations in mothers and their eggs) while accounting for uncertainties and the presence of censored data points (i.e. observations whose value is only known to be within an interval rather than a unique value). Subsequently, we applied the EIV model to the synthesised dataset to statistically analyse the maternal transfer of organic pollutants in reptiles. Different versions of the EIV model accounted for species-specific differences, with the models made available to users with limited statistical background through the \u201cMaternal TRACER\u201d shiny app. Furthermore, a maternal transfer EIV model applicable to alligators is also being integrated into an individual-based modelling framework to simulate the lifelong accumulation of pollutants for populations of alligators under realistic field conditions.<\/p>\n<\/li>\n<\/ul>\n<p class=\"has-medium-font-size\"><strong>3e journ\u00e9e 6 juin 2025 \u00e0 Grenoble (journ\u00e9e soutenue par le RT Math Bio Sant\u00e9)<\/strong><\/p>\n<ul>\n<li>10h-11h : Charline Smadi (INRAE, IF, Grenoble): <em>Muller\u2019s ratchet with binary tournament selection: Clickrates and type frequency profile<\/em>\n<p class=\"has-small-font-size\">Muller\u2019s ratchet, in its prototype version, models a haploid, asexual population whose size is constant over the generations. Slightly deleterious mutations are acquired along the lineages at a constant rate, and individuals carrying less mutations have a selective advantage. In the classical variant, the individual fitness is proportional to the difference between the population average and the individual\u2019s mutation load, whereas in the \u2018tournament ratchet\u2019 the individual fitness results as a sum of binary comparisons of the individual mutation loads. We obtain the asymptotic click rates of the tournament ratchet in a large parameter regime. We also analyse the type frequency profile of a sample drawn at a late time.<br \/>\nThis is based on an undergoing work, as well as on :<br \/>\n\u2013 A. Gonzalez Casanova, C. Smadi, and A. Wakolbinger. Quasi-equilibria and click times for a variant of Muller\u2019s ratchet. Electronic Journal of Probability, 2023.<br \/>\n\u2013 J. Igelbrink, A. Gonzalez Casanova, C. Smadi, and A. Wakolbinger. Muller\u2019s ratchet in a near-critical regime: Tournament versus fitness proportional selection. Theoretical Population Biology, 2024.<\/p>\n<\/li>\n<li>11h15- 12h15 : Magali Richard (TIMC, Grenoble) : <em>Statistical and computational methods for the analysis of tumor heterogeneity <\/em>\n<p class=\"has-small-font-size\">Cancer is a highly heterogeneous disease, with each individual tumor evolving as a multicellular autonomous system. Tumors are composed of cells with different identities and origins, that dynamically interact with each other to form the tumor ecosystem. Heterogeneity in tumor cellular composition is a key factor driving cancer progression yet it remains difficult to observe and quantify. To date, our limited ability to accurately estimate this heterogeneity has hampered our understanding of its role during oncogenic processes.<br \/>\nOur work lies at the intersection of bioinformatics, biostatistics, and oncology. We develop and apply computational methods to analyze high-dimensional, multimodal molecular data. This includes single-cell and spatial transcriptomic datasets, which we use to address key questions in fundamental cancer research. In this talk, I will present some of the methods we have designed to characterise tumor heterogeneity and explore its functional implications. I will also highlight our efforts to promote collaborative algorithm benchmarking and evaluation within the scientific community through data challenge frameworks.<\/p>\n<\/li>\n<li>13h45-14h45 : Thomas Lepoutre (Inria Lyon) : <em>Modelling relaxation experiments <\/em>\n<p class=\"has-small-font-size\">Abstract: We analyze the relaxation dynamics of the CD34 antigen on the surface of TF1-BA cells by conducting two relaxation experiments. We propose that the expression of this gene serves as a reliable marker for cell stemness. In the first experiment, we studied the isolation of the least stem cells, while in the second, the most stem cells. In both cases, it is observed that after approximately 25 days the distribution of stemness returns to the initial stationary state. This highlights the complexity of the stemness process, given its dynamic nature. To model these complex dynamics, we introduced a system of two mechanical equations. We have theoretically derived the asymptotic profile of the solutions of this model. Additionally, utilizing data obtained from the relaxation experiments, we estimated the parameter values. Numerical simulations, based on these parameter values, have shown that the model solutions closely align with the experimental data from the relaxation experiments.<\/p>\n<\/li>\n<li>15h-16h : Sophie Achard (LJK, Grenoble) : <em>Statistical comparisons of spatio-temporal networks<\/em>\n<p class=\"has-small-font-size\"> In the scenario where multiple instances of networks with same nodes are available and nodes are attached to spatial features, it is worth combining both information in order to explain the role of the nodes. The explainability of node role in complex networks is very difficult, however crucial in different application scenarios such as social science, neuroscience, computer science. . . Many efforts have been made on the quantification of hubs revealing particular nodes in a network using a given structural property.<br \/>\nYet, for spatio-temporal networks, the identification of node role remains largely unexplored. In this talk, I will show limitations of classical methods on a real datasets coming from brain connectivity comparing healthy subjects to coma patients. Then, I will present recent work using equivalence relation of the nodal structural properties. Comparisons of graphs with same nodes set is evaluated with a new similarity score based on graph structural patterns. This score provides a nodal index to determine node role distinctiveness in a graph family. Finally, illustrations on different datasets concerning human brain functional connectivity will be described.<\/p>\n<\/li>\n<\/ul>\n<p class=\"has-small-font-size\"> Journ\u00e9e soutenue par le RT Math-Bio-Sant\u00e9.<br \/>\n<strong><a href=\"https:\/\/project.inria.fr\/gdtmathbio\/files\/2025\/02\/logolastcolor.png\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/project.inria.fr\/gdtmathbio\/files\/2025\/02\/logolastcolor-300x85.png\" alt=\"\" width=\"300\" height=\"85\"><\/a><\/strong><\/p>\n<p class=\"has-medium-font-size\"><strong>15 mai 2025 \u00e0 Lyon (ICJ)<\/strong><\/p>\n<li>Laetitia Colombani (ISFA, Lyon): <em>Interacting birth-death processes in adaptation to an environmental change and their lineages<\/em>\n<p class=\"has-small-font-size\">In the last decades, environmental changes and the consequences of the evolution of the population, especially the phenotypic evolution, have been described by different models. In this ongoing study, with Tran and M\u00e9l\u00e9ard, we aim to understand the individual dynamics of a population. In particular, we want to describe the ancestral lineage of a living individual. Some preliminary work has been published by Calvez, Henry, M\u00e9l\u00e9ard and Tran in 2022 when the initial population is well distributed and is close to the stationary solution of a PDE.<br \/>\nIn this talk, I will introduce the model, its construction, and the link with the PDE of the macroscopic dynamics of the phenotypic density. I&rsquo;ll then describe some of the results we obtain when we consider any initial repartition of the population.<\/p>\n<\/li>\n<li>R\u00e9mi Tuffet (LBBE, Lyon): <em>The Paradox of Plasmid Diversity<\/em>\n<p class=\"has-small-font-size\">Plasmids are circular DNA molecules independent of the bacterial chromosome that can be transferred horizontally between bacteria in an autonomous manner. As such, they are the main vector for horizontal gene transfer between bacteria. In particular, they are responsible for the rapid dissemination of many antibiotic resistance genes, as well as some virulence genes. Plasmids are therefore a threat to our healthcare systems, and it is essential to better understand their eco-evolutionary dynamics.<br \/>\nHaving established that there is a wide diversity of plasmids, just as there can be a great diversity of interacting species in communities, we propose to apply the theories and concepts of community ecology to  bacterial plasmids. In particular, we develop models of competition between plasmids to illustrate how the three main theories of biodiversity (ecological niche partitioning theory, neutral biodiversity theory and emergent neutrality theory) can be applied to plasmids.<\/p>\n<\/li>\n<p class=\"has-medium-font-size\"><strong>3 avril 2025 \u00e0 Lyon (UMPA)<\/strong><\/p>\n<li>10h-10h50: Nicolas Alcala (CIRC, Lyon): <em>The mathematics of diversity: theory and applications to anthropology, ecology, and oncology.<\/em>\n<p class=\"has-small-font-size\">Diversity\u2014the degree to which individuals in a populations are different\u2014has a central role in many disciplines, in particular in the life science. In evolutionary biology, genetic and phenotypic diversity drive evolution and are key to understanding human traits. In ecology, diversity reflects ecosystem health and the ability to adapt to environmental changes, such as climate change. In oncology, genetic diversification of tissues plays a central role in tumor initiation and progression, and intra-tumor heterogeneity is a key predictor of response to treatment and relapse. Nevertheless, there is considerable debate regarding which diversity metric should be used to quantify diversity.I will present a recent body of work studying the mathematical properties of various diversity metrics\u2014in particular the conditions under which they are maximized or minimized\u2014and show how this analysis reconciles their sometimes apparently contradictory behaviors. I will show how this allows to lift apparent contradictions in multiple fields, including debates on the extent of genetic differences among Human populations, the level of diversity in threatened species, and the impact of carcinogens on tumor DNA.<\/p>\n<\/li>\n<li>11h-11h50: Youcef Mammeri (ICJ, Saint-Etienne): <em>Du phlo\u00e8me au paysage : quelques probl\u00e8mes de mod\u00e9lisation continue des interactions plantes-ravageurs<\/em>\n<p class=\"has-small-font-size\">Je pr\u00e9senterai quelques r\u00e9sultats concernant la mod\u00e9lisation du d\u00e9veloppement des plantes dans leur environnement. Nous d\u00e9buterons par un nouveau mod\u00e8le d\u00e9crivant la distribution du sucrose dans les arbres, pour ensuite aborder la propagation des ravageurs (v\u00e9g\u00e9taux ou animaux) au sein des paysages agricoles. Mon propos sera centr\u00e9 sur des syst\u00e8mes continus de type advection-r\u00e9action-diffusion.<\/p>\n<\/li>\n<p class=\"has-medium-font-size\"><strong>Journ\u00e9e 2 \u00e0 Marseille le 21 mars 2025 (10h-16h)<br \/>\n<\/strong><\/p>\n<ul>\n<li>Claudia Alvarez (Laboratoire de Math\u00e9matiques d&rsquo;Avignon): <em>Stability of the Chemostat system with interaction between species.<\/em>\n<p class=\"has-small-font-size\">The Chemostat system represents a special class of dynamical systems describing the behavior of multiple species that compete over a same substrate within a reactor. This model finds application in diverse areas, notably in the investigation of wastewater treatment. We are interested in the study of a subclass of Chemostat system where direct interspecies interaction is considered. Such interaction can be related to some underlying mutation processes. Our main objective is to understand the stability properties of such systems considering the interaction between species to be as general as possible.<\/p>\n<\/li>\n<li>Florence Bansept (Laboratoire de Chimie Bact\u00e9rienne, Aix-Marseille): <em>How does intermittent feeding shape the gut microbiome?<\/em>\n<p class=\"has-small-font-size\"> Feeding impacts the composition of the gut microbiome in animal hosts. While most research efforts have been directed towards studying the impact of the nutritional bolus on the microbiome composition, the effective use of probiotics suggests that, at least in some cases, the immigration of microbes through feeding also has the potential to modify its composition. In community ecology, immigration is considered a key factor to maintain the diversity of a local community; furthermore, a diverse gut microbiome is usually considered an important determinant of health. Thus, questions arise: do hosts adapt their feeding behavior so as to manipulate microbial immigration in a way that facilitates the maintenance of a diverse flora? What fluctuations are to be expected in the community composition from feeding intermittence, and should sampling be controlled for it?We develop a mathematical model of microbial communities with birth, death and intermittent migration to study these questions. We show the existence in most cases &#8211; when the number of species is large enough &#8211; of an optimal feeding strategy, characterized by a relationship between the feeding interval and the food microbial content, that maximizes the average of the microbial diversity over time. We developed a linear approximation of the OFS and showed that its existence is a sufficient condition for the existence of an OFS. In addition, we showed that diversity largely correlates with that of the food, and that the optimal feeding parameters converge to values we are able to explain analytically. We plan to compare our theoretical results with experimental studies in vitro and in different animal hosts, as we expect these effects to depend on host characteristics, like typical transit time.<\/p>\n<\/li>\n<li>Apolline Louvet (BioSP &#8211; INRAE)<\/li>\n<li>Elias Ventre (COMPO &#8211; INRIA):<em> Calibration of stochastic models of gene expression from single-cell datasets<\/em>\n<p class=\"has-small-font-size\"> Differentiation is the process by which a cell acquires a certain phenotype, through the expression of genes over time. It is now accepted that this dynamic is largely the result of the action of a gene regulatory network (GRN). Studying the action of this GRN in the cells of an organism is one of the main tasks of the field of systems biology. A particularly interesting approach to this problem is to model the dynamics of a cell under the action of its GRN by a stochastic process: GRN inference can then be seen as the calibration of the model from experimental datasets. A first approach is to use a generic model, such as a system of stochastic differential equations, and to employ non-parametric methods based on optimal transport theory. This approach has the advantage of benefiting from highly efficient existing tools. Another approach is to use a mechanistic model, a system of piecewise deterministic Markov processes directly parameterized by a GRN, which is more suitable for taking into account biological priors, but requires the development of appropriate tools. I&rsquo;ll illustrate the effectiveness of these approaches on simulated and experimental data.<\/p>\n<\/li>\n<\/ul>\n<p class=\"has-medium-font-size\"><strong>6 f\u00e9vrier 2025 \u00e0 Grenoble<\/strong><\/p>\n<div class=\"elementToProof\">10h : Vincent Brault (LJK, Grenoble):&nbsp;<i>Segmentation du Parsimonious Oscillatory Model of Handwriting&nbsp;et application \u00e0 la d\u00e9tection d&rsquo;enfants dysgraphiques<\/i><\/div>\n<p class=\"has-small-font-size\">La ma\u00eetrise de l&rsquo;\u00e9criture manuscrite reste essentielle pour une int\u00e9gration r\u00e9ussie dans la soci\u00e9t\u00e9, mais elle repose sur un long processus d&rsquo;apprentissage. Les troubles de l&rsquo;\u00e9criture, appel\u00e9s dysgraphies, peuvent donc avoir des cons\u00e9quences graves, de la petite enfance \u00e0 l&rsquo;\u00e2ge adulte. En France, la d\u00e9tection de ces troubles se fait g\u00e9n\u00e9ralement \u00e0 l&rsquo;aide du test Brave Handwriting Kinder (ou BHK ; voir voir Hamstra-Bletzet al. (1987) et son adaptation fran\u00e7aise par Charles et al. (2004))) consistant \u00e0 faire \u00e9crire des enfants pendant 5 minutes et \u00e0 faire \u00e9valuer ce texte selon 13 crit\u00e8res par un sp\u00e9cialiste en psychomotricit\u00e9. L&rsquo;un des inconv\u00e9nients de cette proc\u00e9dure est qu&rsquo;elle est longue et fastidieuse et qu&rsquo;un certain nombre d&rsquo;enfants peuvent ne pas \u00eatre diagnostiqu\u00e9s.Pour contourner ce probl\u00e8me, l&rsquo;une des pistes explor\u00e9e dans le cadre du post-doc de Yunjiao Lu est de s&rsquo;appuyer sur le Parsimonious Oscillatory Model of Handwriting (ou mod\u00e8le POMH ; voir Andr\u00e9 et al. (2014)) qui part du principe que l&rsquo;\u00e9criture est le r\u00e9sultat de deux oscillateurs orthogonaux compos\u00e9s de fonctions constantes par morceaux. En trouvant les instants o\u00f9 les fonctions changent de valeurs, les auteurs reconstruisent les traces faites par les enfants. Dans son post-doc, Yunjiao Lu montre que l&rsquo;estimation du nombre et des emplacements des ruptures dans ces fonctions influent sur la reconstruction et semblent varier suivant la qualit\u00e9 de l&rsquo;\u00e9criture (voir Lu et al. (2022)) ; elle essaie notamment d&rsquo;estimer l&rsquo;influence des param\u00e8tres de filtrage sur l&rsquo;aide \u00e0 la pr\u00e9diction d&rsquo;un diagnostic de dysgraphie.Dans cet expos\u00e9, nous \u00e9tudierons une autre piste pour estimer les emplacements de ruptures. Apr\u00e8s avoir expos\u00e9 la probl\u00e9matique, nous montrerons que le mod\u00e8le POMH peut \u00eatre vu comme un mod\u00e8le de segmentation o\u00f9 la programmation dynamique permet d&rsquo;estimer les emplacements de ruptures. Nous d\u00e9montrerons \u00e9galement que la forme particuli\u00e8re du mod\u00e8le permet au maximum de vraisemblance d&rsquo;\u00eatre un estimateur consistant de l&#8217;emplacement mais surtout du nombre de ruptures. Nous terminerons par une \u00e9tude de cette mod\u00e9lisation sur la d\u00e9tection de la dysgraphie.R\u00e9f\u00e9rences<br \/>\nG. Andr\u00e9, V. Kostrubiec, J.-C. Buisson, J.-M. Albaret, et P.-G. Zanone. A parsimonious oscillatory model of handwriting. Biological cybernetics, 108(3):321\u2013336, 2014.<br \/>\nM. Charles, R. Soppelsa, et J.-M. Albaret. Bhk: \u00e9chelle d&rsquo;\u00b4evaluation rapide de l&rsquo;\u00e9criture chez l&rsquo;enfant. Ecpa, 2004.<br \/>\nL. Hamstra-Bletz, J. DeBie, B. Den Brinker, et al. Concise evaluation scale for children&rsquo;s handwriting. Lisse: Swets, 1:623\u2013662, 1987.<br \/>\nY. Lu, J. Boutet, V. Brault, C. Jolly, E. Labyt, R. Lambert, et J.-C. Quinton. Number of zero velocity points: a critical parameter for handwriting model estimation towards dysgraphia diagnosis assistance. Dans 53\u00e8mes journ\u00e9es de statistique, 2022.<\/p>\n<div class=\"elementToProof\">11h : Antoine Fr\u00e9noy (TIMC, Grenoble) :&nbsp;<em>Simulation-based parameter inference in population biology: revisiting Luria Delbr\u00fcck problem through stochastic simulations<br \/>\n<\/em><\/div>\n<p class=\"has-small-font-size\">Genesis and growth of mutants is a central processus in evolutionary biology. The rate at which mutations randomly appear is a key parameter, determining the speed at which genetic diversity is generated. It is classically estimated through a classical experiment called the fluctuation test, where bacteria are growth in a non-selective medium and then exposed to a selective environment to count surviving mutants. Mutation rate is then inferred from the number of surviving mutants, using a now classical mathematical model which makes restrictive assumptions about the demographic processes involved.In this work, we are interested in more general cases not covered by this classical model (more complex demographics). We developed an efficient algorithm for stochastic simulation of this problem, and use it to perform simulation-based inference using approximate bayesian computing methods. We show that these methods can successfully infer one or several parameters of the model in arbitrarily complex growth models.<\/p>\n<p class=\"has-medium-font-size\"><strong>9 janvier 2025 \u00e0 Lyon (ICJ)<\/strong><\/p>\n<div class=\"elementToProof\">10h: Ella Hiesmayr (UMPA, Lyon):&nbsp;<i>Mean-field interacting multi-type birth-death processes with a view to applications in phylodynamics<\/i>.<\/div>\n<div class=\"elementToProof\">11h: Samuel Bernard (Inria Lyon, Musics)<em>: Implication of lipid turnover for the control of energy balance <\/em><\/div>\n<p class=\"has-small-font-size\">The ongoing obesity epidemic is a consequence of a progressive energy imbalance. The energy-balance model (EBM) posits that obesity results from an excess in food intake and circulating fuels. A reversal in causality has been proposed recently in the form of the carbohydrate-insulin model (CIM), according to which fat storage drives energy imbalance. Under the CIM, dietary carbohydrates shift energy use in favour of storage in adipose tissue. The dynamics of lipid storage and mobilisation could therefore be sensitive to changes in carbohydrate intake and represent a measurable component of the CIM. To characterise potential changes in lipid dynamics induced by carbohydrates, mathematical models were<br \/>\nused. Here we propose a coherent mathematical implementation of the CIM (energy deposition model, CIM-EDM), which includes lipid turnover dynamics. Using lipid turnover data previously obtained by radiocarbon dating, we build two cohorts of virtual patients and simulate lipid dynamics during aging and weight loss. We identify clinically testable lipid dynamic parameters that discriminate between the CIM-EDM and an energy in, energy out implementation of the EBM (EBM-IOM). Using a clinically relevant two-month virtual trial, we additionally identify scenarios and propose mechanisms whereby individuals may<br \/>\nrespond differently to low carbohydrate diets. Work in collaboration with Kirsty Spalding (Karolinska Institute)<\/p>\n<p class=\"has-medium-font-size\"><strong>Journ\u00e9e 1 \u00e0 Lyon le 19 d\u00e9cembre 2024<\/strong><\/p>\n<ul>\n<li>10h30: <a href=\"https:\/\/www.normalesup.org\/~bienvenu\/\">Fran\u00e7ois Bienvenu<\/a> (CNRS, Universit\u00e9 de Besan\u00e7on) : <em>The B2 index of galled trees<\/em>\n<p class=\"has-small-font-size\">In recent years, there has been an effort to extend the classical notion of phylogenetic balance, originally defined in the context of trees, to networks. One of the most natural ways to do this is with the so-called B2 index. In this talk, we study the B2 index for a prominent class of phylogenetic networks: galled trees. We show that the B2 index of a uniform leaf-labeled galled tree converges in distribution as the network becomes large, and we characterize the corresponding limiting distribution.This work combines two different and independent approaches, each with its advantages: analytic combinatorics, and local limits. The analytic combinatorics approach is more direct, as it relies on standard tools; but it involves slightly more complex calculations. Because it has not previously been used to study such questions, the local limit approach requires developing an extensive framework beforehand; however, this framework is interesting in itself and can be used to tackle other similar problems. In this talk, we exclusively focus on the local limit approach.<\/p>\n<\/li>\n<\/ul>\n<ul>\n<li>11h30: <a href=\"https:\/\/mathildeeandre.github.io\/\">Mathilde Andr\u00e9<\/a> (Universit\u00e9 de Besan\u00e7on, ENS de Paris) : <em>Directed configuration model with edge lengths: a framework for the spread of epidemics<\/em>\n<p class=\"has-small-font-size\">We introduce a multitype directed configuration model (DCM) as a mathematical framework for understanding the spread of infectious diseases. Building on the inherent versatility of configuration models, our model incorporates a multitype structure by endowing edges with an integer length. These edge lengths represent transmission delays, enabling a detailed exploration of infection dynamics. Through directed breadth-first explorations and coupling with multitype branching processes on countable state spaces, we analyze the dynamics and emergence of geodesics. This work aims to establish conditions under which the successive times of infection between distinguished focal vertices converge weakly, in the large population scaling limit, to the atoms of a Cox point process with a characterized intensity. This result generalizes existing findings on first-passage percolation in configuration models, such as those in [Bhamidi et al., 2017]. Applications to epidemiology are highlighted, demonstrating how this framework allows us to extend previous results on the epidemic curve [Barbour and Reinert, 2013] to a discrete-time setting under minimal assumptions. Finally, the model&rsquo;s relevance is illustrated through biological case studies and simulations.<br \/>\nThis ongoing research is a collaboration with Jean-Jil Duchamps (Besan\u00e7on).<\/p>\n<\/li>\n<\/ul>\n<ul>\n<li>12h30-14h: Repas en salle passerelle.<\/li>\n<\/ul>\n<ul>\n<li>14h: <a href=\"https:\/\/fr.linkedin.com\/in\/landry-duguet-a536b0198\">Landry Duguet<\/a> (LBMC ENS de Lyon, Mosaic): <em>Waves in a 1D canalization model with finite resources<\/em>\n<p class=\"has-small-font-size\">The study of Phyllotaxis (the arrangement of leaves around plant stems) has led the community to observe emergent travelling waves of a morphogen called auxin (Galvan-Ampudia &amp; Cerutti et al. 2020). Models of auxin transport have been proposed to understand several aspect of plant development through the equilibrium patterns they can produce. It is the first time the question of understanding auxin transport dynamically is raised by biological data. We take back a known auxin transport model based on a canalization feedback between auxin fluxes and the auxin efflux carriers, and study its ability to produce emergent traveling waves. A parameter space analysis allows to simulate traveling waves. A continuum limit of the model and a phase space analysis allows to detail the mechanism of traveling wave propagation. It is closely linked to a hysteresis phenomenon&#8230;<\/p>\n<\/li>\n<\/ul>\n<ul>\n<li>15h: <a href=\"https:\/\/fr.linkedin.com\/in\/niami-nasr-a59666266\">Niami Nasr<\/a> (ICJ, Saint-Etienne): <em>M\u00e9thodes num\u00e9riques de fronti\u00e8re immerg\u00e9e pour un probl\u00e8me inverse en imagerie m\u00e9dicale.<\/em>\n<p class=\"has-small-font-size\">La tomographie par imp\u00e9dance \u00e9lectrique (EIT) est une technique d&rsquo;imagerie non invasive visant \u00e0 reconstruire la distribution de conductivit\u00e9 \u00e9lectrique \u00e0 l&rsquo;int\u00e9rieur d&rsquo;un domaine en appliquant des courants \u00e9lectriques au bord de celui-ci \u00e0 travers des \u00e9lectrodes et en mesurant les tensions r\u00e9sultantes. Math\u00e9matiquement, le probl\u00e8me, connu sous le nom de probl\u00e8me de Calder\u00f3n ou probl\u00e8me inverse de conductivit\u00e9, est un probl\u00e8me inverse fortement mal pos\u00e9. L&rsquo;inconnue principale de ce probl\u00e8me inverse est la conductivit\u00e9, mais le manque d&rsquo;informations concernant d&rsquo;autres variables telles que la forme g\u00e9om\u00e9trique du domaine dans lequel nous visons \u00e0 reconstruire la conductivit\u00e9, ainsi que les positions des \u00e9lectrodes, peut influencer la qualit\u00e9 de la reconstruction. Par cons\u00e9quent, nous consid\u00e9rons le probl\u00e8me d&rsquo;EIT avec une g\u00e9om\u00e9trie inconnue mobile.<br \/>\nLa r\u00e9solution d&rsquo;un tel probl\u00e8me peut \u00eatre co\u00fbteuse en termes de calcul, en particulier lors de l&rsquo;utilisation de m\u00e9thodes num\u00e9riques qui n\u00e9cessitent un maillage adapt\u00e9 en raison des \u00e9tapes de remaillage. Pour les \u00e9viter, nous proposons une approche par m\u00e9thode de fronti\u00e8re immerg\u00e9e (IBM) pour la r\u00e9solution num\u00e9rique du mod\u00e8le d&rsquo;\u00e9lectrode complet en Tomographie d&rsquo;Imp\u00e9dance \u00c9lectrique. Cette m\u00e9thode permet l&rsquo;utilisation d&rsquo;un maillage cart\u00e9sien sans n\u00e9cessiter une discr\u00e9tisation pr\u00e9cise de la fronti\u00e8re, ce qui s&rsquo;av\u00e8re utile dans les situations o\u00f9 la fronti\u00e8re est complexe et\/ou mobile. Nous d\u00e9montrons la convergence de notre m\u00e9thode et en illustrons l&rsquo;efficacit\u00e9 dans des probl\u00e8mes directs et inverses en deux dimensions.<br \/>\nL&rsquo;utilisation de m\u00e9thodes de fronti\u00e8re immerg\u00e9e pour r\u00e9soudre le probl\u00e8me direct permet \u00e9galement une parall\u00e9lisation ais\u00e9e de la m\u00e9thode et le d\u00e9veloppement d&rsquo;un code parall\u00e8le d\u00e9di\u00e9 au probl\u00e8me direct. Il est \u00e0 noter que ce travail s&rsquo;inscrit dans le contexte de l&rsquo;imagerie \u00e9lectrocardiographique (ECGi). Pour l&rsquo;ECGi, l&rsquo;inconnue principale est l&rsquo;activit\u00e9 \u00e9lectrique du c\u0153ur. L&rsquo;objectif \u00e0 long terme est d&rsquo;\u00e9valuer si l&rsquo;EIT peut fournir plus d&rsquo;informations sur la conductivit\u00e9 des organes \u00e0 l&rsquo;int\u00e9rieur du volume du torse.<\/p>\n<\/li>\n<\/ul>\n<p class=\"has-medium-font-size\"><strong>14 novembre 2024 \u00e0 Grenoble, Institut Fourier salle B29, 10h-12h<\/strong><\/p>\n<div class=\"elementToProof\">10h : Pierre RECHO (LiPhy, UGA): <em>A mechanical interpretation of the Fisher-KPP equation<\/em><\/div>\n<p class=\"has-small-font-size\">In ecology, the Fisher-KPP equation is often motivated by the proliferation of a population of randomly moving individuals in an environment with finite ressources. In this talk, I will show that this<br \/>\nequation also appears as the limit of a Stefan problem originating from an active gel model of a proliferating cell monolayer with a free boundary. The advancement of the leading edge still relies on cell<br \/>\nproliferation and protrusive activity at the tissue margin but the effective diffusion coefficient has now a direct mechanical interpretation.<\/p>\n<p>11h : Nicolas ZADEH (Universit\u00e9 Libre de Bruxelles): <em>Kinetic description and numerical study of a network of resonate and fire neurons<\/em><\/p>\n<p class=\"has-small-font-size\">An important feature of some neurons is their ability to display resonant-like properties. The resonate and fire (RF) model (Izhikevich, 2001) allows for a simple description of such neurons, for a meager computational cost. We will first present a mean-field description of a network of interconnected RF neurons, following the kinetic formalism.<br \/>\nThen a numerical approximation finite differences scheme designed to tackle the equation will be seen, having mass and positivity preservation properties. Some simulations giving validity to the mean-field approach conclude the talk.<\/p>\n<p class=\"has-medium-font-size\"><strong>10 octobre 2024 \u00e0 l&rsquo;UMPA, ENS Lyon<\/strong><\/p>\n<p>10h : Thao Nguyen (ENS de Lyon, laboratoire LBMC): &nbsp;<em>Multiscale Modeling of Neuroblastoma Organoids: From Gene Regulatory Networks to Spatial Dynamics<\/em><\/p>\n<p class=\"has-small-font-size\">In this talk, I will present a multiscale model of neuroblastoma organoids, which are child tumors of the sympathetic nervous system derived from the primitive neural crest cells. At the molecular level, we implemented a simple gene regulatory network (GRN) in the form of a toggle switch between two genes, one driving the stemness and the other characterizing a differentiated phenotype. This GRN has been encoded as a biologically realistic mechanistic model driven by transcriptional burst for gene expression. Cellular decision-making (proliferation, death, differentiation) is driven by protein concentrations produced by the GRN. To check the realism of the 3D structures obtained, we compared the simulation results, both visually and using appropriate statistics, with immunohistochemistry (IHC) images, using quantitative measurements of spatial distributions.<\/p>\n<p>11h : L\u00e9o Girardin (ICJ, Lyon 1): &nbsp;<em>Persistence and propagation of structured populations in space-time periodic media<\/em><\/p>\n<p class=\"has-small-font-size\">This talk is concerned with asymptotic persistence, extinction and spreading properties for structured population models resulting in non-cooperative Fisher-KPP systems with space-time periodic coefficients. Results are formulated in terms of a family of generalized principal eigenvalues associated with the linearized problem. When the maximal generalized principal eigenvalue is negative, all solutions to the Cauchy problem become locally uniformly positive in long-time, at least one space-time periodic uniformly positive entire solution exists, and solutions with compactly supported initial condition asymptotically spread in space at a speed given by a Freidlin-G\u00e4rtner-type formula. When another, possibly smaller, generalized principal eigenvalue is nonnegative, then on the contrary all solutions to the Cauchy problem vanish uniformly and the zero solution is the unique space-time periodic nonnegative entire solution. When the twogeneralized principal eigenvalues differ and zero is in between, the long-time behavior depends on the decay at infinity of the initial condition. The proofs rely upon double-sided controls by solutions of cooperative systems.&nbsp; The control from below is new for such systems and makes it possible to shorten the proofs and extend the generality of the system simultaneously.<\/p>\n<p class=\"has medium-font-size\"><strong> Journ\u00e9e 3 \u00e0 Grenoble le 21 juin 2024 (10h-16h)<\/strong><\/p>\n<p>10h30 &#8211; 11h30: Julien Chevallier (LJK, Grenoble),<em> Estimation de la densit\u00e9 d\u2019un graphe de d\u00e9pendance en grande dimension<\/em><\/p>\n<p class=\"has-small-font-size\">L\u2019objectif est d\u2019estimer la densit\u00e9 de connexion d\u2019un graphe de d\u00e9pendance entre N agents, dans la limite o\u00f9 N tend vers l\u2019infini, \u00e0 partir de la seule observation de N processus \u00e0 temps discret en interaction. Plus pr\u00e9cis\u00e9ment, le mod\u00e8le que nous proposons poss\u00e8de : 1) un graphe d\u2019Erdos-R\u00e9nyi de param\u00e8tre p, 2) conditionnellement \u00e0 ce graphe latent, les observations forment une chaine de Markov \u00e0 valeurs dans {0,1}^N. Dans ce cadre, l\u2019objectif est d\u2019estimer le param\u00e8tre p.<br \/>\nJe pr\u00e9senterai notre estimateur et sa vitesse de convergence.&nbsp;Si le temps le permet, je pr\u00e9senterai, au choix de l\u2019audience : 1)&nbsp;des&nbsp;arguments heuristiques qui expliquent sa convergence, 2) quelques d\u00e9tails sur des r\u00e9sultats de matrices al\u00e9atoires, 3) quelques d\u00e9tails sur le contr\u00f4le des corr\u00e9lations&nbsp;spatio-temporelles du processus.&nbsp;Enfin, je pr\u00e9senterai des illustrations issues de simulations.Travail en collaboration avec Eva L\u00f6cherbach et Guilherme Ost.<\/p>\n<p>11h30 &#8211; 12h30: Patrick Vallet (INRAE, Grenoble)<\/p>\n<p>13h45 &#8211; 14h45: Clara Lage (ENS de Lyon):<em> Identifying a piecewise affine signal from its nonlinear observation &#8211; application to DNA replication analysis<\/em><\/p>\n<p class=\"has-small-font-size\">An important challenge in DNA replication analysis is to recover a so-called timing profile, that contains important information about the replication dynamics, from nonlinear observations. We show that this can be expressed as a nonlinear inverse problem where the unknown timing profile can be assumed to be piecewise affine. As this problem cannot be directly addressed with techniques for linear inverse problems, we propose a novel formalism and computational approach to harness it. In the noiseless case, we establish sufficient identifiability conditions for the timing profile, and prove that it is the solution of a non-convex optimization problem. These problems are specially challenging because of their multiple local minima. We propose the DNA-Inverse optimization method that is capable of finding their global solution in the noiseless case and proved to be effective in numerical experiments for noisy signals. Comparative analysis against state-of-the-art optimization methods highlights the superior computational efficiency of our approach. The method enables the automatic recovery of all configurations of the replication dynamics, crucial for DNA replication analysis, which was not possible with previous methods.<\/p>\n<p>15h &#8211; 16h: Vincent Miele (CNRS, LECA Chamb\u00e9ry\/Grenoble): <em>ELGRIN, un mod\u00e8le statistique pour quantifier l&rsquo;effet des interactions biotiques sur la distribution des esp\u00e8ces le long de gradients environnementaux.<\/em><\/p>\n<p class=\"has-small-font-size\">We propose a novel statistical model, called ELGRIN (in reference to Charles Elton and Joseph Grinnell) that can handle the effects of both environmental factors and known interspecific interactions (aka a metanetwork) on species distributions. We rely on Markov random fields to handle dependencies between variables using a graph. More specifically, ELGRIN jointly models the presence and absence of all species in a given area in function of environmental covariates and the topological structure of the known metanetwork. It separates the interspecific interaction effects from those of the environment on species distributions.<br \/>\nUsing various simulated and empirical data, we demonstrate the suitability of ELGRIN to address the objectives for various types of interspecific interactions like mutualism, competition and trophic interactions. We then apply the model on vertebrate trophic networks in the European Alps.<\/p>\n<p class=\"has-medium-font-size\"><strong>16 mai 2024 : ICJ, Lyon<\/strong><\/p>\n<p>10h : Audrey Denizot (AIstroSight, Inria Lyon) : <em>Towards elucidating astrocyte function in the brain: insights from stochastic spatially-extended models<\/em><\/p>\n<p class=\"has-small-font-size\">Astrocytes are cells of the brain that have recently emerged as key regulators of signal transmission, taking part in higher brain functions such as memory and learning. Astrocytes communicate with neighboring cells with changes in intracellular calcium concentration: Ca2+ signals. Most of these signals occur at the nanoscale, hindering their study in live tissue, so that computational approaches are essential to gain insights into their dynamics. To take into account the complex morphology of astrocytes and the stochasticity of reactions occuring in the resulting nanoscopic compartments, we have developed reaction-diffusion particle-based and voxel-based models of astrocyte Ca2+ dynamics. Our simulations revealed mechanisms by which spatial factors such as the clustering of Ca2+ channels, Ca2+ buffering, ER shape and distribution influence the spatio-temporal properties of Ca2+ signals. Astrocytes and their Ca2+ signals are essential to the functioning of the nervous system and are altered in most brain disorders. As research has for long focused on treating neurons, little is known about astrocyte (patho-)physiology and better characterizing astrocyte function might lead to the discovery of new treatments for the diseased brain.<\/p>\n<p>11h: Jimmy Garnier (LAMA, Univ. Savoie Mont-Blanc): <em>Mutualism at the leading edge: Insights into the eco-evolutionary dynamics of host-symbiont communities during range expansion<\/em><\/p>\n<p class=\"has-small-font-size\">The evolution of mutualism between host and symbiont communities plays an essential role in maintaining ecosystem function and should therefore have a profound effect on their range expansion dynamics. In particular, the presence of mutualistic symbionts at the leading edge of a host-symbiont community should enhance its propagation in space. I will present a theoretical framework that captures the eco-evolutionary dynamics of host-symbiont communities, and allow us to investigate how the evolution of resource exchange may shape community structure during range expansion.<\/p>\n<p class=\"has-medium-font-size\"><strong>Journ\u00e9e 2 \u00e0 Marseille le 8 avril 2024<\/strong><\/p>\n<p>10h30-11h30: Chlo\u00e9 GUICHARNAUD : <em>Tir\u00e9e ou pouss\u00e9e? \u00c9tude de populations en expansion via l&rsquo;utilisation conjointe de mod\u00e8les individus-centr\u00e9s et d&rsquo;exp\u00e9riences en laboratoire<\/em><br \/>\n11h30-12h30: Nathana\u00ebl BOUTILLON : <em>Une \u00e9quation de Fisher-KPP avec une dimension spatiale et une dimension ph\u00e9notypique : persistance et propagation<\/em><br \/>\n15h30-16h30: Marie Jose CHAAYA : <em>A continuous approach of modeling tumorigenesis and axons regulation for the pancreatic cancer<\/em><\/p>\n<p class=\"has-medium-font-size\"><strong>14 mars 2024 : Institut Fourier salle B29, Grenoble<\/strong><\/p>\n<p>10h : Adeline Leclercq Samson (LJK, UGA) : <em>Some statistical models to quantify the effect of climate change on whales in Greenland<\/em><\/p>\n<p class=\"has-small-font-size\">Human activities have a profound impact on marine ecology in Greenland. In this presentation, I will focus on a study of the impact of these activities on narwhals. I will present different stochastic models to analyze the data from this study: point process with memory, stochastic Langevin diffusions. These diffusion processes can be multidimensional, hypoelliptic (with a degenerate noise) and partially observed. I will discuss the question of parameter estimation when only discrete observations are available.<\/p>\n<p>11h : Sylvain Moinard (LECA, UGA) : <em>Indicateurs de biodiversit\u00e9 robustes pour le m\u00e9tabarcoding et outils math\u00e9matiques associ\u00e9s <\/em><\/p>\n<p class=\"has-small-font-size\">Du fait de l\u2019activit\u00e9 humaine, la biodiversit\u00e9 conna\u00eet un bouleversement rapide \u00e0 l\u2019\u00e9chelle mondiale. Les mesures de conservation n\u00e9cessitent de pouvoir \u00e9valuer l\u2019\u00e9tat de la biodiversit\u00e9 sur un site donn\u00e9. L\u2019\u00e9tude de l\u2019ADN environnemental par m\u00e9tabarcoding permet de remplacer l&rsquo;observation directe des esp\u00e8ces, laborieuse, et fournit une source d\u2019information prometteuse pour am\u00e9liorer la gestion des \u00e9cosyst\u00e8mes. Cependant, l\u2019estimation des abondances relatives des esp\u00e8ces est encore mal \u00e9tablie pour ce type de donn\u00e9es.<br \/>\nJe pr\u00e9senterai d&rsquo;abord un projet de correction des biais d&rsquo;abondance induits par le m\u00e9tabarcoding. Ces travaux sont appuy\u00e9s par une mod\u00e9lisation de la PCR (Polyerase Chain Reaction), cruciale dans ce protocole. Le choix des param\u00e8tres optimaux dudit mod\u00e8le n&rsquo;est pas \u00e9tabli de mani\u00e8re analytique mais repose sur une optimisation num\u00e9rique.<br \/>\nJe pr\u00e9senterai donc dans un second temps un nouvel algorithme d\u2019inf\u00e9rence de param\u00e8tres pour mod\u00e8les al\u00e9atoires appel\u00e9 Fixed Landscape Inference MethOd (flimo). Celui-ci est applicable \u00e0 divers mod\u00e8les utilis\u00e9s en \u00e9cologie. Il fonctionne dans le m\u00eame cadre que les algorithmes d\u2019Approximate Bayesian Computation (ABC) en proc\u00e9dant par simulations du mod\u00e8le sans consid\u00e9rer sa vraisemblance. Sur les exemples \u00e9tudi\u00e9s, les r\u00e9sultats de flimo sont obtenus beaucoup plus vite que pour les algorithmes utilis\u00e9s en comparaison, avec une pr\u00e9cision similaire.<\/p>\n<p class=\"has-medium-font-size\"><strong>15 F\u00e9vrier 2024: ICJ La Doua, Universit\u00e9 de Lyon, salle Fokko du Cloux<\/strong><\/p>\n<p>10h : Charlotte Camus (ICJ, Lyon) : <em>Modeling the mechanisms of antibody mixtures in viral infections: the cases of sequential homologous and heterologous dengue infections<\/em><\/p>\n<p class=\"has-small-font-size\">Les anticorps jouent un r\u00f4le essentiel dans la r\u00e9ponse immunitaire aux infections virales, \u00e0 la vaccination ou \u00e0 la th\u00e9rapie par anticorps. N\u00e9anmoins, ils peuvent avoir un effet protecteur ou nocif au cours de la r\u00e9ponse immunitaire. En outre, la comp\u00e9tition ou la coop\u00e9ration entre les anticorps, lorsqu&rsquo;ils sont m\u00e9lang\u00e9s, peut renforcer ou r\u00e9duire cet effet protecteur ou nocif. En utilisant les lois des r\u00e9actions chimiques pour mod\u00e9liser la liaison des anticorps aux antig\u00e8nes et leurs actions pour neutraliser ou renforcer l&rsquo;infection, nous proposons une nouvelle approche pour mod\u00e9liser l&rsquo;activit\u00e9 du complexe antig\u00e8ne-anticorps. L&rsquo;expression qui en r\u00e9sulte couvre non seulement la liaison purement comp\u00e9titive ou purement ind\u00e9pendante entre les anticorps, mais aussi la liaison synergique qui, selon le type d&rsquo;anticorps, peut favoriser soit la neutralisation, soit le renforcement de l&rsquo;activit\u00e9 virale. Nous int\u00e9grons ensuite cette expression dans un mod\u00e8le intra-h\u00f4te (syst\u00e8me EDO), impliquant \u00e0 la fois des cellules cibles saines et infect\u00e9es, la r\u00e9plication du virus et la production de deux types d&rsquo;anticorps au cours d&rsquo;infections successives. Nous \u00e9tudions l&rsquo;existence d&rsquo;\u00e9quilibres (sans maladie et end\u00e9mique) et leurs stabilit\u00e9s asymptotiques locale et globale.<\/p>\n<p>11h: Romain Aza\u00efs (LBMC, Lyon) : <em>Estimation in spinal Galton-Watson trees<\/em><\/p>\n<p class=\"has-small-font-size\">We consider a Galton-Watson tree whose birth distribution depends on the hidden type of nodes: normal or special. Every special node gives birth to one special child and a number of normal children whose descendance will be normal. Even in such a very structured two-type population, our ability to distinguish the two types and estimate their birth distribution is constrained by a trade-off between the growth-rate of the population and the similarity of the two birth distributions. Indeed, if the growth-rate is too large, large deviations events are likely to be observed in the sampling of the normal individuals preventing us to distinguish them from special ones. The talk will be illustrated by numerical simulations and asymptotic goodness-of-fit tests for surviving subcritical Galton-Watson trees. Joint work with Beno\u00eet Henry.<\/p>\n<p class=\"has-medium-font-size\"><strong>18 Janvier 2024: ENS de Lyon, UMPA salle 435&nbsp;<\/strong><\/p>\n<p>10h : Bastien Boussau (LBBE, Lyon) :&nbsp;<em>Genome scale genotype-phenotype associations along phylogenies<\/em><\/p>\n<p class=\"has-small-font-size\">Identifying the footprints of selection in coding sequences can inform about the importance and function of individual sites. Analyses of the ratio of nonsynonymous to synonymous substitutions (dN\/dS) have been widely used to pinpoint changes in the intensity of selection, but cannot distinguish them from changes in the direction of selection, that is, changes in the fitness of specific amino acids at a given position. We have evaluated several methods that detect changes in directional selection associated to discrete phenotypic changes on a phylogeny, and have found that our method Pelican offers a good trade-off between power and speed, enabling whole genome analyses for hundreds of species (Duchemin et al., MBE 2023, https:\/\/doi.org\/10.1093\/molbev\/msac247). In this presentation we present Pelican, show how its performance compares to other state-of-the-art methods, including in the presence of confounding factors such as GC-biased gene conversion and CpG hypermutability, present an extension to handle continuous phenotypes, and demonstrate its use on several phenotypes on a data set of 116 whole genomes from mammals. Overall, we demonstrate that Pelican can analyze large amounts of data to look for genotype-phenotype associations, at the level of individual sites or individual genes, for both discrete and continuous phenotypes. Looking forward, we expect that the use of such phylogenetic approaches on large genomic data sets will be instrumental to annotating gene function across the tree of life.<\/p>\n<p>11h : Josu\u00e9 Tchouanti-Fotso (UMPA, Lyon) : <em>Detection of neural synchronization and implications for neuroscience experimental design<\/em><\/p>\n<p class=\"has-small-font-size\">Abstract : Two neurons are said to be synchronized when their spike trains coincide more than when they are independent. It is commonly accepted that this phenomenon plays a very important role in the neural activity. The construction of statistical tests for its detection has been the subject of much interest in the literature and in particular with the work of Albert et al. (2015, 2016) on asymptotic tests of Bootstrap and permutation. This presentation is in the same vein, and will focus on the construction of a criterion ensuring the detection of synchonization in the case of a non-asymptotic test. This criterion is constructed in such a way as to ensure control of the first and second kind errors. We also apply this criterion to some classical models of interacting neurons, typically the well known jittering Poisson and Hawkes models, and deduce informations about the choice of some experimental parameters. Joint work with: \u00c9va L\u00f6cherbach, Patricia Reynaud-Bouret and \u00c9tienne Tanr\u00e9.<\/p>\n<p class=\"has-medium-font-size\"><strong>Journ\u00e9e \u00e0 Lyon le 18 d\u00e9cembre 2023 \u00e0 l&rsquo;ENS de Lyon.<\/strong><\/p>\n<p>Charles Medous (Universit\u00e9 Grenoble Alpes) : <em>Construction d&rsquo;\u00e9pines pour des populations stochastiques d&rsquo;individus en interactions.<\/em><\/p>\n<p class=\"has-small-font-size\">Abstract : La biologie des syst\u00e8mes tente d&rsquo;expliquer les observations exp\u00e9rimentales par l&rsquo;identification de m\u00e9canismes sous-jacents pertinents et l&rsquo;utilisation de mod\u00e8les math\u00e9matiques. De la morphog\u00e9n\u00e8se d\u00e9crite par les \u00e9quations de r\u00e9action diffusion de Turing, aux \u00ab\u00a0Genome-wide association studies\u00a0\u00bb, le r\u00f4le de la mod\u00e9lisation math\u00e9matique dans les avanc\u00e9es biologiques n&rsquo;est plus \u00e0 prouver. Dans son livre \u00ab\u00a0What is Life\u00a0\u00bb, Erwin Schr\u00f6dinger met en avant les limites de la mod\u00e9lisation d\u00e9terministe dans l&rsquo;explication des fluctuations et des sauts dans la dynamique des syst\u00e8mes biologiques. En r\u00e9sulte l&rsquo;\u00e9mergence de mod\u00e8les stochastiques, prenant en compte l&rsquo;al\u00e9atoire des m\u00e9canismes et en particulier les processus de branchement pouvant d\u00e9crire les comportements individuels dans une population. Depuis quelques d\u00e9cennies, de nombreuses m\u00e9thodes probabilistes ont \u00e9t\u00e9 d\u00e9velopp\u00e9es pour \u00e9tudier de tels processus: martingales, super-processus, calcul stochastique, \u00e9pine &#8230;<br \/>\nNous nous focaliserons dans cet expos\u00e9, sur les m\u00e9thodes d&rsquo;\u00e9pine, leur construction rigoureuse dans le cas de processus de Galton-Watson ainsi que leurs diverses utilisations dans des mod\u00e8les simples. Nous pr\u00e9senterons dans un deuxi\u00e8me temps les processus de branchement avec interactions, les constructions d&rsquo;\u00e9pines associ\u00e9es et leur utilisation pour obtenir des estimateurs non biais\u00e9s de statistiques d&rsquo;int\u00e9r\u00eat sur des individus \u00e9chantillonn\u00e9s dans la population.<\/p>\n<p>Raluca Eftimie (Universit\u00e9 Franche-Comt\u00e9) : <em>Computational approaches to investigate the impact of heterogeneous immune responses in cancer evolution.<\/em><\/p>\n<p class=\"has-small-font-size\">Abstract : TBA<\/p>\n<p>Bartholom\u00e9 Vieille (Inrae, Avignon) : <em>Une approximation markovienne d\u2019un processus de Hawkes pour la mod\u00e9lisation de propagation \u00e9pid\u00e9mique.<\/em><\/p>\n<p class=\"has-small-font-size\">Abstract : In recent years, numerous studies grounded on Hawkes processes have been carried out in many fields including finance, biology and social network. Hawkes processes form a class of self-exciting simple point processes. In this communication, I will introduce a markovian approximation of a specific hidden multivariate Hawkes process considered in a spatial setting and used to model the spatio-temporal spread of an epidemic. The spatial domain is composed of multiple disjoint regions. The baseline intensity is time-dependent, and the jump size is constant and equal to 1. Furthermore, the exciting function is a general one. The closed-form expression of the multivariate characteristic function of such a markovian process will be presented. This allows us to obtain a closed-form formula for the temporal structure of the first moments. I will also discuss other points such as parameter estimation of the state-space epidemic model by Sequential Monte-Carlo.<\/p>\n<p>Pierre Roux (Centrale Lyon) : <em>Mod\u00e9lisation des cellules de grille par une \u00e9quation de Fokker-Planck non-lin\u00e9aire et non-locale.<\/em><\/p>\n<p class=\"has-small-font-size\">Abstract : Depuis leur d\u00e9couverte en 2005 par Moser, Moser et leurs coll\u00e8gues, les cellules de grilles &#8211; des neurones sp\u00e9cifique du cortex entorhinal qui jouent un r\u00f4le crucial dans la navigation spatiale des mammif\u00e8res &#8211; ont \u00e9t\u00e9 l\u2019objet de nombreuses \u00e9tudes. Un point clef de leur fonctionnement est qu\u2019elles constituent des modules dont l\u2019activit\u00e9 \u00e9lectrique se stabilise en un motif hexagonal (qui constitue une sorte de grille). Dans cet expos\u00e9, je pr\u00e9senterai un mod\u00e8le aux d\u00e9riv\u00e9es partielles de type Fokker-Planck non-lin\u00e9aire, d\u00e9velopp\u00e9 par Carrillo, Clini, Holden et Solem, visant \u00e0 comprendre l&rsquo;apparition du motif hexagonal et \u00e0 \u00e9tudier sa robustesse au bruit. \u00c0 travers un m\u00e9lange de r\u00e9sultats th\u00e9oriques (existence locale et globale, convergence en entropie relative, bifurcations entra\u00een\u00e9es par le bruit) et d&rsquo;explorations num\u00e9riques, Jos\u00e9 Antonio Carrillo, Susanne Solem et moi-m\u00eame avons \u0153uvr\u00e9 \u00e0 am\u00e9liorer la compr\u00e9hension du mod\u00e8le et du ph\u00e9nom\u00e8ne sous-jacent.<\/p>\n<p class=\"has-medium-font-size\"><strong>16 Novembre 2023: Institut Fourier, salle B29, Grenoble<\/strong><\/p>\n<p class=\"has-medium-font-size\">Eugenio Cinquemani (Inria): <em>Power spectral analysis for the optimal design of gene reporter systems<\/em><\/p>\n<p class=\"has-small-font-size\">An established technique for the monitoring of gene expression dynamics is the use of fluorescent reporter proteins. Synthesized in response to promoter activation of the gene of interest, fluorescent proteins provide a visible readout of gene expression that can be quantified over time both at an ensemble population and at a single-cell level. Fluorescent reporter system response to promoter activation can be described as standard transcription-translation reaction networks, taking the form of stochastic models for single cells and deterministic models for population averages. The kinetic rate constants of these systems constitute design parameters for the experimenter that shape the response to promoter activation.<\/p>\n<p class=\"has-small-font-size\">In this talk, reporter systems are analyzed from a signal processing viewpoint. The power spectral transfer function for stochastic (single-cell) response models is developed and compared with the frequency response of corresponding deterministic (population) models. Both response models are shown to be equivalent to a linear filter, with a noise component for single-cell response coming from intrinsic noise of the gene expression process. These results are next used to explore the design of the kinetic rate constants. Assuming additive measurement noise on the observed fluorescent levels, design guidelines are established to optimize information content of the reporter output in spite of measurement noise and, for single-cell monitoring, of intrinsic noise. A final discussion of the results points out fundamental differences between gene expression monitoring in populations and in single cells.<\/p>\n<p class=\"has-medium-font-size\">Lo\u00efc Chalmandrier (UGA, LIPhy): <em>Calibrating process-based biodiversity models with functional traits<\/em><\/p>\n<p class=\"has-small-font-size\">Process-based models are seldom used to identify the mechanisms that structure species-rich biological communities. One reason is that species demography and interactions are often too difficult to estimate in situ or experimentally. Here, I will show how to use functional trait data and biodiversity data instead to infer species demography and interactions. I will present case studies demonstrating the value of this approach to model abiotic filtering and competition in plant communities and present the future directions of my research on that topic.<\/p>\n<p class=\"has-medium-font-size\"><strong>12 Octobre 2023: ICJ La Doua, Universit\u00e9 de Lyon, salle Fokko du Cloux<\/strong><\/p>\n<p>Thomas Koffel (Lyon 1, LBBE) : <em>Connecting local and regional scales with stochastic metacommunity models: Competition, ecological drift, and dispersal. <\/em><\/p>\n<p class=\"has-small-font-size\">R\u00e9sum\u00e9 : Metacommunity ecology extends the metapopulation concept to provide a theoretical framework for understanding multi-species interactions in spatially subdivided landscapes. Despite the interest in metacommunity ecology, the theory is currently loosely organized into disjunct paradigms such as species sorting, patch dynamics, mass effects, and neutral theory. Reconciling these diverse models in a unified framework requires inclusion of three fundamental ecological processes: selection (niche-based processes), ecological drift (stochasticity), and dispersal. I will present a competitive Lotka Volterra metacommunity model that includes all of these processes. First, we look at open systems, where immigrants come from a mainland source population. Then we look at true metacommunities, where immigrants come from other patches in the landscape. Using efficient numerical techniques to calculate equilibria and invasion criteria, we determine how the regional outcome of competition depends on local interactions, dispersal, and local population size.<\/p>\n<p>Julien Clavel (Lyon 1, LEHNA) : <em>Modelling phenotypic traits evolution in deep-times: a phylogenetic approach. <\/em><\/p>\n<p class=\"has-small-font-size\">R\u00e9sum\u00e9 :The use of statistical approaches for modeling the evolution of species traits on phylogenetic trees, also known as phylogenetic comparative methods, have exploded since Felsenstein\u2019s seminal paper in 1985. Developed at the beginning as a statistical fix for comparative analyses, these approaches are now routinely used to address fundamental questions in macroevolution and macroecology from extant and fossil data. However, their use has been often limited to simplistic models assuming that traits or species are evolving independently of each other\u2019s and from their environment. Here, I present a suite of models that we recently developed to infer the effect of inter-specific interactions and past environmental changes on the evolution of phenotypic traits as well as for understanding the evolution of multidimensional traits \u2013 in particular high dimensional multivariate datasets such as 3D geometric morphometrics. These methods show that phylogenies of extant taxa provide valuable information about past and present biodiversity and offer a unified analytical framework for the study of extant and fossil taxa. Future developments of these models and statistical tools will further allow a better integration of data types and research fields for a better understanding of the processes driving the evolution of taxonomic and phenotypic diversity.<\/p>\n<p class=\"has-medium-font-size\"><strong>14 Septembre 2023: ENS de Lyon, UMPA salle 435<\/strong><\/p>\n<p>C\u00e9line Bonnet (Inria, UMPA): <em>A piecewise deterministic and Markovian approach to study the role of quiescence dynamics in blood cancers.<\/em><\/p>\n<p class=\"has-small-font-size\">R\u00e9sum\u00e9 : We will see an approach to study the impact of a small microscopic population of cancer cells on a macroscopic population of healthy cells, with an example inspired by pathological hematopoiesis. Hematopoiesis is the biological phenomenon of blood cells production by differentiation of cells called hematopoietic stem cells (HSCs). Cancer HSCs produce a large number of cancer blood cells but randomly stop to produce them (during such a period, the cancer HSC is called quiescent). We will study the impact of such a quiescent state on the production of cancer blood cells and on healthy cells through regulation. We will describe the evolution over time of the number of healthy and cancer cells using a multi-type Markov process. A single cancer HSC is considered while other populations are in large numbers. We show the convergence in law of this process towards a piecewise deterministic Markov process (PDMP). We then study the long time behavior of this limit process. We show the existence and uniqueness of an invariant probability measure using the works of Benaim and co-authors. We finally identify this measure using the solution of a stationary system of partial differential equations describing the impact of cancer HSC quiescent phases and regulation on the cell density of the hematopoietic system studied.<\/p>\n<p>Guillaume Mestdagh (Inria, RDP) : <em>Contr\u00f4le optimal pour le recalage d&rsquo;organe en chirurgie augment\u00e9e.<\/em><\/p>\n<p class=\"has-small-font-size\">R\u00e9sum\u00e9 : La r\u00e9alit\u00e9 augment\u00e9e est utilis\u00e9e en chirurgie minimalement invasive pour permettre au personnel m\u00e9dical de suivre en temps r\u00e9el les mouvements du foie du patient. Pour mettre \u00e0 jour la d\u00e9formation d\u2019un organe virtuel, une m\u00e9thode de recalage \u00e9lastique aligne un mod\u00e8le biom\u00e9canique pr\u00e9-op\u00e9ratoire du foie avec une surface partielle observ\u00e9e pendant l\u2019op\u00e9ration. Tandis qu\u2019une grande partie des m\u00e9thodes de recalage \u00e9lastique consistent \u00e0 introduire des forces fictives dans le mod\u00e8le direct, notre approche vise \u00e0 reconstruire la vraie densit\u00e9 de forces surfaciques qui a cr\u00e9\u00e9 la d\u00e9formation observ\u00e9e. Nous exprimons le probl\u00e8me de recalage dans le formalisme du contr\u00f4le optimal, en utilisant comme variable d\u2019optimisation la distribution de forces qui s\u2019applique \u00e0 la surface de l\u2019organe. En permettant de d\u00e9finir \u00e0 l\u2019avance un ensemble de forces admissibles, cette approche favorise les champs de d\u00e9placement ayant un sens physique. Nous commen\u00e7ons par \u00e9tudier l\u2019existence de solutions pour le probl\u00e8me continu et nous calculons des conditions d\u2019optimalit\u00e9 de premier ordre. Puis nous pr\u00e9sentons la m\u00e9thode d\u2019adjoint que nous avons impl\u00e9ment\u00e9e afin de traiter le probl\u00e8me num\u00e9riquement. Finalement, nous validons notre m\u00e9thode au moyen de cas-test li\u00e9s \u00e0 l\u2019application en chirurgie augment\u00e9e. Lors de ces essais, nous mesurons l\u2019erreur de recalage, et nous cherchons \u00e9galement, dans un cas particulier, \u00e0 donner un sens \u00e0 la distribution de forces obtenue.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Journ\u00e9e 2 \u00e0 Lyon (UMPA) le 20 mars 2026 (10h30 -16h) 10h30 : Charles Elbar : Including surface tension for tumor growth modeling with the Cahn-Hilliard equation We are motivated by invasive cancer. A common approach is to use Hele-Shaw models with surface tension, these are models where the tumor\u2026<\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/project.inria.fr\/gdtmathbio\/rencontres-passees\/\"><span>Continue reading<\/span><i class=\"crycon-right-dir\"><\/i><\/a> <\/p>\n","protected":false},"author":2368,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-112","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/pages\/112","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/users\/2368"}],"replies":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/comments?post=112"}],"version-history":[{"count":27,"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/pages\/112\/revisions"}],"predecessor-version":[{"id":602,"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/pages\/112\/revisions\/602"}],"wp:attachment":[{"href":"https:\/\/project.inria.fr\/gdtmathbio\/wp-json\/wp\/v2\/media?parent=112"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}