871 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- Centre National de la Recherche ScientifiqueFR34 papers
- Lyon 1 UniversitéFR33 papers
- Université de LyonFR14 papers
- Institut national de recherche en sciences et technologies du numériqueFR10 papers
- École Normale Supérieure de LyonFR6 papers
- Centre Inria de l'Université Grenoble AlpesFR5 papers
- Université Grenoble AlpesFR5 papers
- Institut polytechnique de GrenobleFR4 papers
- Laboratoire de Probabilités, Statistique et ModélisationFR4 papers
- Sorbonne UniversitéFR4 papers
- Université de MontpellierFR4 papers
- Université Paris CitéFR4 papers
51 papers
Likelihood-free inference of phylogenetic tree posterior distributions
Luc Blassel, Noémie Sauvage, Pierre Barrat-Charlaix +3
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-ar…
Largest planar graphs of diameter and fixed maximum degree -- connection with fractional matchings
Antoine Dailly, Sasha Darmon, Ugo Giocanti +2
The degree diameter problem asks for the maximum possible number of vertices in a graph of maximum degree and diameter . In this paper, we focus on planar graphs of diameter…
The expensive son hypothesis
Lucas Invernizzi, Jean-françois Lemaître, Mathieu Douhard
In its initial form, the expensive son hypothesis postulates that sons from male-biased sexually dimorphic species require more food during growth than daughters, which ultimately…
Inner ear morphology in wild versus laboratory house mice
Sabrina Renaud, Léa Amar, Pascale Chevret +4
The semicircular canals of the inner ear are involved in balance and velocity control. Being crucial to ensure efficient mobility, their morphology exhibits an evolutionary conserv…
Complexity of the Swap Median and Swap Closest Problems
Luís Cunha, Thiago Lopes, Arnaud Mary
Genome rearrangement distances provide a combinatorial framework for comparing genomes represented as permutations. Although the swap distance between two permutations is polynomia…
Enumeration of minimal transversals of hypergraphs of bounded VC-dimension
Arnaud Mary
We consider the problem of enumerating all minimal transversals (also called minimal hitting sets) of a hypergraph . An equivalent formulation of this problem known as…
Zero-inflation in the Multivariate Poisson Lognormal Family
Bastien Batardière, Julien Chiquet, François Gindraud +1
Analyzing high-dimensional count data is a challenge and statistical model-based approaches provide an adequate and efficient framework that preserves explainability. The (multivar…
FAIR Data Pipeline: provenance-driven data management for traceable scientific workflows
Sonia Natalie Mitchell, Andrew Lahiff, Nathan Cummings +35
Modern epidemiological analyses to understand and combat the spread of disease depend critically on access to, and use of, data. Rapidly evolving data, such as data streams changin…
Neuronal Network Inference and Membrane Potential Model using Multivariate Hawkes Processes
Anna Bonnet, Charlotte Dion, François Gindraud +1
In this work, we propose to catch the complexity of the membrane potential's dynamic of a motoneuron between its spikes, taking into account the spikes from other neurons around. O…
Quantifying the overall effect of biotic interactions on species distributions along environmental gradients
Marc Ohlmann, Catherine Matias, Giovanni Poggiato +3
Separating environmental effects from those of interspecific interactions on species distributions has always been a central objective of community ecology. Despite years of effort…
Uniform Deconvolution for Poisson Point Processes
Anna Bonnet, Claire Lacour, Franck Picard +1
We focus on the estimation of the intensity of a Poisson process in the presence of a uniform noise. We propose a kernel-based procedure fully calibrated in theory and practice. We…
Convolutional Kernel Networks for Graph-Structured Data
Dexiong Chen, Laurent Jacob, Julien Mairal
We introduce a family of multilayer graph kernels and establish new links between graph convolutional neural networks and kernel methods. Our approach generalizes convolutional ker…
Antioxidant capacity is repeatable across years but does not consistently correlate with a marker of peroxidation in a free-living passerine bird
Charlotte Récapet, Mathilde Arrivé, Blandine Doligez +1
Oxidative stress occurs when reactive oxygen species (ROS) exceed antioxidant defences, which can have deleterious effects on cell function, health and survival. Therefore, organis…
Nine Quick Tips for Analyzing Network Data
Stephane Robin, Vincent Miele, Catherine Matias +1
These tips provide a quick and concentrated guide for beginners in the analysis of network data.
Reconfiguration of graphs with connectivity constraints
Nicolas Bousquet, Arnaud Mary
A graph realizes the degree sequence if the degrees of its vertices is . Hakimi gave a necessary and sufficient condition to guarantee that there exists a connected mult…
Probabilistic Count Matrix Factorization for Single Cell Expression Data Analysis
Ghislain Durif, Laurent Modolo, Jeff E. Mold +2
The development of high throughput single-cell sequencing technologies now allows the investigation of the population level diversity of cellular transcriptomes. This diversity has…
Gene tree reconciliation including transfers with replacement is hard and FPT
Damir Hasic, Eric Tannier
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tre…
Token Jumping in minor-closed classes
Nicolas Bousquet, Arnaud Mary, Aline Parreau
Given two -independent sets and of a graph , one can ask if it is possible to transform the one into the other in such a way that, at any step, we replace one vertex…
Gene tree species tree reconciliation with gene conversion
Damir Hasic, Eric Tannier
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories.…
Revealing the hidden structure of dynamic ecological networks
Vincent Miele, Catherine Matias
Recent technological advances and long-term data studies provide interaction data that can be modelled through dynamic networks, i.e a sequence of different snapshots of an evolvin…
Simulation based estimation of branching models for LTR retrotransposons
Serge Moulin, Nicolas Seux, Stéphane Chrétien +2
Motivation: LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model…
Minimax wavelet estimation for multisample heteroscedastic non-parametric regression
Madison Giacofc, Sophie Lambert-Lacroix, Franck Picard
The problem of estimating the baseline signal from multisample noisy curves is investigated. We consider the functional mixed effects model, and we suppose that the functional fixe…
Efficient enumeration of solutions produced by closure operations
Arnaud Mary, Yann Strozecki
In this paper we address the problem of generating all elements obtained by the saturation of an initial set by some operations. More precisely, we prove that we can generate the c…
Statistical clustering of temporal networks through a dynamic stochastic block model
Catherine Matias, Vincent Miele
Statistical node clustering in discrete time dynamic networks is an emerging field that raises many challenges. Here, we explore statistical properties and frequentist inference in…