Sophie Donnet

Total : 61 publications

2025

Pré-publication, Document de travail

• Common Structure Discovery in Collections of Bipartite Networks: Application to Pollination Systems
  Louis Lacoste, Pierre Barbillon, Sophie Donnet
  Bipartite networks are widely used to encode the ecological interactions. Being able to compare the organization of bipartite networks is a first step...
  hal-05399136 | ⬇️ Télécharger
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• Climatic legacies drive spatial aggregation of plants in drylands
  Benoît Pichon, Sonia Kefi, Isabelle Gounand, Sophie Donnet
  In drylands, vegetation is spatially aggregated in so called patches, separated by bare soil areas. So far, research on vegetation spatial patterns ma...
  hal-05357145 | ⬇️ Télécharger
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• Estimating distances to desertification points from dryland ecosystem images
  Benoît Pichon, Sophie Donnet, Isabelle Gounand, Sonia Kéfi
  Resource-limited ecosystems, such as drylands, can exhibit self-organized spatial patterns. Theory suggests that these patterns can reflect increasing...
  hal-05216054 | ⬇️ Télécharger
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Article dans une revue

• Vegetation patterns pinpoint the least resilient dryland sites
  Benoît Pichon, Sophie Donnet, Isabelle Gounand, Sonia Kéfi
  Abstract Resource‐limited ecosystems, such as drylands, can exhibit self‐organized spatial patterns. Theory suggests that changes in these pattern...
  hal-05389368 | ⬇️ Télécharger
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• Grazing Modulates the Multiscale Spatial Structure of Dryland Vegetation
  Benoît Pichon, Sonia Kéfi, Isabelle Gounand, Nicolas Gross, Yoann Le Bagousse-Pinguet, Josquin Guerber, David Eldridge, Enrique Valencia, César Plaza, Jaime Martínez-Valderrama, Hugo Saiz, Victoria Ochoa, Beatriz Gozalo, Emilio Guirado, Miguel García-Gómez, Juan Gaitán, Sergio Asensio, Betty Josefina Mendoza, Sophie Donnet, Fernando Maestre
  Plants can facilitate their local environment and create a two‐phase spatial structure of vegetation and bare soil in drylands, which largely influe...
  hal-05180398 | ⬇️ Télécharger
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• Hoeffding-type decomposition for U-statistics on bipartite networks
  Tâm Le Minh, Sophie Donnet, François Massol, Stéphane Robin
  
  hal-05215215 | ⬇️ Télécharger
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Chapitre d'ouvrage

• Seed circulation networks, the missing link between crop diversity and sustainable agriculture
  Vanesse Labeyrie, Sophie Donnet, Sophie Caillon, Eric Garine, Christine Raimond
  Smallholder farming systems in the Global South largely rely on crop diversity for their livelihood. Access to crop seeds is based on complex social n...
  hal-05268722
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2024

Article dans une revue

• The interplay of facilitation and competition drives the emergence of multistability in dryland plant communities
  Benoît Pichon, Isabelle Gounand, Sophie Donnet, Sonia Kéfi
  Within communities, species are wrapped in a set of feedbacks with each other and with their environment. When such feedbacks are strong enough they c...
  hal-04668228 | ⬇️ Télécharger
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• Learning common structures in a collection of networks. An application to food webs
  Saint-Clair Chabert-Liddell, Pierre M Barbillon, Sophie Donnet
  Let a collection of networks represent interactions within several (social or ecological) systems. We pursue two objectives: identifying similarities ...
  hal-03685293 | ⬇️ Télécharger
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• Using the multivariate Hawkes process to study interactions between multiple species from camera trap data
  Lisa Nicvert, Sophie Donnet, Mark Keith, Mike Peel, Michael J Somers, Lourens H Swanepoel, Jan Venter, Hervé Fritz, Stéphane Dray
  Interspecific interactions can influence species' activity and movement patterns. In particular, species may avoid or attract each other through react...
  hal-04465235 | ⬇️ Télécharger
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2023

Pré-publication, Document de travail

• Auto-encoding GPS data to reveal individual and collective behaviour
  Saint-Clair Chabert-Liddell, Nicolas Bez, Pierre Gloaguen, Sophie Donnet, Stéphanie Mahévas
  We propose an innovative and generic methodology to analyse individual and collective behaviour through individual trajectory data. The work is motiva...
  hal-04317516 | ⬇️ Télécharger
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Poster de conférence

• Monitoring the ribosome dynamics at the single molecule level
  Véronique Vienne, Baptiste Bouhet, Antonin Tidu, Sandra Blanchet, Charles Truong, Sophie Donnet, François Marquier, Olivier Namy, Franck Martin, Karen Perronet
  
  hal-04240628
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Communication dans un congrès

• Hoeffding-type decomposition for U-statistics on bipartite networks
  Tâm Le Minh, Sophie Donnet, François Massol, Stephane S. Robin
  Bipartite networks are naturally represented by their adjacency matrices. We consider node-exchangeable networks, which means their adjacency matrices...
  hal-04792991 | ⬇️ Télécharger
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2022

Chapitre d'ouvrage

• Chapter 6: Using Latent Block Models to Detect Structure in Ecological Networks
  Julie J. Aubert, Pierre M Barbillon, Sophie Donnet, Vincent Miele
  
  hal-03811607
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Article dans une revue

• Impact of the mesoscale structure of a bipartite ecological interaction network on its robustness through a probabilistic modeling
  Saint-Clair Chabert-Liddell, Pierre M Barbillon, Sophie Donnet
  The robustness of an ecological network quantifies the resilience of the ecosystem it represents to species loss. It corresponds to the proportion of ...
  hal-03259474 | ⬇️ Télécharger
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• A hierarchical Bayesian approach for incorporating expert opinions into parametric survival models: a case study of female Ixodes ricinus ticks exposed to various temperature and relative humidity conditions
  Phrutsamon Wongnak, Severine Bord, Sophie Donnet, Thierry Hoch, Frederic Beugnet, Karine Chalvet-Monfray
  The survival of ectothermic species is heavily dependent on environmental conditions, such as temperature and water balance. Understanding their survi...
  hal-03428117 | ⬇️ Télécharger
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2021

Article dans une revue

• Coupling ecological network analysis with high-throughput sequencing-based surveys: Lessons from the next-generation biomonitoring project
  Maxime Dubart, Pascal Alonso, Didac Barroso-Bergadà, N. Becker, Kévin Béthune, David Bohan, Christophe Boury, Marine Cambon, Elsa Canard, Emilie Chancerel, Julien Chiquet, Patrice David, Natasha de Manincor, Sophie Donnet, Anne Duputié, Benoit Facon, Erwan Guichoux, Tâm Le Minh, Sebastián Ortiz-Martínez, Lucie Piouceau, Ambre Sacco--Martret de Préville, Manuel Plantegenest, Céline Poux, Virginie Ravigné, Stephane S. Robin, Marine Trillat, Corinne Vacher, Christian Vernière, François Massol
  Biomonitoring ecosystems is necessary in order to evaluate risks and to efficiently manage ecosystems and their associated services. Agrosystems are t...
  hal-03634351 | ⬇️ Télécharger
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• A Stochastic Block Model Approach for the Analysis of Multilevel Networks: an Application to the Sociology of Organizations
  Saint-Clair Chabert-Liddell, Pierre Barbillon, Sophie Donnet, Emmanuel Lazega
  A multilevel network is defined as the junction of two interaction networks, one level representing the interactions between individuals and the other...
  hal-02353711 | ⬇️ Télécharger
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• Accelerating Bayesian estimation for network Poisson models using frequentist variational estimates
  Sophie Donnet, Stéphane Robin
  This work is motivated by the analysis of ecological interaction networks. Poisson stochastic block models are widely used in this field to decipher t...
  hal-03202058
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2020

Article dans une revue

• Block models for generalized multipartite networks: Applications in ecology and ethnobiology
  Avner Bar-Hen, Pierre M Barbillon, Sophie Donnet
  Generalized multipartite networks consist in the joint observation of several networks implying some common pre-specified groups of individuals. Such ...
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• Nonparametric Bayesian estimation for multivariate Hawkes processes
  Sophie Donnet, Vincent Rivoirard, Judith Rousseau
  This paper studies nonparametric estimation of parameters of multivariate Hawkes processes. We consider the Bayesian setting and derive posterior conc...
  hal-03320970 | ⬇️ Télécharger
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Logiciel

• sbm: Stochastic Blockmodels
  Julien Chiquet, Pierre Barbillon, Sophie Donnet
  A collection of tools and functions to adjust a variety of stochastic blockmodels (SBM). Supports at the moment Simple, Bipartite, 'Multipartite' and ...
  hal-04440688 | ⬇️ Télécharger
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2019

Pré-publication, Document de travail

• Bayesian inference for network Poisson models
  Sophie Donnet, Stéphane Robin
  This work is motivated by the analysis of ecological interaction networks. Poisson stochastic blockmodels are widely used in this field to decipher th...
  hal-02192621
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Communication dans un congrès

• Modeling Heaping in Marine Surveys : A Bayesian Approach
  Éric É. Parent, Matthieu A Authier, Sophie Donnet, Isabelle Albert, Daouda Ba
  
  hal-02930953
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2018

Pré-publication, Document de travail

• Block model for multipartite networks. Applications in ecology and ethnobiology
  Avner Bar-Hen, P. Barbillon, Sophie Donnet
  Modeling relations between individuals is a classical question in social sciences, ecology, etc. In order to uncover a latent structure in the data, a...
  hal-01850875 | ⬇️ Télécharger
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HDR

• Contributions à l’inférence statistique de modèles complexes
  Sophie Donnet
  
  tel-02789900 | ⬇️ Télécharger
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• Contributions à l’inférence statistique de modèles complexes
  Sophie Donnet
  
  tel-04438090 | ⬇️ Télécharger
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Article dans une revue

• Posterior concentration rates for empirical Bayes procedures with applications to Dirichlet process mixtures
  Sophie Donnet, Vincent Rivoirard, Judith Rousseau, Catia Scricciolo
  We provide conditions on the statistical model and the prior probability law to derive contraction rates of posterior distributions corresponding to d...
  hal-01570308 | ⬇️ Télécharger
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2017

Pré-publication, Document de travail

• Shortened Bridge Sampler: Using deterministic approximations to accelerate SMC for posterior sampling
  Sophie Donnet, Stéphane Robin
  Sequential Monte Carlo has become a standard tool for Bayesian Inference of complex models. This approach can be computationally demanding, especially...
  hal-01566898 | ⬇️ Télécharger
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Communication dans un congrès

• Méthode conjointe de segmentation-classification pour des modèles d'écologie du déplacement
  Sophie Donnet, Julien Chiquet, Marie Pierre Etienne, Adeline Samson
  
  hal-01565530
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• Modèles à blocs latents pour graphe multipartite Application aux interactions entre espèces animales et plantes
  Sophie Donnet, Avner Bar-Hen, Pierre Barbillon
  Dans l’environnement naturel, une grande diversité des types d’interactions entre plantes et espèces animales (parmi lesquels la pollinisation, ...
  hal-01557217
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Article dans une revue

• Stochastic block-models for multiplex networks : An application to a multilevel network of researchers
  Pierre Barbillon, Sophie Donnet, Emmanuel Lazega, Avner Bar-Hen
  Modelling relationships between individuals is a classical question in social sci- ences and clustering individuals according to the observed patterns...
  hal-01520820 | ⬇️ Télécharger
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• Posterior concentration rates for counting processes with Aalen multiplicative intensities
  Sophie Donnet, Vincent Rivoirard, Judith Rousseau, Catia Scricciolo
  We provide general conditions to derive posterior concentration rates for Aalen counting processes. The conditions are designed to resemble those prop...
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2016

Communication dans un congrès

• Discussion on "Recent Developments in Pharmacokinetics and Pharmacodynamic Modeling and Data Analysis
  Sophie Donnet
  Discussion on "Recent Developments in Pharmacokinetics and Pharmacodynamic Modeling and Data Analysis". XXVIII. International Biometric Conference (IB...
  hal-01565528
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Article dans une revue

• Effects of competition on collective learning in advice networks
  Emmanuel Lazega, Avner Bar-Hen, Pierre Barbillon, Sophie Donnet
  This paper looks at the effect of identifying alters as direct competitors on their selection as advisors. We differentiate between two kinds of compe...
  hal-01520660
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• Bayesian analysis of ODEs : solver optimal accuracy and bayes factors
  Marcos A. Capistrán, J. Andrés Christen, Sophie Donnet
  In most cases in the Bayesian analysis of ODE inverse problems, a numerical solver needs to be used. Therefore, we cannot work with the exact theoreti...
  hal-01570310
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• Bayesian inference for partially observed multiplicative intensity processes
  Sophie Donnet, Judith Rousseau
  Poisson processes are used in various applications. In their homogeneous version, the intensity process is a deterministic constant whereas it depends...
  hal-01197643 | ⬇️ Télécharger
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2015

Communication dans un congrès

• Estimation bayésienne non paramétrique pour processus de Hawkes multidimensionnels
  Sophie Donnet, Vincent Rivoirard, Judith Rousseau
  Estimation bayésienne non paramétrique pour processus de Hawkes multidimensionnels. Congrés SMAI 2015...
  hal-01565529
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• Estimation bayésienne non-paramétrique pour les processus de Hawkes
  Sophie Donnet, Vincent Rivoirard
  Les processus de Hawkes multidimensionnels sont utilisés pour la modélisation des potentiels d'actions neuronaux. L'estimation des fonctions d'inten...
  hal-01565526
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2014

Communication dans un congrès

• Non parametric Bayesian estimation for Hawkes processes
  Sophie Donnet, Judith Rousseau, Vincent Rivoirard
  Non parametric Bayesian estimation for Hawkes processes. International Society for Bayesian Analysis World Meeting, ISBA 2014...
  hal-01565527 | ⬇️ Télécharger
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Pré-publication, Document de travail

• Posterior concentration rates for empirical Bayes procedures, with applications to Dirichlet Process mixtures
  Sophie Donnet, Vincent Rivoirard, Judith Rousseau, Catia Scricciolo
  In this paper we provide general conditions to check on the model and the prior to derive posterior concentration rates for data-dependent priors (or ...
  hal-01007444 | ⬇️ Télécharger
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• Posterior concentration rates for empirical Bayes procedures, with applications to Dirichlet Process mixtures. Supplementary material
  Sophie Donnet, Judith Rousseau, Vincent Rivoirard, Catia Scricciolo
  In this paper we provide general conditions to check on the model and the prior to derive posterior concentration rates for data-dependent priors (or ...
  hal-01007554 | ⬇️ Télécharger
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Article dans une revue

• Monkeys time their pauses of movement and not their movement-kinematics during a synchronization-continuation rhythmic task
  Sophie Donnet, Ramon Bartolo, Jose Maria Fernandes, Joao Paulo Silva Cunha, Luis Prado, Hugo Merchant
  A critical question in tapping behavior is to understand whether the temporal control is exerted on the duration and trajectory of the downward-upward...
  hal-01197634
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• Using PMCMC in EM algorithm for stochastic mixed models: theoretical and practical issues
  Sophie Donnet, Adeline Samson
  Biological processes measured repeatedly among a series of individuals are standardly analyzed by mixed models. Recently, stochastic processes have be...
  hal-00950760 | ⬇️ Télécharger
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2013

Article dans une revue

• A review on estimation of stochastic differential equations for pharmacokinetic/pharmacodynamic models
  Sophie Donnet, Adeline Samson
  This paper is a survey of existing estimation methods for pharmacokinetic/pharmacodynamic (PK/PD) models based on stochastic differential equations (S...
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Pré-publication, Document de travail

• Bayesian Inference for Partially Observed Branching Processes
  Sophie Donnet, Judith Rousseau
  Poisson processes are used in various application fields applications (public health biology, reliability and so on). In their homogeneous version, th...
  hal-00776926 | ⬇️ Télécharger
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2012

Rapport

• Book reviews, Winter 2012
  Sophie Donnet, Christian Robert
  This note is made of reviews of the books by Wilkinson (2011), Tu and Gilthorpe (2011), Wardhaugh (2012), Mackenzie (2012), Petersen (2012), and Doxia...
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Article dans une revue

• Review of ''Monte Carlo Simulation for the Pharmaceutical Industry: Concepts, Algorithms, and Case Studies'' by Mark Chang
  Sophie Donnet
  
  hal-00703160
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• Rejoinder
  Isabelle I. Albert, Sophie S. Donnet, Chantal C. Guihenneuc-Jouyaux, Samantha S. Low-Choy, Kerrie K. Mengersen, Judith J. Rousseau
  
  hal-01004758 | ⬇️ Télécharger
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• Combining expert opinions in prior elicitation
  Isabelle I. Albert, Sophie S. Donnet, Chantal C. Guihenneuc-Jouyaux, Samantha S. Low-Choy, Kerrie K. Mengersen, Judith J. Rousseau
  We consider the problem of combining opinions from different experts in an explicitly model-based way to construct a valid subjective prior in a Bayes...
  hal-01004440 | ⬇️ Télécharger
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2011

Article dans une revue

• An empirical Bayes procedure for the selection of Gaussian graphical models
  Sophie Donnet, Jean-Michel Marin
  A new methodology for model determination in decomposable graphical Gaussian models (Dawid and Lauritzen in Ann. Stat. 21(3), 1272-1317, 1993) is deve...
  hal-00658539
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Pré-publication, Document de travail

• EM algorithm coupled with particle filter for maximum likelihood parameter estimation of stochastic differential mixed-effects models
  Sophie Donnet, Adeline Samson
  Biological processes measured repeatedly among a series of individuals are standardly analyzed by mixed models. These biological processes can be adeq...
  hal-00519576 | ⬇️ Télécharger
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2010

Article dans une revue

• Bayesian analysis of growth curves using mixed models defined by stochastic differential equations
  Sophie Donnet, Jean-Louis Foulley, Adeline Samson
  Growth curve data consist of repeated measurements of a continuous growth process over time among a population of individuals. These data are classica...
  hal-00360111 | ⬇️ Télécharger
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• Un cadre de détection-estimation conjointe pour analyser les données individuelles d’IRMf
  Sophie Donnet, Philippe Ciuciu, Laurent Risser, Thomas Vincent
  Dans cet article, nous synthétisons la méthodologie usuelle et des variantes plus élaborées pour analyser des données individuelles d’Imagerie ...
  hal-00703158
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Document associé à des manifestations scientifiques

• Modélisation de pannes sur un réseau électrique souterrain
  Sophie Donnet, Judith Rousseau
  Nous nous intéressons à la modélisation des pannes sur un réseau électrique souterrain, ce réseau étant composé de deux types de matériels : ...
  inria-00510286 | ⬇️ Télécharger
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2009

Communication dans un congrès

• Analyse bayésienne de courbes de croissance par des modèles à effets mixtes définis par équations différentielles stochastiques.
  Sophie Donnet, Jean-Louis Foulley, Adeline Samson
  On désigne par courbes de croissance des mesures répétées au cours du temps d'un processus continu de croissance sur une population d'individus. C...
  inria-00386568 | ⬇️ Télécharger
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2008

Article dans une revue

• Parametric inference for mixed models defined by stochastic differential equations
  Sophie Donnet, Adeline Samson
  Non-linear mixed models defined by stochastic differential equations (SDEs) are consid- ered: the parameters of the diffusion process are random varia...
  hal-00263515 | ⬇️ Télécharger
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2007

Article dans une revue

• Estimation of parameters in incomplete data models defined by dynamical systems.
  Adeline Samson, Sophie Donnet
  Parametric incomplete data models defined by ordinary differential equa- tions (ODEs) are widely used in biostatistics to describe biological proces...
  hal-00263507 | ⬇️ Télécharger
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• Discussion on "Parameter estimation for differential equations: a generalized smoothing approach" (by Ramsay JO, Hooker G, Campbell D and Cao J),
  Sophie Donnet, Adeline Samson
  
  hal-00703159
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2006

Article dans une revue

• Are fMRI event-related response constant in time? A model selection answer
  Sophie Donnet, Marc Lavielle, Jean-Baptiste Poline
  An accurate estimation of the hemodynamic response function (HRF) in functional magnetic resonance imaging (fMRI) is crucial for a precise spatial and...
  hal-00415832
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2000

Rapport

• Parametric Estimation for Diffusion Processes from Discrete-time and Noisy Observations
  Sophie Donnet, M. Samson
  Noisy discretely observed diffusion processes with random drift function parameters are considered. Maximum likelihood and Bayesian estimation methods...
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