arXiv subjects

Stéphane Robin

Publications and source records attributed to Stéphane Robin.

At least 19 recordsLinked to original sources

arXiv2026

Online robust covariance matrix estimation and outlier detection

Robust estimation of the covariance matrix and detection of outliers remain major challenges in statistical data analysis, particularly when the proportion of contaminated observations increases with the size of the dataset. Outliers can severely bias parameter estimates and induce a masking effect, whereby some outliers conceal the presence of other outliers, further complicating their detection. Although many approaches have been proposed for covariance estimation and outlier detection, to our knowledge, none of these methods have been implemented in an online setting. In this paper, we focus on online covariance matrix estimation and outlier detection. Specifically, we propose a new method for simultaneously and online estimating the geometric median and variance, which allows us to calculate the Mahalanobis distance for each incoming data point before deciding whether it should be considered an outlier. To mitigate the masking effect, robust estimation techniques for the mean and variance are required. Our approach uses the geometric median for robust estimation of the location and the median covariance matrix for robust estimation of the dispersion parameters. The new online methods proposed for parameter estimation and outlier detection allow real-time identification of outliers as data are observed sequentially. The performance of our methods is demonstrated on simulated datasets.

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arXiv2025

A Markov switching discrete-time Hawkes process: application to the monitoring of bats behavior

Over the past few decades, the Hawkes process has become a popular framework for modeling temporal events thanks to its flexibility to capture different dependency structures. The objective of this work is to model call sequences emitted by bats for echolocation, whose patterns are known to change depending on the animal's activity. The novelty of the model lies in the combination of a Hawkes-type dependency from past events, as well as a latent variable that encodes changes in bat behavior. More precisely, we consider a discrete-time version of the Hawkes process, with an exponential kernel, where the immigration term varies according to a latent Markov chain. We prove that this model is identifiable and can be reformulated in terms of a Hidden Markov Model, with Poisson emissions. Based on these properties, we show that maximum likelihood inference of the model parameters can be performed using an EM algorithm, which involves a recursive M-step. A simulation study demonstrates the performance of our approach method for estimating the parameters, recovering the number of hidden states and classifying each bin of the trajectory. Finally, we illustrate the use of the proposed modeling to distinguish different behaviors of bats, based on the recording of their cries.

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arXiv2025

Hoeffding-type decomposition for $U$-statistics on bipartite networks

We consider a broad class of random bipartite networks, the distribution of which is invariant under permutation within each type of nodes. We are interested in $U$-statistics defined on the adjacency matrix of such a network, for which we define a new type of Hoeffding decomposition based on the Aldous-Hoover-Kallenberg representation of row-column exchangeable matrices. This decomposition enables us to characterize non-degenerate $U$-statistics -- which are then asymptotically normal -- and provides us with a natural and easy-to-implement estimator of their asymptotic variance. \\ We illustrate the use of this general approach on some typical random graph models and use it to estimate or test some quantities characterizing the topology of the associated network. We also assess the accuracy and the power of the proposed estimates or tests, via a simulation study.

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arXiv2024

A Structured Estimator for large Covariance Matrices in the Presence of Pairwise and Spatial Covariates

We consider the problem of estimating a high-dimensional covariance matrix from a small number of observations when covariates on pairs of variables are available and the variables can have spatial structure. This is motivated by the problem arising in demography of estimating the covariance matrix of the total fertility rate (TFR) of 195 different countries when only 11 observations are available. We construct an estimator for high-dimensional covariance matrices by exploiting information about pairwise covariates, such as whether pairs of variables belong to the same cluster, or spatial structure of the variables, and interactions between the covariates. We reformulate the problem in terms of a mixed effects model. This requires the estimation of only a small number of parameters, which are easy to interpret and which can be selected using standard procedures. The estimator is consistent under general conditions, and asymptotically normal. It works if the mean and variance structure of the data is already specified or if some of the data are missing. We assess its performance under our model assumptions, as well as under model misspecification, using simulations. We find that it outperforms several popular alternatives. We apply it to the TFR dataset and draw some conclusions.

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arXiv2023

Motif-based tests for bipartite networks

Bipartite networks are a natural representation of the interactions between entities from two different types. The organization (or topology) of such networks gives insight to understand the systems they describe as a whole. Here, we rely on motifs which provide a meso-scale description of the topology. Moreover, we consider the bipartite expected degree distribution (B-EDD) model which accounts for both the density of the network and possible imbalances between the degrees of the nodes. Under the B-EDD model, we prove the asymptotic normality of the count of any given motif, considering sparsity conditions. We also provide close-form expressions for the mean and the variance of this count. This allows to avoid computationally prohibitive resampling procedures. Based on these results, we define a goodness-of-fit test for the B-EDD model and propose a family of tests for network comparisons. We assess the asymptotic normality of the test statistics and the power of the proposed tests on synthetic experiments and illustrate their use on ecological data sets.

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arXiv2022

A robust model-based clustering based on the geometric median and the Median Covariation Matrix

Grouping observations into homogeneous groups is a recurrent task in statistical data analysis. We consider Gaussian Mixture Models, which are the most famous parametric model-based clustering method. We propose a new robust approach for model-based clustering, which consists in a modification of the EM algorithm (more specifically, the M-step) by replacing the estimates of the mean and the variance by robust versions based on the median and the median covariation matrix. All the proposed methods are available in the R package RGMM accessible on CRAN.

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arXiv2022

Mixture-based estimation of entropy

The entropy is a measure of uncertainty that plays a central role in information theory. When the distribution of the data is unknown, an estimate of the entropy needs be obtained from the data sample itself. We propose a semi-parametric estimate, based on a mixture model approximation of the distribution of interest. The estimate can rely on any type of mixture, but we focus on Gaussian mixture model to demonstrate its accuracy and versatility. Performance of the proposed approach is assessed through a series of simulation studies. We also illustrate its use on two real-life data examples.

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arXiv2021

Querying multiple sets of $p$-values through composed hypothesis testing

Motivation: Combining the results of different experiments to exhibit complex patterns or to improve statistical power is a typical aim of data integration. The starting point of the statistical analysis often comes as sets of p-values resulting from previous analyses, that need to be combined in a flexible way to explore complex hypotheses, while guaranteeing a low proportion of false discoveries. Results: We introduce the generic concept of composed hypothesis, which corresponds to an arbitrary complex combination of simple hypotheses. We rephrase the problem of testing a composed hypothesis as a classification task, and show that finding items for which the composed null hypothesis is rejected boils down to fitting a mixture model and classify the items according to their posterior probabilities. We show that inference can be efficiently performed and provide a thorough classification rule to control for type I error. The performance and the usefulness of the approach are illustrated on simulations and on two different applications. The method is scalable, does not require any parameter tuning, and provided valuable biological insight on the considered application cases. Availability: The QCH methodology is implemented in the qch R package hosted on CRAN.

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arXiv2020

Accounting for missing actors in interaction network inference from abundance data

Network inference aims at unraveling the dependency structure relating jointly observed variables. Graphical models provide a general framework to distinguish between marginal and conditional dependency. Unobserved variables (missing actors) may induce apparent conditional dependencies.In the context of count data, we introduce a mixture of Poisson log-normal distributions with tree-shaped graphical models, to recover the dependency structure, including missing actors. We design a variational EM algorithm and assess its performance on synthetic data. We demonstrate the ability of our approach to recover environmental drivers on two ecological datasets. The corresponding R package is available from github.com/Rmomal/nestor.

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arXiv2019

Tree-based Inference of Species Interaction Network from Abundance Data

The behavior of ecological systems mainly relies on the interactions between the species it involves. We consider the problem of inferring the species interaction network from abundance data. To be relevant, any network inference methodology needs to handle count data and to account for possible environmental effects. It also needs to distinguish between direct interactions and indirect associations and graphical models provide a convenient framework for this purpose. We introduce a generic statistical model for network inference based on abundance data. The model includes fixed effects to account for environmental covariates and sampling efforts, and correlated random effects to encode species interactions. The inferred network is obtained by averaging over all possible tree-shaped (and therefore sparse) networks, in a computationally efficient manner. An output of the procedure is the probability for each edge to be part of the underlying network. A simulation study shows that the proposed methodology compares well with state-of-the-art approaches, even when the underlying graph strongly differs from a tree. The analysis of two datasets highlights the influence of covariates on the inferred network. Accounting for covariates is critical to avoid spurious edges. The proposed approach could be extended to perform network comparison or to look for missing species.

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arXiv2019

Degree-based goodness-of-fit tests for heterogeneous random graph models : independent and exchangeable cases

The degrees are a classical and relevant way to study the topology of a network. They can be used to assess the goodness-of-fit for a given random graph model. In this paper we introduce goodness-of-fit tests for two classes of models. First, we consider the case of independent graph models such as the heterogeneous Erdös-Rényi model in which the edges have different connection probabilities. Second, we consider a generic model for exchangeable random graphs called the W-graph. The stochastic block model and the expected degree distribution model fall within this framework. We prove the asymptotic normality of the degree mean square under these independent and exchangeable models and derive formal tests. We study the power of the proposed tests and we prove the asymptotic normality under specific sparsity regimes. The tests are illustrated on real networks from social sciences and ecology, and their performances are assessed via a simulation study.

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arXiv2019

Bayesian inference for network Poisson models

This work is motivated by the analysis of ecological interaction networks. Poisson stochastic blockmodels are widely used in this field to decipher the structure that underlies a weighted network, while accounting for covariate effects. Efficient algorithms based on variational approximations exist for frequentist inference, but without statistical guaranties as for the resulting estimates. In absence of variational Bayes estimates, we show that a good proxy of the posterior distribution can be straightforwardly derived from the frequentist variational estimation procedure, using a Laplace approximation. We use this proxy to sample from the true posterior distribution via a sequential Monte-Carlo algorithm. As shown in the simulation study, the efficiency of the posterior sampling is greatly improved by the accuracy of the approximate posterior distribution. The proposed procedure can be easily extended to other latent variable models. We use this methodology to assess the influence of available covariates on the organization of two ecological networks, as well as the existence of a residual interaction structure.

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arXiv2018

A factor model approach for the joint segmentation with between-series correlation

We consider the segmentation of set of correlated time-series, the correlation being allowed to take an arbitrary form but being the same at each time-position. We show that encoding the dependency in a factor model enables us to use the dynamic programming algorithm for the inference of the breakpoints, which remains one the most efficient algorithm. We propose a model selection procedure to determine both the number of breakpoints and the number of factors. This proposed method is implemented in the FASeg R package, which is available on the CRAN. We demonstrate the performances of our procedure through simulation experiments and an application to geodesic data is presented.

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arXiv2018

Variational inference for sparse network reconstruction from count data

In multivariate statistics, the question of finding direct interactions can be formulated as a problem of network inference - or network reconstruction - for which the Gaussian graphical model (GGM) provides a canonical framework. Unfortunately, the Gaussian assumption does not apply to count data which are encountered in domains such as genomics, social sciences or ecology. To circumvent this limitation, state-of-the-art approaches use two-step strategies that first transform counts to pseudo Gaussian observations and then apply a (partial) correlation-based approach from the abundant literature of GGM inference. We adopt a different stance by relying on a latent model where we directly model counts by means of Poisson distributions that are conditional to latent (hidden) Gaussian correlated variables. In this multivariate Poisson lognormal-model, the dependency structure is completely captured by the latent layer. This parametric model enables to account for the effects of covariates on the counts. To perform network inference, we add a sparsity inducing constraint on the inverse covariance matrix of the latent Gaussian vector. Unlike the usual Gaussian setting, the penalized likelihood is generally not tractable, and we resort instead to a variational approach for approximate likelihood maximization. The corresponding optimization problem is solved by alternating a gradient ascent on the variational parameters and a graphical-Lasso step on the covariance matrix. We show that our approach is highly competitive with the existing methods on simulation inspired from microbiological data. We then illustrate on three various data sets how accounting for sampling efforts via offsets and integrating external covariates (which is mostly never done in the existing literature) drastically changes the topology of the inferred network.

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arXiv2018

Variational inference for probabilistic Poisson PCA

Many application domains such as ecology or genomics have to deal with multivariate non Gaussian observations. A typical example is the joint observation of the respective abundances of a set of species in a series of sites, aiming to understand the co-variations between these species. The Gaussian setting provides a canonical way to model such dependencies, but does not apply in general. We consider here the multivariate exponential family framework for which we introduce a generic model with multivariate Gaussian latent variables. We show that approximate maximum likelihood inference can be achieved via a variational algorithm for which gradient descent easily applies. We show that this setting enables us to account for covariates and offsets. We then focus on the case of the Poisson-lognormal model in the context of community ecology. We demonstrate the efficiency of our algorithm on microbial ecology datasets. We illustrate the importance of accounting for the effects of covariates to better understand interactions between species.

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arXiv2018

Incomplete graphical model inference via latent tree aggregation

Graphical network inference is used in many fields such as genomics or ecology to infer the conditional independence structure between variables, from measurements of gene expression or species abundances for instance. In many practical cases, not all variables involved in the network have been observed, and the samples are actually drawn from a distribution where some variables have been marginalized out. This challenges the sparsity assumption commonly made in graphical model inference, since marginalization yields locally dense structures, even when the original network is sparse. We present a procedure for inferring Gaussian graphical models when some variables are unobserved, that accounts both for the influence of missing variables and the low density of the original network. Our model is based on the aggregation of spanning trees, and the estimation procedure on the Expectation-Maximization algorithm. We treat the graph structure and the unobserved nodes as missing variables and compute posterior probabilities of edge appearance. To provide a complete methodology, we also propose several model selection criteria to estimate the number of missing nodes. A simulation study and an illustration flow cytometry data reveal that our method has favorable edge detection properties compared to existing graph inference techniques. The methods are implemented in an R package.

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arXiv2018

Exact and approximate inference in graphical models: variable elimination and beyond

Probabilistic graphical models offer a powerful framework to account for the dependence structure between variables, which is represented as a graph. However, the dependence between variables may render inference tasks intractable. In this paper we review techniques exploiting the graph structure for exact inference, borrowed from optimisation and computer science. They are built on the principle of variable elimination whose complexity is dictated in an intricate way by the order in which variables are eliminated. The so-called treewidth of the graph characterises this algorithmic complexity: low-treewidth graphs can be processed efficiently. The first message that we illustrate is therefore the idea that for inference in graphical model, the number of variables is not the limiting factor, and it is worth checking for the treewidth before turning to approximate methods. We show how algorithms providing an upper bound of the treewidth can be exploited to derive a 'good' elimination order enabling to perform exact inference. The second message is that when the treewidth is too large, algorithms for approximate inference linked to the principle of variable elimination, such as loopy belief propagation and variational approaches, can lead to accurate results while being much less time consuming than Monte-Carlo approaches. We illustrate the techniques reviewed in this article on benchmarks of inference problems in genetic linkage analysis and computer vision, as well as on hidden variables restoration in coupled Hidden Markov Models.

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arXiv2017

Using deterministic approximations to accelerate SMC for posterior sampling

Sequential Monte Carlo has become a standard tool for Bayesian Inference of complex models. This approach can be computationally demanding, especially when initialized from the prior distribution. On the other hand, deter-ministic approximations of the posterior distribution are often available with no theoretical guaranties. We propose a bridge sampling scheme starting from such a deterministic approximation of the posterior distribution and targeting the true one. The resulting Shortened Bridge Sampler (SBS) relies on a sequence of distributions that is determined in an adaptive way. We illustrate the robustness and the efficiency of the methodology on a large simulation study. When applied to network datasets, SBS inference leads to different statistical conclusions from the one supplied by the standard variational Bayes approximation.

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