arXiv subjects

Geneviève Robin

Publications and source records attributed to Geneviève Robin.

12 recordsLinked to original sources

arXiv2026

Inference of Multiscale Gaussian Graphical Model

Gaussian Graphical Models (GGMs) are widely used in high-dimensional data analysis to synthesize the interaction between variables. In many applications, such as genomics or image analysis, graphical models rely on sparsity and clustering to reduce dimensionality and improve performances. This paper explores a slightly different paradigm where clustering is not knowledge-driven but performed simultaneously with the graph inference task. We introduce a novel Multiscale Graphical Lasso (MGLasso) to improve networks interpretability by proposing graphs at different granularity levels. The method estimates clusters through a convex clustering approach - a relaxation of k-means, and hierarchical clustering. The conditional independence graph is simultaneously inferred through a neighborhood selection scheme for undirected graphical models. MGLasso extends and generalizes the sparse group fused lasso problem to undirected graphical models. We use continuation with Nesterov smoothing in a shrinkage-thresholding algorithm (CONESTA) to propose a regularization path of solutions along the group fused Lasso penalty, while the Lasso penalty is kept constant. Extensive experiments on synthetic data compare the performances of our model to state-of-the-art clustering methods and network inference models. Applications to gut microbiome data and poplar's methylation mixed with transcriptomic data are presented.

stat.ML↗

arXiv2025

Distilling foundation models for robust and efficient models in digital pathology

In recent years, the advent of foundation models (FM) for digital pathology has relied heavily on scaling the pre-training datasets and the model size, yielding large and powerful models. While it resulted in improving the performance on diverse downstream tasks, it also introduced increased computational cost and inference time. In this work, we explore the distillation of a large foundation model into a smaller one, reducing the number of parameters by several orders of magnitude. Leveraging distillation techniques, our distilled model, H0-mini, achieves nearly comparable performance to large FMs at a significantly reduced inference cost. It is evaluated on several public benchmarks, achieving 3rd place on the HEST benchmark and 5th place on the EVA benchmark. Additionally, a robustness analysis conducted on the PLISM dataset demonstrates that our distilled model reaches excellent robustness to variations in staining and scanning conditions, significantly outperforming other state-of-the art models. This opens new perspectives to design lightweight and robust models for digital pathology, without compromising on performance.

cs.CV↗

arXiv2025

Optimizing the diffusion coefficient of overdamped Langevin dynamics

Overdamped Langevin dynamics are reversible stochastic differential equations which are commonly used to sample probability measures in high-dimensional spaces, such as the ones appearing in computational statistical physics and Bayesian inference. By varying the diffusion coefficient, there are in fact infinitely many overdamped Langevin dynamics which are reversible with respect to the target probability measure at hand. This suggests to optimize the diffusion coefficient in order to increase the convergence rate of the dynamics, as measured by the spectral gap of the generator associated with the stochastic differential equation. We analytically study this problem here, obtaining in particular necessary conditions on the optimal diffusion coefficient. We also derive an explicit expression of the optimal diffusion in some appropriate homogenized limit. Numerical results, both relying on discretizations of the spectral gap problem and Monte Carlo simulations of the stochastic dynamics, demonstrate the increased quality of the sampling arising from an appropriate choice of the diffusion coefficient.

math.NA↗

arXiv2023

Generative methods for sampling transition paths in molecular dynamics

Molecular systems often remain trapped for long times around some local minimum of the potential energy function, before switching to another one -- a behavior known as metastability. Simulating transition paths linking one metastable state to another one is difficult by direct numerical methods. In view of the promises of machine learning techniques, we explore in this work two approaches to more efficiently generate transition paths: sampling methods based on generative models such as variational autoencoders, and importance sampling methods based on reinforcement learning.

stat.ML↗

arXiv2021

Federated Expectation Maximization with heterogeneity mitigation and variance reduction

The Expectation Maximization (EM) algorithm is the default algorithm for inference in latent variable models. As in any other field of machine learning, applications of latent variable models to very large datasets make the use of advanced parallel and distributed architectures mandatory. This paper introduces FedEM, which is the first extension of the EM algorithm to the federated learning context. FedEM is a new communication efficient method, which handles partial participation of local devices, and is robust to heterogeneous distributions of the datasets. To alleviate the communication bottleneck, FedEM compresses appropriately defined complete data sufficient statistics. We also develop and analyze an extension of FedEM to further incorporate a variance reduction scheme. In all cases, we derive finite-time complexity bounds for smooth non-convex problems. Numerical results are presented to support our theoretical findings, as well as an application to federated missing values imputation for biodiversity monitoring.

math.OC↗

arXiv2021

Technical report: Impact of evaluation metrics and sampling on the comparison of machine learning methods for biodiversity indicators prediction

Machine learning (ML) approaches are used more and more widely in biodiversity monitoring. In particular, an important application is the problem of predicting biodiversity indicators such as species abundance, species occurrence or species richness, based on predictor sets containing, e.g., climatic and anthropogenic factors. Considering the impressive number of different ML methods available in the litterature and the pace at which they are being published, it is crucial to develop uniform evaluation procedures, to allow the production of sound and fair empirical studies. However, defining fair evaluation procedures is challenging: because well-documented, intrinsic properties of biodiversity indicators such as their zero-inflation and over-dispersion, it is not trivial to design good sampling schemes for cross-validation nor good evaluation metrics. Indeed, the classical Mean Squared Error (MSE) fails to capture subtle differences in the performance of different methods, particularly in terms of prediction of very small, or very large values (e.g., zero counts or large counts). In this report, we illustrate this phenomenon by comparing ten statistical and machine learning models on the task of predicting waterbirds abundance in the North-African area, based on geographical, meteorological and spatio-temporal factors. Our results highlight that differnte off-the-shelf evaluation metrics and cross-validation sampling approaches yield drastically different rankings of the metrics, and fail to capture interpretable conclusions.

stat.AP↗

arXiv2020

Outliers Detection in Networks with Missing Links

Outliers arise in networks due to different reasons such as fraudulent behavior of malicious users or default in measurement instruments and can significantly impair network analyses. In addition, real-life networks are likely to be incompletely observed, with missing links due to individual non-response or machine failures. Identifying outliers in the presence of missing links is therefore a crucial problem in network analysis. In this work, we introduce a new algorithm to detect outliers in a network that simultaneously predicts the missing links. The proposed method is statistically sound: we prove that, under fairly general assumptions, our algorithm exactly detects the outliers, and achieves the best known error for the prediction of missing links with polynomial computation cost. It is also computationally efficient: we prove sub-linear convergence of our algorithm. We provide a simulation study which demonstrates the good behavior of the algorithm in terms of outliers detection and prediction of the missing links. We also illustrate the method with an application in epidemiology, and with the analysis of a political Twitter network. The method is freely available as an R package on the Comprehensive R Archive Network.

stat.ML↗

arXiv2019

Main effects and interactions in mixed and incomplete data frames

A mixed data frame (MDF) is a table collecting categorical, numerical and count observations. The use of MDF is widespread in statistics and the applications are numerous from abundance data in ecology to recommender systems. In many cases, an MDF exhibits simultaneously main effects, such as row, column or group effects and interactions, for which a low-rank model has often been suggested. Although the literature on low-rank approximations is very substantial, with few exceptions, existing methods do not allow to incorporate main effects and interactions while providing statistical guarantees. The present work fills this gap. We propose an estimation method which allows to recover simultaneously the main effects and the interactions. We show that our method is near optimal under conditions which are met in our targeted applications. We also propose an optimization algorithm which provably converges to an optimal solution. Numerical experiments reveal that our method, mimi, performs well when the main effects are sparse and the interaction matrix has low-rank. We also show that mimi compares favorably to existing methods, in particular when the main effects are significantly large compared to the interactions, and when the proportion of missing entries is large. The method is available as an R package on the Comprehensive R Archive Network.

stat.ME↗

arXiv2018

Low-rank Interaction with Sparse Additive Effects Model for Large Data Frames

Many applications of machine learning involve the analysis of large data frames-matrices collecting heterogeneous measurements (binary, numerical, counts, etc.) across samples-with missing values. Low-rank models, as studied by Udell et al. [30], are popular in this framework for tasks such as visualization, clustering and missing value imputation. Yet, available methods with statistical guarantees and efficient optimization do not allow explicit modeling of main additive effects such as row and column, or covariate effects. In this paper, we introduce a low-rank interaction and sparse additive effects (LORIS) model which combines matrix regression on a dictionary and low-rank design, to estimate main effects and interactions simultaneously. We provide statistical guarantees in the form of upper bounds on the estimation error of both components. Then, we introduce a mixed coordinate gradient descent (MCGD) method which provably converges sub-linearly to an optimal solution and is computationally efficient for large scale data sets. We show on simulated and survey data that the method has a clear advantage over current practices, which consist in dealing separately with additive effects in a preprocessing step.

stat.ML↗

arXiv2018

Low-rank model with covariates for count data analysis

Count data are collected in many scientific and engineering tasks including image processing, single-cell RNA sequencing and ecological studies. Such data sets often contain missing values, for example because some ecological sites cannot be reached in a certain year. In addition, in many instances, side information is also available, for example covariates about ecological sites or species. Low-rank methods are popular to denoise and impute count data, and benefit from a substantial theoretical background. Extensions accounting for covariates have been proposed, but to the best of our knowledge their theoretical and empirical properties have not been thoroughly studied, and few softwares are available for practitioners. We propose a complete methodology called LORI (Low-Rank Interaction), including a Poisson model, an algorithm, and automatic selection of the regularization parameter, to analyze count tables with covariates. We also derive an upper bound on the estimation error. We provide a simulation study with synthetic data, revealing empirically that LORI improves on state of the art methods in terms of estimation and imputation of the missing values. We illustrate how the method can be interpreted through visual displays with the analysis of a well-know plant abundance data set, and show that the LORI outputs are consistent with known results. Finally we demonstrate the relevance of the methodology by analyzing a water-birds abundance table from the French national agency for wildlife and hunting management (ONCFS). The method is available in the R package lori on the Comprehensive Archive Network (CRAN).

stat.ME↗

arXiv2018

Imputation of mixed data with multilevel singular value decomposition

Statistical analysis of large data sets offers new opportunities to better understand many processes. Yet, data accumulation often implies relaxing acquisition procedures or compounding diverse sources. As a consequence, such data sets often contain mixed data, i.e. both quantitative and qualitative and many missing values. Furthermore, aggregated data present a natural \textit{multilevel} structure, where individuals or samples are nested within different sites, such as countries or hospitals. Imputation of multilevel data has therefore drawn some attention recently, but current solutions are not designed to handle mixed data, and suffer from important drawbacks such as their computational cost. In this article, we propose a single imputation method for multilevel data, which can be used to complete either quantitative, categorical or mixed data. The method is based on multilevel singular value decomposition (SVD), which consists in decomposing the variability of the data into two components, the between and within groups variability, and performing SVD on both parts. We show on a simulation study that in comparison to competitors, the method has the great advantages of handling data sets of various size, and being computationally faster. Furthermore, it is the first so far to handle mixed data. We apply the method to impute a medical data set resulting from the aggregation of several data sets coming from different hospitals. This application falls in the framework of a larger project on Trauma patients. To overcome obstacles associated to the aggregation of medical data, we turn to distributed computation. The method is implemented in an R package.

stat.AP↗

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.

stat.ME↗