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Franck Picard

Publications and source records attributed to Franck Picard.

14 recordsLinked to original sources

Minimax estimation of Functional Principal Components from noisy discretized functional data: the case of smooth processes

We study the minimax estimation of covariance eigenfunctions and eigenvalues in functional principal component analysis when $n$ trajectories are observed at $p$ common grid points with additive noise. We consider covariance kernels with arbitrary H\"older smoothness and no prescribed parametric decay of the eigenvalues. In this setting, kernel smoothness and local spectral separation play distinct roles: a minimax inconsistency result over the smoothness-only class shows that kernel regularity alone is not sufficient for minimax-consistent eigenfunction estimation. To capture this interplay, we introduce a class of processes that jointly controls the H\"older smoothness of the covariance kernel and a local relative inverse eigengap quantity at the target index $\ell$. Over this class, we derive non-asymptotic minimax lower bounds for eigenfunction estimation that disentangle sampling variability, discretization and spectral effects, revealing rates of order $\delta_\ell n^{-1}+p^{-2\alpha}$, where $\delta_\ell$ quantifies the spectral difficulty. We also obtain non-asymptotic lower bounds for eigenvalue estimation under a relative squared-error loss. We then construct a computable wavelet projection estimator based on Coiflet scaling functions and a quadrature scheme designed to accommodate arbitrary H\"older smoothness. For eigenfunction estimation, this estimator matches the minimax dependence on the sample size and grid resolution, up to the natural spectral factor, for any H\"older index $\alpha>0$. Finally, we show that the proposed framework covers several classical Gaussian processes and Karhunen--Lo\`eve constructions. In particular, a Karhunen--Lo\`eve based criterion links spectral decay, eigenfunction regularity and covariance-kernel smoothness, and yields controlled simulation settings illustrating the predicted phase transitions and least-favourable discretization effects.

math.ST

Non-asymptotic two-sample kernel testing with the spectrally truncated normalized MMD

Kernel methods provide a flexible and powerful framework for nonparametric statistical testing by embedding probability distributions into a reproducing kernel Hilbert space (RKHS). In this work, we study the kernel two-sample testing problem and focus on a normalized version of the Maximum Mean Discrepancy (MMD) as a test statistic, which scales the discrepancy by the within-group covariance operator to account for data variability. This normalization has been shown to improve test power in both theoretical and empirical settings. Because this normalization requires regularization, we study the non-asymptotic properties of the spectrally truncated normalized MMD (st-nMMD) and derive an exponential upper bound under the null hypothesis. Thanks to this result we propose a sharp and explicit upper bound for the corresponding non-asymptotic quantile, along with a data-adaptive estimator. We further propose an algorithm to tune the hyperparameters involved in the quantile estimation, including the truncation level, without requiring data splitting. We demonstrate the performance of the st-nMMD through numerical experiments under both the null and alternative hypotheses.

math.ST

Extending Kernel Testing To General Designs

Kernel-based testing has revolutionized the field of non-parametric tests through the embedding of distributions in an RKHS. This strategy has proven to be powerful and flexible, yet its applicability has been limited to the standard two-sample case, while practical situations often involve more complex experimental designs. To extend kernel testing to any design, we propose a linear model in the RKHS that allows for the decomposition of mean embeddings into additive functional effects. We then introduce a truncated kernel Hotelling-Lawley statistic to test the effects of the model, demonstrating that its asymptotic distribution is chi-square, which remains valid with its Nystrom approximation. We discuss a homoscedasticity assumption that, although absent in the standard two-sample case, is necessary for general designs. Finally, we illustrate our framework using a single-cell RNA sequencing dataset and provide kernel-based generalizations of classical diagnostic and exploration tools to broaden the scope of kernel testing in any experimental design.

stat.ME

PCA for Point Processes

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\`{e}ve 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.

math.ST

Kernel-Based Testing for Single-Cell Differential Analysis

Single-cell technologies offer insights into molecular feature distributions, but comparing them poses challenges. We propose a kernel-testing framework for non-linear cell-wise distribution comparison, analyzing gene expression and epigenomic modifications. Our method allows feature-wise and global transcriptome/epigenome comparisons, revealing cell population heterogeneities. Using a classifier based on embedding variability, we identify transitions in cell states, overcoming limitations of traditional single-cell analysis. Applied to single-cell ChIP-Seq data, our approach identifies untreated breast cancer cells with an epigenomic profile resembling persister cells. This demonstrates the effectiveness of kernel testing in uncovering subtle population variations that might be missed by other methods.

stat.ML

Uniform Deconvolution for Poisson Point Processes

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 show that our adaptive estimator is optimal from the oracle and minimax points of view, and provide new lower bounds when the intensity belongs to a Sobolev ball. By developing the Goldenshluger-Lepski methodology in the case of deconvolution for Poisson processes, we propose an optimal data-driven selection of the kernel bandwidth. Our method is illustrated on the spatial distribution of replication origins and sequence motifs along the human genome.

stat.ME

A Probabilistic Graph Coupling View of Dimension Reduction

Most popular dimension reduction (DR) methods like t-SNE and UMAP are based on minimizing a cost between input and latent pairwise similarities. Though widely used, these approaches lack clear probabilistic foundations to enable a full understanding of their properties and limitations. To that extent, we introduce a unifying statistical framework based on the coupling of hidden graphs using cross entropy. These graphs induce a Markov random field dependency structure among the observations in both input and latent spaces. We show that existing pairwise similarity DR methods can be retrieved from our framework with particular choices of priors for the graphs. Moreover this reveals that these methods suffer from a statistical deficiency that explains poor performances in conserving coarse-grain dependencies. Our model is leveraged and extended to address this issue while new links are drawn with Laplacian eigenmaps and PCA.

math.PR

Minimax estimation of Functional Principal Components from noisy discretized functional data

Functional Principal Component Analysis is a reference method for dimension reduction of curve data. Its theoretical properties are now well understood in the simplified case where the sample curves are fully observed without noise. However, functional data are noisy and necessarily observed on a finite discretization grid. Common practice consists in smoothing the data and then to compute the functional estimates, but the impact of this denoising step on the procedure's statistical performance are rarely considered. Here we prove new convergence rates for functional principal component estimators. We introduce a double asymptotic framework: one corresponding to the sampling size and a second to the size of the grid. We prove that estimates based on projection onto histograms show optimal rates in a minimax sense. Theoretical results are illustrated on simulated data and the method is applied to the visualization of genomic data.

stat.ME

Probabilistic Count Matrix Factorization for Single Cell Expression Data Analysis

The development of high throughput single-cell sequencing technologies now allows the investigation of the population level diversity of cellular transcriptomes. This diversity has shown two faces. First, the expression dynamics (gene to gene variability) can be quantified more accurately, thanks to the measurement of lowly-expressed genes. Second, the cell-to-cell variability is high, with a low proportion of cells expressing the same gene at the same time/level. Those emerging patterns appear to be very challenging from the statistical point of view, especially to represent and to provide a summarized view of single-cell expression data. PCA is one of the most powerful framework to provide a suitable representation of high dimensional datasets, by searching for latent directions catching the most variability in the data. Unfortunately, classical PCA is based on Euclidean distances and projections that work poorly in presence of over-dispersed counts that show drop-out events (zero-inflation) like single-cell expression data We propose a probabilistic Count Matrix Factorization (pCMF) approach for single-cell expression data analysis, that relies on a sparse Gamma-Poisson factor model. This hierarchical model is inferred using a variational EM algorithm. It is able to jointly build a low dimensional representation of cells and genes. We show how this probabilistic framework induces a geometry that is suitable for single-cell data visualization, and produces a compression of the data that is very powerful for clustering purposes. Our method is competed against other standard representation methods like t-SNE, and we illustrate its performance for the representation of single-cell data. We especially focus on publicly available single-cell RNA-seq datasets.

stat.ME

Continuous testing for Poisson process intensities: A new perspective on scanning statistics

We propose a novel continuous testing framework to test the intensities of Poisson Processes. This framework allows a rigorous definition of the complete testing procedure, from an infinite number of hypothesis to joint error rates. Our work extends traditional procedures based on scanning windows, by controlling the family-wise error rate and the false discovery rate in a non-asymptotic manner and in a continuous way. The decision rule is based on a \pvalue process that can be estimated by a Monte-Carlo procedure. We also propose new test statistics based on kernels. Our method is applied in Neurosciences and Genomics through the standard test of homogeneity, and the two-sample test.

stat.ME

Minimax wavelet estimation for multisample heteroscedastic non-parametric regression

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 fixed effect belongs to the Besov class. This framework allows us to model curves that can exhibit strong irregularities, such as peaks or jumps for instance. The lower bound for the $L_2$ minimax risk is provided, as well as the upper bound of the minimax rate, that is derived by constructing a wavelet estimator for the functional fixed effect. Our work constitutes the first theoretical functional results in multisample non parametric regression. Our approach is illustrated on realistic simulated datasets as well as on experimental data.

stat.ME

Modelling overdispersion heterogeneity in differential expression analysis using mixtures

Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this probabilistic framework is the reliable estimation of the overdispersion parameter, reinforced by the limited number of replicates generally observable for each gene. Many strategies have been proposed to estimate this parameter, but when differential analysis is the purpose, they often result in procedures based on plug-in estimates, and we show here that this discrepancy between the estimation framework and the testing framework can lead to uncontrolled type-I errors. Instead we propose a mixture model that allows each gene to share information with other genes that exhibit similar variability. Three consistent statistical tests are developed for differential expression analysis. We show that the proposed method improves the sensitivity of detecting differentially expressed genes with respect to the common procedures, since it is the best one in reaching the nominal value for the first-type error, while keeping elevate power. The method is finally illustrated on prostate cancer RNA-seq data.

stat.ME

Spatially-constrained clustering of ecological networks

Spatial ecological networks are widely used to model interactions between georeferenced biological entities (e.g., populations or communities). The analysis of such data often leads to a two-step approach where groups containing similar biological entities are firstly identified and the spatial information is used afterwards to improve the ecological interpretation. We develop an integrative approach to retrieve groups of nodes that are geographically close and ecologically similar. Our model-based spatially-constrained method embeds the geographical information within a regularization framework by adding some constraints to the maximum likelihood estimation of parameters. A simulation study and the analysis of real data demonstrate that our approach is able to detect complex spatial patterns that are ecologically meaningful. The model-based framework allows us to consider external information (e.g., geographic proximities, covariates) in the analysis of ecological networks and appears to be an appealing alternative to consider such data.

stat.AP

Strategies for online inference of model-based clustering in large and growing networks

In this paper we adapt online estimation strategies to perform model-based clustering on large networks. Our work focuses on two algorithms, the first based on the SAEM algorithm, and the second on variational methods. These two strategies are compared with existing approaches on simulated and real data. We use the method to decipher the connexion structure of the political websphere during the US political campaign in 2008. We show that our online EM-based algorithms offer a good trade-off between precision and speed, when estimating parameters for mixture distributions in the context of random graphs.

stat.AP