Bertrand Michel

Anthony Ozier-Lafontaine, Camille Fourneaux, Ghislain Durif et al.

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.

Ziyad Oulhaj, Mathieu Carrière, Bertrand Michel

Unsupervised data representation and visualization using tools from topology is an active and growing field of Topological Data Analysis (TDA) and data science. Its most prominent line of work is based on the so-called Mapper graph, which is a combinatorial graph whose topological structures (connected components, branches, loops) are in correspondence with those of the data itself. While highly generic and applicable, its use has been hampered so far by the manual tuning of its many parameters-among these, a crucial one is the so-called filter: it is a continuous function whose variations on the data set are the main ingredient for both building the Mapper representation and assessing the presence and sizes of its topological structures. However, while a few parameter tuning methods have already been investigated for the other Mapper parameters (i.e., resolution, gain, clustering), there is currently no method for tuning the filter itself. In this work, we build on a recently proposed optimization framework incorporating topology to provide the first filter optimization scheme for Mapper graphs. In order to achieve this, we propose a relaxed and more general version of the Mapper graph, whose convergence properties are investigated. Finally, we demonstrate the usefulness of our approach by optimizing Mapper graph representations on several datasets, and showcasing the superiority of the optimized representation over arbitrary ones.

Anthony Nouy, Bertrand Michel

We consider the problem of approximating a function from $L^2$ by an element of a given $m$-dimensional space $V_m$, associated with some feature map $\boldsymbol{\varphi}$, using evaluations of the function at random points $x_1, \dots,x_n$. After recalling some results on optimal weighted least-squares using independent and identically distributed points, we consider weighted least-squares using projection determinantal point processes (DPP) or volume sampling. These distributions introduce dependence between the points that promotes diversity in the selected features $\boldsymbol{\varphi}(x_i)$. We first provide a generalized version of volume-rescaled sampling yielding quasi-optimality results in expectation with a number of samples $n = O(m\log(m))$, that means that the expected $L^2$ error is bounded by a constant times the best approximation error in $L^2$. Also, further assuming that the function is in some normed vector space $H$ continuously embedded in $L^2$, we further prove that the approximation error in $L^2$ is almost surely bounded by the best approximation error measured in the $H$-norm. This includes the cases of functions from $L^\infty$ or reproducing kernel Hilbert spaces. Finally, we present an alternative strategy consisting in using independent repetitions of projection DPP (or volume sampling), yielding similar error bounds as with i.i.d. or volume sampling, but in practice with a much lower number of samples. Numerical experiments illustrate the performance of the different strategies.

Bertrand Michel, Anthony Nouy

Tree tensor networks, or tree-based tensor formats, are prominent model classes for the approximation of high-dimensional functions in computational and data science. They correspond to sum-product neural networks with a sparse connectivity associated with a dimension tree and widths given by a tuple of tensor ranks. The approximation power of these models has been proved to be (near to) optimal for classical smoothness classes. However, in an empirical risk minimization framework with a limited number of observations, the dimension tree and ranks should be selected carefully to balance estimation and approximation errors. We propose and analyze a complexity-based model selection method for tree tensor networks in an empirical risk minimization framework and we analyze its performance over a wide range of smoothness classes. Given a family of model classes associated with different trees, ranks, tensor product feature spaces and sparsity patterns for sparse tensor networks, a model is selected (à la Barron, Birgé, Massart) by minimizing a penalized empirical risk, with a penalty depending on the complexity of the model class and derived from estimates of the metric entropy of tree tensor networks. This choice of penalty yields a risk bound for the selected predictor. In a least-squares setting, after deriving fast rates of convergence of the risk, we show that our strategy is (near to) minimax adaptive to a wide range of smoothness classes including Sobolev or Besov spaces (with isotropic, anisotropic or mixed dominating smoothness) and analytic functions. We discuss the role of sparsity of the tensor network for obtaining optimal performance in several regimes. In practice, the amplitude of the penalty is calibrated with a slope heuristics method. Numerical experiments in a least-squares regression setting illustrate the performance of the strategy.

Mathieu Carrière, Bertrand Michel

Reeb spaces, as well as their discretized versions called Mappers, are common descriptors used in Topological Data Analysis, with plenty of applications in various fields of science, such as computational biology and data visualization, among others. The stability and quantification of the rate of convergence of the Mapper to the Reeb space has been studied a lot in recent works [BBMW19, CO17, CMO18, MW16], focusing on the case where a scalar-valued filter is used for the computation of Mapper. On the other hand, much less is known in the multivariate case, when the codomain of the filter is $\mathbb{R}^p$, and in the general case, when it is a general metric space $(Z, d_Z)$, instead of $\mathbb{R}$. The few results that are available in this setting [DMW17, MW16] can only handle continuous topological spaces and cannot be used as is for finite metric spaces representing data, such as point clouds and distance matrices. In this article, we introduce a slight modification of the usual Mapper construction and we give risk bounds for estimating the Reeb space using this estimator. Our approach applies in particular to the setting where the filter function used to compute Mapper is also estimated from data, such as the eigenfunctions of PCA. Our results are given with respect to the Gromov-Hausdorff distance, computed with specific filter-based pseudometrics for Mappers and Reeb spaces defined in [DMW17]. We finally provide applications of this setting in statistics and machine learning for different kinds of target filters, as well as numerical experiments that demonstrate the relevance of our approach

Frédéric Chazal, Bertrand Michel

Topological Data Analysis is a recent and fast growing field providing a set of new topological and geometric tools to infer relevant features for possibly complex data. This paper is a brief introduction, through a few selected topics, to basic fundamental and practical aspects of \tda\ for non experts.

Frédéric Chazal, Ilaria Giulini, Bertrand Michel

Approximations of Laplace-Beltrami operators on manifolds through graph Lapla-cians have become popular tools in data analysis and machine learning. These discretized operators usually depend on bandwidth parameters whose tuning remains a theoretical and practical problem. In this paper, we address this problem for the unnormalized graph Laplacian by establishing an oracle inequality that opens the door to a well-founded data-driven procedure for the bandwidth selection. Our approach relies on recent results by Lacour and Massart [LM15] on the so-called Lepski's method.

Stephane Gaiffas, Bertrand Michel

This paper is about variable selection, clustering and estimation in an unsupervised high-dimensional setting. Our approach is based on fitting constrained Gaussian mixture models, where we learn the number of clusters $K$ and the set of relevant variables $S$ using a generalized Bayesian posterior with a sparsity inducing prior. We prove a sparsity oracle inequality which shows that this procedure selects the optimal parameters $K$ and $S$. This procedure is implemented using a Metropolis-Hastings algorithm, based on a clustering-oriented greedy proposal, which makes the convergence to the posterior very fast.

Frédéric Chazal, Marc Glisse, Catherine Labruère et al.

Computational topology has recently known an important development toward data analysis, giving birth to the field of topological data analysis. Topological persistence, or persistent homology, appears as a fundamental tool in this field. In this paper, we study topological persistence in general metric spaces, with a statistical approach. We show that the use of persistent homology can be naturally considered in general statistical frameworks and persistence diagrams can be used as statistics with interesting convergence properties. Some numerical experiments are performed in various contexts to illustrate our results.