Steve Oudot

Julie Mordacq, Vicky Kalogeiton, Steve Oudot

Self-supervised learning (SSL) has emerged as a powerful paradigm for learning meaningful representations from unlabeled data. However, the standard protocol for evaluating these representations, linear probing, is computationally expensive, sensitive to hyperparameters, and provides limited insight into the geometric structure of the representation space. In this work, motivated by connections between neural network generalization and intrinsic dimension (ID) we propose IdEst, a method for estimating the ID of SSL representations via the Minimum Spanning Tree dimension estimator ($\mathrm{dim}_\mathrm{MST}$). Across diverse datasets, architectures, and SSL pretraining objectives, we show that IdEst strongly correlates with downstream linear probe performances. Furthermore, we demonstrate that IdEst enables efficient hyperparameter selection, significantly reducing the computational cost compared to supervised alternatives. Our results highlight intrinsic dimensionality as a principled geometric proxy for assessing SSL representations, complementing standard supervised probing protocols.

David Loiseaux, Luis Scoccola, Mathieu Carrière et al.

Persistent homology (PH) provides topological descriptors for geometric data, such as weighted graphs, which are interpretable, stable to perturbations, and invariant under, e.g., relabeling. Most applications of PH focus on the one-parameter case -- where the descriptors summarize the changes in topology of data as it is filtered by a single quantity of interest -- and there is now a wide array of methods enabling the use of one-parameter PH descriptors in data science, which rely on the stable vectorization of these descriptors as elements of a Hilbert space. Although the multiparameter PH (MPH) of data that is filtered by several quantities of interest encodes much richer information than its one-parameter counterpart, the scarceness of stability results for MPH descriptors has so far limited the available options for the stable vectorization of MPH. In this paper, we aim to bring together the best of both worlds by showing how the interpretation of signed barcodes -- a recent family of MPH descriptors -- as signed measures leads to natural extensions of vectorization strategies from one parameter to multiple parameters. The resulting feature vectors are easy to define and to compute, and provably stable. While, as a proof of concept, we focus on simple choices of signed barcodes and vectorizations, we already see notable performance improvements when comparing our feature vectors to state-of-the-art topology-based methods on various types of data.

Julie Mordacq, Leo Milecki, Maria Vakalopoulou et al.

Multimodality has recently gained attention in the medical domain, where imaging or video modalities may be integrated with biomedical signals or health records. Yet, two challenges remain: balancing the contributions of modalities, especially in cases with a limited amount of data available, and tackling missing modalities. To address both issues, in this paper, we introduce the AnchoreD multimodAl Physiological Transformer (ADAPT), a multimodal, scalable framework with two key components: (i) aligning all modalities in the space of the strongest, richest modality (called anchor) to learn a joint embedding space, and (ii) a Masked Multimodal Transformer, leveraging both inter- and intra-modality correlations while handling missing modalities. We focus on detecting physiological changes in two real-life scenarios: stress in individuals induced by specific triggers and fighter pilots' loss of consciousness induced by $g$-forces. We validate the generalizability of ADAPT through extensive experiments on two datasets for these tasks, where we set the new state of the art while demonstrating its robustness across various modality scenarios and its high potential for real-life applications.

Ethan André, Jingyi Li, David Loiseaux et al.

Given an unknown $\mathbb{R}^n$-valued function $f$ on a metric space $X$, can we approximate the persistent homology of $f$ from a finite sampling of $X$ with known pairwise distances and function values? This question has been answered in the case $n=1$, assuming $f$ is Lipschitz continuous and $X$ is a sufficiently regular geodesic metric space, and using filtered geometric complexes with fixed scale parameter for the approximation. In this paper we answer the question for arbitrary $n$, under similar assumptions and using function-geometric multifiltrations. Our analysis offers a different view on these multifiltrations by focusing on their approximation properties rather than on their stability properties. We also leverage the multiparameter setting to provide insight into the influence of the scale parameter, whose choice is central to this type of approach. From a practical standpoint, we show that our approximation results are robust to input noise, and that function-geometric multifiltrations have good statistical convergence properties. We also provide an algorithm to compute our estimators, and we use its implementation to conduct extensive experiments, on both synthetic and real biological data, in order to validate our theoretical results and to assess the practicality of our approach.

Julie Mordacq, David Loiseaux, Vicky Kalogeiton et al.

Self-supervised learning (SSL) has emerged as a powerful paradigm for learning representations without labeled data, often by enforcing invariance to input transformations such as rotations or blurring. Recent studies have highlighted two pivotal properties for effective representations: (i) avoiding dimensional collapse-where the learned features occupy only a low-dimensional subspace, and (ii) enhancing uniformity of the induced distribution. In this work, we introduce T-REGS, a simple regularization framework for SSL based on the length of the Minimum Spanning Tree (MST) over the learned representation. We provide theoretical analysis demonstrating that T-REGS simultaneously mitigates dimensional collapse and promotes distribution uniformity on arbitrary compact Riemannian manifolds. Several experiments on synthetic data and on classical SSL benchmarks validate the effectiveness of our approach at enhancing representation quality.

Soham Mukherjee, Shreyas N. Samaga, Cheng Xin et al.

End-to-end topological learning using 1-parameter persistence is well-known. We show that the framework can be enhanced using 2-parameter persistence by adopting a recently introduced 2-parameter persistence based vectorization technique called GRIL. We establish a theoretical foundation of differentiating GRIL producing D-GRIL. We show that D-GRIL can be used to learn a bifiltration function on standard benchmark graph datasets. Further, we exhibit that this framework can be applied in the context of bio-activity prediction in drug discovery.

Jacob Leygonie, Mathieu Carrière, Théo Lacombe et al.

We introduce a novel gradient descent algorithm extending the well-known Gradient Sampling methodology to the class of stratifiably smooth objective functions, which are defined as locally Lipschitz functions that are smooth on some regular pieces-called the strata-of the ambient Euclidean space. For this class of functions, our algorithm achieves a sub-linear convergence rate. We then apply our method to objective functions based on the (extended) persistent homology map computed over lower-star filters, which is a central tool of Topological Data Analysis. For this, we propose an efficient exploration of the corresponding stratification by using the Cayley graph of the permutation group. Finally, we provide benchmark and novel topological optimization problems, in order to demonstrate the utility and applicability of our framework.

Théo Lacombe, Marco Cuturi, Steve Oudot

Persistence diagrams (PDs) are now routinely used to summarize the underlying topology of complex data. Despite several appealing properties, incorporating PDs in learning pipelines can be challenging because their natural geometry is not Hilbertian. Indeed, this was recently exemplified in a string of papers which show that the simple task of averaging a few PDs can be computationally prohibitive. We propose in this article a tractable framework to carry out standard tasks on PDs at scale, notably evaluating distances, estimating barycenters and performing clustering. This framework builds upon a reformulation of PD metrics as optimal transport (OT) problems. Doing so, we can exploit recent computational advances: the OT problem on a planar grid, when regularized with entropy, is convex can be solved in linear time using the Sinkhorn algorithm and convolutions. This results in scalable computations that can stream on GPUs. We demonstrate the efficiency of our approach by carrying out clustering with diagrams metrics on several thousands of PDs, a scale never seen before in the literature.

Mathieu Carrière, Marco Cuturi, Steve Oudot

Persistence diagrams (PDs) play a key role in topological data analysis (TDA), in which they are routinely used to describe topological properties of complicated shapes. PDs enjoy strong stability properties and have proven their utility in various learning contexts. They do not, however, live in a space naturally endowed with a Hilbert structure and are usually compared with specific distances, such as the bottleneck distance. To incorporate PDs in a learning pipeline, several kernels have been proposed for PDs with a strong emphasis on the stability of the RKHS distance w.r.t. perturbations of the PDs. In this article, we use the Sliced Wasserstein approximation SW of the Wasserstein distance to define a new kernel for PDs, which is not only provably stable but also provably discriminative (depending on the number of points in the PDs) w.r.t. the Wasserstein distance $d_1$ between PDs. We also demonstrate its practicality, by developing an approximation technique to reduce kernel computation time, and show that our proposal compares favorably to existing kernels for PDs on several benchmarks.

Thomas Bonis, Steve Oudot

In this paper, we propose a new fuzzy clustering algorithm based on the mode-seeking framework. Given a dataset in $\mathbb{R}^d$, we define regions of high density that we call cluster cores. We then consider a random walk on a neighborhood graph built on top of our data points which is designed to be attracted by high density regions. The strength of this attraction is controlled by a temperature parameter $β> 0$. The membership of a point to a given cluster is then the probability for the random walk to hit the corresponding cluster core before any other. While many properties of random walks (such as hitting times, commute distances, etc\dots) have been shown to enventually encode purely local information when the number of data points grows, we show that the regularization introduced by the use of cluster cores solves this issue. Empirically, we show how the choice of $β$ influences the behavior of our algorithm: for small values of $β$ the result is close to hard mode-seeking whereas when $β$ is close to $1$ the result is similar to the output of a (fuzzy) spectral clustering. Finally, we demonstrate the scalability of our approach by providing the fuzzy clustering of a protein configuration dataset containing a million data points in $30$ dimensions.