Johan Mathe

Mathilde Papillon, Mustafa Hajij, Helen Jenne et al.

This paper presents the computational challenge on topological deep learning that was hosted within the ICML 2023 Workshop on Topology and Geometry in Machine Learning. The competition asked participants to provide open-source implementations of topological neural networks from the literature by contributing to the python packages TopoNetX (data processing) and TopoModelX (deep learning). The challenge attracted twenty-eight qualifying submissions in its two-month duration. This paper describes the design of the challenge and summarizes its main findings.

Louisa Cornelis, Johan Mathe, Louis Van Langendonck et al.

Graph Neural Networks (GNNs) have become the dominant framework for inductive graph-level learning. Yet most benchmarks focus on the regime $n \gg p$, where the number of graphs $n$ greatly exceeds the number of nodes per graph $p$. This overlooks biological domains such as omics, which operate in the opposite $n \ll p$ regime, characterized by large graphs of genes, transcripts, or proteins across few patient samples. This raises the question: \textit{how do GNNs perform in this low-sample, high-node omics setting?} We introduce \texttt{OgBench} (Omics-Graph Bench), the first benchmarking platform for graph-level prediction in the $n \ll p$ regime characteristic of omics data. We provide a standardized, end-to-end modular infrastructure from raw omics data to families of featured graphs with varied structural properties. We benchmark classical GNNs, as well as GNNs designed for large graphs and omics applications, alongside MLPs and machine learning baselines to establish reference performances. Our results show that widely used GNNs often do not outperform simple MLPs and classical baselines. These findings challenge the prevailing assumption that graph structure inherently adds value in this domain, fostering a critical reassessment of current learning paradigms. Ultimately, by exposing these limitations, OgBench provides the open-source ecosystem necessary for the community to develop and validate novel architectures explicitly tailored for biological graphs. The code is available at https://github.com/geometric-intelligence/ogbench.

Mathilde Papillon, Sophia Sanborn, Johan Mathe et al.

The enduring legacy of Euclidean geometry underpins classical machine learning, which, for decades, has been primarily developed for data lying in Euclidean space. Yet, modern machine learning increasingly encounters richly structured data that is inherently nonEuclidean. This data can exhibit intricate geometric, topological and algebraic structure: from the geometry of the curvature of space-time, to topologically complex interactions between neurons in the brain, to the algebraic transformations describing symmetries of physical systems. Extracting knowledge from such non-Euclidean data necessitates a broader mathematical perspective. Echoing the 19th-century revolutions that gave rise to non-Euclidean geometry, an emerging line of research is redefining modern machine learning with non-Euclidean structures. Its goal: generalizing classical methods to unconventional data types with geometry, topology, and algebra. In this review, we provide an accessible gateway to this fast-growing field and propose a graphical taxonomy that integrates recent advances into an intuitive unified framework. We subsequently extract insights into current challenges and highlight exciting opportunities for future development in this field.

Johan Mathe, Adele Myers, Simon Mataigne et al.

Many machine learning tasks are invariant under the action of a group $G$ of transformations: signal classification can be invariant under translations, image classification under 2D rotations, and spherical-image classification under 3D rotations. The $G$-bispectrum is a principled complete invariant of a signal (retaining all all signal's information up to the group action) with proven benefits in machine learning and as a pooling layer in deep networks. However, its deployment has been hampered by high computational cost and a patchwork of group-specific implementations. We present bispectrum, an open-source, fully unit-tested PyTorch library that implements selective $G$-bispectra for seven different group actions, as differentiable modules that can be directly incorporated into machine learning pipelines and deep learning architectures. For finite groups $G$, selectivity reduces the computational cost from $O(|G|^2)$ to $O(|G|)$. For planar rotations, we leverage the disk bispectrum. For spherical 3D rotations, we introduce an augmented selective bispectrum at band-limit $L$ which reduces the cost from $O(L^3)$ to $Θ(L^2)$ coefficients. We profile the entire library (for which we implemented various compute optimizations), showing that it delivers near-exact $G$-invariance with its selective $G$-bispectra computed in sub-millisecond time on GPU (up to commonly used bandlimits). We evaluate the benefits of incorporating $G$-bispectra as pooling layers into deep learning architectures on three classical benchmark datasets --comparing against norm pooling, gated pooling, Fourier-ELU pooling, max pooling, and (non-equivariant) data-augmented convolutional baselines. Results show that $G$-bispectra consistently outperform alternatives in the low-data, moderate-capacity regime.

Guillermo Bernárdez, Lev Telyatnikov, Marco Montagna et al.

This paper describes the 2nd edition of the ICML Topological Deep Learning Challenge that was hosted within the ICML 2024 ELLIS Workshop on Geometry-grounded Representation Learning and Generative Modeling (GRaM). The challenge focused on the problem of representing data in different discrete topological domains in order to bridge the gap between Topological Deep Learning (TDL) and other types of structured datasets (e.g. point clouds, graphs). Specifically, participants were asked to design and implement topological liftings, i.e. mappings between different data structures and topological domains --like hypergraphs, or simplicial/cell/combinatorial complexes. The challenge received 52 submissions satisfying all the requirements. This paper introduces the main scope of the challenge, and summarizes the main results and findings.

Simon Mataigne, Johan Mathe, Sophia Sanborn et al.

An important problem in signal processing and deep learning is to achieve \textit{invariance} to nuisance factors not relevant for the task. Since many of these factors are describable as the action of a group $G$ (e.g. rotations, translations, scalings), we want methods to be $G$-invariant. The $G$-Bispectrum extracts every characteristic of a given signal up to group action: for example, the shape of an object in an image, but not its orientation. Consequently, the $G$-Bispectrum has been incorporated into deep neural network architectures as a computational primitive for $G$-invariance\textemdash akin to a pooling mechanism, but with greater selectivity and robustness. However, the computational cost of the $G$-Bispectrum ($\mathcal{O}(|G|^2)$, with $|G|$ the size of the group) has limited its widespread adoption. Here, we show that the $G$-Bispectrum computation contains redundancies that can be reduced into a \textit{selective $G$-Bispectrum} with $\mathcal{O}(|G|)$ complexity. We prove desirable mathematical properties of the selective $G$-Bispectrum and demonstrate how its integration in neural networks enhances accuracy and robustness compared to traditional approaches, while enjoying considerable speeds-up compared to the full $G$-Bispectrum.

Nina Miolane, Alice Le Brigant, Johan Mathe et al.

We introduce Geomstats, an open-source Python toolbox for computations and statistics on nonlinear manifolds, such as hyperbolic spaces, spaces of symmetric positive definite matrices, Lie groups of transformations, and many more. We provide object-oriented and extensively unit-tested implementations. Among others, manifolds come equipped with families of Riemannian metrics, with associated exponential and logarithmic maps, geodesics and parallel transport. Statistics and learning algorithms provide methods for estimation, clustering and dimension reduction on manifolds. All associated operations are vectorized for batch computation and provide support for different execution backends, namely NumPy, PyTorch and TensorFlow, enabling GPU acceleration. This paper presents the package, compares it with related libraries and provides relevant code examples. We show that Geomstats provides reliable building blocks to foster research in differential geometry and statistics, and to democratize the use of Riemannian geometry in machine learning applications. The source code is freely available under the MIT license at \url{geomstats.ai}.

Johan Mathe, Nina Miolane, Nicolas Sebastien et al.

Photovoltaic (PV) power generation has emerged as one of the lead renewable energy sources. Yet, its production is characterized by high uncertainty, being dependent on weather conditions like solar irradiance and temperature. Predicting PV production, even in the 24-hour forecast, remains a challenge and leads energy providers to left idling - often carbon emitting - plants. In this paper, we introduce a Long-Term Recurrent Convolutional Network using Numerical Weather Predictions (NWP) to predict, in turn, PV production in the 24-hour and 48-hour forecast horizons. This network architecture fully leverages both temporal and spatial weather data, sampled over the whole geographical area of interest. We train our model on an NWP dataset from the National Oceanic and Atmospheric Administration (NOAA) to predict spatially aggregated PV production in Germany. We compare its performance to the persistence model and state-of-the-art methods.

Nina Miolane, Johan Mathe, Claire Donnat et al.

We introduce geomstats, a python package that performs computations on manifolds such as hyperspheres, hyperbolic spaces, spaces of symmetric positive definite matrices and Lie groups of transformations. We provide efficient and extensively unit-tested implementations of these manifolds, together with useful Riemannian metrics and associated Exponential and Logarithm maps. The corresponding geodesic distances provide a range of intuitive choices of Machine Learning loss functions. We also give the corresponding Riemannian gradients. The operations implemented in geomstats are available with different computing backends such as numpy, tensorflow and keras. We have enabled GPU implementation and integrated geomstats manifold computations into keras deep learning framework. This paper also presents a review of manifolds in machine learning and an overview of the geomstats package with examples demonstrating its use for efficient and user-friendly Riemannian geometry.