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Johan Mathe

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4 publications

preprint2026arXiv

bispectrum: Selective GG-Bispectra Made Practical

Many machine learning tasks are invariant under the action of a group GG of transformations: signal classification can be invariant under translations, image classification under 2D rotations, and spherical-image classification under 3D rotations. The GG-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 GG-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 GG, selectivity reduces the computational cost from O(∣G∣2)O(|G|^2) to O(∣G∣)O(|G|). For planar rotations, we leverage the disk bispectrum. For spherical 3D rotations, we introduce an augmented selective bispectrum at band-limit LL which reduces the cost from O(L3)O(L^3) to Θ(L2)Θ(L^2) coefficients. We profile the entire library (for which we implemented various compute optimizations), showing that it delivers near-exact GG-invariance with its selective GG-bispectra computed in sub-millisecond time on GPU (up to commonly used bandlimits). We evaluate the benefits of incorporating GG-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 GG-bispectra consistently outperform alternatives in the low-data, moderate-capacity regime.

preprint2026arXiv

OgBench: A Framework for Evaluating Graph Neural Networks on Omics Data

Graph Neural Networks (GNNs) have become the dominant framework for inductive graph-level learning. Yet most benchmarks focus on the regime n≫pn \gg p, where the number of graphs nn greatly exceeds the number of nodes per graph pp. This overlooks biological domains such as omics, which operate in the opposite n≪pn \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≪pn \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.

preprint2022arXiv

ICLR 2022 Challenge for Computational Geometry and Topology: Design and Results

This paper presents the computational challenge on differential geometry and topology that was hosted within the ICLR 2022 workshop ``Geometric and Topological Representation Learning". The competition asked participants to provide implementations of machine learning algorithms on manifolds that would respect the API of the open-source software Geomstats (manifold part) and Scikit-Learn (machine learning part) or PyTorch. The challenge attracted seven teams in its two month duration. This paper describes the design of the challenge and summarizes its main findings.

preprint2020arXiv

Geomstats: A Python Package for Riemannian Geometry in Machine Learning

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}.

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