Louisa Cornelis

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.

Louisa Cornelis, Guillermo Bernárdez, Haewon Jeong et al.

Personalization in machine learning involves tailoring models to individual users by incorporating personal attributes such as demographic or medical data. While personalization can improve prediction accuracy, it may also amplify biases and reduce explainability. This work introduces a unified framework to evaluate the impact of personalization on both prediction accuracy and explanation quality across classification and regression tasks. We derive novel upper bounds for the number of personal attributes that can be used to reliably validate benefits of personalization. Our analysis uncovers key trade-offs. We show that regression models can potentially utilize more personal attributes than classification models. We also demonstrate that improvements in prediction accuracy due to personalization do not necessarily translate to enhanced explainability -- underpinning the importance to evaluate both metrics when personalizing machine learning models in critical settings such as healthcare. Validated with a real-world dataset, this framework offers practical guidance for balancing accuracy, fairness, and interpretability in personalized models.