arXiv subjects

Louisa Cornelis

Publications and source records attributed to Louisa Cornelis.

6 recordsLinked to original sources

arXiv2026

MotionBench-XAI: Benchmarking What Shapes Shapley Explanations in Spatiotemporal Machine Learning

Predicting outcomes from spatiotemporal data, such as assessing Parkinson's severity from human motion, often requires explainability in addition to accuracy. Practitioners need to know what drove the prediction, whether it be spatial (a body joint), temporal (a specific window), or both. Shapley values are attributions computed by treating input features as players in a cooperative game and measuring how the model output changes as coalitions of players are removed. Computing them involves choosing what counts as players, how absent players are imputed, and how the game is evaluated. How these choices affect explanation quality is poorly understood for spatiotemporal data, and real data carries no ground-truth attributions to check against. We present MotionBench-XAI, a benchmark built on i) five synthetic spatiotemporal datasets with exact ground-truth Shapley values, ii) three real datasets across clinical gait, electrocardiogram, and audio, iii) ten attribution methods across three player sets, and iv) three trained architectures. We show that grouping features into players, across time, space, or both, matters more than the choice of imputer. Generative imputers improve explanations only when their conditional models are accurate. On real data, the standard proxy metrics select contradictory best methods. We distill these findings into practical insights and provide an open-source pipeline.

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arXiv2026

From Simulated Fluids to Living Tissue: Zero-Shot Foundation Model Transfer to Perturbed Embryos

Morphogenesis is driven by the interplay of genetic regulation and tissue mechanics. In vivo video data is limited, particularly under genetic mutations and environmental perturbations, making generalization beyond the most representative conditions in the dataset challenging. However, at tissue scales, the dynamics of Drosophila can be described as a continuum flow, motivating the usage of representations learned across other physical systems as priors for developmental dynamics. We investigate finetuning Walrus, a Continuum Dynamics Foundation Model pretrained across a broad set of simulated continuous systems, on tissue velocity fields from only 12 wild-type Drosophila blastoderm videos. We evaluate autoregressive prediction both in-distribution and zero-shot under unseen temperature and genetic perturbations. Zero-shot refers to evaluation on perturbation conditions never seen during wild-type finetuning, without any additional training. In-distribution, a Fourier Neural Operator model trained from scratch achieves best performance on VRMSE. However, Walrus (CRPS) is the strongest model under the most severe distribution shift of unseen samples of mutated embryos and temperature conditions. Interestingly, predictions capture the shape of the mean surface tissue velocity trajectory and its separation between 17°C and 27°C, including the timing of the peak at Germ Band Extension onset, a biologically meaningful milestone of embryo development. Our results provide preliminary support that representations learned from different dynamical systems can transfer to experimental morphogenesis in developmental regimes, provided they admit a continuum description. More broadly, our results motivate further study of physics foundation models as a new complementary tool for the simulation of morphogenesis in low-data regimes.

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arXiv2026

HOPSE: Scalable Higher-Order Positional and Structural Encoder for Combinatorial Representations

While Graph Neural Networks (GNNs) have proven highly effective at modeling relational data, pairwise connections cannot fully capture multi-way relationships naturally present in complex real-world systems. In response to this, Topological Deep Learning (TDL) leverages more general combinatorial representations--such as simplicial or cellular complexes--to accommodate higher-order interactions. Existing TDL methods often extend GNNs through Higher-Order Message Passing (HOMP), but face critical scalability challenges due to the steep complexity overhead of propagating messages through combinatorial structures. To overcome this limitation, we propose HOPSE (Higher-Order Positional and Structural Encoder), a framework free of message passing layers that uses Hasse graph decompositions to derive efficient and expressive encodings over arbitrary higher-order domains. Notably, HOPSE scales linearly with the size of combinatorial representations while preserving the expressive power and permutation equivariance of the HOMP approaches. Experiments on molecular and topological benchmarks show that it matches or surpasses state-of-the-art performance while consistently achieving speedups over HOMP-based models, opening a new path for scalable TDL. The code is available at https://github.com/geometric-intelligence/topobench.git.

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arXiv2026

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 $n \gg p$, 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.

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arXiv2026

When Machine Learning Gets Personal: Evaluating Prediction and Explanation

In high-stakes domains like healthcare, users often expect that sharing personal information with machine learning systems will yield tangible benefits, such as more accurate diagnoses and clearer explanations of contributing factors. However, the validity of this assumption remains largely unexplored. We propose a unified framework to quantify how personalizing a model influences both prediction and explanation. We show that its impacts on prediction and explanation can diverge: a model may become more or less explainable even when prediction is unchanged. For practical settings, we study a standard hypothesis test for detecting personalization effects on demographic groups. We derive a finite-sample lower bound on its probability of error as a function of group sizes, number of personal attributes, and desired benefit from personalization. This provides actionable insights, such as which dataset characteristics are necessary to test an effect, or the maximum effect that can be tested given a dataset. We apply our framework to real-world tabular datasets using feature-attribution methods, uncovering scenarios where effects are fundamentally untestable due to the dataset statistics. Our results highlight the need for joint evaluation of prediction and explanation in personalized models and the importance of designing models and datasets with sufficient information for such evaluation.

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arXiv2025

Beyond Euclid: An Illustrated Guide to Modern Machine Learning with Geometric, Topological, and Algebraic Structures

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.

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