A.1 Cellular WLResults In this section, we assume basic familiarity with the WL test and its higher-order variants. For an introduction to these topics, we refer the reader to the survey of Sato [62]. We begin by introducing a few useful concepts. A cellular colouring is a map c that maps a cell complex X and one of its cells to a colour from a fixed colour palette. Let X,Y be two regular cell complexes and c a cellular colouring. We say that X,Y are c-similar, denoted by cX = cY, if the number of cells in X coloured with a given colour equals the number of cells in Y with the same colour. Otherwise, we have cX 6= cY . We emphasise that in this paper we are interested only in colourings c with the property that any two isomorphic cell complexes are c-similar. A cellular colouring c refines a cellular colouring d, denoted by c v d, if for all cell complexes X and Y and all 2 PX and 2 PY, cX = cY implies dX = dY . Additionally, if d v c, we say the two colourings are equivalent and we represent it by c d. We state the following result from Bodnar et al. [8] about simplicial colourings, which we translate here directly to cell complexes. The proof is however, identical, and we refer the reader to their work for that. Let X,Y be any regular cellular complexes with A PX and B PY . Consider two cellular colourings c,d such that c v d.

Node-level random walk has been widely used to improve Graph Neural Networks.

Topological neural networks have emerged as powerful successors of graph neural networks. However, they typically involve higher-order message passing, which incurs significant computational expense. We circumvent this issue with a novel topological framework that introduces a Laplacian operator on combinatorial complexes (CCs), enabling efficient computation of heat kernels that serve as node descriptors. Our approach captures multiscale information and enables permutation-equivariant representations, allowing easy integration into modern transformer-based architectures. Theoretically, the proposed method is maximally expressive because it can distinguish arbitrary non-isomorphic CCs. Empirically, it significantly outperforms existing topological methods in terms of computational efficiency. Besides demonstrating competitive performance with the state-of-the-art descriptors on standard molecular datasets, it exhibits superior capability in distinguishing complex topological structures and avoiding blind spots on topological benchmarks. Overall, this work advances topological deep learning by providing expressive yet scalable representations, thereby opening up exciting avenues for molecular classification and property prediction tasks.

Predicting the labels of graph-structured data is crucial in scientific applications and is often achieved using graph neural networks (GNNs). However, when data is scarce, GNNs suffer from overfitting, leading to poor performance. Recently, Gaussian processes (GPs) with graph-level inputs have been proposed as an alternative. In this work, we extend the Gaussian process framework to simplicial complexes (SCs), enabling the handling of edge-level attributes and attributes supported on higher-order simplices. We further augment the resulting SC representations by considering their Hodge decompositions, allowing us to account for homological information, such as the number of holes, in the SC. We demonstrate that our framework enhances the predictions across various applications, paving the way for GPs to be more widely used for graph and SC-level predictions.

We introduce Hodge Diffusion Maps, a novel manifold learning algorithm designed to analyze and extract topological information from high-dimensional data-sets. This method approximates the exterior derivative acting on differential forms, thereby providing an approximation of the Hodge Laplacian operator. Hodge Diffusion Maps extend existing non-linear dimensionality reduction techniques, including vector diffusion maps, as well as the theories behind diffusion maps and Laplacian Eigenmaps. Our approach captures higher-order topological features of the data-set by projecting it into lower-dimensional Euclidean spaces using the Hodge Laplacian. We develop a theoretical framework to estimate the approximation error of the exterior derivative, based on sample points distributed over a real manifold. Numerical experiments support and validate the proposed methodology.

Simplicial complexes provide a powerful framework for modeling high-order interactions in structured data, making them particularly suitable for applications such as trajectory prediction and mesh processing. However, existing simplicial neural networks (SNNs), whether convolutional or attention-based, rely primarily on discrete filtering techniques, which can be restrictive. In contrast, partial differential equations (PDEs) on simplicial complexes offer a principled approach to capture continuous dynamics in such structures. In this work, we introduce COntinuous SiMplicial neural netwOrkS (COSMOS), a novel SNN architecture derived from PDEs on simplicial complexes. We provide theoretical and experimental justifications of COSMOS's stability under simplicial perturbations. Furthermore, we investigate the over-smoothing phenomenon, a common issue in geometric deep learning, demonstrating that COSMOS offers better control over this effect than discrete SNNs. Our experiments on real-world datasets of ocean trajectory prediction and regression on partial deformable shapes demonstrate that COSMOS achieves competitive performance compared to state-of-the-art SNNs in complex and noisy environments.

We introduce, for the first time, a cohomology-based Gromov-Hausdorff ultrametric method to analyze 1-dimensional and higher-dimensional (co)homology groups, focusing on loops, voids, and higher-dimensional cavity structures in simplicial complexes, to address typical clustering questions arising in molecular data analysis. The Gromov-Hausdorff distance quantifies the dissimilarity between two metric spaces. In this framework, molecules are represented as simplicial complexes, and their cohomology vector spaces are computed to capture intrinsic topological invariants encoding loop and cavity structures. These vector spaces are equipped with a suitable distance measure, enabling the computation of the Gromov-Hausdorff ultrametric to evaluate structural dissimilarities. We demonstrate the methodology using organic-inorganic halide perovskite (OIHP) structures. The results highlight the effectiveness of this approach in clustering various molecular structures. By incorporating geometric information, our method provides deeper insights compared to traditional persistent homology techniques.

We consider the problem of classifying trajectories on a discrete or discretised 2-dimensional manifold modelled by a simplicial complex. Previous works have proposed to project the trajectories into the harmonic eigenspace of the Hodge Laplacian, and then cluster the resulting embeddings. However, if the considered space has vanishing homology (i.e., no "holes"), then the harmonic space of the 1-Hodge Laplacian is trivial and thus the approach fails. Here we propose to view this issue akin to a sensor placement problem and present an algorithm that aims to learn "optimal holes" to distinguish a set of given trajectory classes. Specifically, given a set of labelled trajectories, which we interpret as edge-flows on the underlying simplicial complex, we search for 2-simplices whose deletion results in an optimal separation of the trajectory labels according to the corresponding spectral embedding of the trajectories into the harmonic space. Finally, we generalise this approach to the unsupervised setting.