Manuel Lecha

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.

Manuel Lecha, Andrea Cavallo, Francesca Dominici et al.

Topological Deep Learning (TDL) has emerged as a paradigm to process and learn from signals defined on higher-order combinatorial topological spaces, such as simplicial or cell complexes. Although many complex systems have an asymmetric relational structure, most TDL models forcibly symmetrize these relationships. In this paper, we first introduce a novel notion of higher-order directionality and we then design Directed Simplicial Neural Networks (Dir-SNNs) based on it. Dir-SNNs are message-passing networks operating on directed simplicial complexes able to leverage directed and possibly asymmetric interactions among the simplices. To our knowledge, this is the first TDL model using a notion of higher-order directionality. We theoretically and empirically prove that Dir-SNNs are more expressive than their directed graph counterpart in distinguishing isomorphic directed graphs. Experiments on a synthetic source localization task demonstrate that Dir-SNNs outperform undirected SNNs when the underlying complex is directed, and perform comparably when the underlying complex is undirected.

Adeela Islam, Stefano Fiorini, Manuel Lecha et al.

3D reassembly is a fundamental geometric problem, and in recent years it has increasingly been challenged by deep learning methods rather than classical optimization. While learning approaches have shown promising results, most still rely primarily on geometric features to assemble a whole from its parts. As a result, methods struggle when geometry alone is insufficient or ambiguous, for example, for small, eroded, or symmetric fragments. Additionally, solutions do not impose physical constraints that explicitly prevent overlapping assemblies. To address these limitations, we introduce E-M3RF, an equivariant multimodal 3D reassembly framework that takes as input the point clouds, containing both point positions and colors of fractured fragments, and predicts the transformations required to reassemble them using SE(3) flow matching. Each fragment is represented by both geometric and color features: i) 3D point positions are encoded as rotationconsistent geometric features using a rotation-equivariant encoder, ii) the colors at each 3D point are encoded with a transformer. The two feature sets are then combined to form a multimodal representation. We experimented on four datasets: two synthetic datasets, Breaking Bad and Fantastic Breaks, and two real-world cultural heritage datasets, RePAIR and Presious, demonstrating that E-M3RF on the RePAIR dataset reduces rotation error by 23.1% and translation error by 13.2%, while Chamfer Distance decreases by 18.4% compared to competing methods.

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.

Lev Telyatnikov, Guillermo Bernardez, Marco Montagna et al.

This work introduces TopoBench, an open-source library designed to standardize benchmarking and accelerate research in topological deep learning (TDL). TopoBench decomposes TDL into a sequence of independent modules for data generation, loading, transforming and processing, as well as model training, optimization and evaluation. This modular organization provides flexibility for modifications and facilitates the adaptation and optimization of various TDL pipelines. A key feature of TopoBench is its support for transformations and lifting across topological domains. Mapping the topology and features of a graph to higher-order topological domains, such as simplicial and cell complexes, enables richer data representations and more fine-grained analyses. The applicability of TopoBench is demonstrated by benchmarking several TDL architectures across diverse tasks and datasets.

Mustafa Hajij, Mathilde Papillon, Florian Frantzen et al.

We introduce TopoX, a Python software suite that provides reliable and user-friendly building blocks for computing and machine learning on topological domains that extend graphs: hypergraphs, simplicial, cellular, path and combinatorial complexes. TopoX consists of three packages: TopoNetX facilitates constructing and computing on these domains, including working with nodes, edges and higher-order cells; TopoEmbedX provides methods to embed topological domains into vector spaces, akin to popular graph-based embedding algorithms such as node2vec; TopoModelX is built on top of PyTorch and offers a comprehensive toolbox of higher-order message passing functions for neural networks on topological domains. The extensively documented and unit-tested source code of TopoX is available under MIT license at https://pyt-team.github.io/}{https://pyt-team.github.io/.

Manuel Lecha, Andrea Cavallo, Francesca Dominici et al.

Graph Neural Networks (GNNs) excel at learning from pairwise interactions but often overlook multi-way and hierarchical relationships. Topological Deep Learning (TDL) addresses this limitation by leveraging combinatorial topological spaces. However, existing TDL models are restricted to undirected settings and fail to capture the higher-order directed patterns prevalent in many complex systems, e.g., brain networks, where such interactions are both abundant and functionally significant. To fill this gap, we introduce Semi-Simplicial Neural Networks (SSNs), a principled class of TDL models that operate on semi-simplicial sets -- combinatorial structures that encode directed higher-order motifs and their directional relationships. To enhance scalability, we propose Routing-SSNs, which dynamically select the most informative relations in a learnable manner. We prove that SSNs are strictly more expressive than standard graph and TDL models. We then introduce a new principled framework for brain dynamics representation learning, grounded in the ability of SSNs to provably recover topological descriptors shown to successfully characterize brain activity. Empirically, SSNs achieve state-of-the-art performance on brain dynamics classification tasks, outperforming the second-best model by up to 27%, and message passing GNNs by up to 50% in accuracy. Our results highlight the potential of principled topological models for learning from structured brain data, establishing a unique real-world case study for TDL. We also test SSNs on standard node classification and edge regression tasks, showing competitive performance. We will make the code and data publicly available.