Extended persistence is a technique from topological data analysis to obtain global multiscale topological information from a graph. This includes information about connected components and cycles that are captured by the so-called persistence barcodes. We introduce extended persistence into a supervised learning framework for graph classification. Global topological information, in the form of a barcode with four different types of bars and their explicit cycle representatives, is combined into the model by the readout function which is computed by extended persistence. The entire model is end-to-end differentiable. We use a link-cut tree data structure and parallelism to lower the complexity of computing extended persistence, obtaining a speedup of more than 60x over the state-of-the-art for extended persistence computation. This makes extended persistence feasible for machine learning. We show that, under certain conditions, extended persistence surpasses both the WL[1] graph isomorphism test and 0-dimensional barcodes in terms of expressivity because it adds more global (topological) information. In particular, arbitrarily long cycles can be represented, which is difficult for finite receptive field message passing graph neural networks. Furthermore, we show the effectiveness of our method on real world datasets compared to many existing recent graph representation learning methods.

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://github.com/pyt-team.

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.

$1$-parameter persistent homology, a cornerstone in Topological Data Analysis (TDA), studies the evolution of topological features such as connected components and cycles hidden in data. It has been applied to enhance the representation power of deep learning models, such as Graph Neural Networks (GNNs). To enrich the representations of topological features, here we propose to study $2$-parameter persistence modules induced by bi-filtration functions. In order to incorporate these representations into machine learning models, we introduce a novel vector representation called Generalized Rank Invariant Landscape (GRIL) for $2$-parameter persistence modules. We show that this vector representation is $1$-Lipschitz stable and differentiable with respect to underlying filtration functions and can be easily integrated into machine learning models to augment encoding topological features. We present an algorithm to compute the vector representation efficiently. We also test our methods on synthetic and benchmark graph datasets, and compare the results with previous vector representations of $1$-parameter and $2$-parameter persistence modules. Further, we augment GNNs with GRIL features and observe an increase in performance indicating that GRIL can capture additional features enriching GNNs. We make the complete code for the proposed method available at https://github.com/soham0209/mpml-graph.

Topological deep learning is a rapidly growing field that pertains to the development of deep learning models for data supported on topological domains such as simplicial complexes, cell complexes, and hypergraphs, which generalize many domains encountered in scientific computations. In this paper, we present a unifying deep learning framework built upon a richer data structure that includes widely adopted topological domains. Specifically, we first introduce combinatorial complexes, a novel type of topological domain. Combinatorial complexes can be seen as generalizations of graphs that maintain certain desirable properties. Similar to hypergraphs, combinatorial complexes impose no constraints on the set of relations. In addition, combinatorial complexes permit the construction of hierarchical higher-order relations, analogous to those found in simplicial and cell complexes. Thus, combinatorial complexes generalize and combine useful traits of both hypergraphs and cell complexes, which have emerged as two promising abstractions that facilitate the generalization of graph neural networks to topological spaces. Second, building upon combinatorial complexes and their rich combinatorial and algebraic structure, we develop a general class of message-passing combinatorial complex neural networks (CCNNs), focusing primarily on attention-based CCNNs. We characterize permutation and orientation equivariances of CCNNs, and discuss pooling and unpooling operations within CCNNs in detail. Third, we evaluate the performance of CCNNs on tasks related to mesh shape analysis and graph learning. Our experiments demonstrate that CCNNs have competitive performance as compared to state-of-the-art deep learning models specifically tailored to the same tasks. Our findings demonstrate the advantages of incorporating higher-order relations into deep learning models in different applications.