Augmenting these graph models with topological features via persistent homology (PH) has gained prominence, but identifying the class of attributed graphs that PH can recognize remains open. We introduce a novel concept of color-separating sets to provide a complete resolution to this important problem.

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Representational limits of message-passing graph neural networks (MP-GNNs), e.g., in terms of the Weisfeiler-Leman (WL) test for isomorphism, are well understood. Augmenting these graph models with topological features via persistent homology (PH) has gained prominence, but identifying the class of attributed graphs that PH can recognize remains open. We introduce a novel concept of color-separating sets to provide a complete resolution to this important problem. Specifically, we establish the necessary and sufficient conditions for distinguishing graphs based on the persistence of their connected components, obtained from filter functions on vertex and edge colors. Our constructions expose the limits of vertex-and edge-level PH, proving that neither category subsumes the other. Leveraging these theoretical insights, we propose RePHINE for learning topological features on graphs. RePHINE efficiently combines vertex-and edge-level PH, achieving a scheme that is provably more powerful than both. Integrating RePHINE into MP-GNNs boosts their expressive power, resulting in gains over standard PH on several benchmarks for graph classification.

Topological data analysis (TDA) is an area of data science that focuses on using invariants from algebraic topology to provide multiscale shape descriptors for geometric data sets such as point clouds. One of the most important such descriptors is persistent homology, which encodes the change in shape as a filtration parameter changes; a typical parameter is the feature scale. For many data sets, it is useful to simultaneously vary multiple filtration parameters, for example feature scale and density. While the theoretical properties of single parameter persistent homology are well understood, less is known about the multiparameter case. A central question is the problem of representing multiparameter persistent homology by elements of a vector space for integration with standard machine learning algorithms.

We introduce graphcodes, a novel multi-scale summary of the topological properties of a dataset that is based on the well-established theory of persistent homology. Graphcodes handle datasets that are filtered along two real-valued scale parameters. Such multi-parameter topological summaries are usually based on complicated theoretical foundations and difficult to compute; in contrast, graphcodes yield an informative and interpretable summary and can be computed as efficient as one-parameter summaries. Moreover, a graphcode is simply an embedded graph and can therefore be readily integrated in machine learning pipelines using graph neural networks. We describe such a pipeline and demonstrate that graphcodes achieve better classification accuracy than state-of-the-art approaches on various datasets.

Machine learning for point clouds has been attracting much attention, with many applications in various fields, such as shape recognition and material science. For enhancing the accuracy of such machine learning methods, it is often effective to incorporate global topological features, which are typically extracted by persistent homology. In the calculation of persistent homology for a point cloud, we choose a filtration for the point cloud, an increasing sequence of spaces. Since the performance of machine learning methods combined with persistent homology is highly affected by the choice of a filtration, we need to tune it depending on data and tasks. In this paper, we propose a framework that learns a filtration adaptively with the use of neural networks. In order to make the resulting persistent homology isometry-invariant, we develop a neural network architecture with such invariance. Additionally, we show a theoretical result on a finite-dimensional approximation of filtration functions, which justifies the proposed network architecture. Experimental results demonstrated the efficacy of our framework in several classification tasks.

Deep learning models have achieved remarkable success across various domains, yet their learned representations and decision-making processes remain largely opaque and hard to interpret. This work introduces HOLE (Homological Observation of Latent Embeddings), a method for analyzing and interpreting deep neural networks through persistent homology. HOLE extracts topological features from neural activations and presents them using a suite of visualization techniques, including Sankey diagrams, heatmaps, dendrograms, and blob graphs. These tools facilitate the examination of representation structure and quality across layers. We evaluate HOLE on standard datasets using a range of discriminative models, focusing on representation quality, interpretability across layers, and robustness to input perturbations and model compression. The results indicate that topological analysis reveals patterns associated with class separation, feature disentanglement, and model robustness, providing a complementary perspective for understanding and improving deep learning systems.

This paper presents a mathematically rigorous framework for brain-inspired representation learning founded on the interplay between persistent topological structures and cohomological flows. Neural computation is reformulated as the evolution of cochain maps over dynamic simplicial complexes, enabling representations that capture invariants across temporal, spatial, and functional brain states. The proposed architecture integrates algebraic topology with differential geometry to construct cohomological operators that generalize gradient-based learning within a homological landscape. Synthetic data with controlled topological signatures and real neural datasets are jointly analyzed using persistent homology, sheaf cohomology, and spectral Laplacians to quantify stability, continuity, and structural preservation. Empirical results demonstrate that the model achieves superior manifold consistency and noise resilience compared to graph neural and manifold-based deep architectures, establishing a coherent mathematical foundation for topology-driven representation learning.

Graph classification has gained significant attention due to its applications in chemistry, social networks, and bioinformatics. While Graph Neural Networks (GNNs) effectively capture local structural patterns, they often overlook global topological features that are critical for robust representation learning. In this work, we propose GraphTCL, a dual-view contrastive learning framework that integrates structural em-beddings from GNNs with topological embeddings derived from persistent homology. By aligning these complementary views through a cross-view contrastive loss, our method enhances representation quality and improves classification performance. Extensive experiments on benchmark datasets, including TU and OGB molecular graphs, demonstrate that GraphTCL consistently outperforms state-of-the-art baselines. This study highlights the importance of topology-aware contrastive learning for advancing graph representation methods.

Inferring topological and geometrical information from data can offer an alternative perspective on machine learning problems. Methods from topological data analysis, e.g., persistent homology, enable us to obtain such information, typically in the form