Contraction and Hourglass Persistence for Learning on Graphs, Simplices, and Cells

We study the grokking phenomenon through the lens of topology. Using persistent homology on point clouds derived from the embedding matrices of a range of models trained on modular arithmetic with varying primes, we identify a clear and consistent topological signature of grokking: a sharp increase in both the maximum and total persistence of first homology ($H_1$). Persistence diagrams reveal the emergence of a dominant long-lived topological feature together with increasingly structured secondary features, reflecting the underlying cyclic structure of the task. Compared to existing spectral and geometric diagnostics -- specifically, Fourier analysis and local intrinsic dimension -- persistent homology provides a unified geometric and topological characterization of representation learning, capturing both local and global multi-scale structure. Ablations across data regimes and control settings show that these topological transitions are tied to generalization rather than memorization. Our results suggest that persistent homology offers a principled and interpretable framework for analyzing how neural networks internalize latent structure during training.

We introduce Topoformer, a lightweight and scalable framework for graph representation learning that encodes topological structure into attention-friendly sequences. At the core of our method is Topo-Scan, a novel module that decomposes a graph into a short, ordered sequence of topological tokens by slicing over node or edge filtrations. These sequences capture multi-scale structural patterns, from local motifs to global organization, and are processed by a Transformer to produce expressive graph-level embeddings. Unlike traditional persistent homology pipelines, Topo-Scan is parallelizable, avoids costly diagram computations, and integrates seamlessly with standard deep learning architectures. We provide theoretical guarantees on the stability of our topological encodings and demonstrate state-of-the-art performance across graph classification and molecular property prediction benchmarks. Our results show that Topoformer matches or exceeds strong GNN and topology-based baselines while offering predictable and efficient compute. This work opens a new path for parallelizable and unifying approaches to graph representation learning that integrate topological inductive biases into attention frameworks.

Message-passing Graph Neural Networks (GNNs) iteratively propagate and aggregate local neighborhood information followed by global readout to learn graph representations. However, their discriminative power is upper-bounded by the Weisfeiler--Lehman (1-WL) graph isomorphism test. This prevents GNNs from distinguishing certain non-isomorphic graphs with identical local neighborhood structures, often leading to similar graph representations. Unified Topological Signatures (UTS) capture compact, multi-scale representation of global graph topology derived from persistent homology. We introduce two complementary UTS signatures: Graph_UTS- a static signature of the input graph topology, and Embedding_UTS- a dynamic signature of the evolving embedding topology. They encode structural information inaccessible to 1-WL-based message-passing GNNs, yet their capabilities are explored solely for post-hoc embedding-space analysis. We integrate UTS into GNN training across three architectural interventions: (i) UTS-Aug: augmenting with standard readout feature that encodes graph's true topology; (ii) UTS-Reg: topological regularizer that constrains representation collapse; (iii) UTS-Pool: topology-guided pooling that retains structurally critical nodes. We further leverage UTS as a layer-wise diagnostic to quantify oversmoothing during GNN training. Theoretically, we show that integrating UTS into GNN optimization strictly extends GNN expressivity beyond the 1-WL hierarchy. Experiments on three graph classification benchmarks show consistent benefits: Graph-UTS, Dual-UTS, and UTS-Pool improve accuracy across all three datasets, Embedding-UTS provides smaller but similarly consistent gains, and UTS-Reg's benefit varies across graph domains. Accuracy improves by up to 5.8% with Graph-UTS augmentation, by up to 1.9% with UTS-Reg, and achieves comparable performance to TOGL with UTS-Pool.