Topological Representation Learning

Many modern datasets mix points, edges, regions, groups, objects, events, hyperedges, and relations. Yet neural architectures often force such data into grids, graphs, or sequences, obscuring higher-order structure and making encoder-decoder designs domain-specific. We view U-Net not as a grid-specific architecture, but as a hierarchical encoder-decoder principle: representation spaces, transport maps between levels, and skip connections between matched levels. Combinatorial complexes naturally supply these ingredients through cells, incidences, and ranks. We introduce TopoU-Net, a rank-path U-Net for topological domains. Given a path from an input rank to a bottleneck rank and back, the encoder lifts cochains upward along incidence maps, the decoder transports them downward, and skip connections merge features at matched ranks. Rank replaces spatial scale: choosing paths through nodes, edges, faces, hyperedges, or global cells becomes the central architectural decision. A key quantity is the bottleneck support ratio, the number of cells at the bottleneck relative to the number of cells at the input rank. This ratio is fixed by the complex and chosen path rather than by arbitrary pooling, and it clarifies when skip connections are optional, useful, or structurally important. Across node classification, graph classification, hypergraph node classification, mesh classification, and image reconstruction, TopoU-Net provides a reusable encoder-decoder template for higher-order structured data. Among the evaluated baselines, it achieves the strongest mean accuracy on six of eight node-classification datasets and four of five hypergraph datasets, with the largest gains on heterophilic graphs. Ablations show that removing skip connections is most damaging under severe bottleneck compression.

Decades of cognitive science establish that humans navigate environments by forming cognitive maps, defined as allocentric and topology-preserving representations of 3D space. While modern Vision-Language Models (VLMs) demonstrate emergent spatial reasoning from 2D egocentric inputs, it remains unclear whether they construct an analogous 3D internal representation. In this paper, we demonstrate that current VLMs do possess a latent topological map of 3D scenes, but it is heavily overshadowed by non-geometric visual semantics, such as color and shape. By isolating this spatial subspace through cross-scene linear feature extraction, we extract a clean spatial subspace that causally controls the model's spatial outputs. We mathematically shape this latent representation and prove its correspondence to the Laplacian eigenmaps of the scene's 3D Gaussian-kernel graph, converging to the physical 3D space in the continuous limit. Motivated by this geometric identification, we further introduce a mathematically principled latent regularization method for VLMs, based on Dirichlet energy. Applying this single-term regularizer to a minimal 500-step supervised VLM fine-tuning (SFT) on simple synthetic data yields significant improvements on real-world spatial benchmarks, outperforming standard SFT and competitive baselines by up to 12.1% in spatial tasks involving scene topology understanding. Source code is available at https://github.com/pittisl/vlm-latent-shaping

Despite an ever-increasing interest in topological deep learning models that target higher-order datasets, there is no consensus on how to evaluate such models. This is exacerbated by the fact that topological objects permit operations, such as structural refinements, that are not appropriate for graph data. In this work, we extend MANTRA, a benchmark dataset containing manifold triangulations, to a larger class of manifolds with more diverse homeomorphism types. We show that, unlike prior claims, both graph neural networks (GNNs) and higher-order message passing (HOMP) methods can saturate the benchmark. However, we find that this is contingent on the right representation and feature assignment, emphasizing their importance in baseline models. We thus provide a novel evaluation protocol based on representational diversity and triangulation refinement. Surprisingly, we find no indication that existing models are capable of generalizing beyond the combinatorial structure of the data. This points towards a research gap in developing models that understand topological structure independent of scale. Our work thus provides the necessary scaffolding to evaluate future models and enable the development of topology-aware inductive biases.

Graph neural tangent kernels give a principled infinite-width theory for graph neural networks, but inherit a basic limitation of graph models: they see only pairwise structure. Many relational systems contain higher-order interactions that are more naturally represented by simplicial complexes. We introduce the Topological Neural Tangent Kernel (TopoNTK), an infinite-width kernel for simplicial message passing on edge features. TopoNTK combines lower Hodge interactions, capturing graph-like coupling through shared vertices, with upper Hodge interactions, capturing coupling through filled simplices. This makes the kernel sensitive to topology invisible to graph kernels, allowing complexes with the same graph but different filled simplices to induce different kernels. Beyond expressivity, the Hodge structure gives the kernel an interpretable learning geometry. Edge signals decompose into gradient-like, harmonic, and local circulation components, and the spectrum of the TopoNTK determines how quickly each component is learned. This yields a topological form of spectral bias: components aligned with large-eigenvalue modes are learned quickly, while global harmonic modes, retained through the residual channel, often lie at smaller eigenvalues and are learned more slowly. We prove expressivity, Hodge-alignment, spectral learning, and stability properties, and validate them on synthetic simplicial tasks and DBLP higher-order link prediction. The results show that topology is not merely extra structure; it can provide coordinates that make relational learning more faithful, interpretable, and effective.

Vision-language models have shown strong performance, but they often generalize poorly to specialized domains. While semi-supervised vision-language learning mitigates this limitation by leveraging a small set of labeled image-text pairs together with abundant unlabeled images, existing methods remain fundamentally pairwise and fail to model the global structure of multimodal representation manifolds. Existing topology-based alignment methods rely on persistence diagram matching, which neither guarantees geometric alignment nor utilizes the image-text pairing information central to vision-language learning. We propose Topology-Aware Multimodal Representation Alignment (ToMA), a framework that uses persistent homology to identify topologically salient edges and aligns them across modalities through available cross-modal correspondences. ToMA leverages both H_0-death edges and lightweight H_1-birth edges, allowing it to capture both connectivity and cycle structure without constructing 2-simplices. Experiments show that ToMA yields stable gains, with clear improvements on remote sensing and modest but consistent benefits on fashion retrieval. Additional analysis shows that ToMA is more stable than alternative topology-based objectives and that lightweight H_1-birth edges provide useful higher-order structural signals.

Dimensionality reduction methods such as UMAP and t-SNE are central tools for visualising high-dimensional data, but their local-neighborhood objectives can preserve sampling noise while distorting global topology. We show that standard local metrics reward this noise memorisation: top-performing embeddings invent cycles and disconnected islands absent from the data. We introduce a topology-faithfulness benchmark based on noisy manifolds with known homology, tune DiRe against it, and find Pareto-optimal configurations that match or beat GPU-accelerated UMAP on classification while recovering exact first Betti numbers on stress tests. On 723K arXiv paper embeddings, DiRe preserves 3-4 times more topological structure than UMAP at comparable wall-clock.

Recent advances in pretraining 3D point cloud encoders (e.g., Point-BERT, Point-MAE) have produced powerful models, whose abilities are typically evaluated on geometric or semantic tasks. At the same time, topological descriptors have been shown to provide informative summaries of a shape's multiscale structure. In this paper we pose the question whether topological information can be derived from features produced by 3D encoders. To address this question, we first introduce DONUT, a synthetic benchmark with controlled topological complexity, and propose FILTR (Filtration Transformer), a learnable framework to predict persistence diagrams directly from frozen encoders. FILTR adapts a transformer decoder to treat diagram generation as a set prediction task. Our analysis on DONUT reveals that existing encoders retain only limited global topological signals, yet FILTR successfully leverages information produced by these encoders to approximate persistence diagrams. Our approach enables, for the first time, data-driven extraction of persistence diagrams from raw point clouds through an efficient learnable feed-forward mechanism.

AlphaGeometry represents a milestone in neuro-symbolic reasoning, yet its architecture faces a log-linear scaling bottleneck within its symbolic deduction engine that limits its efficiency as problem complexity increases. Recent technical reports suggest that current domain-specific languages may be isomorphic as input representations to natural language, interchanging them acts as a performance-invariant transformation, implying that current neural guidance relies on superficial encodings rather than structural understanding. This paper addresses this representation bottleneck by proposing a logic-to-topology encoding designed to reveal the structural invariants of a model's latent space under a transformation of its input space. By leveraging the Logic of Observation, we utilize the duality between provability in observable theories and topologies to propose a logic-to-topology encoder for the input space. We introduce the concept of the "topological dual of a dataset", a transformation that bridges formal logic, topology, and neural processing. This framework serves as a Rosetta Stone for neuro-symbolic AI, providing a principled pathway for the mechanistic interpretability of how models navigate complex discovery paths.

Persistent homology (PH) encodes global information, such as cycles, and is thus increasingly integrated into graph neural networks (GNNs). PH methods in GNNs typically traverse an increasing sequence of subgraphs. In this work, we first expose limitations of this inclusion procedure. To remedy these shortcomings, we analyze contractions as a principled topological operation, in particular, for graph representation learning. We study the persistence of contraction sequences, which we call Contraction Homology (CH). We establish that forward PH and CH differ in expressivity. We then introduce Hourglass Persistence, a class of topological descriptors that interleave a sequence of inclusions and contractions to boost expressivity, learnability, and stability. We also study related families parametrized by two paradigms. We also discuss how our framework extends to simplicial and cellular networks. We further design efficient algorithms that are pluggable into end-to-end differentiable GNN pipelines, enabling consistent empirical improvements over many PH methods across standard real-world graph datasets. Code is available at this https URL.

Category-level object pose estimation is fundamental for embodied intelligence, yet achieving robust generalization to unseen instances remains challenging. However, existing methods mainly rely on simple feature extraction and aggregation, which struggle to capture category-shared topological structures and conduct semantic keypoint modeling, limiting their generalization. To address these, we propose a \textbf{T}opology-Aware Learning with \textbf{S}emantic \textbf{M}amba for Category-Level \textbf{P}ose Estimation framework (TSM-Pose). Specifically, we introduce a Topology Extractor to capture the global topological representation of the point cloud, which is integrated into local geometry features and enables robust category-level structural representation. Simultaneously, we propose a Mamba-based Global Semantic Aggregator that injects semantics priors into keypoints to enhance their expressiveness and leverages multiple TwinMamba blocks to model long-range dependencies for more effective global feature aggregation. Extensive experiments on three benchmark datasets (REAL275, CAMERA25, and HouseCat6D) demonstrate that TSM-Pose outperforms existing state-of-the-art methods.

We present the Global Neural World Model (GNWM), a self-stabilizing framework that achieves topological quantization through balanced continuous entropy constraints. Operating as a continuous, action-conditioned Joint-Embedding Predictive Architecture (JEPA), the GNWM maps environments onto a discrete 2D grid, enforcing translational equivariance without pixel-level reconstruction. Our results show this architecture prevents manifold drift during autoregressive rollouts by using grid ``snapping'' as a native error-correction mechanism. Furthermore, by training via maximum entropy exploration (random walks), the model learns generalized transition dynamics rather than memorizing specific expert trajectories. We validate the GNWM across passive observation, active agent control, and abstract sequence regimes, demonstrating its capacity to act not just as a spatial physics simulator, but as a causal discovery model capable of organizing continuous, predictable concepts into structured topological maps.