Topological Representation Learning

Microsatellite instability-high (MSI-H) and high tumor mutational burden (TMB-H) are clinically relevant biomarkers, yet their histopathological prediction remains challenging when models are transferred across morphologically distinct cancer types. Immune-associated spatial patterns can persist across cancers despite these morphological differences, but foundation-model-based predictors trained on a single cancer do not explicitly use this information, limiting cross-cancer generalization. To address this limitation, we propose TIRA (Tumor Immune Representation Adaptation), a target-free framework that refines frozen foundation-model representations using spatial immune topology, without requiring target-domain data during model development or test-time adaptation. TIRA uses a topology-supervised biology representation to condition tile-level attention while pooling only morphological features for joint MSI and TMB prediction. We train TIRA on TCGA-COAD+READ and evaluate it zero-shot on CPTAC-COAD, TCGA-STAD, TCGA-UCEC, and CPTAC-UCEC, covering cross-site, cross-cancer, and combined cross-cancer-site distribution shifts under UNI2, CONCH, and Virchow2. With UNI2, TIRA improved zero-shot AUROC on TCGA-STAD from 0.633 to 0.766 for MSI and from 0.651 to 0.772 for TMB. Source-derived spatial immune topology improved the cross-cancer robustness of frozen pathology foundation-model representations.

Existing molecular and materials learning approaches often rely on a limited set of structural representations, which may capture only selected aspects of complex three-dimensional structure. Here, we introduce mathematical invariant-enabled topological neural networks (MITNNs), a framework that represents complex structures through multiple complementary mathematical views and integrates them with topological neural architectures. MITNNs combine multiscale invariants from topology, spectral theory, commutative algebra, differential geometry, and discrete curvature, capturing complementary structural information from the same system. Systematic invariant-subset, architecture-subset, and ensemble analyses show that predictive performance depends on how mathematical representations and neural architectures are paired, with selected combinations outperforming individual models and the aggregation of all available components. Across protein-ligand binding, metal-organic framework properties, mutation-induced protein solubility, and molecular toxicity prediction, MITNN consistently outperforms existing methods. These results establish MITNN as a mathematically multimodal framework for scientific machine learning.

Concept-based methods provide a semantic level for interpreting and manipulating learned representations, but existing editing approaches are typically specialized to particular interventions and do not provide a common and editable representation of concept organization. To achieve this, we introduce Topological Concept Representations (TCR), a post-hoc operational abstraction that jointly characterizes the concepts encoded in a learned representation and their relationships. TCR constructs an intermediate concept space from concept recoverability and interaction scores, and compactly encodes its organization through topology. Interventions are expressed through modifications of this abstraction that are propagated back to the underlying learned representation. This allows different concept-level operations to share the same optimization framework and separates the desired concept organization from the mechanism to achieve it. We establish stability and reparameterization-invariance properties of TCR and its connections to existing concept-editing formulations. We use TCR to disentangle concepts as a preprocessing step for existing erasure methods, improving worst-group accuracy by 21.89 on average at comparable concept leakage. We further use TCR to transfer concepts from teacher to student models, improving concept recoverability by up to 5.54 while also improving or maintaining competitive test top-1 accuracy.

Molecular learning models are strongly shaped by their underlying representations. Yet standard sequential and graph formalisms struggle to explicitly encode higher-order topology, such as ring systems and recurring motifs. Existing higher-order representations can capture these structures directly, but they are often computationally demanding and difficult to decode into valid molecules. Here, we introduce Higher-order Grammar Representation (HGR), a principled, topology-aware framework that lifts molecules to combinatorial complexes and parses each complex into a compact sequence of production rules under a context-free higher-order grammar. By serialising higher-order topology into rule sequences, HGR makes these structures directly compatible with standard sequence models, avoiding the computational overhead of explicit higher-order encodings while preserving topological expressiveness. To reduce benchmark bias towards simple ring systems, we construct RingDiv, a ring-enriched benchmark containing 1.18 million molecules, including the curated RingDiv300k subset, and introduce the ring diversity index (RDI) to quantify ring-system coverage. In molecular generation, HGR-based models uniquely combine 100% validity by construction with leading distributional alignment, ranking first in FCD on all five generation benchmarks. In representation learning, HGR-FM achieves the highest mean AUC across seven MoleculeNet benchmarks under both transfer protocols, improving on the strongest baseline by 8.3 and 3.3 AUC points under probing and full fine-tuning, respectively. Collectively, these results establish HGR as an efficient higher-order representation for molecular generation and transferable representation learning.

Topology is, by its nature and design, suited to structure that is nonlinear, multiscale, and nonstationary - however, within machine learning, its use remains largely confined to topological data analysis. We advocate that tools from low-dimensional topology which have remained almost exclusively contained within the domain of pure mathematics (such as Morse theory) offer a strong, complementary, and yet virtually unexplored perspective on the hidden structure of data-generating processes and learning tasks built upon them. Here we introduce concepts from cobordism theory and harness tools from discrete Morse theory to improve the performance of graph diffusion models through our pipeline MG-Diff. Further, we derive theoretical guarantees and sufficient conditions so that under a positive decision-gap, the Morse-theoretic tools and their application for induced diffusion guidance are stable under small perturbations. Finally, we illustrate the utility of discrete Morse theory in application to graph diffusion models for spatio-temporal graph forecasting and graph regeneration, and argue that these applications are only a small window into the part of what low-dimensional topology can offer to the field of machine learning.

Many real-world systems exhibit higher-order interactions among groups of entities that cannot be captured by pairwise relationships alone. Graph Transformers and Graph Neural Networks increasingly rely on positional encodings to enrich graph representations, yet existing positional encodings are computed solely from the original graph and therefore cannot directly capture observed higher-order interactions. Topological Deep Learning addresses this limitation by lifting graphs to simplicial complexes, but typically requires performing message passing or attention on higher-order neural network representations. We introduce a representation learning paradigm that enriches graph representations with higher-order topology through positional encodings, enabling standard graph learning models to exploit lifted incidence structure without modifying the backbone. We derive a theoretical characterization of the expressivity of higher-order positional encodings, proving that node-level operators induced by higher-order lifts can mix graph Laplacian frequencies in ways that scalar graph spectral filters cannot. Guided by this theory, we instantiate higher-order positional encodings using Hodge Laplacians derived from clique complexes. Experiments with Graph Transformers on ZINC and controlled synthetic benchmarks demonstrate improvements in predictive performance, while a fixed-1-skeleton experiment shows that the pipeline can transmit higher-order information when cells are supplied independently of the graph. Together, our results establish higher-order positional encodings as a principled bridge between graph positional encodings and topological deep learning.

Natural Visibility Graph (NVG)-based representations provide a promising approach for capturing structural patterns in sequential network traffic. However, whether different cyber-attack classes exhibit distinctive topological signatures in such representations remains insufficiently understood. This study investigates the discriminative and structural characteristics of NVG-based network traffic representations using the CSE-CIC-IDS2018 dataset. Seventy-six numerical traffic features were independently transformed into NVGs within overlapping frames of 40 observations, and ten graph-theoretic metrics were extracted from each graph, resulting in 760 topological descriptors per frame. The discriminative capability of these representations was evaluated using a multi-branch convolutional neural network (CNN) with stratified five-fold cross-validation. The model achieved an average accuracy of 96.20% and a Matthews correlation coefficient (MCC) of 0.9566. To characterize class-specific topological differences, Kruskal-Wallis and Mann-Whitney U tests were combined with Benjamini-Hochberg false discovery rate correction and effect-size measures. Of the 10,640 attack-versus-benign comparisons, 7,777 (73.1%) remained statistically significant after FDR correction, with 4,844 exhibiting large Cliff's delta effects. The strongest global differences were predominantly associated with backward-traffic and packet-length-related features combined with connectivity, clustering, and centrality measures. These findings indicate that NVG-derived representations can provide strong discriminative capability while revealing class-dependent topological patterns associated with different cyber-attack classes.

Signed graphs arise in trust--distrust networks, financial correlation systems, biological interaction graphs, and many other domains in which edges can be positive or negative and may also be directed. While signed graph neural networks have improved task-specific learning, graph transfer learning on signed graphs remains underdeveloped. In this paper, we introduce TopoSIGN, a pioneer topology-guided graph pre-training and prompt learning framework for signed graphs. TopoSIGN combines a structural encoder built on the magnetic signed Laplacian with a novel persistent-homology branch that summarizes signed topology through Dowker-complex persistence images. The fused embeddings are then transferred to a prompt learning function. Experimental results on synthetic and real-world datasets demonstrate the efficacy of TopoSIGN in extracting useful structural information in signed graphs, as well as the adaptability and flexibility of the proposed general framework.

Cable routing requires coordinated control of global cable topology and changing local contacts. We present CableVLA, an end-to-end multimodal vision-language-action framework that converts simulation-privileged supervision into deployable cable-topology and tactile representations. TopoHead distills node-level physics and current and future cable-topology information into causal visual context for the action expert. TacSense uses complementary frame and taxel branches to learn contact dynamics from resistive arrays, with simulator-derived kinematics and contact events providing supervision beyond the measured force map. A contact gate activates force-tactile residuals that refine the next 8 arm-and-gripper actions of a frozen topology-conditioned policy. Across 345 MuJoCo evaluations, CableVLA improves success from 62.6% for the $π_{0.5}$-V visual baseline to 84.9%. TacSense achieves pronounced gains in slip-transition recognition over a CNN-LSTM baseline with a similar parameter count, and this advantage persists under frozen-encoder probes. Topology prediction and 57-task tactile evaluations assess representation quality, while policy adaptation studies evaluate downstream control performance. Cross-simulator and real-robot comparisons further examine zero-shot policy transfer under changes in dynamics and sensing.

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.

Urban region embeddings have shown promising results in diverse urban sensing tasks such as crime, income, and service-call prediction. Recent methods improve representation quality by integrating mobility data with auxiliary modalities, using cross-view attention or contrastive objectives to align heterogeneous features into a unified region representation. However, leveraging the temporal dynamics of human mobility remains under-explored. Regional inflow and outflow fluctuate throughout the day, and inter-region connections emerge, persist, and dissolve over time. Moreover, prevailing fusion strategies combine views additively and miss the joint signal that emerges only when views co-occur. To address these gaps, we propose Mobility Stream-Structure Synergy (MoSS), which derives complementary views from mobility data: a Sequence view that preserves each region's hourly inflow/outflow profile, and a Structure view based on zigzag persistence diagrams that capture how regional connectivity emerges, persists, and dissolves over time. A synergy module then extracts emergent representations from the co-occurrence of these views through multi-degree interactions, explicitly capturing higher-order signal across views. Extensive experiments on New York City and Chicago show that MoSS achieves state-of-the-art performance across three downstream tasks using mobility data alone, outperforming baselines that rely on auxiliary modalities.

Graph representation learning has largely focused on designing increasingly sophisticated models to transform graph topology into vector representations, or embeddings. However, the extent to which embedding quality depends on model learning, rather than on the underlying topological transformations, remains unclear. Here, we show that informative embeddings can be derived without complicated model design and gradient-based training. Propagating random features through implicit hierarchical structures induced by random walks and anonymous walks yields embeddings that capture node proximity and structural role, respectively. These two training-free embeddings preserve complementary aspects of graph organization and perform competitively with classic and recent methods across various node-, edge-, and graph-level tasks. They often require substantially less computation, resulting in a favorable quality-efficiency trade-off. Combining the two types of embeddings further improves inference quality of some tasks compared with using either embedding type alone. Our results suggest that informative graph embeddings can arise from carefully chosen topological transformations before any learning operation is applied.

Deep networks trained on noisy labels simultaneously generalize on clean data and memorize flipped labels. These are usually conflated as pressures on one capacity. We present Topo^2, a measurement framework that makes them causally separable, measurable, and law-governed. Persistent-homology H1 structure of the representation space separates into a within-class manifold channel (a function of the training stopping point) and a cross-class channel (a monotone readout of memorized flipped samples). An intervention, the FM0 prescription (zero loss on flipped samples from epoch 0), reaches each setting's generalization ceiling while memorizing essentially nothing. Within the framework we establish a law set with graded evidence: (L2) FM0 separation prescription (9/9); (L1) the within-channel as a training-position function (mid-rise 6/6; convergence-back CIFAR 3/3, SVHN 2/3); (L3) a ring-construction identity (definitional, not a law); and TLS (memory-generalization topological layering): memory is causally additive, anchored (silencing clean collapses the representation), invertible (stripping memory restores near-ceiling generalization), and quantitatively billable (the memorization cost law, effective slope coefficient C ~ 0.38 at the reference capacity: CIFAR-10 0.3801 / SVHN 0.3806 / CIFAR-100 0.384 / VGG 0.3715, capacity-dependent in general and traced to clean-sample feature displacement). We also publish the framework's boundaries: a falsification ledger of nine dead ends, and an instrument-vindication section that excludes six families of global statistics as explanations of the within-channel. The framework turns "memorization" from an ill-defined capacity into a measurable, separable, invertible topological layer.

We study the topology of learned representations in predictive coding networks (PCNs), a neuro-inspired bidirectional architecture, using a quantitative layer-wise persistent homology analysis. We train well-performing PCNs on a synthetic classification dataset ($\geq 99.9\%$ test accuracy) and on MNIST ($\geq 95\%$ test accuracy), and measure how topological features change across layers for different architectures and activation functions. We find that smaller PCNs collapse connected components across layers earlier than larger models (Spearman $\unicode{x1D70C} \in [0.72, 0.79]$ across activations), with model size measured as the sum of hidden-layer widths. We also observe a strong negative correlation ($\unicode{x1D70C} = -0.58$) between the depth at which simplification occurs and reconstruction error; i.e., architectures that simplify later reconstruct better. Finally, a seed-level bootstrap comparison across architectures and activations shows that PCNs consistently collapse connected components later than matched MLPs, with an average difference of $3.6$ layers. These results suggest that persistent homology offers a useful quantitative lens on the compression--reconstruction tradeoff in PCNs, and that both model capacity and the recurrent, bidirectional dynamics of predictive coding inference shape when this tradeoff is resolved across layers.

Topological neural networks (TNNs) enable leveraging high-order structures on graphs (e.g., cycles and cliques) to boost the expressive power of message-passing neural networks. In turn, however, these structures are typically identified a priori through an unsupervised graph lifting operation. Notwithstanding, this choice is crucial and may have a drastic impact on a TNN's performance on downstream tasks. To circumvent this issue, we propose $\partial$lift (DiffLift), a general framework for learning graph liftings to hypergraphs and cellular- and simplicial complexes in an end-to-end fashion. In particular, our approach leverages learned vertex-level latent representations to identify and parameterize distributions over candidate higher-order cells for inclusion. This results in a scalable model which can be readily integrated into any TNN. Our experiments show that $\partial$lift outperforms existing lifting methods on multiple benchmarks for graph and node classification across different TNN architectures. Notably, our approach leads to gains of up to 45% over static liftings, including both connectivity- and feature-based ones.

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.

Contemporary machine learning struggles to learn continually, reuse prior knowledge, and expose a comprehensible internal structure. A recently proposed developmental, gradient-free learning framework addresses these limitations by learning a discrete, topological model of its inputs through local variation and selection, yielding an inherent continual-learning guarantee: new observations refine existing structure without overwriting past knowledge, and without replay buffers or predefined task boundaries. Its extension to visual inputs demonstrated this principle on shape recognition, but relied on a feature representation of limited expressivity that capped recognition accuracy. We introduce a new visual feature representation that encodes shape structure across multiple scales, capturing edge and contour features together with their spatial relations, and integrate it with the network-refinement learning process; we further improve the learning dynamics and the read-out used to predict from the learned model. The study targets two-dimensional shape, with class-incremental MNIST as a controlled, interpretable benchmark in which continual-learning behavior can be measured directly. Our approach substantially increases accuracy over the prior representation, matching or exceeding replay- and regularisation-based baselines at comparable storage while storing no past data, and preserves the framework's defining behavior: earlier-learned classes are retained as new ones are introduced, with no destructive adaptation, and the learned representations remain human-interpretable. What separates the methods is retention: the baselines surrender most of a just-trained class within its own cycle and relearn it afterwards, which ours does not. The significance lies in the manner of learning. The system integrates information one sample at a time while provably preserving its responses to...

Semantic ID-based generative recommendation tokenizes each item into a sequence of discrete semantic IDs and predicts the next item by generating semantic IDs. However, existing methods typically regard SIDs as independent discrete symbols, while often overlooking the topology of the learned semantic ID space. We identify a structural mismatch between tokenization and generation: the tokenizer learns a structured code space with semantic neighborhood relations, whereas the generator consumes semantic ID tokens as independent categorical symbols. Consequently, item relatedness is reduced to exact semantic ID overlap, making it difficult to identify semantically similar items whose semantic IDs do not overlap. To address this issue, we propose TopoGR, a topology-preserving generative recommendation framework based on Bit-decomposable Semantic ID(Binary SID). Each Binary SID is learned in a bit-decomposable form and can be deterministically converted to a standard integer SID, while exposing an explicit Hamming geometry. TopoGR exploits this topology at three stages: binary SID features preserve Hamming proximity at the input layer; Hamming soft targets inject topology-aware supervision; and Hamming-consistent reranking aligns candidate items with the predicted binary prototype during inference. We further verify that the Hamming topology can capture item relatedness beyond exact SID matching. Experiments on four benchmark datasets show that TopoGR consistently outperforms existing state-of-the-art baselines in recommendation performance.

Computer aided design (CAD) is ubiquitous: virtually any modern object was designed using editable CAD tools. However, with the shortage of available CAD datasets in its native editable and parametric format, boundary representation (B-Rep), it is ever more important to develop data-efficient methods for this domain. We present a new self-supervised pretraining task, Masked Topology Modeling (MTM), that leverages the face-adjacency graph, an induced structure unique to B-reps that the encoder can be asked to reconstruct. MTM masks a fraction of edges and trains a small head to predict each masked edge's convexity and curve type from the encoder's post-message-passing face features. We combine MTM with a MoCo-style momentum-queue contrastive learning over B-rep-aware augmentations, a BFS-connected face-region masked-reconstruction objective, and pretraining on the ABC dataset and our new procedurally generated dataset to show strong performance on a number of benchmarks.

In this paper, we ask whether vision foundation models construct representations that reflect the intrinsic properties of 3D Euclidean space. Unlike previous works that probe 3D awareness of vision features by regressing image-centric quantities such as depth or normals, we investigate the relation between the structure of the space of visual features and the group of Euclidean transformations $SE(3)$. We propose a set of probes to evaluate this relation from both topological and geometric perspectives: a mutual neighborhood metric that measures the alignment between feature neighborhoods and spatial topology, and a Poincaré Adapter to test the linear accessibility of the geometry of camera motion from latent displacements in static scenes. We show that self-supervised vision models, which, in principle, have not been trained with direct 3D supervision or active agency, possess latent subspaces that are remarkably strongly correlated with three-dimensional Euclidean space, when probed correctly. Building on this insight we propose a new class of "Latent-Space Navigation" techniques that perform visual odometry and localization purely in the latent space, bypassing the need for explicit 3D reconstruction.

Current electroencephalography (EEG)-based dream detection relies on power spectral density (PSD) and statistical moment features, achieving a state-of-the-art area under the receiver operating characteristic curve (AUC) of approximately 0.70 on the DREAM database (Wong et al., 2025, Nature Communications). We introduce PHINN-EEG (Persistent Homology Inspired Neural Network for EEG), the first topological time-series framework for dream mentation analysis. Using sliding-window Takens delay embeddings and Vietoris-Rips filtrations on multichannel pre-awakening EEG epochs, we extract Dynamic Betti Curves that characterize the geometric architecture of neural activity, not merely its energy. These topological invariants, combined with topology-conditioned flow matching, are analytically projected to outperform existing PSD and catch22 benchmarks, targeting AUC = 0.82-0.90 on the 1,462-awakening open-access subset of the DREAM database (drawn from a full registry of 3,191 total awakenings from 263 participants across 20 independent laboratories). We further introduce a topology-conditioned rectified flow model for dream-state EEG synthesis-with a spectral-conditioned flow model of comparable feature dimensionality as an additional ablation baseline to isolate the value of topological conditioning specifically-and propose a set of candidate Betti transition archetypes linking topology to phenomenological dream report categories, presented as an exploratory hypothesis space pending empirical validation. If validated, this work represents a paradigm shift from spectral energy to phase-space geometry in neural rare-event detection, with potential future implications for wearable BCI dream monitoring.

Topological data analysis (TDA), particularly persistent homology (PH), captures geometric structural properties in medical images (e.g., connected components, loops, shape characteristics), which conventional pixel-level deep learning approaches often neglect. While many topological descriptors are known for converting persistence diagrams (PDs) or raw images into topological feature vectors, existing methods mostly default to a single fixed descriptor (e.g., persistence images), leaving the diversity of topological representations largely unexplored. To the best of our knowledge, there is no known large language model (LLM)-based agentic framework that can automatically determine the most suitable topological descriptors for a given image dataset and produce the corresponding topological feature vectors for downstream tasks. To fill this gap, we propose \textbf{TopoAgent}, an LLM-based agentic framework that automates topology learning for medical image analysis.TopoAgent operates through a Perception--Reasoning--Action--Reflection loop supported by 21 domain-specific tools and dual memory that accumulates experience across runs. Its skill set is distilled from systematic evaluation of 15 topological descriptors across 26 datasets with six classifiers. TopoAgent analyzes input images and their topological characteristics, reasons about which topological descriptors best suit the input, and determines the optimal descriptor and its configuration, all without task-specific training.

Autoregressive Transformers dominate high-quality mesh generation by producing artist-worthy topologies, yet their inherent sequential decoding induces substantial computational overhead, falling orders of magnitude slower than parallel generative models. On the other hand, while continuous diffusion and flow-matching methods support efficient parallel synthesis across a variety of domains, they cannot be directly applied to meshes: mesh connectivity is inherently discrete and incompatible with standard continuous noise injection and denoising operations. To resolve this fundamental incompatibility, we introduce a compact topology embedder that projects discrete mesh vertex positions and normals into continuous per-vertex embeddings, where the original discrete adjacency information can be faithfully recovered via spacetime distance thresholding. After pretraining and freezing this embedder, any raw mesh can be fully converted into a continuous per-vertex state space unifying position, normal, and implicit topological attributes. Built upon this novel continuous mesh representation, we present PolyFlow, a Transformer-based flow-matching framework that achieves fully parallel vertex state denoising conditioned on extracted point-cloud features. During inference, our model completes generation rapidly via an ODE solver, and supports explicit, precise control over output mesh resolution by directly specifying the target vertex count. Extensive evaluations on the Toys4K benchmark demonstrate that PolyFlow surpasses state-of-the-art autoregressive baselines in both Chamfer Distance and Hausdorff Distance.

Real-time process monitoring requires methods that extract actionable information from high-dimensional time-series data. In this work, we present a new approach for process monitoring that combines tools of topological data analysis (TDA) and machine learning. In the proposed approach, we represent multivariate time-series data as manifolds and use topological descriptors to summarize the structure of such data; we then use a neural ordinary differential equation to learn the dynamic evolution of the topological structure of the system. Using real data from an industrial process, we show that this trajectory-based event detection approach is effective at detecting diverse types of events. We contrast this approach against reconstruction-based approaches such as principal component analysis and autoencoders and against a trajectory-based approach that uses Koopman autoencoders.

While persistent Laplacians (PL) offer a richer geometric representation of data than persistent homology, utilizing their full eigenspectrum for learning tasks is often hampered by high dimensionality and the ``varying length'' problem across different filtration scales. We propose a compact spectral representation that distills the persistent Laplacian into three mathematically grounded invariants: Betti numbers, the spectral gap, and analytic torsion. Across benchmark datasets including MNIST, QM-3D, and SKEMPI WT, we demonstrate that this reduced feature space captures the essential predictive signal of the full spectrum, and in some cases outperforms it, while significantly reducing computational overhead and preventing the noise introduced by higher-frequency eigenvalues. Our results suggest that these invariants provide a principled, fixed-length interface between spectral geometry and topological learning.

The Euler Characteristic Curve (ECC) records the Euler characteristic of a linearly embedded cell complex as a function of filtration height in a given direction, and the Euler Characteristic Transform (ECT) is the injective shape descriptor obtained by collecting ECCs over many directions. How the ECT is encoded for a neural network is itself an inductive bias, conventionally fixed by discretizing each ECC. We introduce a continuous encoding: for each direction and each vertex it records the net Euler-characteristic change attributed to that vertex, producing a per-direction token sequence that a small transformer maps to a feature vector. We separate the resulting pipeline into two stages on orthogonal axes: an ECC encoder that acts within each direction, mapping its curve to a fixed-length vector, and an ECT representation that acts across directions, aggregating the per-direction vectors into one. We study six ECT representation architectures spanning a range of inductive biases, from a structure-agnostic feedforward baseline to convolutional and complex-valued models that preserve equivariance under planar rotations. Across six classification benchmarks covering point clouds, graphs, cubical complexes, and meshes, the continuous encoding improves accuracy on five of six datasets, and control experiments attribute the gain to the tokenization itself rather than to the added transformer capacity. The representation architecture matters less than the encoding, and the payoff from its inductive biases depends on the encoding: a feedforward network performs best under continuous encoding but is less robust under discretization than convolutional architectures.

Variational autoencoders (VAEs) learn low-dimensional latent representations of high-dimensional data. When the data lies on a manifold with non-Euclidean topology, the standard Gaussian prior introduces a topological mismatch that degrades reconstruction quality and prevents faithful representation. We present a constructive mathematical framework that resolves this mismatch for all manifolds that admit a product covering space. These are manifolds expressible as products of elementary factors (circles, intervals, or lines) or as quotients of such products by a finite symmetry group. The class includes cylinders, tori, Möbius strips, Klein bottles, and real projective spaces. Factorized distributions over the elementary factors yield product topologies with closed-form, decoupled KL divergences, so that each latent factor can be shaped independently while keeping training tractable. We catalogue reparametrizable encoder-prior pairs for periodic, bounded, and unbounded supports, and provide coordinate transformations that allow standard neural networks to output non-Euclidean parameters with smooth gradients. For quotient manifolds, the decoder receives group-invariant features of the covering-space coordinates, so that identified points produce identical outputs. Anchor constraints fix the coordinate system relative to the data or create soft topological holes. Experiments on synthetic manifolds and real-image datasets (rotated and cyclically shifted MNIST) confirm that a topology-matched prior aligns KL regularization with the data manifold. The resulting topology-aware models outperform the Gaussian baseline at all practically relevant regularization strengths. The code is available at https://github.com/JvHulst/VAE-Topology.

Deep neural networks learn representations where individual features often lack interpretable meaning; a single neuron may activate for scattered, unrelated inputs. We introduce coherence, a geometric property inspired by neural coding in the brain, where neurons like grid cells and head direction cells respond to contiguous regions of state space. A non-negative matrix is coherent if each row (sample) attends to geometrically clustered columns (features) and vice versa, and in addition every sample is well described by some feature and every feature is needed by some sample. We prove that coherent matrices induce a bounded interleaving between the Vietoris-Rips filtrations of samples and features, guaranteeing that both spaces share compatible topological structure. This geometric constraint facilitates interpretability. For example, if data lies on a circle, coherent features must tile that circle into contiguous arcs. We introduce Coh, a differentiable objective function based on Fréchet variance that enforces coherence during training. Unlike sparsity, which bounds how many samples a feature activates on, coherence bounds which samples, requiring geometric connectivity rather than only rarity. This yields not just interpretable features but an interpretable feature space. We validate Coh in an auto-encoder using synthetic and rotated MNIST datasets and in a token embedding of BERT using language data.

Self-supervised pre-training methods in medical imaging typically treat each individual as an isolated instance, learning representations through augmentation-based objectives or masked reconstruction. They often do not adequately capitalize on a key characteristic of physiological features: anatomical structures maintain consistent spatial relationships across individuals (instances), such as the thalamus being medial to the basal ganglia, regardless of variations in brain size, shape, or pathology. We propose leveraging this cross-instance topological consistency as a supervisory signal. The challenge arises from the inherent variability in medical imaging, which can differ significantly across instances and modalities. To tackle this, we focus on two alignment regimes. (i) Intra-instance: with pixel-level correspondences available, a cross-modal triplet objective explicitly preserves local neighborhood topology. (ii) Inter-instance: without such supervision, we derive pseudo-correspondences to control partial neighborhood alignment and prevent topology collapse across modalities. We validate our approach across 7 downstream multi-modal tasks, achieving average improvements of 1.1% and 5.94% in segmentation and classification tasks, respectively, and demonstrating significantly better robustness when modalities are missing at test time.

The Nearest Class Mean (NCM) classifier is widely favored in Class-Incremental Learning (CIL) for its superior resistance to catastrophic forgetting compared to Fully Connected layers. While Neural Collapse (NC) theory supports NCM's optimality by assuming features collapse into single points, non-linear feature drift and insufficient training in CIL often prevent this ideal state. Consequently, classes manifest as complex manifolds rather than collapsed points, rendering the single-point NCM suboptimal. To address this, we propose Hierarchical-Cluster SOINN (HC-SOINN), a novel classifier that captures the topological structure of these manifolds via a ``local-to-global'' representation. Furthermore, we introduce Structure-Topology Alignment via Residuals (STAR) method, which employs a fine-grained pointwise trajectory tracking mechanism to actively deform the learned topology, allowing it to adapt precisely to complex non-linear feature drift. Theoretical analysis and Procrustes distance experiments validate our framework's resilience to manifold deformations. We integrated HC-SOINN into seven state-of-the-art methods by replacing their original classifiers, achieving consistent improvements that highlight the effectiveness and robustness of our approach. Code is available at https://github.com/yhyet/HC_SOINN.