Persistent Homology

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Latest papers 46

5 papers in the last four weeks, up 67% on the four weeks before. 0.0% of all new papers.

May 4, 2026

A Closed-Form Persistence-Landmark Pipeline for Certified Point-Cloud and Graph Classification

We introduce PLACE (Persistence-Landmark Analytic Classification Engine), a closed-form pipeline for classifying point clouds and graphs through their persistent-homology signatures. Three quantitative guarantees -- a margin-based excess-risk rate, a closed-form descriptor-selection rule, and a per-prediction certificate -- are derived from training labels alone, with no learned weights or held-out calibration. The embedding sums Mitra-Virk single-point coordinate functions over a sparse landmark grid; the closed-form weight rule

w_k^2 \propto (d_{k+1}^2 - d_k^2)/R_k^2

maximizes the distortion slope in Mitra-Virk's affine certificate under

ν

-coherence. (i) An

O(kR/(Δ\sqrt{m_{\min}}))

margin bound, driven by class-mean separation

Δ

and embedding radius

R

, matched in the sample-starved regime

m \lesssim R/Δ

by a Le Cam minimax lower bound. (ii) The Mahalanobis margin under Ledoit-Wolf-shrunk covariance is the strongest closed-form ranker on a 64-descriptor chemical-graph pool (mean Spearman

ρ= +0.56

across 11 benchmarks, positive on 10 of 11); the isotropic surrogate

Δ/\sqrt{\ell}

admits a closed-form selection-consistency rate on the homogeneous protein/social pools. (iii) A training-time-decided certificate, with no per-prediction overhead, in three concrete radii (Pinelis, Gaussian plug-in, and variance-aware Pinelis-Bernstein). Empirically, PLACE is the strongest diagram-based method on Orbit5k and matches the strongest topology-based baseline within statistical noise on MUTAG and COX2; remaining gaps fall into two diagnosable regimes (descriptor blindness on NCI1/NCI109; pool-coverage limits elsewhere). The Pinelis-Bernstein radius fires on 8 of the 12 benchmarks; on MUTAG the empirical and population nearest-centroid rules agree on every one of 940 held-out test predictions, validating the certificate's mechanism.

Sushovan Majhi, Atish Mitra, Žiga Virk +1

Data Science, George Washington University, USA · Department of Mathematical Sciences, Montana Technological University, USA · Faculty of Computer and Information Science, University of Ljubljana, Institute IMFM, Slovenia +1

Point Cloud Classification Classification Graph Classification Persistent Homology Statistical Learning Theory

Apr 24, 2026

FILTR: Extracting Topological Features from Pretrained 3D Models

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.

Louis Martinez, Maks Ovsjanikov

LIX, ´Ecole Polytechnique, IP Paris

Point Cloud Learning 3D Representation Learning Persistent Homology Topological Representation Learning Topological Data Analysis

Apr 23, 2026

Fixation Sequences as Time Series: A Topological Approach to Dyslexia Detection

Persistent homology, a method from topological data analysis, extracts robust, multi-scale features from data. It produces stable representations of time series by applying varying thresholds to their values (a process known as a filtration). We develop novel filtrations for time series and introduce topological methods for the analysis of eye-tracking data, by interpreting fixation sequences as time series, and constructing ``hybrid models'' that combine topological features with traditional statistical features. We empirically evaluate our method by applying it to the task of dyslexia detection from eye-tracking-while-reading data using the Copenhagen Corpus, which contains scanpaths from dyslexic and non-dyslexic L1 and L2 readers. Our hybrid models outperform existing approaches that rely solely on traditional features, showing that persistent homology captures complementary information encoded in fixation sequences. The strength of these topological features is further underscored by their achieving performance comparable to established baseline methods. Importantly, our proposed filtrations outperform existing ones.

Marius Huber, David R. Reich, Lena A. Jäger

Department of Computational Linguistics, University of Zürich, Switzerland

Time Series Classification Eye Tracking Persistent Homology Topological Data Analysis

Apr 19, 2026

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

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.

Mattie Ji, Indradyumna Roy, Vikas Garg

University of Pennsylvania · Aalto University · Indian Institute of Technology Bombay +1

Graph Neural Networks Graph Representation Learning Persistent Homology Topological Representation Learning Topological Data Analysis

Apr 5, 2026

A Persistent Homology Design Space for 3D Point Cloud Deep Learning

Persistent Homology (PH) offers stable, multi-scale descriptors of intrinsic shape structure by capturing connected components, loops, and voids that persist across scales, providing invariants that complement purely geometric representations of 3D data. Yet, despite strong theoretical guarantees and increasing empirical adoption, its integration into deep learning for point clouds remains largely ad hoc and architecturally peripheral. In this work, we introduce a unified design space for Persistent-Homology driven learning in 3D point clouds (3DPHDL), formalizing the interplay between complex construction, filtration strategy, persistence representation, neural backbone, and prediction task. Beyond the canonical pipeline of diagram computation and vectorization, we identify six principled injection points through which topology can act as a structural inductive bias reshaping sampling, neighborhood graphs, optimization dynamics, self-supervision, output calibration, and even internal network regularization. We instantiate this framework through a controlled empirical study on ModelNet40 classification and ShapeNetPart segmentation, systematically augmenting representative backbones (PointNet, DGCNN, and Point Transformer) with persistence diagrams, images, and landscapes, and analyzing their impact on accuracy, robustness to noise and sampling variation, and computational scalability. Our results demonstrate consistent improvements in topology-sensitive discrimination and part consistency, while revealing meaningful trade-offs between representational expressiveness and combinatorial complexity. By viewing persistent homology not merely as an auxiliary feature but as a structured component within the learning pipeline, this work provides a systematic framework for incorporating topological reasoning into 3D point cloud learning.

Prachi Kudeshia, Jiju Poovvancheri, Amr Ghoneim +1

Saint Mary’s University, Halifax, Canada · Nanjing Forestry University, China

Persistent Homology Topological Representation Learning Point Cloud Learning Point Cloud Classification

Mar 30, 2026

How much of persistent homology is topology? A quantitative decomposition for spin model phase transitions

Point-cloud persistent homology (PH) -- computing alpha or Rips complexes on spin-position point clouds -- has been widely applied to detect phase transitions in classical spin models since Donato et al. (2016), with subsequent studies attributing the detection to the topological content of the persistence diagram. We ask a simple question that has not been posed: what fraction of the PH signal is genuinely topological? We introduce f_topo, a quantitative decomposition that separates the density-driven and topological contributions to any PH statistic by comparing real spin configurations against density-matched shuffled null models. Across the 2D Ising model (system sizes L = 16-128, ten temperatures) and Potts models (q = 3, 5), we find that H_0 statistics -- total persistence, persistence entropy, feature count -- are 94-100% density-driven (f_topo < 0.07). The density-matched shuffled null detects T_c at the identical location and with comparable peak height as real configurations, showing that density alone is sufficient for phase transition detection. However, H_1 statistics are partially topological: the topological fraction grows with system size as delta(TP_{H_1}) ~ L^{0.53} and follows a finite-size scaling collapse delta(T, L) = L^{0.53} g(tL^{1/nu}) with collapse quality CV = 0.27. The longest persistence bar is strongly topological (f_topo > 1) and scales with the correlation length. A scale-resolved analysis reveals that the topological excess shifts from large-scale to small-scale features as L increases. We propose that the TDA-for-phase-transitions community adopt shuffled null models as standard practice, and that H_1 rather than H_0 statistics be used when genuine topological information is sought.

Matthew Loftus

Cedar Loop LLC, Washington, USA

Persistent Homology Topological Data Analysis Phase Transitions

Mar 29, 2026

Persistence diagrams of random matrices via Morse theory: universality and a new spectral diagnostic

We prove that the persistence diagram of the sublevel set filtration of the quadratic form f(x) = x^T M x restricted to the unit sphere S^{n-1} is analytically determined by the eigenvalues of the symmetric matrix M. By Morse theory, the diagram has exactly n-1 finite bars, with the k-th bar living in homological dimension k-1 and having length equal to the k-th eigenvalue spacing s_k = λ_{k+1} - λ_k. This identification transfers random matrix theory (RMT) universality to persistence diagram universality: for matrices drawn from the Gaussian Orthogonal Ensemble (GOE), we derive the closed-form persistence entropy PE = log(8n/π) - 1, and verify numerically that the coefficient of variation of persistence statistics decays as n^{-0.6}. Different random matrix ensembles (GOE, GUE, Wishart) produce distinct universal persistence diagrams, providing topological fingerprints of RMT universality classes. As a practical consequence, we show that persistence entropy outperforms the standard level spacing ratio \langle r \rangle for discriminating GOE from GUE matrices (AUC 0.978 vs. 0.952 at n = 100, non-overlapping bootstrap 95% CIs), and detects global spectral perturbations in the Rosenzweig-Porter model to which \langle r \rangle is blind. These results establish persistence entropy as a new spectral diagnostic that captures complementary information to existing RMT tools.

Matthew Loftus

Cedar Loop LLC, Washington, USA

Random Matrix Theory Persistent Homology

Mar 21, 2026

GraPHFormer: A Multimodal Graph Persistent Homology Transformer for the Analysis of Neuroscience Morphologies

Neuronal morphology encodes critical information about circuit function, development, and disease, yet current methods analyze topology or graph structure in isolation. We introduce GraPHFormer, a multimodal architecture that unifies these complementary views through CLIP-style contrastive learning. Our vision branch processes a novel three-channel persistence image encoding unweighted, persistence-weighted, and radius-weighted topological densities via DINOv2-ViT-S. In parallel, a TreeLSTM encoder captures geometric and radial attributes from skeleton graphs. Both project to a shared embedding space trained with symmetric InfoNCE loss, augmented by persistence-space transformations that preserve topological semantics. Evaluated on six benchmarks (BIL-6, ACT-4, JML-4, N7, M1-Cell, M1-REG) spanning self-supervised and supervised settings, GraPHFormer achieves state-of-the-art performance on five benchmarks, significantly outperforming topology-only, graph-only, and morphometrics baselines. We demonstrate practical utility by discriminating glial morphologies across cortical regions and species, and detecting signatures of developmental and degenerative processes. Code: https://github.com/Uzshah/GraPHFormer

Uzair Shah, Marco Agus, Mahmoud Gamal +5

Hamad Bin Khalifa University, Qatar · University of Turin, Italy · Neuroscience Institute Cavalieri Ottolenghi, Italy +3

Topological Representation Learning Multimodal Graph Learning Graph Neural Networks Persistent Homology Multimodal Contrastive Learning

Mar 16, 2026

Persistence Spheres: a Bi-continuous Linear Representation of Measures for Partial Optimal Transport

We improve and extend persistence spheres, introduced in~\cite{pegoraro2025persistence}. Persistence spheres map an integrable measure

μ

on the upper half-plane, including persistence diagrams (PDs) as counting measures, to a function

S(μ)\in C(\mathbb{S}^2)

, and the map is stable with respect to 1-Wasserstein partial transport distance

\mathrm{POT}_1

. Moreover, to the best of our knowledge, persistence spheres are the first explicit representation used in topological machine learning for which continuity of the inverse on the image is established at every compactly supported target. Recent bounded-cardinality bi-Lipschitz embedding results in partial transport spaces, despite being powerful, are not given by the kind of explicit summary map considered here. Our construction is rooted in convex geometry: for positive measures, the defining ReLU integral is the support function of the lift zonoid. Building on~\cite{pegoraro2025persistence}, we refine the definition to better match the

\mathrm{POT}_1

deletion mechanism, encoding partial transport via a signed diagonal augmentation. In particular, for integrable

μ

, the uniform norm between

S(0)

and

S(μ)

depends only on the persistence of

μ

, without any need of ad-hoc re-weightings, reflecting optimal transport to the diagonal at persistence cost. This yields a parameter-free representation at the level of measures (up to numerical discretization), while accommodating future extensions where

μ

is a smoothed measure derived from PDs (e.g., persistence intensity functions~\citep{wu2024estimation}). Across clustering, regression, and classification tasks involving functional data, time series, graphs, meshes, and point clouds, the updated persistence spheres are competitive and often improve upon persistence images, persistence landscapes, persistence splines, and sliced Wasserstein kernel baselines.

Matteo Pegoraro

Institute of Computing, Faculty of Informatics, Università della Svizzera Italiana

Topological Representation Learning Persistent Homology Optimal Transport

Mar 15, 2026

Beyond Distance: Quantifying Point Cloud Dynamics with Persistent Homology and Dynamic Optimal Transport

We introduce a framework for analyzing topological tipping in time-evolutionary point clouds by extending the recently proposed Topological Optimal Transport (TpOT) distance. While TpOT unifies geometric, homological, and higher-order relations into one metric, its global scalar distance can obscure transient, localized structural reorganizations during dynamic phase transitions. To overcome this limitation, we present a hierarchical dynamic evaluation framework driven by a novel topological and hypergraph reconstruction strategy. Instead of directly interpolating abstract network parameters, our method interpolates the underlying spatial geometry and rigorously recomputes the valid topological structures, ensuring physical fidelity. Along this geodesic, we introduce a set of multi-scale indicators: macroscopic metrics (Topological Distortion and Persistence Entropy) to capture global shifts, and a novel mesoscopic dual-perspective Hypergraph Entropy (node-perspective and edge-perspective) to detect highly sensitive, asynchronous local rewirings. We further propagate the cycle-level entropy change onto individual vertices to form a point-level topological field. Extensive evaluations on physical dynamical systems (Rayleigh-Van der Pol limit cycles, Double-Well cluster fusion), high-dimensional biological aggregation (D'Orsogna model), and longitudinal stroke fMRI data demonstrate the utility of combining transport-based alignment with multi-scale entropy diagnostics for dynamic topological analysis.

Yixin Wang, Ting Gao, Jinqiao Duan

School of Mathematics and Statistics, Huazhong University of Science and Technology, Wuhan, China · Center for Mathematical Science, Huazhong University of Science and Technology, Wuhan, China · Steklov-Wuhan Institute for Mathematical Exploration, Huazhong University of Science and Technology, China +2

Topological Data Analysis Optimal Transport Persistent Homology

Mar 15, 2026

Beyond Means: Topological Causal Effects under Persistent-Homology Ignorability

Average treatment effects (ATE) and conditional average treatment effects (CATE) are foundational causal estimands, but they target changes in expected outcomes and can miss treatment-induced changes in the shape of outcome distributions. A canonical failure mode occurs when control outcomes are unimodal, treated outcomes become bimodal, and both distributions have the same mean. In such cases mean-based causal estimands are zero even though the geometry and topology of the outcome law change substantially. This paper develops a topological causal framework based on persistent homology. We formalize a persistent-homology ignorability condition, define topological analogues of CATE and ATE, and prove that these estimands are identifiable up to an explicit error bound under approximate topological ignorability. We also clarify a subtle but important point: a marginal persistence-diagram effect is not identified from conditional topological ignorability alone because persistent homology does not in general commute with mixtures over covariates. To preserve the original intuition while ensuring scientific correctness, we retain the marginal effect as a motivating quantity, but place the mathematically sound conditional estimands at the center of the theory. A synthetic experiment with mean-preserving topology change shows that mean-based causal estimands remain near zero while the proposed topological effect increases sharply and remains recoverable after adjustment for confounding.

Amir Saki, Usef Faghihi

Université du Québec à Trois-Rivières (UQTR).

Causal Effect Estimation Causal Identifiability Conditional Average Treatment Effect Estimation Persistent Homology

Mar 12, 2026

The Density of Cross-Persistence Diagrams and Its Applications

Topological Data Analysis (TDA) provides powerful tools to explore the shape and structure of data through topological features such as clusters, loops, and voids. Persistence diagrams are a cornerstone of TDA, capturing the evolution of these features across scales. While effective for analyzing individual manifolds, persistence diagrams do not account for interactions between pairs of them. Cross-persistence diagrams (cross-barcodes), introduced recently, address this limitation by characterizing relationships between topological features of two point clouds. In this work, we present the first systematic study of the density of cross-persistence diagrams. We prove its existence, establish theoretical foundations for its statistical use, and design the first machine learning framework for predicting cross-persistence density directly from point cloud coordinates and distance matrices. Our statistical approach enables the distinction of point clouds sampled from different manifolds by leveraging the linear characteristics of cross-persistence diagrams. Interestingly, we find that introducing noise can enhance our ability to distinguish point clouds, uncovering its novel utility in TDA applications. We demonstrate the effectiveness of our methods through experiments on diverse datasets, where our approach consistently outperforms existing techniques in density prediction and achieves superior results in point cloud distinction tasks. Our findings contribute to a broader understanding of cross-persistence diagrams and open new avenues for their application in data analysis, including potential insights into time-series domain tasks and the geometry of AI-generated texts. Our code is publicly available at https://github.com/Verdangeta/TDA_experiments

Alexander Mironenko, Evgeny. Burnaev, Serguei Barannikov

Skolkovo Institute of Science and Technology, Moscow 121205, Russia · AIRI, Moscow 123317, Russia · CNRS, IMJ, Paris University, Paris 75205, France

Topological Data Analysis Density Estimation Persistent Homology

Feb 20, 2026

G-LoG Bi-filtration for Medical Image Classification

Building practical filtrations on objects to detect topological and geometric features is an important task in the field of Topological Data Analysis (TDA). In this paper, leveraging the ability of the Laplacian of Gaussian operator to enhance the boundaries of medical images, we define the G-LoG (Gaussian-Laplacian of Gaussian) bi-filtration to generate the features more suitable for multi-parameter persistence module. By modeling volumetric images as bounded functions, then we prove the interleaving distance on the persistence modules obtained from our bi-filtrations on the bounded functions is stable with respect to the maximum norm of the bounded functions. Finally, we conduct experiments on the MedMNIST dataset, comparing our bi-filtration against single-parameter filtration and the established deep learning baselines, including Google AutoML Vision, ResNet, AutoKeras and auto-sklearn. Experiments results demonstrate that our bi-filtration significantly outperforms single-parameter filtration. Notably, a simple Multi-Layer Perceptron (MLP) trained on the topological features generated by our bi-filtration achieves performance comparable to complex deep learning models trained on the original dataset.

Qingsong Wang, Jiaxing He, Bingzhe Hou +3

Topological Data Analysis Medical Image Classification Persistent Homology

Feb 8, 2026

Persistent Entropy as a Detector of Phase Transitions

Persistent entropy is a scalar summary of persistence barcodes widely used to detect regime changes, yet there is no account of when a structural change in a barcode must produce a detectable change in entropy. We establish a model-agnostic theorem supplying such conditions. Treating persistence diagrams as random objects indexed by a control parameter, we identify a dispersion-condensation mechanism in the normalized persistence weights and derive an explicit lower bound on the entropy difference between the two regimes, valid with high probability at finite sample size and insensitive to the absolute scale of bar lifetimes. We also give a procedure for verifying the hypotheses on empirical barcodes. Applied to convolutional networks, the criterion shows that the circular organization of learned filters reported by Gabrielsson and Carlsson emerges through a sharp topological phase transition, and locates its onset: within a few hundred iterations on MNIST, but an order of magnitude later on CIFAR-10. The same criterion detects the Kuramoto synchronization and Vicsek order-disorder transitions.

Marcos Gutierrez-del-Pozo, Eduardo Paluzo-Hidalgo, Matteo Rucco

Phase Transitions Persistent Homology Topological Data Analysis

Dec 29, 2025

Finite Topological Space Filtrations: A Topological Framework for Data Analysis

We introduce a data-analysis framework based on filtrations of finite topological spaces. Starting from a finite metric data set, we construct a sequence of coarsening topologies on the same set of points. These topologies give persistence modules and barcodes in the usual way, but they also retain information that is lost when the filtration is reduced to homology. At each level one can examine, for example, which points are topologically indistinguishable, how their minimal neighbourhoods overlap, how connected components merge, and how these features change from one level to the next. We develop the basic theory of these filtrations, establish stability results under suitable hypotheses, and give practical constructions starting directly from a distance matrix. We then study what can be learned from the resulting finite topologies. On synthetic data with known clusters of different shapes, sizes, and densities, we examine how these regions appear among the finite-topological structures and how they merge as the topology coarsens. We also study what happens when points that become uncovered early in the construction are removed and the analysis is repeated. For one-dimensional homology, we use paths in the finite-topological structure to locate cycles and to examine how their appearance is related to the geometry of the data. We finally apply these ideas to two real data sets with quite different structures. On the Paul15 single-cell data, we use the evolving finite topology to examine fine cellular states, their overlaps and relations, their assembly into larger groups, and the effect of removing points that connect these structures. On COIL20, where images of an object are sampled through a full rotation, we study how the cyclic organization of the images is reflected in the finite-topological evolution and in the associated one-dimensional homology.

Selçuk Kayacan

Bahçeşehir University, Faculty of Engineering and Natural Sciences, Istanbul, Turkey

Clustering Persistent Homology Topological Data Analysis

Jun 17, 2025

Topological data analysis using persistent discrete homology

We propose persistent discrete homology as a tool for topological data analysis and discuss its advantages over the existing methods. In particular, we provide empirical evidence that persistent discrete homology is more noise-resistant than persistent homology of the Vietoris-Rips complex for data coming from non-metric settings.

Chris Kapulkin, Nathan Kershaw

Noise Robustness Persistent Homology Topological Data Analysis