Understanding temporal patterns in online search behavior is crucial for real-time marketing and trend forecasting. Google Trends offers a rich proxy for public interest, yet the high dimensionality and noise of its time-series data present challenges for effective clustering. This study evaluates three unsupervised clustering approaches, Symbolic Aggregate approXimation (SAX), enhanced SAX (eSAX), and Topological Data Analysis (TDA), applied to 20 Google Trends keywords representing major consumer categories. Our results show that while SAX and eSAX offer fast and interpretable clustering for stable time series, they struggle with volatility and complexity, often producing ambiguous ``catch-all'' clusters. TDA, by contrast, captures global structural features through persistent homology and achieves more balanced and meaningful groupings. We conclude with practical guidance for using symbolic and topological methods in consumer analytics and suggest that hybrid approaches combining both perspectives hold strong potential for future applications.
Persistent Laplacians are matrix operators that track how the shape and structure of data transform across scales and are popularly adopted in biology, physics, and machine learning. Their eigenvalues are concise descriptors of geometric and topological features in a filtration. Although earlier work established global algebraic stability for these operators, the precise change in a single eigenvalue when one simplex, such as a vertex, edge, or triangle, is added has remained unknown. This is important because downstream tools, including heat-kernel signatures and spectral neural networks, depend directly on these eigenvalues. We close this gap by proving a uniform Lipschitz bound: after inserting one simplex, every up-persistent Laplacian eigenvalue can vary by at most twice the Euclidean norm of that simplex's boundary, independent of filtration scale and complex size. This result delivers the first eigenvalue-level robustness guarantee for spectral topological data analysis. It guarantees that spectral features remain stable under local updates and enables reliable error control in dynamic data settings.
Point cloud-based object/place recognition remains a problem of interest in applications such as autonomous driving, scene reconstruction, and localization. Extracting meaningful local descriptors from a query point cloud that can be matched with the descriptors of the collected point clouds is a challenging problem. Furthermore, when the query point cloud is noisy or has been transformed (e.g., rotated), it adds to the complexity. To this end, we propose a novel methodology, named TDACloud, using Topological Data Analysis (TDA) for local descriptor extraction from a point cloud, which does not need resource-intensive GPU-based machine learning training. More specifically, we used the ATOL vectorization method to generate vectors for point clouds. Unlike voxelization, our proposed technique can take raw point clouds as inputs and outputs a fixed-size TDA-descriptor vector. To test the quality of the proposed TDACloud technique, we have implemented it on multiple real-world (e.g., Oxford RobotCar, KITTI-360) and realistic (e.g., ShapeNet) point cloud datasets for object and place recognition. We have also tested TDACloud on noisy and transformed test cases where the query point cloud has been scaled, translated, or rotated. Our results demonstrate high recognition accuracies in noisy conditions and large-scale real-world place recognition while outperforming the baselines by up to approximately 14%.
Ground Penetrating Radar (GPR) is a widely used Non-Destructive Testing (NDT) technique for subsurface exploration, particularly in infrastructure inspection and maintenance. However, conventional interpretation methods are often limited by noise sensitivity and a lack of structural awareness. This study presents a novel framework that enhances the detection of underground utilities, especially pipelines, by integrating shape-aware topological features derived from B-scan GPR images using Topological Data Analysis (TDA), with the spatial detection capabilities of the YOLOv5 deep neural network (DNN). We propose a novel shape-aware topological representation that amplifies structural features in the input data, thereby improving the model's responsiveness to the geometrical features of buried objects. To address the scarcity of annotated real-world data, we employ a Sim2Real strategy that generates diverse and realistic synthetic datasets, effectively bridging the gap between simulated and real-world domains. Experimental results demonstrate significant improvements in mean Average Precision (mAP), validating the robustness and efficacy of our approach. This approach underscores the potential of TDA-enhanced learning in achieving reliable, real-time subsurface object detection, with broad applications in urban planning, safety inspection, and infrastructure management.
We explore the role of torsion in hybrid deep learning models that incorporate topological data analysis, focusing on autoencoders. While most TDA tools use field coefficients, this conceals torsional features present in integer homology. We show that torsion can be lost during encoding, altered in the latent space, and in many cases, not reconstructed by standard decoders. Using both synthetic and high-dimensional data, we evaluate torsion sensitivity to perturbations and assess its recoverability across several autoencoder architectures. Our findings reveal key limitations of field-based approaches and underline the need for architectures or loss terms that preserve torsional information for robust data representation.
We present a tractable, incremental framework for topological dialogue semantics based on finite, discrete semantic spaces. Building on the intuition that utterances correspond to open sets and their combinatorial relations form a simplicial complex (the dialogue nerve), we give a rigorous foundation, a provably correct incremental algorithm for nerve updates, and a reference implementation in the Wolfram Language. The framework supports negative nerve computation (inconsistency tracking), consequence extraction, and a transparent, set-theoretic ranking of entailments. We clarify which combinatorial properties hold in the discrete case, provide motivating examples, and outline limitations and prospects for richer logical and categorical extensions.
In medical image analysis, feature engineering plays an important role in the design and performance of machine learning models. Persistent homology (PH), from the field of topological data analysis (TDA), demonstrates robustness and stability to data perturbations and addresses the limitation from traditional feature extraction approaches where a small change in input results in a large change in feature representation. Using PH, we store persistent topological and geometrical features in the form of the persistence barcode whereby large bars represent global topological features and small bars encapsulate geometrical information of the data. When multiple barcodes are computed from 2D or 3D medical images, two approaches can be used to construct the final topological feature vector in each dimension: aggregating persistence barcodes followed by featurization or concatenating topological feature vectors derived from each barcode. In this study, we conduct a comprehensive analysis across diverse medical imaging datasets to compare the effects of the two aforementioned approaches on the performance of classification models. The results of this analysis indicate that feature concatenation preserves detailed topological information from individual barcodes, yields better classification performance and is therefore a preferred approach when conducting similar experiments.
Understanding how protein mutations affect protein-nucleic acid binding is critical for unraveling disease mechanisms and advancing therapies. Current experimental approaches are laborious, and computational methods remain limited in accuracy. To address this challenge, we propose a novel topological machine learning model (TopoML) combining persistent Laplacian (from topological data analysis) with multi-perspective features: physicochemical properties, topological structures, and protein Transformer-derived sequence embeddings. This integrative framework captures robust representations of protein-nucleic acid binding interactions. To validate the proposed method, we employ two datasets, a protein-DNA dataset with 596 single-point amino acid mutations, and a protein-RNA dataset with 710 single-point amino acid mutations. We show that the proposed TopoML model outperforms state-of-the-art methods in predicting mutation-induced binding affinity changes for protein-DNA and protein-RNA complexes.
Topological data analysis (TDA) offers novel mathematical tools for deep learning. Inspired by Carlsson et al., this study designs topology-aware convolutional kernels that significantly improve speech recognition networks. Theoretically, by investigating orthogonal group actions on kernels, we establish a fiber-bundle decomposition of matrix spaces, enabling new filter generation methods. Practically, our proposed Orthogonal Feature (OF) layer achieves superior performance in phoneme recognition, particularly in low-noise scenarios, while demonstrating cross-domain adaptability. This work reveals TDA's potential in neural network optimization, opening new avenues for mathematics-deep learning interdisciplinary studies.
Understanding how adversarial conditions affect language models requires techniques that capture both global structure and local detail within high-dimensional activation spaces. We propose persistent homology (PH), a tool from topological data analysis, to systematically characterize multiscale latent space dynamics in LLMs under two distinct attack modes -- backdoor fine-tuning and indirect prompt injection. By analyzing six state-of-the-art LLMs, we show that adversarial conditions consistently compress latent topologies, reducing structural diversity at smaller scales while amplifying dominant features at coarser ones. These topological signatures are statistically robust across layers, architectures, model sizes, and align with the emergence of adversarial effects deeper in the network. To capture finer-grained mechanisms underlying these shifts, we introduce a neuron-level PH framework that quantifies how information flows and transforms within and across layers. Together, our findings demonstrate that PH offers a principled and unifying approach to interpreting representational dynamics in LLMs, particularly under distributional shift.
The Hough transform is a popular and classical technique in computer vision for the detection of lines (or more general objects). It maps a pixel into a dual space -- the Hough space: each pixel is mapped to the set of lines through this pixel, which forms a curve in Hough space. The detection of lines then becomes a voting process to find those lines that received many votes by pixels. However, this voting is done by thresholding, which is susceptible to noise and other artifacts. In this work, we present an alternative voting technique to detect peaks in the Hough space based on persistent homology, which very naturally addresses limitations of simple thresholding. Experiments on synthetic data show that our method significantly outperforms the original method, while also demonstrating enhanced robustness. This work seeks to inspire future research in two key directions. First, we highlight the untapped potential of Topological Data Analysis techniques and advocate for their broader integration into existing methods, including well-established ones. Secondly, we initiate a discussion on the mathematical stability of the Hough transform, encouraging exploration of mathematically grounded improvements to enhance its robustness.
We present a generalised Hanson-Wright inequality and use it to establish new statistical insights into the geometry of data point-clouds. In the setting of a general random function model of data, we clarify the roles played by three notions of dimensionality: ambient intrinsic dimension $p_{\mathrm{int}}$, which measures total variability across orthogonal feature directions; correlation rank, which measures functional complexity across samples; and latent intrinsic dimension, which is the dimension of manifold structure hidden in data. Our analysis shows that in order for persistence diagrams to reveal latent homology and for manifold structure to emerge it is sufficient that $p_{\mathrm{int}}\gg \log n$, where $n$ is the sample size. Informed by these theoretical perspectives, we revisit the ground-breaking neuroscience discovery of toroidal structure in grid-cell activity made by Gardner et al. (Nature, 2022): our findings reveal, for the first time, evidence that this structure is in fact isometric to physical space, meaning that grid cell activity conveys a geometrically faithful representation of the real world.
Spatial transcriptomics studies are becoming increasingly large and commonplace, necessitating the analysis of a large number of spatially resolved variables. With spatial transcriptomics data sets typically containing data on thousands of different genes, on increasingly large numbers of samples, there is a need for bioinformatics tools that enable the comparison of spatial structure across large numbers of variables. Here we present PersiST, an exploratory tool that uses topology to automatically compute a continuous measure of spatial structure for each gene in a spatial transcriptomics sample. This quantification can be used for analytical tasks such as spatially variable gene identification, or searching for spatial differences in the expression of a gene between samples. We use PersiST to derive biologically meaningful insights into two public spatial transcriptomics data sets, and we experiment with applying PersiST to a spatial metabolomics data set, making use of PersiST's non-parametric approach to enable application across different measurement types. Our work showcases the advantages of using a continuous quantification of spatial structure over p-value based approaches to SVG identification, the potential for developing unified methods for the analysis of different spatial `omics modalities, and the utility of persistent homology in big data applications.
Semiconductor manufacturing generates vast amounts of image data, crucial for defect identification and yield optimization, yet often exceeds manual inspection capabilities. Traditional clustering techniques struggle with high-dimensional, unlabeled data, limiting their effectiveness in capturing nuanced patterns. This paper introduces an advanced clustering framework that integrates deep Topological Data Analysis (TDA) with self-supervised and transfer learning techniques, offering a novel approach to unsupervised image clustering. TDA captures intrinsic topological features, while self-supervised learning extracts meaningful representations from unlabeled data, reducing reliance on labeled datasets. Transfer learning enhances the framework's adaptability and scalability, allowing fine-tuning to new datasets without retraining from scratch. Validated on synthetic and open-source semiconductor image datasets, the framework successfully identifies clusters aligned with defect patterns and process variations. This study highlights the transformative potential of combining TDA, self-supervised learning, and transfer learning, providing a scalable solution for proactive process monitoring and quality control in semiconductor manufacturing and other domains with large-scale image datasets.
Comparing mathematical models offers a means to evaluate competing scientific theories. However, exact methods of model calibration are not applicable to many probabilistic models which simulate high-dimensional spatio-temporal data. Approximate Bayesian Computation is a widely-used method for parameter inference and model selection in such scenarios, and it may be combined with Topological Data Analysis to study models which simulate data with fine spatial structure. We develop a flexible pipeline for parameter inference and model selection in spatio-temporal models. Our pipeline identifies topological summary statistics which quantify spatio-temporal data and uses them to approximate parameter and model posterior distributions. We validate our pipeline on models of tumour-induced angiogenesis, inferring four parameters in three established models and identifying the correct model in synthetic test-cases.
Multiplexed imaging allows multiple cell types to be simultaneously visualised in a single tissue sample, generating unprecedented amounts of spatially-resolved, biological data. In topological data analysis, persistent homology provides multiscale descriptors of ``shape" suitable for the analysis of such spatial data. Here we propose a novel visualisation of persistence homology (PH) and fine-tune vectorisations thereof (exploring the effect of different weightings for persistence images, a prominent vectorisation of PH). These approaches offer new biological interpretations and promising avenues for improving the analysis of complex spatial biological data especially in multiple cell type data. To illustrate our methods, we apply them to a lung data set from fatal cases of COVID-19 and a data set from lupus murine spleen.
Nonlinear dynamical systems are complex and typically only simple systems can be analytically studied. In applications, these systems are usually defined with a set of tunable parameters and as the parameters are varied the system response undergoes significant topological changes or bifurcations. In a high dimensional parameter space, it is difficult to determine which direction to vary the system parameters to achieve a desired system response or state. In this paper, we introduce a new approach for optimally navigating a dynamical system parameter space that is rooted in topological data analysis. Specifically we use the differentiability of persistence diagrams to define a topological language for intuitively promoting or deterring different topological features in the state space response of a dynamical system and use gradient descent to optimally move from one point in the parameter space to another. The end result is a path in this space that guides the system to a set of parameters that yield the desired topological features defined by the loss function. We show a number of examples by applying the methods to different dynamical systems and scenarios to demonstrate how to promote different features and how to choose the hyperparameters to achieve different outcomes.
In this paper we evaluate the performance of topological features for generalizable and robust classification of firn image data, with the broader goal of understanding the advantages, pitfalls, and trade-offs in topological featurization. Firn refers to layers of granular snow within glaciers that haven't been compressed into ice. This compactification process imposes distinct topological and geometric structure on firn that varies with depth within the firn column, making topological data analysis (TDA) a natural choice for understanding the connection between depth and structure. We use two classes of topological features, sublevel set features and distance transform features, together with persistence curves, to predict sample depth from microCT images. A range of challenging training-test scenarios reveals that no one choice of method dominates in all categories, and uncoveres a web of trade-offs between accuracy, interpretability, and generalizability.
We investigate predictions of stochastic compartmental models on the severity of disease outbreaks. The models we consider are the Susceptible-Infected-Susceptible (SIS) for bacterial infections, and the Susceptible -Infected-Removed (SIR) for airborne diseases. Stochasticity enters the compartmental models as random fluctuations of the contact rate, to account for uncertainties in the disease spread. We consider three types of noise to model the random fluctuations: the Gaussian white and Ornstein-Uhlenbeck noises, and the logarithmic Ornstein-Uhlenbeck (logOU). The advantages of logOU noise are its positivity and its ability to model the presence of superspreaders. We utilize homological bifurcation plots from Topological Data Analysis to automatically determine the shape of the long-time distributions of the number of infected for the SIS, and removed for the SIR model, over a range of basic reproduction numbers and relative noise intensities. LogOU noise results in distributions that stay close to the endemic deterministic equilibrium even for high noise intensities. For low reproduction rates and increasing intensity, the distribution peak shifts towards zero, that is, disease eradication, for all three noises; for logOU noise the shift is the slowest. Our study underlines the sensitivity of model predictions to the type of noise considered in contact rate.
We introduce a very general approach to the analysis of signals from their noisy measurements from the perspective of Topological Data Analysis (TDA). While TDA has emerged as a powerful analytical tool for data with pronounced topological structures, here we demonstrate its applicability for general problems of signal processing, without any a-priori geometric feature. Our methods are well-suited to a wide array of time-dependent signals in different scientific domains, with acoustic signals being a particularly important application. We invoke time-frequency representations of such signals, focusing on their zeros which are gaining salience as a signal processing tool in view of their stability properties. Leveraging state-of-the-art topological concepts, such as stable and minimal volumes, we develop a complete suite of TDA-based methods to explore the delicate stochastic geometry of these zeros, capturing signals based on the disruption they cause to this rigid, hyperuniform spatial structure. Unlike classical spatial data tools, TDA is able to capture the full spectrum of the stochastic geometry of the zeros, thereby leading to powerful inferential outcomes that are underpinned by a principled statistical foundation. This is reflected in the power and versatility of our applications, which include competitive performance in processing. a wide variety of audio signals (esp. in low SNR regimes), effective detection and reconstruction of gravitational wave signals (a reputed signal processing challenge with non-Gaussian noise), and medical time series data from EEGs, indicating a wide horizon for the approach and methods introduced in this paper.