Distributed Computation of Persistent Homology from Partitioned Big Data

The use of laser scanning techniques has become a common way to measure the real world. Millions of points could be generated by this system, which brings forth the problem of visualizing and eventually performing analyses on them. In the open source domain, various software packages exist to visualize 3D point clouds. However, most of these software packages do not allow the real-time rendering of large point clouds. Few of them also allow visualization in an immersive manner. The research aims to create an open source viewer for large 3D point clouds, which enables a dynamic and immersive visualization. In order to do so, rendering and point cloud management strategies must be implemented to avoid overloading the computer’s memory. The rendering is done using OpenGL engine by utilizing the graphic card’s memory in order to perform faster visualization. The program consists of a pre-processing stage in which the point cloud files are divided into quadtrees and then subsampled using the random tree sampling method. The visualization itself will calculate the distance between the point of view and the center of nodes generated by the pre-processing stage. The amount of points rendered within each node will depend on this distance; the farther away the node is from the point of view, the fewer points are rendered. A loading and unloading function enables the point cloud to be rendered dynamically. With the point cloud management algorithm implemented, the resulting program is able to load large point clouds generated by a mobile laser scanner using an ordinary computer. The resulting program as well as the source code will be available for the public due to its open source nature.

In this paper we develop an alternative topological data analysis (TDA) approach for studying graph representations of time series of dynamical systems. Specifically, we show how persistent homology, a tool from TDA, can be used to yield a compressed, multi-scale representation of the graph that can distinguish between dynamic states such as periodic and chaotic behavior. We show the approach for two graph constructions obtained from the time series. In the first approach the time series is embedded into a point cloud which is then used to construct an undirected k-nearest-neighbor graph. The second construct relies on the recently developed ordinal partition framework. In either case, a pairwise distance matrix is then calculated using the shortest path between the graph's nodes, and this matrix is utilized to define a filtration of a simplicial complex that enables tracking the changes in homology classes over the course of the filtration. These changes are summarized in a persistence diagram's two-dimensional summary of changes in the topological features. We then extract existing as well as new geometric and entropy point summaries from the persistence diagram and compare to other commonly used network characteristics. Our results show that persistence-based point summaries yield a clearer distinction of the dynamic behavior and are more robust to noise than existing graph-based scores, especially when combined with ordinal graphs.

We present TransLPC, a novel detection model for large point clouds that is based on a transformer architecture. While object detection with transformers has been an active field of research, it has proved difficult to apply such models to point clouds that span a large area, e.g. those that are common in autonomous driving, with lidar or radar data. TransLPC is able to remedy these issues: The structure of the transformer model is modified to allow for larger input sequence lengths, which are sufficient for large point clouds. Besides this, we propose a novel query refinement technique to improve detection accuracy, while retaining a memory-friendly number of transformer decoder queries. The queries are repositioned between layers, moving them closer to the bounding box they are estimating, in an efficient manner. This simple technique has a significant effect on detection accuracy, which is evaluated on the challenging nuScenes dataset on real-world lidar data. Besides this, the proposed method is compatible with existing transformer-based solutions that require object detection, e.g. for joint multi-object tracking and detection, and enables them to be used in conjunction with large point clouds.

• A novel foundation for topological pattern recognition of point cloud data, through persistent homology of graph approximations. • An extension of persistent homology to point cloud data of metric trees, including theoretical and experimental verification. • The first charting of cell trajectory data sets that explains some of the difficulties this field is confronted with. The rising field of Topological Data Analysis (TDA) provides a new approach to learning from data through persistence diagrams , which are topological signatures that quantify topological properties of data in a comparable manner. For point clouds, these diagrams are often derived from the Vietoris-Rips filtration—based on the metric equipped on the data—which allows one to deduce topological patterns such as components and cycles of the underlying space. In metric trees these diagrams often fail to capture other crucial topological properties, such as the present leaves and multifurcations. Prior methods and results for persistent homology attempting to overcome this issue mainly target Rips graphs, which are often unfavorable in case of non-uniform density across our point cloud. We therefore introduce a new theoretical foundation for learning a wider variety of topological patterns through any given graph . Given particular powerful functions defining persistence diagrams to summarize topological patterns, including the normalized centrality or eccentricity , we prove a new stability result, explicitly bounding the bottleneck distance between the true and empirical diagrams for metric trees. This bound is tight if the metric distortion obtained through the graph and its maximal edge-weight are small. Through a case study of gene expression data, we demonstrate that our newly introduced diagrams provide novel quality measures and insights into cell trajectory inference.

This chapter describes a new approach for studying the stability of stochastic delay equations by investigating their time series using topological data analysis (TDA). The approach is illustrated utilizing two stochastic delay equations. The first model equation is the stochastic version of Hayes equation—a scalar autonomous delay equation—where the noise is an additive term. The second model equation is the stochastic version of Mathieu’s equation—a time-periodic delay equation. In the latter, noise is added via a multiplicative term in the time-periodic coefficient. The time series is generated using Euler–Maruyama method and a corresponding point cloud is obtained using the Takens’ embedding. The point cloud is then analyzed using a tool from TDA known as persistent homology. The results of this study show that the described approach can be used for analyzing datasets of delay dynamical systems that are described using constant as well as time-periodic coefficients. The presented approach can be used for signals generated from both numerical simulation and experiments. It can be used as a tool to study the stability of stochastic delay equations for which there are currently a limited number of analysis tools.

Extracting roads from dense point clouds in large scale urban environment

Cytometry experiments yield high-dimensional point cloud data that is difficult to interpret manually. Boolean gating techniques coupled with comparisons of relative abundances of cellular subsets is the current standard for cytometry data analysis. However, this approach is unable to capture more subtle topological features hidden in data, especially if those features are further masked by data transforms or significant batch effects or donor-to-donor variations in clinical data. We present that persistent homology, a mathematical structure that summarizes the topological features, can distinguish different sources of data, such as from groups of healthy donors or patients, effectively. Analysis of publicly available cytometry data describing non-naïve CD8+ T cells in COVID-19 patients and healthy controls shows that systematic structural differences exist between single cell protein expressions in COVID-19 patients and healthy controls. We identify proteins of interest by a decision-tree based classifier, sample points randomly and compute persistence diagrams from these sampled points. The resulting persistence diagrams identify regions in cytometry datasets of varying density and identify protruded structures such as ‘elbows’. We compute Wasserstein distances between these persistence diagrams for random pairs of healthy controls and COVID-19 patients and find that systematic structural differences exist between COVID-19 patients and healthy controls in the expression data for T-bet, Eomes, and Ki-67. Further analysis shows that expression of T-bet and Eomes are significantly downregulated in COVID-19 patient non-naïve CD8+ T cells compared to healthy controls. This counter-intuitive finding may indicate that canonical effector CD8+ T cells are less prevalent in COVID-19 patients than healthy controls. This method is applicable to any cytometry dataset for discovering novel insights through topological data analysis which may be difficult to ascertain otherwise with a standard gating strategy or existing bioinformatic tools.

Topological Data Analysis (TDA) is used to extract topological features such as rings from point clouds. Recent works have identified that existing methods, which construct persistence diagrams in TDA, are not robust to noise and varied densities in a point cloud. This causes these methods to obtain incorrect topological features. We analyze the necessary properties of an approach that can address these two issues, and propose a new filter function for TDA based on a new data-dependent kernel that possesses these properties. Our empirical evaluation reveals that (i) the proposed kernel provides a better mean for UMAP dimensionality reduction (ii) the proposed filter function can significantly improve the performance of Topological Point Cloud Clustering (iii) the proposed filter function is a more effective way of constructing Persistence Diagram for t-SNE visualization and SVM classification than three existing methods of TDA, In addition, we explore the proposed filter’s performance on a more complex deformation named Riemannian stretching. Our proposed filter equipped with Sample Fermat distance outperforms all the other filters when noise and Riemannian stretching coexist. Code is available at https://github.com/IsolationKernel/Codes/tree/main/Lambda-kernel.

In reverse engineering, the point cloud data processing is the key, it will directly affect the quality and efficiency of the subsequent reconstruction of the surface. However, the amount of data obtained by three-dimensional laser scanning is often larger and redundant, which will increase the difficulty of the surface reconstruction, therefore, the point cloud data is needed to streamline. Depth analysis of the efficiency and accuracy of curvature grid method, a secondary streamlined algorithm is proposed, which take use of non-uniform grid streamline law based on octree to streamline to the point cloud, and re-use curvature streamline method based on B-spline surface fitting to streamline it. This method, whose streamline ratio is relatively high, can effectively retain the feature point cloud data, providing a great convenience for the follow-up of reverse engineering.

Topological Data Analysis (TDA) and its mainstay computational device, persistent homology (PH), has established a strong track record of providing researchers across the data-driven sciences with new insights and methodologies by characterizing low-dimensional geometric structures in high-dimensional data. When combined with machine learning (ML) methods, PH is valued as a discriminating-feature extraction tool. This work highlights many of the recent successes at the intersection of TDA and ML, introduces some of the foundational mathematics underpinning TDA, and summarizes the efforts to strengthen the bridge between TDA and ML. Thus, this document is a launching point for experimentalists and theoreticians to consider what can be learned from the shape of their data.

Recently, various applications leveraging topological data analysis, in particular, persistent homology (PH), have been presented in many fields since PH provides a novel point cloud analysis method. In this work, we apply PH to LiDAR-based ego-vehicle localization applications. PH can extract translation and rotation invariant features from a point cloud. These features do not maintain local information of the point cloud, such as the edges and lines; however, they can abstract the global structure of the point cloud. A persistence image (PI) vectorizes the features and allows us to obtain fixed-size vectors despite the sizes of the source point clouds being different. Additionally, the size of the PI is not large even though the source point cloud is extremely big. We consider that these advantages are effective to loop closure detection, place categorization, and end-to-end global localization applications. Results reveal that it is difficult to improve the localization accuracy by simply applying PH owing to the basic concept of the topology that does not focus on exact shapes of the geometry. Therefore, we discuss how the advantages of PH can be utilized for the localization.

Abstract: Neurodegenerative diseases, such as Alzheimer's and Parkinson's, are characterized by progressive neuronal deterioration, leading to cognitive and motor impairments. Early detection is crucial for effective intervention and management. This study proposes a novel framework utilizing Topological Data Analysis (TDA), particularly persistent homology, to identify early biomarkers from neuroimaging and physiological data. This study explores the application of TDA techniques—specifically persistent homology and topological invariants—for the early detection of neurodegenerative diseases such as Alzheimer's. By analyzing functional brain connectivity, gait dynamics, and molecular structures associated with disease progression, the research demonstrates that TDA can capture subtle, yet critical, topological signatures indicative of early neurodegenerative changes. Layer-wise topological complexity in neural networks and persistent homology in clinical datasets reveal distinct structural degradation patterns. The integration of TDA with machine learning models enhances diagnostic accuracy, interpretability, and generalization, offering a promising direction for non-invasive, data-driven diagnostics in neurology.By capturing the intrinsic topological features of brain networks, the framework aims to distinguish between healthy and early-stage neurodegenerative conditions, offering a robust tool for early diagnosis.Topological Data Analysis (TDA) offers a robust mathematical framework for extracting shape-based features from high-dimensional and noisy biomedical data. Keywords: Topological Data Analysis, Persistent Homology, Neurodegenerative Disease, Alzheimer's, Brain Connectivity, Early Diagnosis, Betti Numbers, Gait Analysis, Functional Networks, Machine Learning, Biomedical Data

Single-cell technologies have revolutionized our ability to interrogate biological systems at unprecedented resolution, revealing complex cellular heterogeneity and dynamic processes that underlie development, disease, and immune responses. However, the high dimensionality and nonlinear structure of single-cell data present substantial analytical challenges. Topological data analysis offers a powerful mathematical framework for capturing the intrinsic shape of data, providing novel insights that complement and extend traditional statistical and machine learning methods. By leveraging tools such as persistent homology and the Mapper algorithm, TDA enables the detection of subtle, multiscale patterns – including rare cell populations, transitional states, and branching trajectories – that are often obscured by conventional approaches. In this review, we explore the theoretical foundations of topological data analysis and examine its emerging applications across single-cell transcriptomics, proteomics, and spatial biology. We highlight how this approach can unveil previously unrecognized biological phenomena, from alternative differentiation paths to complex tissue architectures, and discuss the growing ecosystem of computational tools that support its use. As single-cell datasets become increasingly large and multimodal, topological data analysis stands out as a uniquely robust and interpretable approach, with the potential to deepen our understanding of cellular identity and function in health and disease. TDA is specially suited for fields such as systems immunology since it can capture the complex, nonlinear structures inherent in high-dimensional immune data helping to identify distinct immune cell states, differentiation pathways, and dynamic responses to infection or therapy. This topological perspective complements traditional statistical approaches, providing a robust, scale-invariant framework for uncovering hidden organization within the immune system’s complexity.

This paper presents a system that can automatically segment objects in large scale 3D point clouds obtained from urban ranging images. The system consists of three steps: The first one involves a ground detection process that can detect relatively complex terrain and separate it from other objects. The second step superpixelizes the remaining objects to speed up the segmentation process. In the final step, a manifold embedded mode seeking method is adopted to segment the point clouds. Even though the segmentation of urban objects is a challenging problem in terms of accuracy and problem scale, our system can efficiently generate very good segmentation results. The proposed manifold learning effectively improves the segmentation performance due to the fact that continuous artificial objects often have manifold-like structures.

Persistent homology is a powerful tool in topological data analysis (TDA) to compute, study and encode efficiently multi-scale topological features and is being increasingly used in digital image classification. The topological features represent number of connected components, cycles, and voids that describe the shape of data. Persistent homology extracts the birth and death of these topological features through a filtration process. The lifespan of these features can represented using persistent diagrams (topological signatures). Cubical homology is a more efficient method for extracting topological features from a 2D image and uses a collection of cubes to compute the homology, which fits the digital image structure of grids. In this research, we propose a cubical homology-based algorithm for extracting topological features from 2D images to generate their topological signatures. Additionally, we propose a score, which measures the significance of each of the sub-simplices in terms of persistence. Also, gray level co-occurrence matrix (GLCM) and contrast limited adapting histogram equalization (CLAHE) are used as a supplementary method for extracting features. Machine learning techniques are then employed to classify images using the topological signatures. Among the eight tested algorithms with six published image datasets with varying pixel sizes, classes, and distributions, our experiments demonstrate that cubical homology-based machine learning with deep residual network (ResNet 1D) and Light Gradient Boosting Machine (lightGBM) shows promise with the extracted topological features.