Application Of Topological Data Analysis Research Articles

Enhancing the Vietoris–Rips simplicial complex for topological data analysis: applications in cancer gene expression datasets

AbstractThe aim of this study is to enhance the extraction of informative features from complex data through the application of topological data analysis (TDA) using novel topological overlapping measures. Topological data analysis has emerged as a promising methodology for extracting meaningful insights from complex datasets. Existing approaches in TDA often involve extrapolating data points using distance correlation measures, which subsequently constrain downstream predictive tasks. Our objective is to improve the construction of the Vietoris–Rips simplicial complex by introducing topological overlapping measures. These measures take into account the interplay of direct connection strengths and shared neighbours, leading to the identification of persistent topological features. We propose the utilisation of topological overlapping measures to optimise the construction of the Vietoris–Rips simplicial complex, offering a more refined representation of complex data structures. The application of topological overlapping measures results in the identification of plentiful persistent topological features. This enhancement contributes to an improvement of up to 20% in cancer phenotype prediction across different cancer types. Our study demonstrates the effectiveness of utilising topological overlapping measures in optimising the construction of the Vietoris–Rips simplicial complex. The identified persistent topological features significantly enhance the predictive accuracy of cancer phenotypes. This novel approach has the potential to advance the field of topological data analysis and improve our understanding of complex data structures, particularly in the context of cancer research and predictive modelling. Further exploration and application of these measures may yield valuable insights in various domains dealing with intricate datasets.

Geometric and topological characterization of the cytoarchitecture of islets of Langerhans.

The islets of Langerhans are critical endocrine micro-organs that secrete hormones regulating energy metabolism in animals. Insulin and glucagon, secreted by beta and alpha cells, respectively, are responsible for metabolic switching between fat and glucose utilization. Dysfunction in their secretion and/or counter-regulatory influence leads to diabetes. Debate in the field centers on the cytoarchitecture of islets, as the signaling that governs hormonal secretion depends on structural and functional factors, including electrical connectivity, innervation, vascularization, and physical proximity. Much effort has therefore been devoted to elucidating which architectural features are significant for function and how derangements in these features are correlated or causative for dysfunction, especially using quantitative network science or graph theory characterizations. Here, we ask if there are non-local features in islet cytoarchitecture, going beyond standard network statistics, that are relevant to islet function. An example is ring structures, or cycles, of α and δ cells surrounding β cell clusters or the opposite, β cells surrounding α and δ cells. These could appear in two-dimensional islet section images if a sphere consisting of one cell type surrounds a cluster of another cell type. To address these issues, we developed two independent computational approaches, geometric and topological, for such characterizations. For the latter, we introduce an application of topological data analysis to determine locations of topological features that are biologically significant. We show that both approaches, applied to a large collection of islet sections, are in complete agreement in the context both of developmental and diabetes-related changes in islet characteristics. The topological approach can be applied to three-dimensional imaging data for islets as well.

An application of topological data analysis in predicting sumoylation sites.

Sumoylation is a reversible post-translational modification that regulates certain significant biochemical functions in proteins. The protein alterations caused by sumoylation are associated with the incidence of some human diseases. Therefore, identifying the sites of sumoylation in proteins may provide a direction for mechanistic research and drug development. Here, we propose a new computational approach for identifying sumoylation sites using an encoding method based on topological data analysis. The features of our model captured the key physical and biological properties of proteins at multiple scales. In a 10-fold cross validation, the outcomes of our model showed 96.45% of sensitivity (Sn), 94.65% of accuracy (Acc), 0.8946 of Matthew's correlation coefficient (MCC), and 0.99 of area under curve (AUC). The proposed predictor with only topological features achieves the best MCC and AUC in comparison to the other released methods. Our results suggest that topological information is an additional parameter that can assist in the prediction of sumoylation sites and provide a novel perspective for further research in protein sumoylation.

Big data to support geoscience recruitment: Novel adoption of topological data analysis in geoscience education

As the need for a well-trained science, technology, engineering, and mathematics (STEM) workforce continuously grows, the need for science majors—including geoscience majors—is ever increasing. Despite this, low numbers of majors across geoscience programs continue to persist and may be the result of many students not being exposed to geoscience concepts early in their education or having misconceptions about who is able to participate in geoscience and what these careers may look like. The application of topological data analysis (TDA), an algorithm that allows researchers to explore multidimensional data with more nuance than traditional clustering methods, represents a new tool for quantitative investigation within geoscience education. The results of TDA from a large-n survey of students in introductory geoscience classes about their perceptions of geoscience and likelihood of pursuing geoscience careers provides insight into students, including those traditionally underrepresented in geoscience, who could be recruited into the discipline. Insights into this novel application of data science methodology to educational research are provided alongside recruitment recommendations for students traditionally underrepresented in the geosciences.

Applications of Topological Data Analysis in Economics

Applications of Topological Data Analysis in Economics

Application of topological data analysis to flood disaster management in Nigeria

The importance of this research to the literature lies in the ability to develop a hybrid method of Topological Data Analysis and Unsupervised Machine Learning (TDA-uML) for flood detection. The working method in TDA-uML entails collection and loading of datasets, feature representation, data preprocessing (i.e., training, testing, computation, and validation), and data classification. Three properties make TDA distinct from traditional methods: coordinate-invariance, deformative-invariance, and compressed-representative. Formerly utilized hydrologic, hydraulic, and statistical models for flood control were frequently erroneous in their forecasts, lacked the use of hybrid models, and were not validated. The main research objective is to develop a hybrid method for predicting floods. The motivation is to fill research gaps by using TDA-uML methods for persistent homology (PH) and synthetic k-means clustering. The results will be used to compare and categorize the features that are produced. Seven states were selected based on Nigeria’s flood history and affected population. The 7 states are located within the 8 hydrological areas of Nigeria. The efficiency of the resultant validity was 91%. The findings contributed to the development of a model for flood prediction and management; topological features were extracted from the data to predict and categorize the risk.

Topological Data Analysis Helps to Improve Accuracy of Deep Learning Models for Fake News Detection Trained on Very Small Training Sets

Topological data analysis has recently found applications in various areas of science, such as computer vision and understanding of protein folding. However, applications of topological data analysis to natural language processing remain under-researched. This study applies topological data analysis to a particular natural language processing task: fake news detection. We have found that deep learning models are more accurate in this task than topological data analysis. However, assembling a deep learning model with topological data analysis significantly improves the model’s accuracy if the available training set is very small.

Applying topological data analysis to local search problems

<p style='text-indent:20px;'>We present an application of topological data analysis (TDA) to discrete optimization problems, which we show can improve the performance of the 2-opt local search method for the traveling salesman problem by simply applying standard Vietoris-Rips construction to a data set of trials. We then construct a simplicial complex which is specialized for this sort of simulated data set, determined by a stochastic matrix with a steady state vector <inline-formula><tex-math id="M1">\begin{document}$ (P,\pi) $\end{document}</tex-math></inline-formula>. When <inline-formula><tex-math id="M2">\begin{document}$ P $\end{document}</tex-math></inline-formula> is induced from a random walk on a finite metric space, this complex exhibits similarities with standard constructions such as Vietoris-Rips on the data set, but is not sensitive to outliers, as sparsity is a natural feature of the construction. We interpret the persistent homology groups in several examples coming from random walks and discrete optimization, and illustrate how higher dimensional Betti numbers can be used to classify connected components, i.e. zero dimensional features in higher dimensions.</p>

Pore Characterization of Organic-Rich Shales through Application of Topological Data Analysis and Persistent Homology

This paper discusses pore characterization of organic-rich shales using 3D high-resolution imaging and a topological data analysis (TDA) framework. In particular, our focus is on persistent homolog...

Erratum: Spatial applications of topological data analysis: Cities, snowflakes, random structures, and spiders spinning under the influence [Phys. Rev. Research 2 , 033426 (2020)]

Received 23 April 2021DOI:https://doi.org/10.1103/PhysRevResearch.3.029003Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.Published by the American Physical SocietyPhysics Subject Headings (PhySH)Research AreasNetwork structurePatterns in complex systemsPhysical SystemsReal world networksRoad networksStochastic networksWatts-Strogatz networkTechniquesSpreading modelsInterdisciplinary PhysicsNetworks

Applications of Topological Data Analysis in Oncology.

The emergence of the information age in the last few decades brought with it an explosion of biomedical data. But with great power comes great responsibility: there is now a pressing need for new data analysis algorithms to be developed to make sense of the data and transform this information into knowledge which can be directly translated into the clinic. Topological data analysis (TDA) provides a promising path forward: using tools from the mathematical field of algebraic topology, TDA provides a framework to extract insights into the often high-dimensional, incomplete, and noisy nature of biomedical data. Nowhere is this more evident than in the field of oncology, where patient-specific data is routinely presented to clinicians in a variety of forms, from imaging to single cell genomic sequencing. In this review, we focus on applications involving persistent homology, one of the main tools of TDA. We describe some recent successes of TDA in oncology, specifically in predicting treatment responses and prognosis, tumor segmentation and computer-aided diagnosis, disease classification, and cellular architecture determination. We also provide suggestions on avenues for future research including utilizing TDA to analyze cancer time-series data such as gene expression changes during pathogenesis, investigation of the relation between angiogenic vessel structure and treatment efficacy from imaging data, and experimental confirmation that geometric and topological connectivity implies functional connectivity in the context of cancer.

On the Application of Topological Data Analysis and Machine Learning to Flood Incidents, and Decision Making

On the Application of Topological Data Analysis and Machine Learning to Flood Incidents, and Decision Making

Warning Ahead of Market Crashes: The Application of Topological Data Analysis

Warning Ahead of Market Crashes: The Application of Topological Data Analysis

The Application of Topological Data Analysis in Practice and Its Effectiveness

Topological Data Analysis(TDA) is a new and fast growing field in data science. TDA provides an approach to analyze data sets and derive their relevant feature out of complex high-dimensional data, which greatly improves the working efficiency in many fields. In this paper, the author mainly discusses some mathematics concepts about topology, methods in TDA and the relation between these topological concepts and data sets (how to apply topological concepts on data). The problems of TDA, mathematical algorithm using in TDA and two application-examples are introduced in this paper. In addition, the advantages, limitations, and the direction of future development of TDA are discussed.

Spatial applications of topological data analysis: Cities, snowflakes, random structures, and spiders spinning under the influence

Spatial networks are ubiquitous in social, geographical, physical, and biological applications. To understand the large-scale structure of networks, it is important to develop methods that allow one to directly probe the effects of space on structure and dynamics. Historically, algebraic topology has provided one framework for rigorously and quantitatively describing the global structure of a space, and recent advances in topological data analysis (TDA) have given scholars a new lens for analyzing network data. In this paper, we study a variety of spatial networks -- including both synthetic and natural ones -- using novel topological methods that we recently developed for analyzing spatial networks. We demonstrate that our methods are able to capture meaningful quantities, with specifics that depend on context, in spatial networks and thereby provide useful insights into the structure of those networks, including a novel approach for characterizing them based on their topological structures. We illustrate these ideas with examples of synthetic networks and dynamics on them, street networks in cities, snowflakes, and webs spun by spiders under the influence of various psychotropic substances.

Forman-Ricci curvature and persistent homology of unweighted complex networks

We present the application of topological data analysis (TDA) to study unweighted complex networks via their persistent homology. By endowing appropriate weights that capture the inherent topological characteristics of such a network, we convert an unweighted network into a weighted one. Standard TDA tools are then used to compute their persistent homology. To this end, we use two main quantifiers: a local measure based on Forman's discretized version of Ricci curvature, and a global measure based on edge betweenness centrality. We have employed these methods to study various model and real-world networks. Our results show that persistent homology can be used to distinguish between model and real networks with different topological properties.

Simplicial degree in complex networks. Applications of topological data analysis to network science

Network Science provides a universal formalism for modelling and studying complex systems based on pairwise interactions between agents. However, many real networks in the social, biological or computer sciences involve interactions among more than two agents, having thus an inherent structure of a simplicial complex. We propose new notions of higher-order degrees of adjacency for simplices in a simplicial complex, allowing any dimensional comparison among them and their faces, which as far as we know were lacked in the literature. We introduce multi-parameter boundary and coboundary operators in an oriented simplicial complex and also a novel multi-combinatorial Laplacian is defined, which generalises the graph and combinatorial Laplacian. To illustrate the potential applications of these theoretical results, we perform a structural analysis of higher-order connectivity in simplicial-complex networks by studying the associated distributions with these simplicial degrees in 17 real-world datasets coming from different domains such as coauthor networks, cosponsoring Congress bills, contacts in schools, drug abuse warning networks, e-mail networks or publications and users in online forums. We find rich and diverse higher-order connectivity structures and observe that datasets of the same type reflect similar higher-order collaboration patterns. Furthermore, we show that if we use what we have called the maximal simplicial degree (which counts the distinct maximal communities in which our simplex and all its strict sub-communities are contained), then its degree distribution is, in general, surprisingly different from the classical node degree distribution.

Centrality measures in simplicial complexes: Applications of topological data analysis to network science

Abstract Many real networks in social sciences, biological and biomedical sciences or computer science have an inherent structure of simplicial complexes reflecting many-body interactions. Therefore, to analyse topological and dynamical properties of simplicial complex networks centrality measures for simplices need to be proposed. Many of the classical complex networks centralities are based on the degree of a node, so in order to define degree centrality measures for simplices (which would characterise the relevance of a simplicial community in a simplicial network), a different definition of adjacency between simplices is required, since, contrarily to what happens in the vertex case (where there is only upper adjacency), simplices might also have other types of adjacency. The aim of these notes is threefold: first we will use the recently introduced notions of higher order simplicial degrees to propose new degree based centrality measures in simplicial complexes. These theoretical centrality measures, such as the simplicial degree centrality or the eigenvector centrality would allow not only to study the relevance of a simplicial community and the quality of its higher-order connections in a simplicial network, but also they might help to elucidate topological and dynamical properties of simplicial networks; sencond, we define notions of walks and distances in simplicial complexes in order to study connectivity of simplicial networks and to generalise, to the simplicial case, the well known closeness and betweenness centralities (needed for instance to study the relevance of a simplicial community in terms of its ability of transmitting information); third, we propose a new clustering coefficient for simplices in a simplicial network, different from the one knows so far and which generalises the standard graph clustering of a vertex. This measure should be essential to know the density of a simplicial network in terms of its simplicial communities.

The shape of things to come: Topological data analysis and biology, from molecules to organisms.

Shape is data and data is shape. Biologists are accustomed to thinking about how the shape of biomolecules, cells, tissues, and organisms arise from the effects of genetics, development, and the environment. Less often do we consider that data itself has shape and structure, or that it is possible to measure the shape of data and analyze it. Here, we review applications of topological data analysis (TDA) to biology in a way accessible to biologists and applied mathematicians alike. TDA uses principles from algebraic topology to comprehensively measure shape in data sets. Using a function that relates the similarity of data points to each other, we can monitor the evolution of topological features—connected components, loops, and voids. This evolution, a topological signature, concisely summarizes large, complex data sets. We first provide a TDA primer for biologists before exploring the use of TDA across biological sub‐disciplines, spanning structural biology, molecular biology, evolution, and development. We end by comparing and contrasting different TDA approaches and the potential for their use in biology. The vision of TDA, that data are shape and shape is data, will be relevant as biology transitions into a data‐driven era where the meaningful interpretation of large data sets is a limiting factor.

Topological data analysis in investment decisions

This article explores the applications of Topological Data Analysis (TDA) in the finance field, especially addressing the primordial problem of asset allocation. Firstly, we build a rationale on why TDA can be a better alternative to traditional risk indicators such as standard deviation using real data sets. We apply Takens embedding theorem to reconstruct the time series of returns in a high dimensional space. We adopt the sliding window approach to draw the time-dependent point cloud data sets and associate a topological space with them. We then apply the persistent homology to discover the topological patterns that appear in the multidimensional time series. The temporal changes in the persistence landscapes, which are the real-valued functions that encode the persistence of topological patterns, are captured via Lp norm. The time series of the Lp norms shows that it is better at measuring the dynamics of returns than the standard deviation.Inspired by our findings, we explore an application of TDA in Enhanced Indexing (EI) that aims to build a portfolio of fewer assets than that in the index to outperform the latter. We propose a two-step procedure to accomplish this task. In step one, we utilize the Lp norms of the assets to propose a filtration technique of selecting a few assets from a larger pool of assets. In step two, we propose an optimization model to construct an optimal portfolio from the class of filtered assets for EI. To test the efficiency of this enhanced algorithm, experiments are carried out on ten data sets from financial markets across the globe. Our extensive empirical analysis exhibits that the proposed strategy delivers superior performance on several measures, including excess mean returns from the benchmark index and tail reward-risk ratios than some of the existing models of EI in the literature. The proposed filtering strategy is also noted to be beneficial for both risk-seeking and risk-averse investors.