Topological data analysis of continuum percolation with disks

Homology groups of embedded fractional Brownian motion

A well-known class of nonstationary self-similar time series is the fractional Brownian motion (fBm) considered to model ubiquitous stochastic processes in nature. Due to noise and trends superimposed on data and even sample size and irregularity impacts, the well-known computational algorithm to compute the Hurst exponent (H) has encountered superior results. Motivated by this discrepancy, we examine the homology groups of high-dimensional point cloud data (PCD), a subset of the unit D-dimensional cube, constructed from synthetic fBm data as a pipeline to compute the H exponent. We compute topological measures for embedded PCD as a function of the associated Hurst exponent for different embedding dimensions, time delays, and amount of irregularity existing in the dataset in various scales. Our results show that for a regular synthetic fBm, the higher value of the embedding dimension leads to increasing the H dependency of topological measures based on zeroth and first homology groups. To achieve a reliable classification of fBm, we should consider the small value of time delay irrespective of the irregularity presented in the data. More interestingly, the value of the scale for which the PCD to be path connected and the postloopless regime scale are more robust concerning irregularity for distinguishing the fBm signal. Such robustness becomes less for the higher value of the embedding dimension. Finally, the associated Hurst exponents for our topological feature vector for the S&P500 were computed, and the results are consistent with the detrended fluctuation analysis method.

A hands-on tutorial on network and topological neuroscience

The brain is an extraordinarily complex system that facilitates the optimal integration of information from different regions to execute its functions. With the recent advances in technology, researchers can now collect enormous amounts of data from the brain using neuroimaging at different scales and from numerous modalities. With that comes the need for sophisticated tools for analysis. The field of network neuroscience has been trying to tackle these challenges, and graph theory has been one of its essential branches through the investigation of brain networks. Recently, topological data analysis has gained more attention as an alternative framework by providing a set of metrics that go beyond pairwise connections and offer improved robustness against noise. In this hands-on tutorial, our goal is to provide the computational tools to explore neuroimaging data using these frameworks and to facilitate their accessibility, data visualisation, and comprehension for newcomers to the field. We will start by giving a concise (and by no means complete) overview of the field to introduce the two frameworks and then explain how to compute both well-established and newer metrics on resting-state functional magnetic resonance imaging. We use an open-source language (Python) and provide an accompanying publicly available Jupyter Notebook that uses the 1000 Functional Connectomes Project dataset. Moreover, we would like to highlight one part of our notebook dedicated to the realistic visualisation of high order interactions in brain networks. This pipeline provides three-dimensional (3-D) plots of pairwise and higher-order interactions projected in a brain atlas, a new feature tailor-made for network neuroscience.

Quantitative analysis of phase transitions in two-dimensional XY models using persistent homology

We use persistent homology and persistence images as an observable of three variants of the two-dimensional XY model to identify and study their phase transitions. We examine models with the classical XY action, a topological lattice action, and an action with an additional nematic term. In particular, we introduce a way of computing the persistent homology of lattice spin model configurations and, by considering the fluctuations in the output of logistic regression and k-nearest neighbor models trained on persistence images, we develop a methodology to extract estimates of the critical temperature and the critical exponent of the correlation length. We put particular emphasis on finite-size scaling behavior and producing estimates with quantifiable error. For each model we successfully identify its phase transition(s) and are able to get an accurate determination of the critical temperatures and critical exponents of the correlation length.

Persistent homology of fractional Gaussian noise

In this paper, we employ the persistent homology (PH) technique to examine the topological properties of fractional Gaussian noise (fGn). We develop the weighted natural visibility graph algorithm, and the associated simplicial complexes through the filtration process are quantified by PH. The evolution of the homology group dimension represented by Betti numbers demonstrates a strong dependency on the Hurst exponent (H). The coefficients of the birth and death curves of the k-dimensional topological holes (k-holes) at a given threshold depend on H which is almost not affected by finite sample size. We show that the distribution function of a lifetime for k-holes decays exponentially and the corresponding slope is an increasing function versus H and, more interestingly, the sample size effect completely disappears in this quantity. The persistence entropy logarithmically grows with the size of the visibility graph of a system with almost H-dependent prefactors. On the contrary, the local statistical features are not able to determine the corresponding Hurst exponent of fGn data, while the moments of eigenvalue distribution (M_{n}) for n≥1 reveal a dependency on H, containing the sample size effect. Finally, the PH shows the correlated behavior of electroencephalography for both healthy and schizophrenic samples.

Noise-driven topological changes in chaotic dynamics

Noise modifies the behavior of chaotic systems in both quantitative and qualitative ways. To study these modifications, the present work compares the topological structure of the deterministic Lorenz (1963) attractor with its stochastically perturbed version. The deterministic attractor is well known to be "strange" but it is frozen in time. When driven by multiplicative noise, the Lorenz model's random attractor (LORA) evolves in time. Algebraic topology sheds light on the most striking effects involved in such an evolution. In order to examine the topological structure of the snapshots that approximate LORA, we use branched manifold analysis through homologies-a technique originally introduced to characterize the topological structure of deterministically chaotic flows-which is being extended herein to nonlinear noise-driven systems. The analysis is performed for a fixed realization of the driving noise at different time instants in time. The results suggest that LORA's evolution includes sharp transitions that appear as topological tipping points.

Topological persistence machine of phase transitions

The study of phase transitions using data-driven approaches is challenging, especially when little prior knowledge of the system is available. Topological data analysis is an emerging framework for characterizing the shape of data and has recently achieved success in detecting structural transitions in material science, such as the glass-liquid transition. However, data obtained from physical states may not have explicit shapes as structural materials. We thus propose a general framework, termed "topological persistence machine," to construct the shape of data from correlations in states, so that we can subsequently decipher phase transitions via qualitative changes in the shape. Our framework enables an effective and unified approach in phase transition analysis. We demonstrate the efficacy of the approach in detecting the Berezinskii-Kosterlitz-Thouless phase transition in the classical XY model and quantum phase transitions in the transverse Ising and Bose-Hubbard models. Interestingly, while these phase transitions have proven to be notoriously difficult to analyze using traditional methods, they can be characterized through our framework without requiring prior knowledge of the phases. Our approach is thus expected to be widely applicable and will provide practical insights for exploring the phases of experimental physical systems.

Topological data analysis of collective and individual epithelial cells using persistent homology of loops

Interacting, self-propelled particles such as epithelial cells can dynamically self-organize into complex multicellular patterns, which are challenging to classify without a priori information. Classically, different phases and phase transitions have been described based on local ordering, which may not capture structural features at larger length scales. Instead, topological data analysis (TDA) determines the stability of spatial connectivity at varying length scales (i.e. persistent homology), and can compare different particle configurations based on the "cost" of reorganizing one configuration into another. Here, we demonstrate a topology-based machine learning approach for unsupervised profiling of individual and collective phases based on large-scale loops. We show that these topological loops (i.e. dimension 1 homology) are robust to variations in particle number and density, particularly in comparison to connected components (i.e. dimension 0 homology). We use TDA to map out phase diagrams for simulated particles with varying adhesion and propulsion, at constant population size as well as when proliferation is permitted. Next, we use this approach to profile our recent experiments on the clustering of epithelial cells in varying growth factor conditions, which are compared to our simulations. Finally, we characterize the robustness of this approach at varying length scales, with sparse sampling, and over time. Overall, we envision TDA will be broadly applicable as a model-agnostic approach to analyze active systems with varying population size, from cytoskeletal motors to motile cells to flocking or swarming animals.

Consensus on simplicial complexes: Results on stability and synchronization

We consider a nonlinear flow on simplicial complexes related to the simplicial Laplacian and show that it is a generalization of various consensus and synchronization models commonly studied on networks. In particular, our model allows us to formulate flows on simplices of any dimension so that it includes edge flows, triangle flows, etc. We show that the system can be represented as the gradient flow of an energy functional and use this to deduce the stability of various steady states of the model. Finally, we demonstrate that our model contains higher-dimensional analogs of structures seen in related network models.

Homological percolation and the Euler characteristic

In this paper we study the connection between the zeros of the expected Euler characteristic curve and the phenomenon which we refer to as homological percolation-the formation of "giant" cycles in persistent homology, which is intimately related to classical notions of percolation. We perform an experimental study that covers four different models: site percolation on the cubical and permutahedral lattices, the Poisson-Boolean model, and Gaussian random fields. All the models are generated on the flat torus T^{d} for d=2,3,4. The simulation results strongly indicate that the zeros of the expected Euler characteristic curve approximate the critical values for homological percolation. Our results also provide some insight about the approximation error. Further study of this connection could have powerful implications both in the study of percolation theory and in the field of topological data analysis.

Effect of volume growth on the percolation threshold in random directed acyclic graphs with a given degree distribution

In every network, a distance between a pair of nodes can be defined as the length of the shortest path connecting these nodes, and therefore one may speak of a ball, its volume, and how it grows as a function of the radius. Spatial networks tend to feature peculiar volume scaling functions, as well as other topological features, including clustering, degree-degree correlation, clique complexes, and heterogeneity. Here we investigate a nongeometric random graph with a given degree distribution and an additional constraint on the volume scaling function. We show that such structures fall into the category of m-colored random graphs and study the percolation transition by using this theory. We prove that for a given degree distribution the percolation threshold for weakly connected components is not affected by the volume growth function. Additionally, we show that the size of the giant component and the cyclomatic number are not affected by volume scaling. These findings may explain the surprisingly good performance of network models that neglect volume scaling. Even though this paper focuses on the implications of the volume growth, the model is generic and might lead to insights in the field of random directed acyclic graphs and their applications.

Topological phase transitions in functional brain networks

Functional brain networks are often constructed by quantifying correlations between time series of activity of brain regions. Their topological structure includes nodes, edges, triangles, and even higher-dimensional objects. Topological data analysis (TDA) is the emerging framework to process data sets under this perspective. In parallel, topology has proven essential for understanding fundamental questions in physics. Here we report the discovery of topological phase transitions in functional brain networks by merging concepts from TDA, topology, geometry, physics, and network theory. We show that topological phase transitions occur when the Euler entropy has a singularity, which remarkably coincides with the emergence of multidimensional topological holes in the brain network. The geometric nature of the transitions can be interpreted, under certain hypotheses, as an extension of percolation to high-dimensional objects. Due to the universal character of phase transitions and noise robustness of TDA, our findings open perspectives toward establishing reliable topological and geometrical markers for group and possibly individual differences in functional brain network organization.