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Motivated by the study of the recurrent orbits in a Morse set of a Morse decomposition, we introduce the concept of Morse predecomposition of an isolated invariant set in the setting of combinatorial and classical dynamical systems. We prove that a Morse predecomposition indexed by a poset is a Morse decomposition and we show how a Morse predecomposition may be condensed back to a Morse decomposition., Comment: 29 pages (31 with bibliography), 9 figures

Recurrence is a fundamental characteristic of complicated deterministic dynamical systems. Understanding its structure is challenging, especially if the system of interest has many degrees of freedom so that visualizations of trajectories are of limited use. To analyze recurrent phenomena, we propose a computational method to identify oscillations and the transitions between them. To this end, we introduce the concept of cycling signature, which is a topological descriptor of a trajectory segment. The advantage of a topological approach, in particular in an application setting, is that it is robust to noise. Cycling signatures are computable from data and provide a comprehensive global description of oscillations through their statistics over many trajectory segments. We demonstrate this through three examples. In particular, we identify and analyze six oscillations in a four-dimensional system with a hyperchaotic attractor., Comment: main paper: 11 pages, 7 figures; appendix: 9 pages, 8 figures

Estimating the region of attraction (${\tt RoA}$) for a robot controller is essential for safe application and controller composition. Many existing methods require a closed-form expression that limit applicability to data-driven controllers. Methods that operate only over trajectory rollouts tend to be data-hungry. In prior work, we have demonstrated that topological tools based on ${\it Morse Graphs}$ (directed acyclic graphs that combinatorially represent the underlying nonlinear dynamics) offer data-efficient ${\tt RoA}$ estimation without needing an analytical model. They struggle, however, with high-dimensional systems as they operate over a state-space discretization. This paper presents ${\it Mo}$rse Graph-aided discovery of ${\it R}$egions of ${\it A}$ttraction in a learned ${\it L}$atent ${\it S}$pace (${\tt MORALS}$). The approach combines auto-encoding neural networks with Morse Graphs. ${\tt MORALS}$ shows promising predictive capabilities in estimating attractors and their ${\tt RoA}$s for data-driven controllers operating over high-dimensional systems, including a 67-dim humanoid robot and a 96-dim 3-fingered manipulator. It first projects the dynamics of the controlled system into a learned latent space. Then, it constructs a reduced form of Morse Graphs representing the bistability of the underlying dynamics, i.e., detecting when the controller results in a desired versus an undesired behavior. The evaluation on high-dimensional robotic datasets indicates data efficiency in ${\tt RoA}$ estimation., Comment: The first two authors contributed equally to this paper

In an increasingly changing world, predicting the fate of species across the globe has become a major concern. Understanding how the population dynamics of various species and communities will unfold requires predictive tools that experimental data alone can not capture. Here, we introduce our combinatorial framework, Widespread Ecological Networks and their Dynamical Signatures (WENDyS) which, using data on the relative strengths of interactions and growth rates within a community of species predicts all possible long-term outcomes of the community. To this end, WENDyS partitions the multidimensional parameter space (formed by the strengths of interactions and growth rates) into a finite number of regions, each corresponding to a unique set of coarse population dynamics. Thus, WENDyS ultimately creates a library of all possible outcomes for the community. On the one hand, our framework avoids the typical ``parameter sweeps'' that have become ubiquitous across other forms of mathematical modeling, which can be computationally expensive for ecologically realistic models and examples. On the other hand, WENDyS opens the opportunity for interdisciplinary teams to use standard experimental data (i.e., strengths of interactions and growth rates) to filter down the possible end states of a community. To demonstrate the latter, here we present a case study from the Indonesian Coral Reef. We analyze how different interactions between anemone and anemonefish species lead to alternative stable states for the coral reef community, and how competition can increase the chance of exclusion for one or more species. WENDyS, thus, can be used to anticipate ecological outcomes and test the effectiveness of management (e.g., conservation) strategies., Comment: 25 pages, 9 figures

This paper concerns the computation and identification of the (homological) Conley index over the integers, in the context of discrete dynamical systems generated by continuous maps. We discuss the significance with respect to nonlinear dynamics of using integer, as opposed to field, coefficients. We translate the problem into the language of commutative ring theory. More precisely, we relate shift equivalence in the category of finitely generated abelian groups to the classification of $\mathbb{Z}[t]$-modules whose underlying abelian group is given. We provide tools to handle the classification problem, but also highlight the associated computational challenges.

This paper proposes an integration of surrogate modeling and topology to significantly reduce the amount of data required to describe the underlying global dynamics of robot controllers, including closed-box ones. A Gaussian Process (GP), trained with randomized short trajectories over the state-space, acts as a surrogate model for the underlying dynamical system. Then, a combinatorial representation is built and used to describe the dynamics in the form of a directed acyclic graph, known as {\it Morse graph}. The Morse graph is able to describe the system's attractors and their corresponding regions of attraction (\roa). Furthermore, a pointwise confidence level of the global dynamics estimation over the entire state space is provided. In contrast to alternatives, the framework does not require estimation of Lyapunov functions, alleviating the need for high prediction accuracy of the GP. The framework is suitable for data-driven controllers that do not expose an analytical model as long as Lipschitz-continuity is satisfied. The method is compared against established analytical and recent machine learning alternatives for estimating \roa s, outperforming them in data efficiency without sacrificing accuracy. Link to code: https://go.rutgers.edu/49hy35en

We study a Weiner process that is conditioned to pass through a finite set of points and consider the dynamics generated by iterating a sample path from this process. Using topological techniques we are able to characterize the global dynamics and deduce the existence, structure and approximate location of invariant sets. Most importantly, we compute the probability that this characterization is correct. This work is probabilistic in nature and intended to provide a theoretical foundation for the statistical analysis of dynamical systems which can only be queried via finite samples., Comment: 18 pages, 3 figures

We introduce a novel procedure that, given sparse data generated from a stationary deterministic nonlinear dynamical system, can characterize specific local and/or global dynamic behavior with rigorous probability guarantees. More precisely, the sparse data is used to construct a statistical surrogate model based on a Gaussian process (GP). The dynamics of the surrogate model is interrogated using combinatorial methods and characterized using algebraic topological invariants (Conley index). The GP predictive distribution provides a lower bound on the confidence that these topological invariants, and hence the characterized dynamics, apply to the unknown dynamical system (a sample path of the GP). The focus of this paper is on explaining the ideas, thus we restrict our examples to one-dimensional systems and show how to capture the existence of fixed points, periodic orbits, connecting orbits, bistability, and chaotic dynamics.

In this paper we describe a combined combinatorial/numerical approach to studying equilibria and bifurcations in network models arising in Systems Biology. ODE models of the dynamics suffer from high dimensional parameters which presents a significant obstruction to studying the global dynamics via numerical methods. The main point of this paper is to demonstrate that combining classical techniques with recently developed combinatorial methods provides a richer picture of the global dynamics despite the high parameter dimension. Given a network topology describing state variables which regulate one another via monotone and bounded functions, we first use the Dynamic Signatures Generated by Regulatory Networks (DSGRN) software to obtain a combinatorial summary of the dynamics. This summary is coarse but global and we use this information as a first pass to identify "interesting'' subsets of parameters in which to focus. We construct an associated ODE model with high parameter dimension using our {\em Network Dynamics Modeling and Analysis} (NDMA) Python library. We introduce algorithms for efficiently investigating the dynamics in these ODE models restricted to these parameter subsets. Finally, we perform a statistical validation of the method and several interesting dynamical applications including finding saddle-node bifurcations in a 54 parameter model.

Understanding the global dynamics of a robot controller, such as identifying attractors and their regions of attraction (RoA), is important for safe deployment and synthesizing more effective hybrid controllers. This paper proposes a topological framework to analyze the global dynamics of robot controllers, even data-driven ones, in an effective and explainable way. It builds a combinatorial representation representing the underlying system's state space and non-linear dynamics, which is summarized in a directed acyclic graph, the Morse graph. The approach only probes the dynamics locally by forward propagating short trajectories over a state-space discretization, which needs to be a Lipschitz-continuous function. The framework is evaluated given either numerical or data-driven controllers for classical robotic benchmarks. It is compared against established analytical and recent machine learning alternatives for estimating the RoAs of such controllers. It is shown to outperform them in accuracy and efficiency. It also provides deeper insights as it describes the global dynamics up to the discretization's resolution. This allows to use the Morse graph to identify how to synthesize controllers to form improved hybrid solutions or how to identify the physical limitations of a robotic system.

Understanding how the structure of within-system interactions affects the dynamics of the system is important in many areas of science. We extend a network dynamics modeling platform DSGRN, which combinatorializes both dynamics and parameter space to construct finite but accurate summaries of network dynamics, to new types of interactions. While the standard DSGRN assumes that each network edge controls the rate of abundance of the target node, the new edges may control either activity level or a decay rate of its target. While motivated by processes of post-transcriptional modification and ubiquitination in systems biology, our extension is applicable to the dynamics of any signed directed network.

Deep learning models evolve through training to learn the manifold in which the data exists to satisfy an objective. It is well known that evolution leads to different final states which produce inconsistent predictions of the same test data points. This calls for techniques to be able to empirically quantify the difference in the trajectories and highlight problematic regions. While much focus is placed on discovering what models learn, the question of how a model learns is less studied beyond theoretical landscape characterizations and local geometric approximations near optimal conditions. Here, we present a toolkit for the Dynamical Organization Of Deep Learning Loss Landscapes, or DOODL3. DOODL3 formulates the training of neural networks as a dynamical system, analyzes the learning process, and presents an interpretable global view of trajectories in the loss landscape. Our approach uses the coarseness of topology to capture the granularity of geometry to mitigate against states of instability or elongated training. Overall, our analysis presents an empirical framework to extract the global dynamics of a model and to use that information to guide the training of neural networks., Comment: 9 pages, 3 figures, Supplementary

We introduce the notion of a template for discrete Morse theory. Templates provide a memory efficient approach to the computation of homological invariants (e.g., homology, persistent homology, Conley complexes) of cell complexes. We demonstrate the effectiveness of templates in two settings: first, by computing the homology of certain cubical complexes which are homotopy equivalent to $\mathbb{S}^d$ for $1\leq d \leq 20$, and second, by computing Conley complexes and connection matrices for a collection of examples arising from a Conley-Morse theory on spaces of braids diagrams., Comment: Updated timing information for improved version of PyCHomP

For a fixed $N$, we analyze the space of all sequences $z=(z_1,\dots,z_N)$, approximating a continuous function on the circle, with a given persistence diagram $P$, and show that the typical components of this space are homotopy equivalent to $S^1$. We also consider the space of functions on $Y$-shaped (resp., star-shaped) trees with a 2-point persistence diagram, and show that this space is homotopy equivalent to $S^1$ (resp., to a bouquet of circles).

In this paper we investigate equilibria of continuous differential equation models of network dynamics. The motivation comes from gene regulatory networks where each directed edge represents either down- or up-regulation, and is modeled by a sigmoidal nonlinear function. We show that the existence and stability of equilibria of a sigmoidal system is determined by a combinatorial analysis of the limiting switching system with piece-wise constant non-linearities. In addition, we describe a local decomposition of a switching system into a product of simpler cyclic feedback systems, where the cycles in each decomposition correspond to a particular subset of network loops., Comment: 29 pages, 3 figures, submitted to SIAM Journal on Applied Dynamical Systems

We demonstrate a modeling and computational framework that allows for rapid screening of thousands of potential network designs for particular dynamic behavior. To illustrate this capability we consider the problem of hysteresis, a prerequisite for construction of robust bistable switches and hence a cornerstone for construction of more complex synthetic circuits. We evaluate and rank most three node networks according to their ability to robustly exhibit hysteresis where robustness is measured with respect to parameters over multiple dynamic phenotypes. Focusing on the highest ranked networks, we demonstrate how additional robustness and design constraints can be applied. We compare our results to more traditional methods based on specific parameterization of ordinary differential equation models and demonstrate a strong qualitative match at a small fraction of the computational cost.

In this paper we consider the classical problem of computing linear extensions of a given poset which is well known to be a difficult problem. However, in our setting the elements of the poset are multivariate polynomials, and only a small "admissible" subset of these linear extensions, determined implicitly by the evaluation map, are of interest. This seemingly novel problem arises in the study of global dynamics of gene regulatory networks in which case the poset is a Boolean lattice. We provide an algorithm for solving this problem using linear programming for arbitrary partial orders of linear polynomials. This algorithm exploits this additional algebraic structure inherited from the polynomials to efficiently compute the admissible linear extensions. The biologically relevant problem involves multilinear polynomials and we provide a construction for embedding it into an instance of the linear problem.

We describe a computational method for constructing a coarse combinatorial model of some dynamical system in which the macroscopic states are given by elementary cycling motions of the system. Our method is in particular applicable to time series data. We illustrate the construction by a perturbed double well Hamiltonian as well as the Lorenz system., Comment: Replacement of the accidentally submitted v2

The theory of bounded, distributive lattices provides the appropriate language for describing directionality and asymptotics in dynamical systems. For bounded, distributive lattices the general notion of `set-difference' taking values in a semilattice is introduced, and is called the Conley form. The Conley form is used to build concrete, set-theoretical models of spectral, or Priestley spaces, of bounded, distributive lattices and their finite coarsenings. Such representations build order-theoretic models of dynamical systems, which are used to develop tools for computing global characteristics of a dynamical system.

The topological method for the reconstruction of dynamics from time series [K. Mischaikow, M. Mrozek, J. Reiss, A. Szymczak. Construction of Symbolic Dynamics from Experimental Time Series, Physical Review Letters, 82 (1999), 1144-1147] is reshaped to improve its range of applicability, particularly in the presence of sparse data and strong expansion. The improvement is based on a multivalued map representation of the data. However, unlike the previous approach, it is not required that the representation has a continuous selector. Instead of a selector, a recently developed new version of Conley index theory for multivalued maps [B. Batko and M. Mrozek. Weak index pairs and the Conley index for discrete multivalued dynamical systems, SIAM J. Applied Dynamical Systems 15 (2016), 1143-1162], [B.Batko. Weak index pairs and the Conley index for discrete multivalued dynamical systems. Part II: properties of the Index, SIAM J. Applied Dynamical Systems 16 (2017), 1587-1617] is used in computations. The existence of a continuous, single-valued generator of the relevant dynamics is guaranteed in the vicinity of the graph of the multivalued map constructed from data. Some numerical examples based on time series derived from the iteration of H\'enon type maps are presented.

Dense, stabilized, frictional particulate suspensions in a viscous liquid undergo increasingly strong continuous shear thickening (CST) as the solid packing fraction, $\phi$, increases above a critical volume fraction, and discontinuous shear thickening (DST) is observed for even higher packing fractions. Recent studies have related shear thickening to a transition from mostly lubricated to predominantly frictional contacts with the increase in stress. The rheology and networks of frictional forces from two and three-dimensional simulations of shear-thickening suspensions are studied. These are analyzed using measures of the topology of the network, including tools of persistent homology. We observe that at low stress the frictional interaction networks are predominantly quasi-linear along the compression axis. With an increase in stress, the force networks become more isotropic, forming loops in addition to chain-like structures. The topological measures of Betti numbers and total persistence provide a compact means of describing the mean properties of the frictional force networks and provide a key link between macroscopic rheology and the microscopic interactions. A total persistence measure describing the significance of loops in the force network structure, as a function of stress and packing fraction, shows behavior similar to that of relative viscosity and displays a scaling law near the jamming fraction for both dimensionalities simulated., Comment: 15 pages

To make progress in understanding the issue of memory loss and history dependence in evolving complex systems, we consider the mixing rate that specifies how fast the future states become independent of the initial condition. We propose a simple measure for assessing the mixing rate that can be directly applied to experimental data observed in any metric space $X$. For a compact phase space $X \subset R^M$, we prove the following statement. If the underlying dynamical system has a unique physical measure and its dynamics is strongly mixing with respect to this measure, then our method provides an upper bound of the mixing rate. We employ our method to analyze memory loss for the system of slowly sheared granular particles with a small inertial number $I$. The shear is induced by the moving walls as well as by the linear motion of the support surface that ensures approximately linear shear throughout the sample. We show that even if $I$ is kept fixed, the rate of memory loss (considered at the time scale given by the inverse shear rate) depends erratically on the shear rate. Our study suggests a presence of bifurcations at which the rate of memory loss increases with the shear rate while it decreases away from these points. We also find that the memory loss is not a smooth process. Its rate is closely related to frequency of the sudden transitions of the force network. The loss of memory, quantified by observing evolution of force networks, is found to be correlated with the loss of correlation of shear stress measured on the system scale. Thus, we have established a direct link between the evolution of force networks and macroscopic properties of the considered system.

This work is motivated by the following question in data-driven study of dynamical systems: given a dynamical system that is observed via time series of persistence diagrams that encode topological features of solutions snapshots, what conclusions can be drawn about solutions of the original dynamical system? In this paper we provide a definition of a persistence diagram for a point in $\mathbb{R}^N$ modeled on piecewise monotone functions. We then provide conditions under which time series of persistence diagrams can be used to guarantee the existence of a fixed point of the flow on $\mathbb{R}^N$ that generates the time series. To obtain this result requires an understanding of the preimage of the persistence map. The main theorem of this paper gives conditions under which these preimages are contractible simplicial complexes., Comment: 12 pages, 3 figures

We explore the chaotic dynamics of Rayleigh-B\'enard convection using large-scale, parallel numerical simulations for experimentally accessible conditions. We quantify the connections between the spatiotemporal dynamics of the leading-order Lyapunov vector and different measures of the flow field pattern's topology and dynamics. We use a range of pattern diagnostics to describe the spatiotemporal features of the flow field structures which includes many of the traditional diagnostics used to describe convection as well as some diagnostics tailored to capture the dynamics of the patterns. Using precision-recall curves, we quantify the complex relationship between the pattern diagnostics and the regions where the magnitude of the leading-order Lyapunov vector is significant.

The connection matrix is a powerful algebraic topological tool from Conley index theory that captures relationships between isolated invariant sets. Conley index theory is a topological generalization of Morse theory in which the connection matrix subsumes the role of the Morse boundary operator. Over the last few decades, the ideas of Conley have been cast into a purely computational form. In this paper we introduce a computational, categorical framework for the connection matrix theory. This contribution transforms the computational Conley theory into a computational homological theory for dynamical systems. More specifically, within this paper we have two goals: 1) We cast the connection matrix theory into appropriate categorical, homotopy-theoretic language. We identify objects of the appropriate categories which correspond to connection matrices and may be computed within the computational Conley theory paradigm by using the technique of reductions. 2) We describe an algorithm for this computation based on algebraic-discrete Morse theory., Comment: Updated to address comments from referees, updated title, updated references

We present a generalization of the induced matching theorem and use it to prove a generalization of the algebraic stability theorem for $\mathbb{R}$-indexed pointwise finite-dimensional persistence modules. Via numerous examples, we show how the generalized algebraic stability theorem enables the computation of rigorous error bounds in the space of persistence diagrams that go beyond the typical formulation in terms of bottleneck (or log bottleneck) distance.

We carry out a direct comparison of experimental and numerical realizations of the exact same granular system as it undergoes shear jamming. We adjust the numerical methods used to optimally represent the experimental settings and outcomes up to microscopic contact force dynamics. Measures presented here range form microscopic, through mesoscopic to system-wide characteristics of the system. Topological properties of the mesoscopic force networks provide a key link between micro and macro scales. We report two main findings: the number of particles in the packing that have at least two contacts is a good predictor for the mechanical state of the system, regardless of strain history and packing density. All measures explored in both experiments and numerics, including stress tensor derived measures and contact numbers depend in a universal manner on the fraction of non-rattler particles, $f_{NR}$. The force network topology also tends to show this universality, yet the shape of the master curve depends much more on the details of the numerical simulations. In particular we show that adding force noise to the numerical data set can significantly alter the topological features in the data. We conclude that both $f_{NR}$ and topological metrics are useful measures to consider when quantifying the state of a granular system., Comment: 8 pages, 8 figures

We show how a graph algorithm for finding matching labeled paths in pairs of labeled directed graphs can be used to perform model validation for a class of dynamical systems including regulatory network models of relevance to systems biology. In particular, we extract a partial order of events describing local minima and local maxima of observed quantities from experimental time-series data from which we produce a labeled directed graph we call the pattern graph for which every path from root to leaf corresponds to a plausible sequence of events. We then consider the regulatory network model, which can be itself rendered into a labeled directed graph we call the search graph via techniques previously developed in computational dynamics. Labels on the pattern graph correspond to experimentally observed events, while labels on the search graph correspond to mathematical facts about the model. We give a theoretical guarantee that failing to find a match invalidates the model. As an application we consider gene regulatory models for the yeast S. cerevisiae.

In this paper, we prove that Wright's equation $y'(t) = - \alpha y(t-1) \{1 + y(t)\}$ has a unique slowly oscillating periodic solution (SOPS) for all parameter values $\alpha \in [ 1.9,6.0]$, up to time translation. Our proof is based on a same strategy employed earlier by Xie [27]; show that every SOPS is asymptotically stable. We first introduce a branch and bound algorithm to control all SOPS using bounding functions at all parameter values $\alpha \in [ 1.9,6.0]$. Once the bounding functions are constructed, we then control the Floquet multipliers of all possible SOPS by solving rigorously an eigenvalue problem, again using a formulation introduced by Xie. Using these two main steps, we prove that all SOPS of Wright's equation are asymptotically stable for $\alpha \in [ 1.9,6.0]$, and the proof follows. This result is a step toward the proof of the Jones' Conjecture formulated in 1962., Comment: 23 pages, 2 figures

When dense granular systems are exposed to external forcing, they evolve on the time scale that is typically related to the externally imposed one (shear or compression rate, for example). This evolution could be characterized by observing temporal evolution of contact networks. However, it is not immediately clear whether the force networks, defined on contact networks by considering force interactions between the particles, evolve on a similar time scale. To analyze the evolution of these networks, we carry out discrete element simulations of a system of soft frictional disks exposed to compression that leads to jamming. By using the tools of computational topology, we show that close to jamming transition, the force networks evolve on the time scale which is much faster than the externally imposed one. The presentation will discuss the factors that determine this fast time scale., Comment: to appear in Powders and Grains, 2017

We describe the theoretical and computational framework for the Dynamic Signatures for Genetic Regulatory Network (DSGRN) database. The motivation stems from urgent need to understand the global dynamics of biologically relevant signal transduction/gene regulatory networks that have at least 5 to 10 nodes, involve multiple interactions, and decades of parameters. The input to the database computations is a regulatory network, i.e.\ a directed graph with edges indicating up or down regulation, from which a computational model based on switching networks is generated. The phase space dimension equals the number of nodes. The associated parameter space consists of one parameter for each node (a decay rate), and three parameters for each edge (low and high levels of expression, and a threshold at which expression levels change). Since the nonlinearities of switching systems are piece-wise constant, there is a natural decomposition of phase space into cells from which the dynamics can be described combinatorially in terms of a state transition graph. This in turn leads to compact representation of the global dynamics called an annotated Morse graph that identifies recurrent and nonrecurrent. The focus of this paper is on the construction of a natural computable finite decomposition of parameter space into domains where the annotated Morse graph description of dynamics is constant. We use this decomposition to construct an SQL database that can be effectively searched for dynamic signatures such as bistability, stable or unstable oscillations, and stable equilibria. We include two simple 3-node networks to provide small explicit examples of the type information stored in the DSGRN database. To demonstrate the computational capabilities of this system we consider a simple network associated with p53 that involves 5-nodes and a 29-dimensional parameter space.

Conley indices and Morse decompositions of flows can be found by using algorithms which rigorously analyze discrete dynamical systems. This usually involves integrating a time discretization of the flow using interval arithmetic. We compare the old idea of fixing a time step as a parameters to a time step continuously varying in phase space. We present an example where this second strategy necessarily yields better numerical outputs and prove that our outputs yield a valid Morse decomposition of the given flow.

We introduce a novel approach to obtaining mathematically rigorous results on the global dynamics of ordinary differential equations. Motivated by models of regulatory networks, we construct a state transition graph from a piecewise affine ordinary differential equation. We use efficient graph algorithms to compute an associated Morse graph that codifies the recurrent and gradient-like dynamics. We prove that for 2-dimensional systems, the Morse graph defines a Morse decomposition for the dynamics of any smooth differential equation that is sufficiently close to the original piecewise affine ordinary differential equation.

We use persistent homology to build a quantitative understanding of large complex systems that are driven far-from-equilibrium; in particular, we analyze image time series of flow field patterns from numerical simulations of two important problems in fluid dynamics: Kolmogorov flow and Rayleigh-B\'enard convection. For each image we compute a persistence diagram to yield a reduced description of the flow field; by applying different metrics to the space of persistence diagrams, we relate characteristic features in persistence diagrams to the geometry of the corresponding flow patterns. We also examine the dynamics of the flow patterns by a second application of persistent homology to the time series of persistence diagrams. We demonstrate that persistent homology provides an effective method both for quotienting out symmetries in families of solutions and for identifying multiscale recurrent dynamics. Our approach is quite general and it is anticipated to be applicable to a broad range of open problems exhibiting complex spatio-temporal behavior.

We implement methods from computational homology to obtain a topological signal of singularity formation in a selection of geometries evolved numerically by Ricci flow. Our approach, based on persistent homology, produces precise, quantitative measures describing the behavior of an entire collection of data across a discrete sample of times. We analyze the topological signals of geometric criticality obtained numerically from the application of persistent homology to models manifesting singularities under Ricci flow. The results we obtain for these numerical models suggest that the topological signals distinguish global singularity formation (collapse to a round point) from local singularity formation (neckpinch). Finally, we discuss the interpretation and implication of these results and future applications., Comment: 24 pages, 14 figures

We study the homomorphism induced in homology by a closed correspondence between topological spaces, using projections from the graph of the correspondence to its domain and codomain. We provide assumptions under which the homomorphism induced by an outer approximation of a continuous map coincides with the homomorphism induced in homology by the map. In contrast to more classical results we do not require that the projection to the domain have acyclic preimages. Moreover, we show that it is possible to retrieve correct homological information from a correspondence even if some data is missing or perturbed. Finally, we describe an application to combinatorial maps that are either outer approximations of continuous maps or reconstructions of such maps from a finite set of data points.

The algebraic structure of the attractors in a dynamical system determine much of its global dynamics. The collection of all attractors has a natural lattice structure, and this structure can be detected through attracting neighborhoods, which can in principle be computed. Indeed, there has been much recent work on developing and implementing general computational algorithms for global dynamics, which are capable of computing attracting neighborhoods efficiently. Here we address the question of whether all of the algebraic structure of attractors can be captured by these methods.

Social and biological contagions are influenced by the spatial embeddedness of networks. Historically, many epidemics spread as a wave across part of the Earth's surface; however, in modern contagions long-range edges -- for example, due to airline transportation or communication media -- allow clusters of a contagion to appear in distant locations. Here we study the spread of contagions on networks through a methodology grounded in topological data analysis and nonlinear dimension reduction. We construct "contagion maps" that use multiple contagions on a network to map the nodes as a point cloud. By analyzing the topology, geometry, and dimensionality of manifold structure in such point clouds, we reveal insights to aid in the modeling, forecast, and control of spreading processes. Our approach highlights contagion maps also as a viable tool for inferring low-dimensional structure in networks., Comment: Main Text and Supplementary Information

We introduce novel sets of measures with the goal of describing dynamical properties of force networks in dense particulate systems. The presented approach is based on persistent homology and allows for extracting precise, quantitative measures that describe the evolution of geometric features of the interparticle forces, without necessarily considering the details related to individual contacts between particles. The networks considered emerge from discrete element simulations of two dimensional particulate systems consisting of compressible frictional circular disks. We quantify the evolution of the networks for slowly compressed systems undergoing jamming transition. The main findings include uncovering significant but localized changes of force networks for unjammed systems, global (system-wide) changes as the systems evolve through jamming, to be followed by significantly less dramatic evolution for the jammed states. We consider both connected components, related in loose sense to force chains, and loops, and find that both measures provide a significant insight into the evolution of force networks. In addition to normal, we consider also tangential forces between the particles and find that they evolve in the consistent manner. Consideration of both frictional and frictionless systems leads us to the conclusion that friction plays a significant role in determining the dynamical properties of the considered networks. We find that the proposed approach describes the considered networks in a precise yet tractable manner, allowing to identify novel features which could be difficult or impossible to describe using other approaches.

From a sufficiently large point sample lying on a compact Riemannian submanifold of Euclidean space, one can construct a simplicial complex which is homotopy-equivalent to that manifold with high confidence. We describe a corresponding result for a Lipschitz-continuous function between two such manifolds. That is, we outline the construction of a simplicial map which recovers the induced maps on homotopy and homology groups with high confidence using only finite sampled data from the domain and range, as well as knowledge of the image of every point sampled from the domain. We provide explicit bounds on the size of the point samples required for such reconstruction in terms of intrinsic properties of the domain, the co-domain and the function. This reconstruction is robust to certain types of bounded sampling and evaluation noise., Comment: 15 pages, To Appear in the Journal of Computational Dynamics (2014)

We describe the basic lattice structures of attractors and repellers in dynamical systems. The structure of distributive lattices allows for an algebraic treatment of gradient-like dynamics in general dynamical systems, both invertible and noninvertible. We separate those properties which rely solely on algebraic structures from those that require some topological arguments, in order to lay a foundation for the development of algorithms to manipulate these structures computationally.

Topological measurements are increasingly being accepted as an important tool for quantifying complex structures. In many applications, these structures can be expressed as nodal domains of real-valued functions and are obtained only through experimental observation or numerical simulations. In both cases, the data on which the topological measurements are based are derived via some form of finite sampling or discretization. In this paper, we present a probabilistic approach to quantifying the number of components of generalized nodal domains of nonhomogeneous random processes on the real line via finite discretizations, that is, we consider excursion sets of a random process relative to a nonconstant deterministic threshold function. Our results furnish explicit probabilistic a priori bounds for the suitability of certain discretization sizes and also provide information for the choice of location of the sampling points in order to minimize the error probability. We illustrate our results for a variety of random processes, demonstrate how they can be used to sample the classical nodal domains of deterministic functions perturbed by additive noise and discuss their relation to the density of zeros., Comment: Published in at http://dx.doi.org/10.1214/09-AAP652 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org)

We use a quantitative topological characterization of complex dynamics to measure geometric structures. This approach is used to analyze the weakly turbulent state of spiral defect chaos in experiments on Rayleigh-Benard convection. Different attractors of spiral defect chaos are distinguished by their homology. The technique reveals pattern asymmetries that are not revealed using statistical measures. In addition we observe global stochastic ergodicity for system parameter values where locally chaotic dynamics has been observed previously., Comment: 5 pages, 5 figures

Homology has long been accepted as an important computable tool for quantifying complex structures. In many applications, these structures arise as nodal domains of real-valued functions and are therefore amenable only to a numerical study based on suitable discretizations. Such an approach immediately raises the question of how accurate the resulting homology computations are. In this paper, we present a probabilistic approach to quantifying the validity of homology computations for nodal domains of random fields in one and two space dimensions, which furnishes explicit probabilistic a priori bounds for the suitability of certain discretization sizes. We illustrate our results for the special cases of random periodic fields and random trigonometric polynomials., Comment: Published at http://dx.doi.org/10.1214/105051607000000050 in the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org)

Algebraic topology (homology) is used to analyze the weakly turbulent state of spiral defect chaos in both laboratory experiments and numerical simulations of Rayleigh-Benard convection.The analysis reveals topological asymmetries that arise when non-Boussinesq effects are present., Comment: 21 pages with 6 figures