arXiv subjects

Konstantin Mischaikow

Publications and source records attributed to Konstantin Mischaikow.

At least 37 records · Page 2Linked to original sources

arXiv2021

Equilibria and their Stability in Networks with Steep Sigmoidal Nonlinearities

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.

math.DS↗

arXiv2021

Morse Theoretic Templates for High Dimensional Homology Computation

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.

math.AT↗

arXiv2021

A computational framework for connection matrix theory

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.

math.AT↗

arXiv2021

Extracting Global Dynamics of Loss Landscape in Deep Learning Models

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.

math.DS↗

arXiv2021

Rational design of complex phenotype via network models

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.

math.DS↗

arXiv2021

Persistent homology with non-contractible preimages

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).

math.AT↗

arXiv2021

Computing linear extensions for polynomial posets subject to algebraic constraints

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.

math.CO↗

arXiv2020

Contractibility of a persistence map preimage

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.

math.AT↗

arXiv2019

Lattice Structures for Attractors III

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.

math.DS↗

arXiv2019

Conley index approach to sampled dynamics

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 Hénon type maps are presented.

math.DS↗

arXiv2019

Interaction network analysis in shear thickening suspensions

Dense, stabilized, frictional particulate suspensions in a viscous liquid undergo increasingly strong continuous shear thickening (CST) as the solid packing fraction, $ϕ$, 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.

cond-mat.soft↗

arXiv2019

Quantitative Measure of Memory Loss in Complex Spatio-Temporal Systems

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.

cond-mat.stat-mech↗

arXiv2018

Connecting Lyapunov Vectors with the Pattern Dynamics of Chaotic Rayleigh-Bénard Convection

We explore the chaotic dynamics of Rayleigh-Bénard 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.

physics.flu-dyn↗

arXiv2018

A Comparison Framework for Interleaved Persistence Modules

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.

math.AT↗

arXiv2018

Characterizing Granular Networks Using Topological Metrics

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.

cond-mat.soft↗

arXiv2017

Topological Signals of Singularities in Ricci Flow

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.

math.AT↗

arXiv2017

Model rejection and parameter reduction via time series

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.

math.DS↗

arXiv2017

Stability and Uniqueness of Slowly Oscillating Periodic Solutions to Wright's Equation

In this paper, we prove that Wright's equation $y'(t) = - αy(t-1) \{1 + y(t)\}$ has a unique slowly oscillating periodic solution (SOPS) for all parameter values $α\in [ 1.9,6.0]$, 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 $α\in [ 1.9,6.0]$. 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 $α\in [ 1.9,6.0]$, and the proof follows. This result is a step toward the proof of the Jones' Conjecture formulated in 1962.

math.DS↗