@article{9821, abstract = {Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode.}, author = {Graff, Grzegorz and Graff, Beata and Pilarczyk, Pawel and Jablonski, Grzegorz and Gąsecki, Dariusz and Narkiewicz, Krzysztof}, issn = {19326203}, journal = {PLoS ONE}, number = {7}, publisher = {Public Library of Science}, title = {{Persistent homology as a new method of the assessment of heart rate variability}}, doi = {10.1371/journal.pone.0253851}, volume = {16}, year = {2021}, } @article{1149, abstract = {We study the usefulness of two most prominent publicly available rigorous ODE integrators: one provided by the CAPD group (capd.ii.uj.edu.pl), the other based on the COSY Infinity project (cosyinfinity.org). Both integrators are capable of handling entire sets of initial conditions and provide tight rigorous outer enclosures of the images under a time-T map. We conduct extensive benchmark computations using the well-known Lorenz system, and compare the computation time against the final accuracy achieved. We also discuss the effect of a few technical parameters, such as the order of the numerical integration method, the value of T, and the phase space resolution. We conclude that COSY may provide more precise results due to its ability of avoiding the variable dependency problem. However, the overall cost of computations conducted using CAPD is typically lower, especially when intervals of parameters are involved. Moreover, access to COSY is limited (registration required) and the rigorous ODE integrators are not publicly available, while CAPD is an open source free software project. Therefore, we recommend the latter integrator for this kind of computations. Nevertheless, proper choice of the various integration parameters turns out to be of even greater importance than the choice of the integrator itself. © 2016 IMACS. Published by Elsevier B.V. All rights reserved.}, author = {Miyaji, Tomoyuki and Pilarczyk, Pawel and Gameiro, Marcio and Kokubu, Hiroshi and Mischaikow, Konstantin}, journal = {Applied Numerical Mathematics}, pages = {34 -- 47}, publisher = {Elsevier}, title = {{A study of rigorous ODE integrators for multi scale set oriented computations}}, doi = {10.1016/j.apnum.2016.04.005}, volume = {107}, year = {2016}, } @inproceedings{1237, abstract = {Bitmap images of arbitrary dimension may be formally perceived as unions of m-dimensional boxes aligned with respect to a rectangular grid in ℝm. Cohomology and homology groups are well known topological invariants of such sets. Cohomological operations, such as the cup product, provide higher-order algebraic topological invariants, especially important for digital images of dimension higher than 3. If such an operation is determined at the level of simplicial chains [see e.g. González-Díaz, Real, Homology, Homotopy Appl, 2003, 83-93], then it is effectively computable. However, decomposing a cubical complex into a simplicial one deleteriously affects the efficiency of such an approach. In order to avoid this overhead, a direct cubical approach was applied in [Pilarczyk, Real, Adv. Comput. Math., 2015, 253-275] for the cup product in cohomology, and implemented in the ChainCon software package [http://www.pawelpilarczyk.com/chaincon/]. We establish a formula for the Steenrod square operations [see Steenrod, Annals of Mathematics. Second Series, 1947, 290-320] directly at the level of cubical chains, and we prove the correctness of this formula. An implementation of this formula is programmed in C++ within the ChainCon software framework. We provide a few examples and discuss the effectiveness of this approach. One specific application follows from the fact that Steenrod squares yield tests for the topological extension problem: Can a given map A → Sd to a sphere Sd be extended to a given super-complex X of A? In particular, the ROB-SAT problem, which is to decide for a given function f: X → ℝm and a value r > 0 whether every g: X → ℝm with ∥g - f ∥∞ ≤ r has a root, reduces to the extension problem.}, author = {Krcál, Marek and Pilarczyk, Pawel}, location = {Marseille, France}, pages = {140 -- 151}, publisher = {Springer}, title = {{Computation of cubical Steenrod squares}}, doi = {10.1007/978-3-319-39441-1_13}, volume = {9667}, year = {2016}, } @article{1252, abstract = {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.}, author = {Harker, Shaun and Kokubu, Hiroshi and Mischaikow, Konstantin and Pilarczyk, Pawel}, issn = {1088-6826}, journal = {Proceedings of the American Mathematical Society}, number = {4}, pages = {1787 -- 1801}, publisher = {American Mathematical Society}, title = {{Inducing a map on homology from a correspondence}}, doi = {10.1090/proc/12812}, volume = {144}, year = {2016}, } @article{1254, abstract = {We use rigorous numerical techniques to compute a lower bound for the exponent of expansivity outside a neighborhood of the critical point for thousands of intervals of parameter values in the quadratic family. We first compute a radius of the critical neighborhood outside which the map is uniformly expanding. This radius is taken as small as possible, yet large enough for our numerical procedure to succeed in proving that the expansivity exponent outside this neighborhood is positive. Then, for each of the intervals, we compute a lower bound for this expansivity exponent, valid for all the parameters in that interval. We illustrate and study the distribution of the radii and the expansivity exponents. The results of our computations are mathematically rigorous. The source code of the software and the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/.}, author = {Golmakani, Ali and Luzzatto, Stefano and Pilarczyk, Pawel}, journal = {Experimental Mathematics}, number = {2}, pages = {116 -- 124}, publisher = {Taylor and Francis}, title = {{Uniform expansivity outside a critical neighborhood in the quadratic family}}, doi = {10.1080/10586458.2015.1048011}, volume = {25}, year = {2016}, } @article{1555, abstract = {We show that incorporating spatial dispersal of individuals into a simple vaccination epidemic model may give rise to a model that exhibits rich dynamical behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as a basis, we describe the spread of an infectious disease in a population split into two regions. In each subpopulation, both forward and backward bifurcations can occur. This implies that for disconnected regions the two-patch system may admit several steady states. We consider traveling between the regions and investigate the impact of spatial dispersal of individuals on the model dynamics. We establish conditions for the existence of multiple nontrivial steady states in the system, and we study the structure of the equilibria. The mathematical analysis reveals an unusually rich dynamical behavior, not normally found in the simple epidemic models. In addition to the disease-free equilibrium, eight endemic equilibria emerge from backward transcritical and saddle-node bifurcation points, forming an interesting bifurcation diagram. Stability of steady states, their bifurcations, and the global dynamics are investigated with analytical tools, numerical simulations, and rigorous set-oriented numerical computations.}, author = {Knipl, Diána and Pilarczyk, Pawel and Röst, Gergely}, issn = {1536-0040}, journal = {SIAM Journal on Applied Dynamical Systems}, number = {2}, pages = {980 -- 1017}, publisher = {Society for Industrial and Applied Mathematics }, title = {{Rich bifurcation structure in a two patch vaccination model}}, doi = {10.1137/140993934}, volume = {14}, year = {2015}, } @article{1563, abstract = {For a given self-map $f$ of $M$, a closed smooth connected and simply-connected manifold of dimension $m\geq 4$, we provide an algorithm for estimating the values of the topological invariant $D^m_r[f]$, which equals the minimal number of $r$-periodic points in the smooth homotopy class of $f$. Our results are based on the combinatorial scheme for computing $D^m_r[f]$ introduced by G. Graff and J. Jezierski [J. Fixed Point Theory Appl. 13 (2013), 63-84]. An open-source implementation of the algorithm programmed in C++ is publicly available at {\tt http://www.pawelpilarczyk.com/combtop/}.}, author = {Graff, Grzegorz and Pilarczyk, Pawel}, journal = {Topological Methods in Nonlinear Analysis}, number = {1}, pages = {273 -- 286}, publisher = {Juliusz Schauder Center for Nonlinear Studies}, title = {{An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds}}, doi = {10.12775/TMNA.2015.014}, volume = {45}, year = {2015}, } @article{451, abstract = {We introduce algorithms for the computation of homology, cohomology, and related operations on cubical cell complexes, using the technique based on a chain contraction from the original chain complex to a reduced one that represents its homology. This work is based on previous results for simplicial complexes, and uses Serre’s diagonalization for cubical cells. An implementation in C++ of the introduced algorithms is available at http://www.pawelpilarczyk.com/chaincon/ together with some examples. The paper is self-contained as much as possible, and is written at a very elementary level, so that basic knowledge of algebraic topology should be sufficient to follow it.}, author = {Pawel Pilarczyk and Real, Pedro}, journal = {Advances in Computational Mathematics}, number = {1}, pages = {253 -- 275}, publisher = {Kluwer}, title = {{Computation of cubical homology, cohomology, and (co)homological operations via chain contraction}}, doi = {10.1007/s10444-014-9356-1}, volume = {41}, year = {2014}, }