Asymptotics of conduction velocity restitution in models of electrical excitation in the heart

We extend a non-Tikhonov asymptotic embedding, proposed earlier, for calculation of conduction velocity restitution curves in ionic models of cardiac excitability. Conduction velocity restitution is the simplest non-trivial spatially extended problem in excitable media, and in the case of cardiac tissue it is an important tool for prediction of cardiac arrhythmias and fibrillation. An idealized conduction velocity restitution curve requires solving a non-linear eigenvalue problem with periodic boundary conditions, which in the cardiac case is very stiff and calls for the use of asymptotic methods. We compare asymptotics of restitution curves in four examples, two generic excitable media models, and two ionic cardiac models. The generic models include the classical FitzHugh–Nagumo model and its variation by Barkley. They are treated with standard singular perturbation techniques. The ionic models include a simplified “caricature” of Noble (J. Physiol. Lond. 160:317–352, 1962) model and Beeler and Reuter (J. Physiol. Lond. 268:177–210, 1977) model, which lead to non-Tikhonov problems where known asymptotic results do not apply. The Caricature Noble model is considered with particular care to demonstrate the well-posedness of the corresponding boundary-value problem. The developed method for calculation of conduction velocity restitution is then applied to the Beeler–Reuter model. We discuss new mathematical features appearing in cardiac ionic models and possible applications of the developed method

Reduction of dynamical biochemical reaction networks in computational biology

Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multi-scaleness is another property of these networks, that can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to simpler networks, in a way that depends only on the orders of magnitude and not on the exact values of the kinetic parameters. The main idea used for such robust simplifications of networks is the concept of dominance among model elements, allowing hierarchical organization of these elements according to their effects on the network dynamics. This concept finds a natural formulation in tropical geometry. We revisit, in the light of these new ideas, the main approaches to model reduction of reaction networks, such as quasi-steady state and quasi-equilibrium approximations, and provide practical recipes for model reduction of linear and nonlinear networks. We also discuss the application of model reduction to backward pruning machine learning techniques

MODEL ORDER REDUCTION OF NONLINEAR DYNAMIC SYSTEMS USING MULTIPLE PROJECTION BASES AND OPTIMIZED STATE-SPACE SAMPLING

Model order reduction (MOR) is a very powerful technique that is used to deal with the increasing complexity of dynamic systems. It is a mature and well understood field of study that has been applied to large linear dynamic systems with great success. However, the continued scaling of integrated micro-systems, the use of new technologies, and aggressive mixed-signal design has forced designers to consider nonlinear effects for more accurate model representations. This has created the need for a methodology to generate compact models from nonlinear systems of high dimensionality, since only such a solution will give an accurate description for current and future complex systems.The goal of this research is to develop a methodology for the model order reduction of large multidimensional nonlinear systems. To address a broad range of nonlinear systems, which makes the task of generalizing a reduction technique difficult, we use the concept of transforming the nonlinear representation into a composite structure of well defined basic functions from multiple projection bases.We build upon the concept of a training phase from the trajectory piecewise-linear (TPWL) methodology as a practical strategy to reduce the state exploration required for a large nonlinear system. We improve upon this methodology in two important ways: First, with a new strategy for the use of multiple projection bases in the reduction process and their coalescence into a unified base that better captures the behavior of the overall system; and second, with a novel strategy for the optimization of the state locations chosen during training. This optimization technique is based on using the Hessian of the system as an error bound metric.Finally, in order to treat the overall linear/nonlinear reduction task, we introduce a hierarchical approach using a block projection base. These three strategies together offer us a new perspective to the problem of model order reduction of nonlinear systems and the tracking or preservation of physical parameters in the final compact model

Basic Types of Coarse-Graining

We consider two basic types of coarse-graining: the Ehrenfests' coarse-graining and its extension to a general principle of non-equilibrium thermodynamics, and the coarse-graining based on uncertainty of dynamical models and Epsilon-motions (orbits). Non-technical discussion of basic notions and main coarse-graining theorems are presented: the theorem about entropy overproduction for the Ehrenfests' coarse-graining and its generalizations, both for conservative and for dissipative systems, and the theorems about stable properties and the Smale order for Epsilon-motions of general dynamical systems including structurally unstable systems. Computational kinetic models of macroscopic dynamics are considered. We construct a theoretical basis for these kinetic models using generalizations of the Ehrenfests' coarse-graining. General theory of reversible regularization and filtering semigroups in kinetics is presented, both for linear and non-linear filters. We obtain explicit expressions and entropic stability conditions for filtered equations. A brief discussion of coarse-graining by rounding and by small noise is also presented.Comment: 60 pgs, 11 figs., includes new analysis of coarse-graining by filtering. A talk given at the research workshop: "Model Reduction and Coarse-Graining Approaches for Multiscale Phenomena," University of Leicester, UK, August 24-26, 200

Shape basis interpretation for monocular deformable 3D reconstruction

© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.In this paper, we propose a novel interpretable shape model to encode object non-rigidity. We first use the initial frames of a monocular video to recover a rest shape, used later to compute a dissimilarity measure based on a distance matrix measurement. Spectral analysis is then applied to this matrix to obtain a reduced shape basis, that in contrast to existing approaches, can be physically interpreted. In turn, these pre-computed shape bases are used to linearly span the deformation of a wide variety of objects. We introduce the low-rank basis into a sequential approach to recover both camera motion and non-rigid shape from the monocular video, by simply optimizing the weights of the linear combination using bundle adjustment. Since the number of parameters to optimize per frame is relatively small, specially when physical priors are considered, our approach is fast and can potentially run in real time. Validation is done in a wide variety of real-world objects, undergoing both inextensible and extensible deformations. Our approach achieves remarkable robustness to artifacts such as noisy and missing measurements and shows an improved performance to competing methods.Peer ReviewedPostprint (author's final draft

A geometric method for model reduction of biochemical networks with polynomial rate functions

Model reduction of biochemical networks relies on the knowledge of slow and fast variables. We provide a geometric method, based on the Newton polytope, to identify slow variables of a biochemical network with polynomial rate functions. The gist of the method is the notion of tropical equilibration that provides approximate descriptions of slow invariant manifolds. Compared to extant numerical algorithms such as the intrinsic low dimensional manifold method, our approach is symbolic and utilizes orders of magnitude instead of precise values of the model parameters. Application of this method to a large collection of biochemical network models supports the idea that the number of dynamical variables in minimal models of cell physiology can be small, in spite of the large number of molecular regulatory actors