Nonlinear Filtering based on Log-homotopy Particle Flow : Methodological Clarification and Numerical Evaluation

The state estimation of dynamical systems based on measurements is an ubiquitous problem. This is relevant in applications like robotics, industrial manufacturing, computer vision, target tracking etc. Recursive Bayesian methodology can then be used to estimate the hidden states of a dynamical system. The procedure consists of two steps: a process update based on solving the equations modelling the state evolution, and a measurement update in which the prior knowledge about the system is improved based on the measurements. For most real world systems, both the evolution and the measurement models are nonlinear functions of the system states. Additionally, both models can also be perturbed by random noise sources, which could be non-Gaussian in their nature. Unlike linear Gaussian models, there does not exist any optimal estimation scheme for nonlinear/non-Gaussian scenarios. This thesis investigates a particular method for nonlinear and non-Gaussian data assimilation, termed as the log-homotopy based particle flow. Practical filters based on such flows have been known in the literature as Daum Huang filters (DHF), named after the developers. The key concept behind such filters is the gradual inclusion of measurements to counter a major drawback of single step update schemes like the particle filters i.e. namely the degeneracy. This could refer to a situation where the likelihood function has its probability mass well seperated from the prior density, and/or is peaked in comparison. Conventional sampling or grid based techniques do not perform well under such circumstances and in order to achieve a reasonable accuracy, could incur a high processing cost. DHF is a sampling based scheme, which provides a unique way to tackle this challenge thereby lowering the processing cost. This is achieved by dividing the single measurement update step into multiple sub steps, such that particles originating from their prior locations are graduated incrementally until they reach their final locations. The motion is controlled by a differential equation, which is numerically solved to yield the updated states. DH filters, even though not new in the literature, have not been fully explored in the detail yet. They lack the in-depth analysis that the other contemporary filters have gone through. Especially, the implementation details for the DHF are very application specific. In this work, we have pursued four main objectives. The first objective is the exploration of theoretical concepts behind DHF. Secondly, we build an understanding of the existing implementation framework and highlight its potential shortcomings. As a sub task to this, we carry out a detailed study of important factors that affect the performance of a DHF, and suggest possible improvements for each of those factors. The third objective is to use the improved implementation to derive new filtering algorithms. Finally, we have extended the DHF theory and derived new flow equations and filters to cater for more general scenarios. Improvements in the implementation architecture of a standard DHF is one of the key contributions of this thesis. The scope of the applicability of DHF is expanded by combining it with other schemes like the Sequential Markov chain Monte Carlo and the tensor decomposition based solution of the Fokker Planck equation, resulting in the development of new nonlinear filtering algorithms. The standard DHF, using improved implementation and the newly derived algorithms are tested in challenging simulated test scenarios. Detailed analysis have been carried out, together with the comparison against more established filtering schemes. Estimation error and the processing time are used as important performance parameters. We show that our new filtering algorithms exhibit marked performance improvements over the traditional schemes

Markov field models of molecular kinetics

Computer simulations such as molecular dynamics (MD) provide a possible means to understand protein dynamics and mechanisms on an atomistic scale. The resulting simulation data can be analyzed with Markov state models (MSMs), yielding a quantitative kinetic model that, e.g., encodes state populations and transition rates. However, the larger an investigated system, the more data is required to estimate a valid kinetic model. In this work, we show that this scaling problem can be escaped when decomposing a system into smaller ones, leveraging weak couplings between local domains. Our approach, termed independent Markov decomposition (IMD), is a first-order approximation neglecting couplings, i.e., it represents a decomposition of the underlying global dynamics into a set of independent local ones. We demonstrate that for truly independent systems, IMD can reduce the sampling by three orders of magnitude. IMD is applied to two biomolecular systems. First, synaptotagmin-1 is analyzed, a rapid calcium switch from the neurotransmitter release machinery. Within its C2A domain, local conformational switches are identified and modeled with independent MSMs, shedding light on the mechanism of its calcium-mediated activation. Second, the catalytic site of the serine protease TMPRSS2 is analyzed with a local drug-binding model. Equilibrium populations of different drug-binding modes are derived for three inhibitors, mirroring experimentally determined drug efficiencies. IMD is subsequently extended to an end-to-end deep learning framework called iVAMPnets, which learns a domain decomposition from simulation data and simultaneously models the kinetics in the local domains. We finally classify IMD and iVAMPnets as Markov field models (MFM), which we define as a class of models that describe dynamics by decomposing systems into local domains. Overall, this thesis introduces a local approach to Markov modeling that enables to quantitatively assess the kinetics of large macromolecular complexes, opening up possibilities to tackle current and future computational molecular biology questions

Generalized averaged Gaussian quadrature and applications

A simple numerical method for constructing the optimal generalized averaged Gaussian quadrature formulas will be presented. These formulas exist in many cases in which real positive GaussKronrod formulas do not exist, and can be used as an adequate alternative in order to estimate the error of a Gaussian rule. We also investigate the conditions under which the optimal averaged Gaussian quadrature formulas and their truncated variants are internal

MS FT-2-2 7 Orthogonal polynomials and quadrature: Theory, computation, and applications

Quadrature rules find many applications in science and engineering. Their analysis is a classical area of applied mathematics and continues to attract considerable attention. This seminar brings together speakers with expertise in a large variety of quadrature rules. It is the aim of the seminar to provide an overview of recent developments in the analysis of quadrature rules. The computation of error estimates and novel applications also are described

Theoretical Concepts of Quantum Mechanics

Quantum theory as a scientific revolution profoundly influenced human thought about the universe and governed forces of nature. Perhaps the historical development of quantum mechanics mimics the history of human scientific struggles from their beginning. This book, which brought together an international community of invited authors, represents a rich account of foundation, scientific history of quantum mechanics, relativistic quantum mechanics and field theory, and different methods to solve the Schrodinger equation. We wish for this collected volume to become an important reference for students and researchers

Nonlinear filter design using Fokker-Planck propagator in Kronecker tensor format

We consider the general continuous-discrete nonlinear filtering problem. In particular, the prediction step involving the numerical solution of the Fokker-Planck equation for the time evolution of the state probability density is known to be a challenging problem as it suffers from the curse of dimensionality. In this contribution a novel approach based on Kronecker tensor decomposition of the matrix exponential of the Fokker-Planck operator is presented. This approach allows solving high dimensional filtering problems while enlarging considerably the time propagation step size compared with finite-difference time stepping methods. We show results from simulations for a passive tracking example involving a four dimensional state vector and compare with other tensor decomposition based approaches

References, Appendices & All Parts Merged

Includes: Appendix MA: Selected Mathematical Formulas; Appendix CA: Selected Physical Constants; References; EGP merged file (all parts, appendices, and references)https://commons.library.stonybrook.edu/egp/1007/thumbnail.jp

Three Risky Decades: A Time for Econophysics?

Our Special Issue we publish at a turning point, which we have not dealt with since World War II. The interconnected long-term global shocks such as the coronavirus pandemic, the war in Ukraine, and catastrophic climate change have imposed significant humanitary, socio-economic, political, and environmental restrictions on the globalization process and all aspects of economic and social life including the existence of individual people. The planet is trapped—the current situation seems to be the prelude to an apocalypse whose long-term effects we will have for decades. Therefore, it urgently requires a concept of the planet's survival to be built—only on this basis can the conditions for its development be created. The Special Issue gives evidence of the state of econophysics before the current situation. Therefore, it can provide excellent econophysics or an inter-and cross-disciplinary starting point of a rational approach to a new era