Energy Minimization of Discrete Protein Titration State Models Using Graph Theory

There are several applications in computational biophysics which require the optimization of discrete interacting states; e.g., amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very time-consuming as it scales exponentially in the number of sites to be optimized. In this paper, we describe a new polynomial-time algorithm for optimization of discrete states in macromolecular systems. This algorithm was adapted from image processing and uses techniques from discrete mathematics and graph theory to restate the optimization problem in terms of "maximum flow-minimum cut" graph analysis. The interaction energy graph, a graph in which vertices (amino acids) and edges (interactions) are weighted with their respective energies, is transformed into a flow network in which the value of the minimum cut in the network equals the minimum free energy of the protein, and the cut itself encodes the state that achieves the minimum free energy. Because of its deterministic nature and polynomial-time performance, this algorithm has the potential to allow for the ionization state of larger proteins to be discovered

SamACO: variable sampling ant colony optimization algorithm for continuous optimization

An ant colony optimization (ACO) algorithm offers algorithmic techniques for optimization by simulating the foraging behavior of a group of ants to perform incremental solution constructions and to realize a pheromone laying-and-following mechanism. Although ACO is first designed for solving discrete (combinatorial) optimization problems, the ACO procedure is also applicable to continuous optimization. This paper presents a new way of extending ACO to solving continuous optimization problems by focusing on continuous variable sampling as a key to transforming ACO from discrete optimization to continuous optimization. The proposed SamACO algorithm consists of three major steps, i.e., the generation of candidate variable values for selection, the ants’ solution construction, and the pheromone update process. The distinct characteristics of SamACO are the cooperation of a novel sampling method for discretizing the continuous search space and an efficient incremental solution construction method based on the sampled values. The performance of SamACO is tested using continuous numerical functions with unimodal and multimodal features. Compared with some state-of-the-art algorithms, including traditional ant-based algorithms and representative computational intelligence algorithms for continuous optimization, the performance of SamACO is seen competitive and promising

Estimation of discrete choice models with hybrid stochastic adaptive batch size algorithms

The emergence of Big Data has enabled new research perspectives in the discrete choice community. While the techniques to estimate Machine Learning models on a massive amount of data are well established, these have not yet been fully explored for the estimation of statistical Discrete Choice Models based on the random utility framework. In this article, we provide new ways of dealing with large datasets in the context of Discrete Choice Models. We achieve this by proposing new efficient stochastic optimization algorithms and extensively testing them alongside existing approaches. We develop these algorithms based on three main contributions: the use of a stochastic Hessian, the modification of the batch size, and a change of optimization algorithm depending on the batch size. A comprehensive experimental comparison of fifteen optimization algorithms is conducted across ten benchmark Discrete Choice Model cases. The results indicate that the HAMABS algorithm, a hybrid adaptive batch size stochastic method, is the best performing algorithm across the optimization benchmarks. This algorithm speeds up the optimization time by a factor of 23 on the largest model compared to existing algorithms used in practice. The integration of the new algorithms in Discrete Choice Models estimation software will significantly reduce the time required for model estimation and therefore enable researchers and practitioners to explore new approaches for the specification of choice models.Comment: 43 page

Solutions to Wiener Filtering and Stationary LQG Problem via H₂ Control Theory - Part II : Discrete - Time System

This paper derives the solutions to the Wiener filtering and stationary LQG problem for a discrete-time system by applying the state-space techniques developed for H₂H∞ optimal controls. As mathematical preliminaries, we collect useful operations for the transfer function matrices. We also provide a new proof for the inner-outer factorization algorithm that appears in the discrete-time H₂ optimization

Applications of ℓ\u3csub\u3e1\u3c/sub\u3e and Mixed H\u3csub\u3e2\u3c/sub\u3e/ℓ\u3csub\u3e1\u3c/sub\u3e Optimization

This thesis explores the use of ℓ1 and mixed H2/ℓ1 optimization methods to design flight control systems. ℓ1 optimization is used to handle tracking issues in the design of digital compensators. Control deflection and rate limitations, overshoot and undershoot limitations and steady-state error requirements are discussed. Model-matching techniques which produce acceptable tracking results with lower order controllers are also examined. New numerical methods for continuous H2/L1 and discrete H2/ℓ1 optimization are presented. These methods are used to design an aircraft controller in continuous and discrete time and the results are compared

Consistent approximations of the zeno behaviour in affine-type switched dynamic systems

This paper proposes a new theoretic approach to a specific interaction of continuous and discrete dynamics in switched control systems known as a Zeno behaviour. We study executions of switched control systems with affine structure that admit infinitely many discrete transitions on a finite time interval. Although the real world processes do not present the corresponding behaviour, mathematical models of many engineering systems may be Zeno due to the used formal abstraction. We propose two useful approximative approaches to the Zeno dynamics, namely, an analytic technique and a variational description of this phenomenon. A generic trajectory associated with the Zeno dynamics can finally be characterized as a result of a specific projection or/and an optimization procedure applied to the original dynamic model. The obtained analytic and variational techniques provide an effective methodology for constructive approximations of the general Zeno-type behaviour. We also discuss shortly some possible applications of the proposed approximation schemes