Parameters identification of unknown delayed genetic regulatory networks by a switching particle swarm optimization algorithm

The official published version can be found at the link below.This paper presents a novel particle swarm optimization (PSO) algorithm based on Markov chains and competitive penalized method. Such an algorithm is developed to solve global optimization problems with applications in identifying unknown parameters of a class of genetic regulatory networks (GRNs). By using an evolutionary factor, a new switching PSO (SPSO) algorithm is first proposed and analyzed, where the velocity updating equation jumps from one mode to another according to a Markov chain, and acceleration coefficients are dependent on mode switching. Furthermore, a leader competitive penalized multi-learning approach (LCPMLA) is introduced to improve the global search ability and refine the convergent solutions. The LCPMLA can automatically choose search strategy using a learning and penalizing mechanism. The presented SPSO algorithm is compared with some well-known PSO algorithms in the experiments. It is shown that the SPSO algorithm has faster local convergence speed, higher accuracy and algorithm reliability, resulting in better balance between the global and local searching of the algorithm, and thus generating good performance. Finally, we utilize the presented SPSO algorithm to identify not only the unknown parameters but also the coupling topology and time-delay of a class of GRNs.This research was partially supported by the National Natural Science Foundation of PR China (Grant No. 60874113), the Research Fund for the Doctoral Program of Higher Education (Grant No. 200802550007), the Key Creative Project of Shanghai Education Community (Grant No. 09ZZ66), the Key Foundation Project of Shanghai (Grant No. 09JC1400700), the Engineering and Physical Sciences Research Council EPSRC of the UK under Grant No. GR/S27658/01, the International Science and Technology Cooperation Project of China under Grant No. 2009DFA32050, an International Joint Project sponsored by the Royal Society of the UK, and the Alexander von Humboldt Foundation of Germany

Modeling and Analysis Generic Interface for eXternal numerical codes (MAGIX)

The modeling and analysis generic interface for external numerical codes (MAGIX) is a model optimizer developed under the framework of the coherent set of astrophysical tools for spectroscopy (CATS) project. The MAGIX package provides a framework of an easy interface between existing codes and an iterating engine that attempts to minimize deviations of the model results from available observational data, constraining the values of the model parameters and providing corresponding error estimates. Many models (and, in principle, not only astrophysical models) can be plugged into MAGIX to explore their parameter space and find the set of parameter values that best fits observational/experimental data. MAGIX complies with the data structures and reduction tools of ALMA (Atacama Large Millimeter Array), but can be used with other astronomical and with non-astronomical data.Comment: 12 pages, 15 figures, 2 tables, paper is also available at http://www.aanda.org/articles/aa/pdf/forth/aa20063-12.pd

Global parameter identification of stochastic reaction networks from single trajectories

We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from live-cell fluorescence microscopy in image-based systems biology. In addition, fluctuation time-courses from, e.g., fluorescence correlation spectroscopy provide additional information about the system dynamics that can be used to more robustly infer parameters than when considering only mean concentrations. Estimating model parameters from a single experimental trajectory enables single-cell measurements and quantification of cell--cell variability. We propose a novel combination of an adaptive Monte Carlo sampler, called Gaussian Adaptation, and efficient exact stochastic simulation algorithms that allows parameter identification from single stochastic trajectories. We benchmark the proposed method on a linear and a non-linear reaction network at steady state and during transient phases. In addition, we demonstrate that the present method also provides an ellipsoidal volume estimate of the viable part of parameter space and is able to estimate the physical volume of the compartment in which the observed reactions take place.Comment: Article in print as a book chapter in Springer's "Advances in Systems Biology

Genetic Optimization Using Derivatives: The rgenoud Package for R

genoud is an R function that combines evolutionary algorithm methods with a derivative-based (quasi-Newton) method to solve difficult optimization problems. genoud may also be used for optimization problems for which derivatives do not exist. genoud solves problems that are nonlinear or perhaps even discontinuous in the parameters of the function to be optimized. When the function to be optimized (for example, a log-likelihood) is nonlinear in the model's parameters, the function will generally not be globally concave and may have irregularities such as saddlepoints or discontinuities. Optimization methods that rely on derivatives of the objective function may be unable to find any optimum at all. Multiple local optima may exist, so that there is no guarantee that a derivative-based method will converge to the global optimum. On the other hand, algorithms that do not use derivative information (such as pure genetic algorithms) are for many problems needlessly poor at local hill climbing. Most statistical problems are regular in a neighborhood of the solution. Therefore, for some portion of the search space, derivative information is useful. The function supports parallel processing on multiple CPUs on a single machine or a cluster of computers.

A Shuffled Complex Evolution Metropolis algorithm for optimization and uncertainty assessment of hydrologic model parameters

Markov Chain Monte Carlo (MCMC) methods have become increasingly popular for estimating the posterior probability distribution of parameters in hydrologic models. However, MCMC methods require the a priori definition of a proposal or sampling distribution, which determines the explorative capabilities and efficiency of the sampler and therefore the statistical properties of the Markov Chain and its rate of convergence. In this paper we present an MCMC sampler entitled the Shuffled Complex Evolution Metropolis algorithm (SCEM-UA), which is well suited to infer the posterior distribution of hydrologic model parameters. The SCEM-UA algorithm is a modified version of the original SCE-UA global optimization algorithm developed by Duan et al. [1992]. The SCEM-UA algorithm operates by merging the strengths of the Metropolis algorithm, controlled random search, competitive evolution, and complex shuffling in order to continuously update the proposal distribution and evolve the sampler to the posterior target distribution. Three case studies demonstrate that the adaptive capability of the SCEM-UA algorithm significantly reduces the number of model simulations needed to infer the posterior distribution of the parameters when compared with the traditional Metropolis-Hastings samplers

Linear Convergence of Comparison-based Step-size Adaptive Randomized Search via Stability of Markov Chains

In this paper, we consider comparison-based adaptive stochastic algorithms for solving numerical optimisation problems. We consider a specific subclass of algorithms that we call comparison-based step-size adaptive randomized search (CB-SARS), where the state variables at a given iteration are a vector of the search space and a positive parameter, the step-size, typically controlling the overall standard deviation of the underlying search distribution.We investigate the linear convergence of CB-SARS on\emph{scaling-invariant} objective functions. Scaling-invariantfunctions preserve the ordering of points with respect to their functionvalue when the points are scaled with the same positive parameter (thescaling is done w.r.t. a fixed reference point). This class offunctions includes norms composed with strictly increasing functions aswell as many non quasi-convex and non-continuousfunctions. On scaling-invariant functions, we show the existence of ahomogeneous Markov chain, as a consequence of natural invarianceproperties of CB-SARS (essentially scale-invariance and invariance tostrictly increasing transformation of the objective function). We thenderive sufficient conditions for \emph{global linear convergence} ofCB-SARS, expressed in terms of different stability conditions of thenormalised homogeneous Markov chain (irreducibility, positivity, Harrisrecurrence, geometric ergodicity) and thus define a general methodologyfor proving global linear convergence of CB-SARS algorithms onscaling-invariant functions. As a by-product we provide aconnexion between comparison-based adaptive stochasticalgorithms and Markov chain Monte Carlo algorithms.Comment: SIAM Journal on Optimization, Society for Industrial and Applied Mathematics, 201

New insights on neutral binary representations for evolutionary optimization

This paper studies a family of redundant binary representations NNg(l, k), which are based on the mathematical formulation of error control codes, in particular, on linear block codes, which are used to add redundancy and neutrality to the representations. The analysis of the properties of uniformity, connectivity, synonymity, locality and topology of the NNg(l, k) representations is presented, as well as the way an (1+1)-ES can be modeled using Markov chains and applied to NK fitness landscapes with adjacent neighborhood.The results show that it is possible to design synonymously redundant representations that allow an increase of the connectivity between phenotypes. For easy problems, synonymously NNg(l, k) representations, with high locality, and where it is not necessary to present high values of connectivity are the most suitable for an efficient evolutionary search. On the contrary, for difficult problems, NNg(l, k) representations with low locality, which present connectivity between intermediate to high and with intermediate values of synonymity are the best ones. These results allow to conclude that NNg(l, k) representations with better performance in NK fitness landscapes with adjacent neighborhood do not exhibit extreme values of any of the properties commonly considered in the literature of evolutionary computation. This conclusion is contrary to what one would expect when taking into account the literature recommendations. This may help understand the current difficulty to formulate redundant representations, which are proven to be successful in evolutionary computation. (C) 2016 Elsevier B.V. All rights reserved

Experimentally Attainable Optimal Pulse Shapes Obtained with the Aid of Genetic Algorithms

We propose a methodology to design optimal pulses for achieving quantum optimal control on molecular systems. Our approach constrains pulse shapes to linear combinations of a fixed number of experimentally relevant pulse functions. Quantum optimal control is obtained by maximizing a multi-target fitness function with genetic algorithms. As a first application of the methodology we generated an optimal pulse that successfully maximized the yield on a selected dissociation channel of a diatomic molecule. Our pulse is obtained as a linear combination of linearly chirped pulse functions. Data recorded along the evolution of the genetic algorithm contained important information regarding the interplay between radiative and diabatic processes. We performed a principal component analysis on these data to retrieve the most relevant processes along the optimal path. Our proposed methodology could be useful for performing quantum optimal control on more complex systems by employing a wider variety of pulse shape functions.Comment: 7 pages, 6 figure