Variable-free exploration of stochastic models: a gene regulatory network example

Finding coarse-grained, low-dimensional descriptions is an important task in the analysis of complex, stochastic models of gene regulatory networks. This task involves (a) identifying observables that best describe the state of these complex systems and (b) characterizing the dynamics of the observables. In a previous paper [13], we assumed that good observables were known a priori, and presented an equation-free approach to approximate coarse-grained quantities (i.e, effective drift and diffusion coefficients) that characterize the long-time behavior of the observables. Here we use diffusion maps [9] to extract appropriate observables ("reduction coordinates") in an automated fashion; these involve the leading eigenvectors of a weighted Laplacian on a graph constructed from network simulation data. We present lifting and restriction procedures for translating between physical variables and these data-based observables. These procedures allow us to perform equation-free coarse-grained, computations characterizing the long-term dynamics through the design and processing of short bursts of stochastic simulation initialized at appropriate values of the data-based observables.Comment: 26 pages, 9 figure

Dominance-Based Multiobjective Simulated Annealing

Copyright © 2008 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.Simulated annealing is a provably convergent optimizer for single-objective problems. Previously proposed multiobjective extensions have mostly taken the form of a single-objective simulated annealer optimizing a composite function of the objectives. We propose a multiobjective simulated annealer utilizing the relative dominance of a solution as the system energy for optimization, eliminating problems associated with composite objective functions. We also propose a method for choosing perturbation scalings promoting search both towards and across the Pareto front. We illustrate the simulated annealer's performance on a suite of standard test problems and provide comparisons with another multiobjective simulated annealer and the NSGA-II genetic algorithm. The new simulated annealer is shown to promote rapid convergence to the true Pareto front with a good coverage of solutions across it comparing favorably with the other algorithms. An application of the simulated annealer to an industrial problem, the optimization of a code-division-multiple access (CDMA) mobile telecommunications network's air interface, is presented and the simulated annealer is shown to generate nondominated solutions with an even and dense coverage that outperforms single objective genetic algorithm optimizers

Practical Combinatorial Interaction Testing: Empirical Findings on Efficiency and Early Fault Detection

Combinatorial interaction testing (CIT) is important because it tests the interactions between the many features and parameters that make up the configuration space of software systems. Simulated Annealing (SA) and Greedy Algorithms have been widely used to find CIT test suites. From the literature, there is a widely-held belief that SA is slower, but produces more effective tests suites than Greedy and that SA cannot scale to higher strength coverage. We evaluated both algorithms on seven real-world subjects for the well-studied two-way up to the rarely-studied six-way interaction strengths. Our findings present evidence to challenge this current orthodoxy: real-world constraints allow SA to achieve higher strengths. Furthermore, there was no evidence that Greedy was less effective (in terms of time to fault revelation) compared to SA; the results for the greedy algorithm are actually slightly superior. However, the results are critically dependent on the approach adopted to constraint handling. Moreover, we have also evaluated a genetic algorithm for constrained CIT test suite generation. This is the first time strengths higher than 3 and constraint handling have been used to evaluate GA. Our results show that GA is competitive only for pairwise testing for subjects with a small number of constraints

Surrogate time series

Before we apply nonlinear techniques, for example those inspired by chaos theory, to dynamical phenomena occurring in nature, it is necessary to first ask if the use of such advanced techniques is justified "by the data". While many processes in nature seem very unlikely a priori to be linear, the possible nonlinear nature might not be evident in specific aspects of their dynamics. The method of surrogate data has become a very popular tool to address such a question. However, while it was meant to provide a statistically rigorous, foolproof framework, some limitations and caveats have shown up in its practical use. In this paper, recent efforts to understand the caveats, avoid the pitfalls, and to overcome some of the limitations, are reviewed and augmented by new material. In particular, we will discuss specific as well as more general approaches to constrained randomisation, providing a full range of examples. New algorithms will be introduced for unevenly sampled and multivariate data and for surrogate spike trains. The main limitation, which lies in the interpretability of the test results, will be illustrated through instructive case studies. We will also discuss some implementational aspects of the realisation of these methods in the TISEAN (http://www.mpipks-dresden.mpg.de/~tisean) software package.Comment: 28 pages, 23 figures, software at http://www.mpipks-dresden.mpg.de/~tisea