Alexandru-Adrian Tantar

EVOLVE- A Bridge between Probability, Set Oriented Numerics and Evolutionary Computation

The aim of this book is to provide a strong theoretical support for understanding and analyzing the behavior of evolutionary algorithms, as well as for creating a bridge between probability, set-oriented numerics and evolutionary computation. The volume encloses a collection of contributions that were presented at the EVOLVE 2011 international workshop, held in Luxembourg, May 25-27, 2011, coming from invited speakers and also from selected regular submissions. The aim of EVOLVE is to unify the perspectives offered by probability, set oriented numerics and evolutionary computation. EVOLVE focuses on challenging aspects that arise at the passage from theory to new paradigms and practice, elaborating on the foundations of evolutionary algorithms and theory-inspired methods merged with cutting-edge techniques that ensure performance guarantee factors. EVOLVE is also intended to foster a growing interest for robust and efficient methods with a sound theoretical background. The chapters enclose challenging theoretical findings, concrete optimization problems as well as new perspectives. By gathering contributions from researchers with different backgrounds, the book is expected to set the basis for a unified view and vocabulary where theoretical advancements may echo in different domains.

Recent development and biomedical applications of probabilistic Boolean networks

Probabilistic Boolean network (PBN) modelling is a semi-quantitative approach widely used for the study of the topology and dynamic aspects of biological systems. The combined use of rule-based representation and probability makes PBN appealing for large-scale modelling of biological networks where degrees of uncertainty need to be considered.A considerable expansion of our knowledge in the field of theoretical research on PBN can be observed over the past few years, with a focus on network inference, network intervention and control. With respect to areas of applications, PBN is mainly used for the study of gene regulatory networks though with an increasing emergence in signal transduction, metabolic, and also physiological networks. At the same time, a number of computational tools, facilitating the modelling and analysis of PBNs, are continuously developed.A concise yet comprehensive review of the state-of-the-art on PBN modelling is offered in this article, including a comparative discussion on PBN versus similar models with respect to concepts and biomedical applications. Due to their many advantages, we consider PBN to stand as a suitable modelling framework for the description and analysis of complex biological systems, ranging from molecular to physiological levels.

A parallel hybrid genetic algorithm for protein structure prediction on the computational grid

Solving the structure prediction problem for complex proteins is difficult and computationally expensive. In this paper, we propose a bicriterion parallel hybrid genetic algorithm (GA) in order to efficiently deal with the problem using the computational grid. The use of a near-optimal metaheuristic, such as a GA, allows a significant reduction in the number of explored potential structures. However, the complexity of the problem remains prohibitive as far as large proteins are concerned, making the use of parallel computing on the computational grid essential for its efficient resolution. A conjugated gradient-based Hill Climbing local search is combined with the GA in order to intensify the search in the neighborhood of its provided configurations. In this paper we consider two molecular complexes: the tryptophan-cage protein (Brookhaven Protein Data Bank ID 1L2Y) and @a-cyclodextrin. The experimentation results obtained on a computational grid show the effectiveness of the approach.

A grid-based genetic algorithm combined with an adaptive simulated annealing for protein structure prediction

A hierarchical hybrid model of parallel metaheuristics is proposed, combining an evolutionary algorithm and an adaptive simulated annealing. The algorithms are executed inside a grid environment with different parallelization strategies: the synchronous multi-start model, parallel evaluation of different solutions and an insular model with asynchronous migrations. Furthermore, a conjugated gradient local search method is employed at different stages of the exploration process. The algorithms were evaluated using the protein structure prediction problem, having as benchmarks the tryptophan-cage protein (Brookhaven Protein Data Bank ID: 1L2Y), the tryptophan-zipper protein (PDB ID: 1LE1) and the α-Cyclodextrin complex. Experimentations were performed on a nation-wide grid infrastructure, over six distinct administrative domains and gathering nearly 1,000 CPUs. The complexity of the protein structure prediction problem remains prohibitive as far as large proteins are concerned, making the use of parallel computing on the computational grid essential for its efficient resolution.

optPBN: An Optimisation Toolbox for Probabilistic Boolean Networks

Background There exist several computational tools which allow for the optimisation and inference of biological networks using a Boolean formalism. Nevertheless, the results from such tools yield only limited quantitative insights into the complexity of biological systems because of the inherited qualitative nature of Boolean networks. Results We introduce optPBN, a Matlab-based toolbox for the optimisation of probabilistic Boolean networks (PBN) which operates under the framework of the BN/PBN toolbox. optPBN offers an easy generation of probabilistic Boolean networks from rule-based Boolean model specification and it allows for flexible measurement data integration from multiple experiments. Subsequently, optPBN generates integrated optimisation problems which can be solved by various optimisers. In term of functionalities, optPBN allows for the construction of a probabilistic Boolean network from a given set of potential constitutive Boolean networks by optimising the selection probabilities for these networks so that the resulting PBN fits experimental data. Furthermore, the optPBN pipeline can also be operated on large-scale computational platforms to solve complex optimisation problems. Apart from exemplary case studies which we correctly inferred the original network, we also successfully applied optPBN to study a large-scale Boolean model of apoptosis where it allows identifying the inverse correlation between UVB irradiation, NFκB and Caspase 3 activations, and apoptosis in primary hepatocytes quantitatively. Also, the results from optPBN help elucidating the relevancy of crosstalk interactions in the apoptotic network. Summary The optPBN toolbox provides a simple yet comprehensive pipeline for integrated optimisation problem generation in the PBN formalism that can readily be solved by various optimisers on local or grid-based computational platforms. optPBN can be further applied to various biological studies such as the inference of gene regulatory networks or the identification of the interactions relevancy in signal transduction networks.

On dynamic multi-objective optimization, classification and performance measures

In this work we focus on defining how dynamism can be modeled in the context of multi-objective optimization. Based on this, we construct a component oriented classification for dynamic multi-objective optimization problems. For each category we provide synthetic examples that depict in a more explicit way the defined model. We do this either by positioning existing synthetic benchmarks with respect to the proposed classification or through new problem formulations. In addition, an online dynamic MNK-landscape formulation is introduced together with a new comparative metric for the online dynamic multi-objective context.

Sparse Antenna Array Optimization With the Cross-Entropy Method

The interest in sparse antenna arrays is growing, mainly due to cost concerns, array size limitations, etc. Formally, it can be shown that their design can be expressed as a constrained multidimensional nonlinear optimization problem. Generally, through lack of convex property, such a multiextrema problem is very tricky to solve by usual deterministic optimization methods. In this article, a recent stochastic approach, called Cross-Entropy method, is applied to the continuous constrained design problem. The method is able to construct a random sequence of solutions which converges probabilistically to the optimal or the near-optimal solution. Roughly speaking, it performs adaptive changes to probability density functions according to the Kullback-Leibler cross-entropy. The approach efficiency is illustrated in the design of a sparse antenna array with various requirements.

The Influence of Mutation on Protein-Ligand Docking Optimization: A Locality Analysis

Evolutionary approaches to protein-ligand docking typically use a real-value encoding and mutation operators based on Gaussian and Cauchy distributions. The choice of mutation is important for an efficient algorithm for this problem. We investigate the effect of mutation operators by locality analysis. High locality means that small variations in the genotype imply small variations in the phenotype. Results show that Gaussian-based operators have stronger locality than Cauchy-based ones, especially if an annealing scheme is used to control the variance.

Computational intelligence for cloud management current trends and opportunities

The development of large scale data center and cloud computing optimization models led to a wide range of complex issues like scaling, operation cost and energy efficiency. Different approaches were proposed to this end, including classical resource allocation heuristics, machine learning or stochastic optimization. No consensus exists but a trend towards using many-objective stochastic models became apparent over the past years. This work reviews in brief some of the more recent studies on cloud computing modeling and optimization, and points at notions on stability, convergence, definitions or results that could serve to analyze, respectively build accurate cloud computing models. A very brief discussion of simulation frameworks that include support for energy-aware components is also given.

A classification of dynamic multi-objective optimization problems

A classification of dynamic multi-objective optimization problems is proposed in this article. As compared to previous studies, we focus not on the changes or the effects that are induced in the Pareto optimal front or set but on the components that lead to the observed dynamic behaviour. Four main classes are identified, including parameter and function time-dependent evolution as well as state-dependent parameter and function transforms or environment changes.