Kyriakos Kentzoglanakis

Bio: Kyriakos Kentzoglanakis is an academic researcher from University of Portsmouth. The author has contributed to research in topics: Particle swarm optimization & Swarm intelligence. The author has an hindex of 3, co-authored 6 publications receiving 112 citations.

A Swarm Intelligence Framework for Reconstructing Gene Networks: Searching for Biologically Plausible Architectures

Abstract: In this paper, we investigate the problem of reverse engineering the topology of gene regulatory networks from temporal gene expression data. We adopt a computational intelligence approach comprising swarm intelligence techniques, namely particle swarm optimization (PSO) and ant colony optimization (ACO). In addition, the recurrent neural network (RNN) formalism is employed for modeling the dynamical behavior of gene regulatory systems. More specifically, ACO is used for searching the discrete space of network architectures and PSO for searching the corresponding continuous space of RNN model parameters. We propose a novel solution construction process in the context of ACO for generating biologically plausible candidate architectures. The objective is to concentrate the search effort into areas of the structure space that contain architectures which are feasible in terms of their topological resemblance to real-world networks. The proposed framework is initially applied to the reconstruction of a small artificial network that has previously been studied in the context of gene network reverse engineering. Subsequently, we consider an artificial data set with added noise for reconstructing a subnetwork of the genetic interaction network of S. cerevisiae (yeast). Finally, the framework is applied to a real-world data set for reverse engineering the SOS response system of the bacterium Escherichia coli. Results demonstrate the relative advantage of utilizing problem-specific knowledge regarding biologically plausible structural properties of gene networks over conducting a problem-agnostic search in the vast space of network architectures.

Particle swarm optimization with an oscillating inertia weight

Abstract: In this paper, we propose an alternative strategy of adapting the inertia weight parameter during the course of particle swarm optimization, by means of a non-monotonic inertia weight function of time. Results demonstrate that an oscillating inertia weight function is competitive and in some cases better than established inertia weight functions, in terms of consistency and speed of convergence.

Incorporating Heuristics in a Swarm Intelligence Framework for Inferring Gene Regulatory Networks from Gene Expression Time Series

Abstract: In this paper, we address the problem of reverse-engineering a gene regulatory network from gene expression time series. We approach the problem by implementing an ant system to generate candidate network structures. The quality of a candidate structure is evaluated using a particle swarm optimization algorithm that tunes the parameters of the corresponding model, by minimizing the error between the actual time series and the trained model's output. We extend this approach by incorporating domain-specific heuristics to the ant system, as a mechanism that has the potential to bias the pheromone amplification effect towards biologically plausible relationships. We apply the method to a subset of genes from a real world data set and report on the results.

VAR model training using particle swarm optimisation: evidence from macro-finance data

Abstract: This paper examines the empirical relationship between CPI, oil prices, stock market and unemployment in EU15 using a new computational approach. In particular, we propose a novel approach to train the well-known vector autoregressive (VAR) model using a particle swarm optimisation (PSO) method. Results demonstrate that PSO succeeds in training the model parameters. Furthermore, as the prediction error is found to be low, this strengthens the validity and usability of PSO as a model training method. The empirical results suggest that oil is an important determinant of CPI and stock market changes. Oil price changes affect CPI positively and stock market negatively. Finally, we report no evidence that CPI and unemployment have a negative effect on stock market performance.

Gene network inference using a swarm intelligence framework

Abstract: In this paper, we present a framework for inferring gene regulatory networks from gene expression time series. A model-based approach is adopted, according to which the quality of a candidate architecture is evaluated by assessing the ability of the corresponding trained model to reproduce the available dynamics. Candidate architectures are generated in the context of the ant colony optimization (ACO) meta-heuristic and model training is performed using particle swarm optimization (PSO). We propose a novel solution construction heuristic for artificial ants, based on growth and preferential attachment, in order to generate candidate structures that adhere to well-known gene network properties. Preliminary results using an artificial network demonstrate the potential of the framework to infer the underlying network architecture to a promising degree of success.

Inertia Weight strategies in Particle Swarm Optimization

Abstract: Particle Swarm Optimization is a popular heuristic search algorithm which is inspired by the social learning of birds or fishes. It is a swarm intelligence technique for optimization developed by Eberhart and Kennedy [1] in 1995. Inertia weight is an important parameter in PSO, which significantly affects the convergence and exploration-exploitation trade-off in PSO process. Since inception of Inertia Weight in PSO, a large number of variations of Inertia Weight strategy have been proposed. In order to propose one or more than one Inertia Weight strategies which are efficient than others, this paper studies 15 relatively recent and popular Inertia Weight strategies and compares their performance on 05 optimization test problems.

Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization

Abstract: The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology, and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing power that usually overtakes the capability of standard desktop computers. In this work we present coagSODA, a CUDA-powered computational tool that was purposely developed for the analysis of a large mechanistic model of the blood coagulation cascade (BCC), defined according to both mass-action kinetics and Hill functions. coagSODA allows the execution of parallel simulations of the dynamics of the BCC by automatically deriving the system of ordinary differential equations and then exploiting the numerical integration algorithm LSODA. We present the biological results achieved with a massive exploration of perturbed conditions of the BCC, carried out with one-dimensional and bi-dimensional parameter sweep analysis, and show that GPU-accelerated parallel simulations of this model can increase the computational performances up to a 181× speedup compared to the corresponding sequential simulations.

On the Performance of Linear Decreasing Inertia Weight Particle Swarm Optimization for Global Optimization

Abstract: Linear decreasing inertia weight (LDIW) strategy was introduced to improve on the performance of the original particle swarm optimization (PSO). However, linear decreasing inertia weight PSO (LDIW-PSO) algorithm is known to have the shortcoming of premature convergence in solving complex (multipeak) optimization problems due to lack of enough momentum for particles to do exploitation as the algorithm approaches its terminal point. Researchers have tried to address this shortcoming by modifying LDIW-PSO or proposing new PSO variants. Some of these variants have been claimed to outperform LDIW-PSO. The major goal of this paper is to experimentally establish the fact that LDIW-PSO is very much efficient if its parameters are properly set. First, an experiment was conducted to acquire a percentage value of the search space limits to compute the particle velocity limits in LDIW-PSO based on commonly used benchmark global optimization problems. Second, using the experimentally obtained values, five well-known benchmark optimization problems were used to show the outstanding performance of LDIW-PSO over some of its competitors which have in the past claimed superiority over it. Two other recent PSO variants with different inertia weight strategies were also compared with LDIW-PSO with the latter outperforming both in the simulation experiments conducted.