Parallel ant colony optimization for the training of cell signaling networks

[Abstract]: Acquiring a functional comprehension of the deregulation of cell signaling networks in disease allows progress in the development of new therapies and drugs. Computational models are becoming increasingly popular as a systematic tool to analyze the functioning of complex biochemical networks, such as those involved in cell signaling. CellNOpt is a framework to build predictive logic-based models of signaling pathways by training a prior knowledge network to biochemical data obtained from perturbation experiments. This training can be formulated as an optimization problem that can be solved using metaheuristics. However, the genetic algorithm used so far in CellNOpt presents limitations in terms of execution time and quality of solutions when applied to large instances. Thus, in order to overcome those issues, in this paper we propose the use of a method based on ant colony optimization, adapted to the problem at hand and parallelized using a hybrid approach. The performance of this novel method is illustrated with several challenging benchmark problems in the study of new therapies for liver cancer

An Efficient Ant Colony Optimization Framework for HPC Environments

Financiado para publicación en acceso aberto: Universidade da Coruña/CISUG[Abstract] Combinatorial optimization problems arise in many disciplines, both in the basic sciences and in applied fields such as engineering and economics. One of the most popular combinatorial optimization methods is the Ant Colony Optimization (ACO) metaheuristic. Its parallel nature makes it especially attractive for implementation and execution in High Performance Computing (HPC) environments. Here we present a novel parallel ACO strategy making use of efficient asynchronous decentralized cooperative mechanisms. This strategy seeks to fulfill two objectives: (i) acceleration of the computations by performing the ants’ solution construction in parallel; (ii) convergence improvement through the stimulation of the diversification in the search and the cooperation between different colonies. The two main features of the proposal, decentralization and desynchronization, enable a more effective and efficient response in environments where resources are highly coupled. Examples of such infrastructures include both traditional HPC clusters, and also new distributed environments, such as cloud infrastructures, or even local computer networks. The proposal has been evaluated using the popular Traveling Salesman Problem (TSP), as a well-known NP-hard problem widely used in the literature to test combinatorial optimization methods. An exhaustive evaluation has been carried out using three medium and large size instances from the TSPLIB library, and the experiments show encouraging results with superlinear speedups compared to the sequential algorithm (e.g. speedups of 18 with 16 cores), and a very good scalability (experiments were performed with up to 384 cores improving execution time even at that scale).This work was supported by the Ministry of Science and Innovation of Spain (PID2019-104184RB-I00 / AEI / 10.13039/501100011033), and by Xunta de Galicia and FEDER funds of the EU (Centro de Investigación de Galicia accreditation 2019–2022, ref. ED431G 2019/01; Consolidation Program of Competitive Reference Groups, ref. ED431C 2021/30). JRB acknowledges funding from the Ministry of Science and Innovation of Spain MCIN / AEI / 10.13039/501100011033 through grant PID2020-117271RB-C22 (BIODYNAMICS), and from MCIN / AEI / 10.13039/501100011033 and “ERDF A way of making Europe” through grant DPI2017-82896-C2-2-R (SYNBIOCONTROL). Authors also acknowledge the Galician Supercomputing Center (CESGA) for the access to its facilities. Funding for open access charge: Universidade da Coruña/CISUGXunta de Galicia; ED431G 2019/01Xunta de Galicia; ED431C 2021/3

Ant Colony Optimization

Ant Colony Optimization (ACO) is the best example of how studies aimed at understanding and modeling the behavior of ants and other social insects can provide inspiration for the development of computational algorithms for the solution of difficult mathematical problems. Introduced by Marco Dorigo in his PhD thesis (1992) and initially applied to the travelling salesman problem, the ACO field has experienced a tremendous growth, standing today as an important nature-inspired stochastic metaheuristic for hard optimization problems. This book presents state-of-the-art ACO methods and is divided into two parts: (I) Techniques, which includes parallel implementations, and (II) Applications, where recent contributions of ACO to diverse fields, such as traffic congestion and control, structural optimization, manufacturing, and genomics are presented

Ant Colony Optimization para la resolución del Problema de Steiner Generalizado

Esta tesis presenta un estudio de la metaheurïstica Ant Colony Optimization (ACO) y de la aplicación de técnicas de computación de alto desempeño a dicha metaheurïstica. En particular, se aborda la aplicación de ACO a la resolución del Problema de Steiner Generalizado (GSP). El GSP consiste en el diseño de una subred de costo mínimo que verifique ciertos requerimientos prefijados de conexión entre pares de nodos distinguidos. En el trabajo se presentan versiones ACO con dos enfoques constructivos de la solución distintos. El primero de los enfoques se basa en incorporar aristas hasta completar un camino, mientras que el segundo determina los K caminos más cortos y realiza una selección entre ellos. También se propone una novedosa formulación de un modelo celular aplicado a la metaheurística ACO y su posible paralelización Se incluye los resultados de un estudio experimental exhaustivo de todas las propuestas formuladas en este trabajo, comprendiendo la evaluación de los enfoques basados en aristas y en caminos y el analizas del efecto del tamaño de la población, de la cantidad de caminos y de incorporar operadores de búsqueda local para el enfoque basado en caminos. El estudio permitió comprobar que la utilización de un enfoque basado en caminos con la incorporación del operador de búsqueda local iterado obtiene resultados competitivos con las mejores técnicas disponibles en la actualidad. Asimismo, se evaluaron las versiones secuencial y paralela del modelo celular propuesto, constatándose que el desempeño computacional de la implementación paralela es muy promisoria, aunque se producen leves pérdidas en la calidad de las soluciones con relación a estructurar la población en la forma tradiciona