Multimethod Optimization for Reverse Engineering of Complex Biological Networks

Publication :PBio 2018: Proceedings of the 6th International Workshop on Parallelism in Bioinformatics[Abstract] Optimization problems appears in different areas of science and engineering. This paper considers the general problem of reverse engineering in computational biology by means of mixed-integer nonlinear dynamic optimization (MIDO). Although this kind of problems are typically hard, solutions can be achieved for rather complex networks by applying global optimization metaheuristics. The main objective of this work is to handle them by means of multimethod optimization, in which different metaheuristics cooperate to outperform the results obtained by any of them isolated. For its preliminary evaluation we consider a synthetic signaling pathway case study and we assess the performance of the proposal on a public cloud. These results open up new possibilities for other MIDO-based large-scale applications in computational systems biology.Gobierno de España; DPI2017-82896-C2-2-RGobierno de España; TIN2016-75845-PXunta de Galicia; R2016/045Xunta de Galicia; ED431C 2017/0

Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology

[Abstract] This paper describes and assesses a parallel multimethod hyperheuristic for the solution of complex global optimization problems. In a multimethod hyperheuristic, different metaheuristics cooperate to outperform the results obtained by any of them isolated. The results obtained show that the cooperation of individual parallel searches modifies the systemic properties of the hyperheuristic, achieving significant performance improvements versus the sequential and the non-cooperative parallel solutions. Here we present and evaluate a hybrid parallel scheme of the multimethod, using both message-passing (MPI) and shared memory (OpenMP) models. The hybrid parallelization allows to achieve a better trade-off between performance and computational resources, through a compromise between diversity (number of islands) and intensity (number of threads per island). For the performance evaluation, we considered the general problem of reverse engineering nonlinear dynamic models in systems biology, which yields very large mixed-integer dynamic optimization problems. In particular, three very challenging problems from the domain of dynamic modeling of cell signaling were used as case studies. In addition, experiments have been carried out in a local cluster, a large supercomputer and a public cloud, to show the suitability of the proposed solution in different execution platforms.Gobierno de España; DPI2017-82896-C2-2-RGobierno de España; TIN2016-75845-PXunta de Galicia; R2016/045Xunta de Galicia; ED431C 2017/0

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

Composite Match Index with Application of Interior Deformation Field Measurement from Magnetic Resonance Volumetric Images of Human Tissues

Whereas a variety of different feature-point matching approaches have been reported in computer vision, few feature-point matching approaches employed in images from nonrigid, nonuniform human tissues have been reported. The present work is concerned with interior deformation field measurement of complex human tissues from three-dimensional magnetic resonance (MR) volumetric images. To improve the reliability of matching results, this paper proposes composite match index (CMI) as the foundation of multimethod fusion methods to increase the reliability of these various methods. Thereinto, we discuss the definition, components, and weight determination of CMI. To test the validity of the proposed approach, it is applied to actual MR volumetric images obtained from a volunteer’s calf. The main result is consistent with the actual condition

Evolutionary algorithms and other metaheuristics in water resources: Current status, research challenges and future directions

Copyright © 2014 Elsevier. NOTICE: this is the author’s version of a work that was accepted for publication in Environmental Modelling and Software. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Environmental Modelling and Software Vol. 62 (2014), DOI: 10.1016/j.envsoft.2014.09.013The development and application of evolutionary algorithms (EAs) and other metaheuristics for the optimisation of water resources systems has been an active research field for over two decades. Research to date has emphasized algorithmic improvements and individual applications in specific areas (e.g. model calibration, water distribution systems, groundwater management, river-basin planning and management, etc.). However, there has been limited synthesis between shared problem traits, common EA challenges, and needed advances across major applications. This paper clarifies the current status and future research directions for better solving key water resources problems using EAs. Advances in understanding fitness landscape properties and their effects on algorithm performance are critical. Future EA-based applications to real-world problems require a fundamental shift of focus towards improving problem formulations, understanding general theoretic frameworks for problem decompositions, major advances in EA computational efficiency, and most importantly aiding real decision-making in complex, uncertain application contexts

Daydreaming factories

Optimisation of factories, a cornerstone of production engineering for the past half century, relies on formulating the challenges with limited degrees of freedom. In this paper, technological advances are reviewed to propose a “daydreaming” framework for factories that use their cognitive capacity for looking into the future or “foresighting”. Assessing and learning from the possible eventualities enable breakthroughs with many degrees of freedom and make daydreaming factories antifragile. In these factories with augmented and reciprocal learning and foresighting processes, revolutionary reactions to external and internal stimuli are unnecessary and industrial co-evolution of people, processes and products will replace industrial revolutions

UFGM - 2006 Annual Report

INGV, SEZIONE DI CATANIAPublished2.6. TTC - Laboratorio di gravimetria, magnetismo ed elettromagnetismo in aree attiveope

Exploring foundations for using simulations in IS research

Simulation has been adopted in many disciplines as a means for understanding the behavior of a system by imitating it through an artificial object that exhibits a nearly identical behavior. Although simulation approaches have been widely adopted for theory building in disciplines such as engineering, computer science, management, and social sciences, their potential in the IS field is often overlooked. The aim of this paper is to understand how different simulation approaches are used in IS research, thereby providing insights and methodological recommendations for future studies. A literature review of simulation studies published in top-tier IS journals leads to the definition of three classes of simulations, namely the self-organizing, the elementary, and the situated. A set of stylized facts is identified for characterizing the ways in which the premise, the inference, and the contribution are presented in IS simulation studies. As a result, this study provides guidance to future simulation researchers in designing and presenting findings