Model Exploration Using OpenMOLE - a workflow engine for large scale distributed design of experiments and parameter tuning

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. In this work, we briefly expose the strong assets of OpenMOLE and demonstrate its efficiency at exploring the parameter set of an agent simulation model. We perform a multi-objective optimisation on this model using computationally expensive Genetic Algorithms (GA). OpenMOLE hides the complexity of designing such an experiment thanks to its DSL, and transparently distributes the optimisation process. The example shows how an initialisation of the GA with a population of 200,000 individuals can be evaluated in one hour on the European Grid Infrastructure.Comment: IEEE High Performance Computing and Simulation conference 2015, Jun 2015, Amsterdam, Netherland

Half a billion simulations: evolutionary algorithms and distributed computing for calibrating the SimpopLocal geographical model

Multi-agent geographical models integrate very large numbers of spatial interactions. In order to validate those models large amount of computing is necessary for their simulation and calibration. Here a new data processing chain including an automated calibration procedure is experimented on a computational grid using evolutionary algorithms. This is applied for the first time to a geographical model designed to simulate the evolution of an early urban settlement system. The method enables us to reduce the computing time and provides robust results. Using this method, we identify several parameter settings that minimise three objective functions that quantify how closely the model results match a reference pattern. As the values of each parameter in different settings are very close, this estimation considerably reduces the initial possible domain of variation of the parameters. The model is thus a useful tool for further multiple applications on empirical historical situations

Evolutionary model type selection for global surrogate modeling

Due to the scale and computational complexity of currently used simulation codes, global surrogate (metamodels) models have become indispensable tools for exploring and understanding the design space. Due to their compact formulation they are cheap to evaluate and thus readily facilitate visualization, design space exploration, rapid prototyping, and sensitivity analysis. They can also be used as accurate building blocks in design packages or larger simulation environments. Consequently, there is great interest in techniques that facilitate the construction of such approximation models while minimizing the computational cost and maximizing model accuracy. Many surrogate model types exist ( Support Vector Machines, Kriging, Neural Networks, etc.) but no type is optimal in all circumstances. Nor is there any hard theory available that can help make this choice. In this paper we present an automatic approach to the model type selection problem. We describe an adaptive global surrogate modeling environment with adaptive sampling, driven by speciated evolution. Different model types are evolved cooperatively using a Genetic Algorithm ( heterogeneous evolution) and compete to approximate the iteratively selected data. In this way the optimal model type and complexity for a given data set or simulation code can be dynamically determined. Its utility and performance is demonstrated on a number of problems where it outperforms traditional sequential execution of each model type

Distributed evolutionary algorithms and their models: A survey of the state-of-the-art

The increasing complexity of real-world optimization problems raises new challenges to evolutionary computation. Responding to these challenges, distributed evolutionary computation has received considerable attention over the past decade. This article provides a comprehensive survey of the state-of-the-art distributed evolutionary algorithms and models, which have been classified into two groups according to their task division mechanism. Population-distributed models are presented with master-slave, island, cellular, hierarchical, and pool architectures, which parallelize an evolution task at population, individual, or operation levels. Dimension-distributed models include coevolution and multi-agent models, which focus on dimension reduction. Insights into the models, such as synchronization, homogeneity, communication, topology, speedup, advantages and disadvantages are also presented and discussed. The study of these models helps guide future development of different and/or improved algorithms. Also highlighted are recent hotspots in this area, including the cloud and MapReduce-based implementations, GPU and CUDA-based implementations, distributed evolutionary multiobjective optimization, and real-world applications. Further, a number of future research directions have been discussed, with a conclusion that the development of distributed evolutionary computation will continue to flourish

Enhanced parallel Differential Evolution algorithm for problems in computational systems biology

[Abstract] Many key problems in computational systems biology and bioinformatics can be formulated and solved using a global optimization framework. The complexity of the underlying mathematical models require the use of efficient solvers in order to obtain satisfactory results in reasonable computation times. Metaheuristics are gaining recognition in this context, with Differential Evolution (DE) as one of the most popular methods. However, for most realistic applications, like those considering parameter estimation in dynamic models, DE still requires excessive computation times. Here we consider this latter class of problems and present several enhancements to DE based on the introduction of additional algorithmic steps and the exploitation of parallelism. In particular, we propose an asynchronous parallel implementation of DE which has been extended with improved heuristics to exploit the specific structure of parameter estimation problems in computational systems biology. The proposed method is evaluated with different types of benchmarks problems: (i) black-box global optimization problems and (ii) calibration of non-linear dynamic models of biological systems, obtaining excellent results both in terms of quality of the solution and regarding speedup and scalability.Ministerio de Economía y Competitividad; DPI2011-28112-C04-03Consejo Superior de Investigaciones Científicas; PIE-201170E018Ministerio de Ciencia e Innovación; TIN2013-42148-PGalicia. Consellería de Cultura, Educación e Ordenación Universitaria; GRC2013/05