A GPU-based multi-criteria optimization algorithm for HDR brachytherapy

Currently in HDR brachytherapy planning, a manual fine-tuning of an objective function is necessary to obtain case-specific valid plans. This study intends to facilitate this process by proposing a patient-specific inverse planning algorithm for HDR prostate brachytherapy: GPU-based multi-criteria optimization (gMCO). Two GPU-based optimization engines including simulated annealing (gSA) and a quasi-Newton optimizer (gL-BFGS) were implemented to compute multiple plans in parallel. After evaluating the equivalence and the computation performance of these two optimization engines, one preferred optimization engine was selected for the gMCO algorithm. Five hundred sixty-two previously treated prostate HDR cases were divided into validation set (100) and test set (462). In the validation set, the number of Pareto optimal plans to achieve the best plan quality was determined for the gMCO algorithm. In the test set, gMCO plans were compared with the physician-approved clinical plans. Over 462 cases, the number of clinically valid plans was 428 (92.6%) for clinical plans and 461 (99.8%) for gMCO plans. The number of valid plans with target V100 coverage greater than 95% was 288 (62.3%) for clinical plans and 414 (89.6%) for gMCO plans. The mean planning time was 9.4 s for the gMCO algorithm to generate 1000 Pareto optimal plans. In conclusion, gL-BFGS is able to compute thousands of SA equivalent treatment plans within a short time frame. Powered by gL-BFGS, an ultra-fast and robust multi-criteria optimization algorithm was implemented for HDR prostate brachytherapy. A large-scale comparison against physician approved clinical plans showed that treatment plan quality could be improved and planning time could be significantly reduced with the proposed gMCO algorithm.Comment: 18 pages, 7 figure

A Parallel Divide-and-Conquer based Evolutionary Algorithm for Large-scale Optimization

Large-scale optimization problems that involve thousands of decision variables have extensively arisen from various industrial areas. As a powerful optimization tool for many real-world applications, evolutionary algorithms (EAs) fail to solve the emerging large-scale problems both effectively and efficiently. In this paper, we propose a novel Divide-and-Conquer (DC) based EA that can not only produce high-quality solution by solving sub-problems separately, but also highly utilizes the power of parallel computing by solving the sub-problems simultaneously. Existing DC-based EAs that were deemed to enjoy the same advantages of the proposed algorithm, are shown to be practically incompatible with the parallel computing scheme, unless some trade-offs are made by compromising the solution quality.Comment: 12 pages, 0 figure

Cooperative Coevolution for Non-Separable Large-Scale Black-Box Optimization: Convergence Analyses and Distributed Accelerations

Given the ubiquity of non-separable optimization problems in real worlds, in this paper we analyze and extend the large-scale version of the well-known cooperative coevolution (CC), a divide-and-conquer optimization framework, on non-separable functions. First, we reveal empirical reasons of why decomposition-based methods are preferred or not in practice on some non-separable large-scale problems, which have not been clearly pointed out in many previous CC papers. Then, we formalize CC to a continuous game model via simplification, but without losing its essential property. Different from previous evolutionary game theory for CC, our new model provides a much simpler but useful viewpoint to analyze its convergence, since only the pure Nash equilibrium concept is needed and more general fitness landscapes can be explicitly considered. Based on convergence analyses, we propose a hierarchical decomposition strategy for better generalization, as for any decomposition there is a risk of getting trapped into a suboptimal Nash equilibrium. Finally, we use powerful distributed computing to accelerate it under the multi-level learning framework, which combines the fine-tuning ability from decomposition with the invariance property of CMA-ES. Experiments on a set of high-dimensional functions validate both its search performance and scalability (w.r.t. CPU cores) on a clustering computing platform with 400 CPU cores

SBSI:an extensible distributed software infrastructure for parameter estimation in systems biology

Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI’s use of standard data formats

Massively Parallel Genetic Optimization through Asynchronous Propagation of Populations

We present Propulate, an evolutionary optimization algorithm and software package for global optimization and in particular hyperparameter search. For efficient use of HPC resources, Propulate omits the synchronization after each generation as done in conventional genetic algorithms. Instead, it steers the search with the complete population present at time of breeding new individuals. We provide an MPI-based implementation of our algorithm, which features variants of selection, mutation, crossover, and migration and is easy to extend with custom functionality. We compare Propulate to the established optimization tool Optuna. We find that Propulate is up to three orders of magnitude faster without sacrificing solution accuracy, demonstrating the efficiency and efficacy of our lazy synchronization approach. Code and documentation are available at https://github.com/Helmholtz-AI-Energy/propulateComment: 18 pages, 5 figures submitted to ISC High Performance 202

Various island-based parallel genetic algorithms for the 2-page drawing problem

Genetic algorithms have been applied to solve the 2-page drawing problem successfully, but they work with one global population, so the search time and space are limited. Parallelization provides an attractive prospect in improving the efficiency and solution quality of genetic algorithms. One of the most popular tools for parallel computing is Message Passing Interface (MPI). In this paper, we present four island models of Parallel Genetic Algorithms with MPI: island models with linear, grid, random graph topologies, and island model with periodical synchronisation. We compare their efficiency and quality of solutions for the 2-page drawing problem on a variety of graphs