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

A cloud-based enhanced differential evolution algorithm for parameter estimation problems in computational systems biology

This is a post-peer-review, pre-copyedit version of an article published in Cluster Computing. The final authenticated version is available online at: https://doi.org/10.1007/s10586-017-0860-1[Abstract] Metaheuristics are gaining increasing recognition in many research areas, computational systems biology among them. Recent advances in metaheuristics can be helpful in locating the vicinity of the global solution in reasonable computation times, with Differential Evolution (DE) being one of the most popular methods. However, for most realistic applications, DE still requires excessive computation times. With the advent of Cloud Computing effortless access to large number of distributed resources has become more feasible, and new distributed frameworks, like Spark, have been developed to deal with large scale computations on commodity clusters and cloud resources. In this paper we propose a parallel implementation of an enhanced DE using Spark. The proposal drastically reduces the execution time, by means of including a selected local search and exploiting the available distributed resources. The performance of the proposal has been thoroughly assessed using challenging parameter estimation problems from the domain of computational systems biology. Two different platforms have been used for the evaluation, a local cluster and the Microsoft Azure public cloud. Additionally, it has been also compared with other parallel approaches, another cloud-based solution (a MapReduce implementation) and a traditional HPC solution (a MPI implementation)Ministerio de Economía y Competitividad; DPI2014-55276-C5-2-RMinisterio de Economía y Competitividad; TIN2013-42148-PMinisterio de Economía y Competitividad; TIN2016-75845-PXunta de Galicia ; R2016/045Xunta de Galicia; GRC2013/05

Fast micro-differential evolution for topological active net optimization

This paper studies the optimization problem of topological active net (TAN), which is often seen in image segmentation and shape modeling. A TAN is a topological structure containing many nodes, whose positions must be optimized while a predefined topology needs to be maintained. TAN optimization is often time-consuming and even constructing a single solution is hard to do. Such a problem is usually approached by a ``best improvement local search'' (BILS) algorithm based on deterministic search (DS), which is inefficient because it spends too much efforts in nonpromising probing. In this paper, we propose the use of micro-differential evolution (DE) to replace DS in BILS for improved directional guidance. The resultant algorithm is termed deBILS. Its micro-population efficiently utilizes historical information for potentially promising search directions and hence improves efficiency in probing. Results show that deBILS can probe promising neighborhoods for each node of a TAN. Experimental tests verify that deBILS offers substantially higher search speed and solution quality not only than ordinary BILS, but also the genetic algorithm and scatter search algorithm

Differential evolution with an evolution path: a DEEP evolutionary algorithm

Utilizing cumulative correlation information already existing in an evolutionary process, this paper proposes a predictive approach to the reproduction mechanism of new individuals for differential evolution (DE) algorithms. DE uses a distributed model (DM) to generate new individuals, which is relatively explorative, whilst evolution strategy (ES) uses a centralized model (CM) to generate offspring, which through adaptation retains a convergence momentum. This paper adopts a key feature in the CM of a covariance matrix adaptation ES, the cumulatively learned evolution path (EP), to formulate a new evolutionary algorithm (EA) framework, termed DEEP, standing for DE with an EP. Without mechanistically combining two CM and DM based algorithms together, the DEEP framework offers advantages of both a DM and a CM and hence substantially enhances performance. Under this architecture, a self-adaptation mechanism can be built inherently in a DEEP algorithm, easing the task of predetermining algorithm control parameters. Two DEEP variants are developed and illustrated in the paper. Experiments on the CEC'13 test suites and two practical problems demonstrate that the DEEP algorithms offer promising results, compared with the original DEs and other relevant state-of-the-art EAs

Pyramid: Enhancing Selectivity in Big Data Protection with Count Featurization

Protecting vast quantities of data poses a daunting challenge for the growing number of organizations that collect, stockpile, and monetize it. The ability to distinguish data that is actually needed from data collected "just in case" would help these organizations to limit the latter's exposure to attack. A natural approach might be to monitor data use and retain only the working-set of in-use data in accessible storage; unused data can be evicted to a highly protected store. However, many of today's big data applications rely on machine learning (ML) workloads that are periodically retrained by accessing, and thus exposing to attack, the entire data store. Training set minimization methods, such as count featurization, are often used to limit the data needed to train ML workloads to improve performance or scalability. We present Pyramid, a limited-exposure data management system that builds upon count featurization to enhance data protection. As such, Pyramid uniquely introduces both the idea and proof-of-concept for leveraging training set minimization methods to instill rigor and selectivity into big data management. We integrated Pyramid into Spark Velox, a framework for ML-based targeting and personalization. We evaluate it on three applications and show that Pyramid approaches state-of-the-art models while training on less than 1% of the raw data

Finding High-Dimensional D-OptimalDesigns for Logistic Models via Differential Evolution

D-optimal designs are frequently used in controlled experiments to obtain the most accurateestimate of model parameters at minimal cost. Finding them can be a challenging task, especially whenthere are many factors in a nonlinear model. As the number of factors becomes large and interact withone another, there are many more variables to optimize and the D-optimal design problem becomes highdimensionaland non-separable. Consequently, premature convergence issues arise. Candidate solutions gettrapped in local optima and the classical gradient-based optimization approaches to search for the D-optimaldesigns rarely succeed. We propose a specially designed version of differential evolution (DE) which is arepresentative gradient-free optimization approach to solve such high-dimensional optimization problems.The proposed specially designed DE uses a new novelty-based mutation strategy to explore the variousregions in the search space. The exploration of the regions will be carried out differently from the previouslyexplored regions and the diversity of the population can be preserved. The proposed novelty-based mutationstrategy is collaborated with two common DE mutation strategies to balance exploration and exploitationat the early or medium stage of the evolution. Additionally, we adapt the control parameters of DE as theevolution proceeds. Using logistic models with several factors on various design spaces as examples, oursimulation results show our algorithm can find D-optimal designs efficiently and the algorithm outperformsits competitors. As an application, we apply our algorithm and re-design a 10-factor car refueling experimentwith discrete and continuous factors and selected pairwise interactions. Our proposed algorithm was able toconsistently outperform the other algorithms and find a more efficient D-optimal design for the problem

Adaptive multimodal continuous ant colony optimization

Seeking multiple optima simultaneously, which multimodal optimization aims at, has attracted increasing attention but remains challenging. Taking advantage of ant colony optimization algorithms in preserving high diversity, this paper intends to extend ant colony optimization algorithms to deal with multimodal optimization. First, combined with current niching methods, an adaptive multimodal continuous ant colony optimization algorithm is introduced. In this algorithm, an adaptive parameter adjustment is developed, which takes the difference among niches into consideration. Second, to accelerate convergence, a differential evolution mutation operator is alternatively utilized to build base vectors for ants to construct new solutions. Then, to enhance the exploitation, a local search scheme based on Gaussian distribution is self-adaptively performed around the seeds of niches. Together, the proposed algorithm affords a good balance between exploration and exploitation. Extensive experiments on 20 widely used benchmark multimodal functions are conducted to investigate the influence of each algorithmic component and results are compared with several state-of-the-art multimodal algorithms and winners of competitions on multimodal optimization. These comparisons demonstrate the competitive efficiency and effectiveness of the proposed algorithm, especially in dealing with complex problems with high numbers of local optima

On the use of biased-randomized algorithms for solving non-smooth optimization problems

Soft constraints are quite common in real-life applications. For example, in freight transportation, the fleet size can be enlarged by outsourcing part of the distribution service and some deliveries to customers can be postponed as well; in inventory management, it is possible to consider stock-outs generated by unexpected demands; and in manufacturing processes and project management, it is frequent that some deadlines cannot be met due to delays in critical steps of the supply chain. However, capacity-, size-, and time-related limitations are included in many optimization problems as hard constraints, while it would be usually more realistic to consider them as soft ones, i.e., they can be violated to some extent by incurring a penalty cost. Most of the times, this penalty cost will be nonlinear and even noncontinuous, which might transform the objective function into a non-smooth one. Despite its many practical applications, non-smooth optimization problems are quite challenging, especially when the underlying optimization problem is NP-hard in nature. In this paper, we propose the use of biased-randomized algorithms as an effective methodology to cope with NP-hard and non-smooth optimization problems in many practical applications. Biased-randomized algorithms extend constructive heuristics by introducing a nonuniform randomization pattern into them. Hence, they can be used to explore promising areas of the solution space without the limitations of gradient-based approaches, which assume the existence of smooth objective functions. Moreover, biased-randomized algorithms can be easily parallelized, thus employing short computing times while exploring a large number of promising regions. This paper discusses these concepts in detail, reviews existing work in different application areas, and highlights current trends and open research lines

The SOS Platform: Designing, Tuning and Statistically Benchmarking Optimisation Algorithms

open access articleWe present Stochastic Optimisation Software (SOS), a Java platform facilitating the algorithmic design process and the evaluation of metaheuristic optimisation algorithms. SOS reduces the burden of coding miscellaneous methods for dealing with several bothersome and time-demanding tasks such as parameter tuning, implementation of comparison algorithms and testbed problems, collecting and processing data to display results, measuring algorithmic overhead, etc. SOS provides numerous off-the-shelf methods including: (1) customised implementations of statistical tests, such as the Wilcoxon rank-sum test and the Holm–Bonferroni procedure, for comparing the performances of optimisation algorithms and automatically generating result tables in PDF and formats; (2) the implementation of an original advanced statistical routine for accurately comparing couples of stochastic optimisation algorithms; (3) the implementation of a novel testbed suite for continuous optimisation, derived from the IEEE CEC 2014 benchmark, allowing for controlled activation of the rotation on each testbed function. Moreover, we briefly comment on the current state of the literature in stochastic optimisation and highlight similarities shared by modern metaheuristics inspired by nature. We argue that the vast majority of these algorithms are simply a reformulation of the same methods and that metaheuristics for optimisation should be simply treated as stochastic processes with less emphasis on the inspiring metaphor behind them