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

Local search: A guide for the information retrieval practitioner

There are a number of combinatorial optimisation problems in information retrieval in which the use of local search methods are worthwhile. The purpose of this paper is to show how local search can be used to solve some well known tasks in information retrieval (IR), how previous research in the field is piecemeal, bereft of a structure and methodologically flawed, and to suggest more rigorous ways of applying local search methods to solve IR problems. We provide a query based taxonomy for analysing the use of local search in IR tasks and an overview of issues such as fitness functions, statistical significance and test collections when conducting experiments on combinatorial optimisation problems. The paper gives a guide on the pitfalls and problems for IR practitioners who wish to use local search to solve their research issues, and gives practical advice on the use of such methods. The query based taxonomy is a novel structure which can be used by the IR practitioner in order to examine the use of local search in IR

Parallel delay multiply and sum algorithm for microwave medical imaging using spark big data framework

Microwave imaging systems are currently being investigated for breast cancer, brain stroke and neurodegenerative disease detection due to their low cost, portable and wearable nature. At present, commonly used radar-based algorithms for microwave imaging are based on the delay and sum algorithm. These algorithms use ultra-wideband signals to reconstruct a 2D image of the targeted object or region. Delay multiply and sum is an extended version of the delay and sum algorithm. However, it is computationally expensive and time-consuming. In this paper, the delay multiply and sum algorithm is parallelised using a big data framework. The algorithm uses the Spark MapReduce programming model to improve its efficiency. The most computational part of the algorithm is pixel value calculation, where signals need to be multiplied in pairs and summed. The proposed algorithm broadcasts the input data and executes it in parallel in a distributed manner. The Spark-based parallel algorithm is compared with sequential and Python multiprocessing library implementation. The experimental results on both a standalone machine and a high-performance cluster show that Spark significantly accelerates the image reconstruction process without affecting its accuracy

Literature Review on Big Data Analytics Methods

Companies and industries are faced with a huge amount of raw data, which have information and knowledge in their hidden layer. Also, the format, size, variety, and velocity of generated data bring complexity for industries to apply them in an efficient and effective way. So, complexity in data analysis and interpretation incline organizations to deploy advanced tools and techniques to overcome the difficulties of managing raw data. Big data analytics is the advanced method that has the capability for managing data. It deploys machine learning techniques and deep learning methods to benefit from gathered data. In this research, the methods of both ML and DL have been discussed, and an ML/DL deployment model for IOT data has been proposed

Spatial Optimization Methods And System For Redistricting Problems

Redistricting is the process of dividing space into districts or zones while optimizing a set of spatial criteria under certain constraints. Example applications of redistricting include political redistricting, school redistricting, business service planning, and city management, among many others. Redistricting is a mission-critical component in operating governments and businesses alike. In research fields, redistricting (or region building) are also widely used, such as climate zoning, traffic zone analysis, and complex network analysis. However, as a combinatorial optimization problem, redistricting optimization remains one of the most difficult research challenges. There are currently few automated redistricting methods that have the optimization capability to produce solutions that meet practical needs. The absence of effective and efficient computational approaches for redistricting makes it extremely time-consuming and difficult for an individual person to consider multiple criteria/constraints and manually create solutions using a trial-and-error approach. To address both the scientific and practical challenges in solving real-world redistricting problems, this research advances the methodology and application of redistricting by developing a new computational spatial optimization method and a system platform that can address a wide range of redistricting problems, in an automated and computation-assisted manner. The research has three main contributions. First, an efficient and effective spatial optimization method is developed for redistricting. The new method is based on a spatially constrained and Tabu-based heuristics, which can optimize multiple criteria under multiple constraints to construct high-quality optimization solutions. The new approach is evaluated with real-world redistricting applications and compared with existing methods. Evaluation results show that the new optimization algorithm is more efficient (being able to allow real-time user interaction), more flexible (considering multiple user-expressed criteria and constraints), and more powerful (in terms of optimization quality) than existing methods. As such, it has the potential to enable general users to perform complex redistricting tasks. Second, a redistricting system, iRedistrict, is developed based on the newly developed spatial optimization method to provide user-friendly visual interface for defining redistricting problems, incorporating domain knowledge, configuring optimization criteria and methodology parameters, and ultimately meeting the needs of real-world applications for tackling complex redistricting tasks. It is particularly useful for users of different skill levels, including researchers, practitioners, and the general public, and thus enables public participation in challenging redistricting tasks that are of immense public interest. Performance evaluations with real-world case studies are carried out. Further computational strategies are developed and implemented to handle large datasets. Third, the newly developed spatial optimization method is extended to solve a different spatial optimization problem, i.e., spatial community structure detection in complex networks, which is to partition networks to discover spatial communities by optimizing an objective function. Moreover, a series of new evaluations are carried out with synthetic datasets. This set of evaluations is different from the previous evaluations with case studies in that, the optimal solution is known with synthetic data and therefore it is possible to evaluate (1) whether the optimization method can discover the true pattern (global optima), and (2) how different data characteristics may affect the performance of the method. Evaluation results reveal that existing non-spatial methods are not robust in detecting spatial community structure, which may produce dramatically different outcomes for the same data with different characteristics, such as different spatial aggregations, sampling rates, or noise levels. The new optimization method with spatial constraints is significantly more stable and consistent. In addition to evaluations with synthetic datasets, a case study is also carried out to detect urban community structure with human movements, to demonstrate the application and effectiveness of the approach

Knowledge management overview of feature selection problem in high-dimensional financial data: Cooperative co-evolution and Map Reduce perspectives

The term big data characterizes the massive amounts of data generation by the advanced technologies in different domains using 4Vs volume, velocity, variety, and veracity-to indicate the amount of data that can only be processed via computationally intensive analysis, the speed of their creation, the different types of data, and their accuracy. High-dimensional financial data, such as time-series and space-Time data, contain a large number of features (variables) while having a small number of samples, which are used to measure various real-Time business situations for financial organizations. Such datasets are normally noisy, and complex correlations may exist between their features, and many domains, including financial, lack the al analytic tools to mine the data for knowledge discovery because of the high-dimensionality. Feature selection is an optimization problem to find a minimal subset of relevant features that maximizes the classification accuracy and reduces the computations. Traditional statistical-based feature selection approaches are not adequate to deal with the curse of dimensionality associated with big data. Cooperative co-evolution, a meta-heuristic algorithm and a divide-And-conquer approach, decomposes high-dimensional problems into smaller sub-problems. Further, MapReduce, a programming model, offers a ready-To-use distributed, scalable, and fault-Tolerant infrastructure for parallelizing the developed algorithm. This article presents a knowledge management overview of evolutionary feature selection approaches, state-of-The-Art cooperative co-evolution and MapReduce-based feature selection techniques, and future research directions

Multi-Objective Optimization of Input Machining Parameters to Machined AISI D2 Tool Steel Material

Poor surface finish on die and mould transfers the bad quality to processed parts. High surface roughness is an example of bad surface finish that is normally reduced by manual polishing after conventional milling machining process. Therefore, in order to avoid disadvantages by manual polishing and disadvantage by the machining, a sequence of two machining operations is proposed. The main operation is run by the machining and followed by Rotary Ultrasonic Machining Assisted Milling (RUMAM). However, this sequence operation requires optimum input parameters to generate the lowest surface roughness. Hence, this paper aims to optimize the input parameters for both machining operations by three soft-computing approaches – Genetic Algorithm, Tabu Search, and Particle Swarm Optimization. The method adopted in this paper begins with a fitness function development, optimization approach usage and ends up with result evaluation and validation. The soft-computing approaches result outperforms the experiment result in having minimum surface roughness. Based on the findings, the conclusion suggests that the lower surface roughness can be obtained by applying the input parameters at maximum for the cutting speed and vibration frequency, and at minimum for machining feed rate. This finding assists manufacturers to apply proper input values to obtain parts with minimum surface roughness