Framing Apache Spark in life sciences

Advances in high-throughput and digital technologies have required the adoption of big data for handling complex tasks in life sciences. However, the drift to big data led researchers to face technical and infrastructural challenges for storing, sharing, and analysing them. In fact, this kind of tasks requires distributed computing systems and algorithms able to ensure efficient processing. Cutting edge distributed programming frameworks allow to implement flexible algorithms able to adapt the computation to the data over on-premise HPC clusters or cloud architectures. In this context, Apache Spark is a very powerful HPC engine for large-scale data processing on clusters. Also thanks to specialised libraries for working with structured and relational data, it allows to support machine learning, graph-based computation, and stream processing. This review article is aimed at helping life sciences researchers to ascertain the features of Apache Spark and to assess whether it can be successfully used in their research activities

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

Facilitating High Performance Code Parallelization

With the surge of social media on one hand and the ease of obtaining information due to cheap sensing devices and open source APIs on the other hand, the amount of data that can be processed is as well vastly increasing. In addition, the world of computing has recently been witnessing a growing shift towards massively parallel distributed systems due to the increasing importance of transforming data into knowledge in today’s data-driven world. At the core of data analysis for all sorts of applications lies pattern matching. Therefore, parallelizing pattern matching algorithms should be made efficient in order to cater to this ever-increasing abundance of data. We propose a method that automatically detects a user’s single threaded function call to search for a pattern using Java’s standard regular expression library, and replaces it with our own data parallel implementation using Java bytecode injection. Our approach facilitates parallel processing on different platforms consisting of shared memory systems (using multithreading and NVIDIA GPUs) and distributed systems (using MPI and Hadoop). The major contributions of our implementation consist of reducing the execution time while at the same time being transparent to the user. In addition to that, and in the same spirit of facilitating high performance code parallelization, we present a tool that automatically generates Spark Java code from minimal user-supplied inputs. Spark has emerged as the tool of choice for efficient big data analysis. However, users still have to learn the complicated Spark API in order to write even a simple application. Our tool is easy to use, interactive and offers Spark’s native Java API performance. To the best of our knowledge and until the time of this writing, such a tool has not been yet implemented

Heterogeneity-aware scheduling and data partitioning for system performance acceleration

Over the past decade, heterogeneous processors and accelerators have become increasingly prevalent in modern computing systems. Compared with previous homogeneous parallel machines, the hardware heterogeneity in modern systems provides new opportunities and challenges for performance acceleration. Classic operating systems optimisation problems such as task scheduling, and application-specific optimisation techniques such as the adaptive data partitioning of parallel algorithms, are both required to work together to address hardware heterogeneity. Significant effort has been invested in this problem, but either focuses on a specific type of heterogeneous systems or algorithm, or a high-level framework without insight into the difference in heterogeneity between different types of system. A general software framework is required, which can not only be adapted to multiple types of systems and workloads, but is also equipped with the techniques to address a variety of hardware heterogeneity. This thesis presents approaches to design general heterogeneity-aware software frameworks for system performance acceleration. It covers a wide variety of systems, including an OS scheduler targeting on-chip asymmetric multi-core processors (AMPs) on mobile devices, a hierarchical many-core supercomputer and multi-FPGA systems for high performance computing (HPC) centers. Considering heterogeneity from on-chip AMPs, such as thread criticality, core sensitivity, and relative fairness, it suggests a collaborative based approach to co-design the task selector and core allocator on OS scheduler. Considering the typical sources of heterogeneity in HPC systems, such as the memory hierarchy, bandwidth limitations and asymmetric physical connection, it proposes an application-specific automatic data partitioning method for a modern supercomputer, and a topological-ranking heuristic based schedule for a multi-FPGA based reconfigurable cluster. Experiments on both a full system simulator (GEM5) and real systems (Sunway Taihulight Supercomputer and Xilinx Multi-FPGA based clusters) demonstrate the significant advantages of the suggested approaches compared against the state-of-the-art on variety of workloads."This work is supported by St Leonards 7th Century Scholarship and Computer Science PhD funding from University of St Andrews; by UK EPSRC grant Discovery: Pattern Discovery and Program Shaping for Manycore Systems (EP/P020631/1)." -- Acknowledgement

An Improved Parallelized mRMR for Gene Subset Selection in Cancer Classification

DNA microarray technique has become a more attractive tool for cancer classification in the scientific and industrial fields. Based on the previous researchers, the conventional approach for cancer classification is primarily based on morphological appearance of the tumor. The limitations of this approach are bias in identify the tumors by expert and faced the difficulty in differentiate the cancer subtypes due to most cancers being highly related to the specific biological insight.  Thus, this study propose an improved parallelized Minimum Redundancy Maximum Relevance (mRMR), which is a particularly fast feature selection method for finding a set of both relevant and complementary features. The mRMR can identify genes more relevance to biological context that leads to richer biological interpretations. The proposed method is expected to achieve accurate classification performance using small number of predictive genes when tested using two datasets from Cancer Genome Project and compared to previous methods

Ant Colony Optimization

Ant Colony Optimization (ACO) is the best example of how studies aimed at understanding and modeling the behavior of ants and other social insects can provide inspiration for the development of computational algorithms for the solution of difficult mathematical problems. Introduced by Marco Dorigo in his PhD thesis (1992) and initially applied to the travelling salesman problem, the ACO field has experienced a tremendous growth, standing today as an important nature-inspired stochastic metaheuristic for hard optimization problems. This book presents state-of-the-art ACO methods and is divided into two parts: (I) Techniques, which includes parallel implementations, and (II) Applications, where recent contributions of ACO to diverse fields, such as traffic congestion and control, structural optimization, manufacturing, and genomics are presented