Towards a parallel computationally efficient approach to scaling up data stream classification

Advances in hardware technologies allow to capture and process data in real-time and the resulting high throughput data streams require novel data mining approaches. The research area of Data Stream Mining (DSM) is developing data mining algorithms that allow us to analyse these continuous streams of data in real-time. The creation and real-time adaption of classification models from data streams is one of the most challenging DSM tasks. Current classifiers for streaming data address this problem by using incremental learning algorithms. However, even so these algorithms are fast, they are challenged by high velocity data streams, where data instances are incoming at a fast rate. This is problematic if the applications desire that there is no or only a very little delay between changes in the patterns of the stream and absorption of these patterns by the classifier. Problems of scalability to Big Data of traditional data mining algorithms for static (non streaming) datasets have been addressed through the development of parallel classifiers. However, there is very little work on the parallelisation of data stream classification techniques. In this paper we investigate K-Nearest Neighbours (KNN) as the basis for a real-time adaptive and parallel methodology for scalable data stream classification tasks.

A parallel DNA fragment assembly algorithm based on eulerian superpath approach

Fragments assembly is among the core problems in the research of Genome. Although many assembly tools based on the "overlap-layout-consensus" paradigm are widely used such as in the Human Genome Project currently, they still can not resolve the "repeats problem" in the DNA sequencing. For the purpose of resolving such problem, Pevzner et al. put forward a new Euler Superpath assembly algorithm. But it needs a big and complex de Bruijin graph which consumes large amounts of memories i.e. becomes the bottleneck of the performance. We present a parallel DNA fragment assembly algorithm based on the Eularian Superpath theory and solve the bottleneck in the current assembly program. The experimental results demonstrate that our approach has a good scalability, and can be used in DNA assembly of middle and large size of eukaryote genome.

Speedup and scalability analysis of Master-Slave applications on large heterogeneous clusters

Although cluster environments have an enormous potential processing power, real applications that take advantage of this power remain an elusive goal. This is due, in part, to the lack of understanding about the characteristics of the applications best suited for these environments. This paper focuses on Master/Slave applications for large heterogeneous clusters. It defines application, cluster and execution models to derive an analytic expression for the execution time. It defines speedup and derives speedup bounds based on the inherent parallelism of the application and the aggregated computing power of the cluster. The paper derives an analytical expression for efficiency and uses it to define scalability of the algorithm-cluster combination based on the isoefficiency metric. Furthermore, the paper establishes necessary and sufficient conditions for an algorithm-cluster combination to be scalable which are easy to verify and use in practice. Finally, it covers the impact of network contention as the number of processors grow. (C) 2007 Elsevier B.V. All rights reserved.

An Efficient Parallel Algorithm for Multiple Sequence Similarities Calculation Using a Low Complexity Method

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Particle methods parallel implementations by GP-GPU strategies

This paper outlines the problems found in the parallelization of SPH (Smoothed Particle Hydrodynamics) algorithms using Graphics Processing Units. Different results of some parallel GPU implementations in terms of the speed-up and the scalability compared to the CPU sequential codes are shown. The most problematic stage in the GPU-SPH algorithms is the one responsible for locating neighboring particles and building the vectors where this information is stored, since these specific algorithms raise many dificulties for a data-level parallelization. Because of the fact that the neighbor location using linked lists does not show enough data-level parallelism, two new approaches have been pro- posed to minimize bank conflicts in the writing and subsequent reading of the neighbor lists. The first strategy proposes an efficient coordination between CPU-GPU, using GPU algorithms for those stages that allow a straight forward parallelization, and sequential CPU algorithms for those instructions that involve some kind of vector reduction. This coordination provides a relatively orderly reading of the neighbor lists in the interactions stage, achieving a speed-up factor of x47 in this stage. However, since the construction of the neighbor lists is quite expensive, it is achieved an overall speed-up of x41. The second strategy seeks to maximize the use of the GPU in the neighbor's location process by executing a specific vector sorting algorithm that allows some data-level parallelism. Al- though this strategy has succeeded in improving the speed-up on the stage of neighboring location, the global speed-up on the interactions stage falls, due to inefficient reading of the neighbor vectors. Some changes to these strategies are proposed, aimed at maximizing the computational load of the GPU and using the GPU texture-units, in order to reach the maximum speed-up for such codes. Different practical applications have been added to the mentioned GPU codes. First, the classical dam-break problem is studied. Second, the wave impact of the sloshing fluid contained in LNG vessel tanks is also simulated as a practical example of particle methods

StreamCloud: An Elastic Parallel-Distributed Stream Processing Engine

In recent years, applications in domains such as telecommunications, network security or large scale sensor networks showed the limits of the traditional store-then-process paradigm. In this context, Stream Processing Engines emerged as a candidate solution for all these applications demanding for high processing capacity with low processing latency guarantees. With Stream Processing Engines, data streams are not persisted but rather processed on the fly, producing results continuously. Current Stream Processing Engines, either centralized or distributed, do not scale with the input load due to single-node bottlenecks. Moreover, they are based on static configurations that lead to either under or over-provisioning. This Ph.D. thesis discusses StreamCloud, an elastic paralleldistributed stream processing engine that enables for processing of large data stream volumes. Stream- Cloud minimizes the distribution and parallelization overhead introducing novel techniques that split queries into parallel subqueries and allocate them to independent sets of nodes. Moreover, Stream- Cloud elastic and dynamic load balancing protocols enable for effective adjustment of resources depending on the incoming load. Together with the parallelization and elasticity techniques, Stream- Cloud defines a novel fault tolerance protocol that introduces minimal overhead while providing fast recovery. StreamCloud has been fully implemented and evaluated using several real word applications such as fraud detection applications or network analysis applications. The evaluation, conducted using a cluster with more than 300 cores, demonstrates the large scalability, the elasticity and fault tolerance effectiveness of StreamCloud. Resumen En los útimos años, aplicaciones en dominios tales como telecomunicaciones, seguridad de redes y redes de sensores de gran escala se han encontrado con múltiples limitaciones en el paradigma tradicional de bases de datos. En este contexto, los sistemas de procesamiento de flujos de datos han emergido como solución a estas aplicaciones que demandan una alta capacidad de procesamiento con una baja latencia. En los sistemas de procesamiento de flujos de datos, los datos no se persisten y luego se procesan, en su lugar los datos son procesados al vuelo en memoria produciendo resultados de forma continua. Los actuales sistemas de procesamiento de flujos de datos, tanto los centralizados, como los distribuidos, no escalan respecto a la carga de entrada del sistema debido a un cuello de botella producido por la concentración de flujos de datos completos en nodos individuales. Por otra parte, éstos están basados en configuraciones estáticas lo que conducen a un sobre o bajo aprovisionamiento. Esta tesis doctoral presenta StreamCloud, un sistema elástico paralelo-distribuido para el procesamiento de flujos de datos que es capaz de procesar grandes volúmenes de datos. StreamCloud minimiza el coste de distribución y paralelización por medio de una técnica novedosa la cual particiona las queries en subqueries paralelas repartiéndolas en subconjuntos de nodos independientes. Ademas, Stream- Cloud posee protocolos de elasticidad y equilibrado de carga que permiten una optimización de los recursos dependiendo de la carga del sistema. Unidos a los protocolos de paralelización y elasticidad, StreamCloud define un protocolo de tolerancia a fallos que introduce un coste mínimo mientras que proporciona una rápida recuperación. StreamCloud ha sido implementado y evaluado mediante varias aplicaciones del mundo real tales como aplicaciones de detección de fraude o aplicaciones de análisis del tráfico de red. La evaluación ha sido realizada en un cluster con más de 300 núcleos, demostrando la alta escalabilidad y la efectividad tanto de la elasticidad, como de la tolerancia a fallos de StreamCloud.

Modelling continuum mechanics phenomena using three dimensional unstructured meshes on massively parallel processors

The difficulties encountered in implementing large scale CM codes on multiprocessor systems are now fairly well understood. Despite the claims of shared memory architecture manufacturers to provide effective parallelizing compilers, these have not proved to be adequate for large or complex programs. Significant programmer effort is usually required to achieve reasonable parallel efficiencies on significant numbers of processors. The paradigm of Single Program Multi Data (SPMD) domain decomposition with message passing, where each processor runs the same code on a subdomain of the problem, communicating through exchange of messages, has for some time been demonstrated to provide the required level of efficiency, scalability, and portability across both shared and distributed memory systems, without the need to re-author the code into a new language or even to support differing message passing implementations. Extension of the methods into three dimensions has been enabled through the engineering of PHYSICA, a framework for supporting 3D, unstructured mesh and continuum mechanics modeling. In PHYSICA, six inspectors are used. Part of the challenge for automation of parallelization is being able to prove the equivalence of inspectors so that they can be merged into as few as possible.

An efficient mapreduce-based parallel clustering algorithm for distributed traffic subarea division

Traffic subarea division is vital for traffic system management and traffic network analysis in intelligent transportation systems (ITSs). Since existing methods may not be suitable for big traffic data processing, this paper presents a MapReduce-based Parallel Three-Phase K -Means (Par3PKM) algorithm for solving traffic subarea division problem on a widely adopted Hadoop distributed computing platform. Specifically, we first modify the distance metric and initialization strategy of K -Means and then employ a MapReduce paradigm to redesign the optimized K -Means algorithm for parallel clustering of large-scale taxi trajectories. Moreover, we propose a boundary identifying method to connect the borders of clustering results for each cluster. Finally, we divide traffic subarea of Beijing based on real-world trajectory data sets generated by 12,000 taxis in a period of one month using the proposed approach. Experimental evaluation results indicate that when compared with K -Means, Par2PK-Means, and ParCLARA, Par3PKM achieves higher efficiency, more accuracy, and better scalability and can effectively divide traffic subarea with big taxi trajectory data.

A parallel random forest algorithm for big data in a spark cloud computing environment

With the emergence of the big data age, the issue of how to obtain valuable knowledge from a dataset efficiently and accurately has attracted increasingly attention from both academia and industry. This paper presents a Parallel Random Forest (PRF) algorithm for big data on the Apache Spark platform. The PRF algorithm is optimized based on a hybrid approach combining data-parallel and task-parallel optimization. From the perspective of data-parallel optimization, a vertical data-partitioning method is performed to reduce the data communication cost effectively, and a data-multiplexing method is performed is performed to allow the training dataset to be reused and diminish the volume of data. From the perspective of task-parallel optimization, a dual parallel approach is carried out in the training process of RF, and a task Directed Acyclic Graph (DAG) is created according to the parallel training process of PRF and the dependence of the Resilient Distributed Datasets (RDD) objects. Then, different task schedulers are invoked for the tasks in the DAG. Moreover, to improve the algorithm's accuracy for large, high-dimensional, and noisy data, we perform a dimension-reduction approach in the training process and a weighted voting approach in the prediction process prior to parallelization. Extensive experimental results indicate the superiority and notable advantages of the PRF algorithm over the relevant algorithms implemented by Spark MLlib and other studies in terms of the classification accuracy, performance, and scalability.

A framework for fully decentralised cycle stealing

Ordinary desktop computers continue to obtain ever more resources – in-creased processing power, memory, network speed and bandwidth – yet these resources spend much of their time underutilised. Cycle stealing frameworks harness these resources so they can be used for high-performance computing. Traditionally cycle stealing systems have used client-server based architectures which place significant limits on their ability to scale and the range of applica-tions they can support. By applying a fully decentralised network model to cycle stealing the limits of centralised models can be overcome. Using decentralised networks in this manner presents some difficulties which have not been encountered in their previous uses. Generally decentralised ap-plications do not require any significant fault tolerance guarantees. High-performance computing on the other hand requires very stringent guarantees to ensure correct results are obtained. Unfortunately mechanisms developed for traditional high-performance computing cannot be simply translated because of their reliance on a reliable storage mechanism. In the highly dynamic world of P2P computing this reliable storage is not available. As part of this research a fault tolerance system has been created which provides considerable reliability without the need for a persistent storage. As well as increased scalability, fully decentralised networks offer the ability for volunteers to communicate directly. This ability provides the possibility of supporting applications whose tasks require direct, message passing style communication. Previous cycle stealing systems have only supported embarrassingly parallel applications and applications with limited forms of communication so a new programming model has been developed which can support this style of communication within a cycle stealing context. In this thesis I present a fully decentralised cycle stealing framework. The framework addresses the problems of providing a reliable fault tolerance sys-tem and supporting direct communication between parallel tasks. The thesis includes a programming model for developing cycle stealing applications with direct inter-process communication and methods for optimising object locality on decentralised networks.

Cognitive assessment in closed head injury : stability, validity and parallel forms for two neuropsychological measures of recovery

Investigated the psychometric properties of the original and alternate sets of the Trail Making Test (TMT) and the Controlled Oral Word Association Test (COWAT; A. L. Benton and D. Hamsher, 1978) in 50 orthopedic and 15 closed head injured (1 yr after trauma) patients (aged 15–59 yrs). Although the alternate forms of both measures proved to be stable and consistent with each other in both groups, only the parallel sets of TMT reliably discriminated the clinical group from controls. Practice effects in the head injured were significant only for Trail B of TMT. Factor analysis of the control group's results identified Verbal Knowledge as a major contributor to performance on COWAT, whereas TMT was more dependent on Rapid Visual Search and Visuomotor Sequencing.