Kenli Li

Bio: Kenli Li is an academic researcher from Hunan University. The author has contributed to research in topics: Computer science & Scheduling (computing). The author has an hindex of 48, co-authored 478 publications receiving 8784 citations. Previous affiliations of Kenli Li include National University of Defense Technology & Agency for Science, Technology and Research.

iProX: an integrated proteome resource.

Abstract: Sharing of research data in public repositories has become best practice in academia. With the accumulation of massive data, network bandwidth and storage requirements are rapidly increasing. The ProteomeXchange (PX) consortium implements a mode of centralized metadata and distributed raw data management, which promotes effective data sharing. To facilitate open access of proteome data worldwide, we have developed the integrated proteome resource iProX (http://www.iprox.org) as a public platform for collecting and sharing raw data, analysis results and metadata obtained from proteomics experiments. The iProX repository employs a web-based proteome data submission process and open sharing of mass spectrometry-based proteomics datasets. Also, it deploys extensive controlled vocabularies and ontologies to annotate proteomics datasets. Users can use a GUI to provide and access data through a fast Aspera-based transfer tool. iProX is a full member of the PX consortium; all released datasets are freely accessible to the public. iProX is based on a high availability architecture and has been deployed as part of the proteomics infrastructure of China, ensuring long-term and stable resource support. iProX will facilitate worldwide data analysis and sharing of proteomics experiments.

A Parallel Random Forest Algorithm for Big Data in a Spark Cloud Computing Environment

Abstract: 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. With the expansion of the scale of the random forest model and the Spark cluster, the advantage of the PRF algorithm is more obvious.

A genetic algorithm for task scheduling on heterogeneous computing systems using multiple priority queues

Abstract: On parallel and distributed heterogeneous computing systems, a heuristic-based task scheduling algorithm typically consists of two phases: task prioritization and processor selection. In a heuristic based task scheduling algorithm, different prioritization will produce different makespan on a heterogeneous computing system. Therefore, a good scheduling algorithm should be able to efficiently assign a priority to each subtask depending on the resources needed to minimize makespan. In this paper, a task scheduling scheme on heterogeneous computing systems using a multiple priority queues genetic algorithm (MPQGA) is proposed. The basic idea of our approach is to exploit the advantages of both evolutionary-based and heuristic-based algorithms while avoiding their drawbacks. The proposedalgorithm incorporates a genetic algorithm (GA) approach to assign a priority to each subtask while using a heuristic-based earliest finish time (EFT) approach to search for a solution for the task-to-processor mapping. The MPQGA method also designs crossover, mutation, and fitness function suitable for the scenario of directed acyclic graph (DAG) scheduling. The experimental results for large-sized problems from a large set of randomly generated graphs as well as graphs of real-world problems with various characteristics show that the proposed MPQGA algorithm outperforms two non-evolutionary heuristics and a random search method in terms of schedule quality.

Hyperspectral Anomaly Detection With Attribute and Edge-Preserving Filters

Abstract: A novel method for anomaly detection in hyperspectral images is proposed. The method is based on two ideas. First, compared with the surrounding background, objects with anomalies usually appear with small areas and distinct spectral signatures. Second, for both the background and the objects with anomalies, pixels in the same class are usually highly correlated in the spatial domain. In this paper, the pixels with specific area property and distinct spectral signatures are first detected with attribute filtering and a Boolean map-based fusion approach in order to obtain an initial pixel-wise detection result. Then, the initial detection result is refined with edge-preserving filtering to make full use of the spatial correlations among adjacent pixels. Compared with other widely used anomaly detection methods, the experimental results obtained on real hyperspectral data sets including airport, beach, and urban scenes demonstrate that the performance of the proposed method is quite competitive in terms of computing time and detection accuracy.

vCUDA: GPU-Accelerated High-Performance Computing in Virtual Machines

Abstract: This paper describes vCUDA, a general-purpose graphics processing unit (GPGPU) computing solution for virtual machines (VMs). vCUDA allows applications executing within VMs to leverage hardware acceleration, which can be beneficial to the performance of a class of high-performance computing (HPC) applications. The key insights in our design include API call interception and redirection and a dedicated RPC system for VMs. With API interception and redirection, Compute Unified Device Architecture (CUDA) applications in VMs can access a graphics hardware device and achieve high computing performance in a transparent way. In the current study, vCUDA achieved a near-native performance with the dedicated RPC system. We carried out a detailed analysis of the performance of our framework. Using a number of unmodified official examples from CUDA SDK and third-party applications in the evaluation, we observed that CUDA applications running with vCUDA exhibited a very low performance penalty in comparison with the native environment, thereby demonstrating the viability of vCUDA architecture.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fundamentals of Queueing Theory

Abstract: Praise for the Third Edition: "This is one of the best books available. Its excellent organizational structure allows quick reference to specific models and its clear presentation . . . solidifies the understanding of the concepts being presented."IIE Transactions on Operations EngineeringThoroughly revised and expanded to reflect the latest developments in the field, Fundamentals of Queueing Theory, Fourth Edition continues to present the basic statistical principles that are necessary to analyze the probabilistic nature of queues. Rather than presenting a narrow focus on the subject, this update illustrates the wide-reaching, fundamental concepts in queueing theory and its applications to diverse areas such as computer science, engineering, business, and operations research.This update takes a numerical approach to understanding and making probable estimations relating to queues, with a comprehensive outline of simple and more advanced queueing models. Newly featured topics of the Fourth Edition include:Retrial queuesApproximations for queueing networksNumerical inversion of transformsDetermining the appropriate number of servers to balance quality and cost of serviceEach chapter provides a self-contained presentation of key concepts and formulae, allowing readers to work with each section independently, while a summary table at the end of the book outlines the types of queues that have been discussed and their results. In addition, two new appendices have been added, discussing transforms and generating functions as well as the fundamentals of differential and difference equations. New examples are now included along with problems that incorporate QtsPlus software, which is freely available via the book's related Web site.With its accessible style and wealth of real-world examples, Fundamentals of Queueing Theory, Fourth Edition is an ideal book for courses on queueing theory at the upper-undergraduate and graduate levels. It is also a valuable resource for researchers and practitioners who analyze congestion in the fields of telecommunications, transportation, aviation, and management science.