Yuhong Zhang

Ph.D, Assitant Professor

College of Information Science and Engineering

Henan University of Technology

E-mail:yhzhang@haut.edu.cn

Visiting Scholar
Department of Electrical Engineering and Computer Science
Northwestern University

Research Interests

Data mining algorithm design and it's application in Bioinformatics
Acceleration of data mining kernels using hardware/software techniques
Social Network and its Graph Algorithms
Acceleration of Bioinformatics computation using HPC techniques ( such as many-core GPU and muti-core CPU )

Recent Publications:

Yuhong Zhang, Sanchit Misra, Daniel Honbo, Ankit Agrawal, Wei-keng Liao, and Alok Choudhary. Efficient Pairwise Statistical Significance Estimation for Local Sequence Alignment Using GPU. In the 1st IEEE International Conference on Computational Advances in Bio and medical Sciences, pp. 226-231, February 2011.

Yuhong Zhang, Sanchit Misra, Ankit Agrawal, Md. Mostofa Ali Patwary, Wei-keng Liao, Zhiguang Qin, and Alok Choudhary. Accelerating Pairwise Statistical Significance Estimation for Local Alignment by Harvesting GPU's Power. BMC Bioinformatics, 2012, BMC Bioinformatics, 13(Suppl 5):S3 doi:10.1186/1471-2105-13-S5-S3.

Yuhong Zhang, Md. Mostofa Ali Patwary, Sanchit Misra, Ankit Agrawal, Wei-keng Liao, and Alok Choudhary. Enhancing Parallelism of Pairwise Statistical Significance Estimation for Local Sequence Alignment. Proceedings of HiPC Workshops, Workshop on Hybrid Multi-core Computing, pp. 1-8, Dec. 2011.

Software 1: CUDA-PSSE

CUDA-PSSE is a GPU implementation to accelerate Pairwise Statistical Significance Estimation (PSSE) for local sequence alignment using standard substitution matrix and position specific score matrix (PSSM). This software of PSSE takes advantage of NVIDIA's CUDA programming environment and the OpenMP parallel programming model.

Software Requirements:

1. CUDA toolkits and SDK 4.0

2. Single or multiple CUDA-enabled GPUs with compute capability 2.0 and higher

3. GCC 4.4+

4. Linux-based Operating System

Download CUDA-PSSE source code

Software 2: OpenMP/MPI-PSSE

OpenMP/MPI is a multi-core based implementation to accelerate Pairwise Statistical Significance Estimation (PSSE) for local sequence alignment. This software reap the benefits of multi-core by using MPI or/and OpenMP paradigms. The software also outputs a number of statistics about the sequence alignment technique used, which can be used to compare retrieval accuracy of PSSE.

Software Requirements:

1. GCC 4.4+

2. Linux-based Operating System

Download MPI/OpenMP-PSSE source code

Sample of output statistics file(.scv file)

Contact Information

E-mail: yuhong AT eecs.northwestern.edu

L470 Technological Institute
2145 Sheridan Road
Department of Electrical Engineering and Computer Science
Northwestern University
Evanston, IL 60208-3118