Hierarchical clustering of gene expression profiles with graphics hardware acceleration

Authors:
Qiong Zhang;Yingsha Zhang
Affiliations:
College of Computer Science and Technology, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang 310027, China;Medical School, University of Wisconsin-Madison, USA
Venue:
Pattern Recognition Letters
Year:
2006

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Abstract

Hierarchical clustering is becoming a de facto standard for analyzing gene expression data. But high computational complexity limits its application in high throughput processing of massive microarray data. An implementation based on commodity graphics hardware is proposed to accelerate this process by employing the parallelism and programmability in graphics pipeline. Significant acceleration is achieved by careful design and implementations, especially in the distance calculation part. The performance comparison between CPU and GPU implementation gives inspiring results.