An Efficient Convex Nonnegative Network Component Analysis for Gene Regulatory Network Reconstruction

Authors:
Jisheng Dai;Chunqi Chang;Zhongfu Ye;Yeung Sam Hung
Affiliations:
Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong and Department of Electronic Engineering and Information Science, University of Science and Technology o ...;Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong;Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, P.R. China;Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong
Venue:
PRIB '09 Proceedings of the 4th IAPR International Conference on Pattern Recognition in Bioinformatics
Year:
2009

Citing 5
Cited 1

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Abstract

A systems biology problem of reconstructing gene regulatory network from time-course gene expression microarray data via network component analysis (NCA) is investigated in this paper. Inspired by the idea that each column of the connectivity matrix can be estimated independently, we try to propose a fast and stable convex approach for nonnegative NCA (nnNCA). Compared with the existing method, our new method reduces the computational cost substantially, whereas maintains a reasonable accuracy. Both the simulation results and experimental results demonstrate the effectiveness of our method.