High-throughput multi-dimensional scaling (HiT-MDS) for cDNA-array expression data

Authors:
M. Strickert;S. Teichmann;N. Sreenivasulu;U. Seiffert
Affiliations:
Pattern Recognition Group, Gene Expression Group, Institute of Plant Genetics and Crop Plant Research Gatersleben;University of Osnabrück;Pattern Recognition Group, Gene Expression Group, Institute of Plant Genetics and Crop Plant Research Gatersleben;Pattern Recognition Group, Gene Expression Group, Institute of Plant Genetics and Crop Plant Research Gatersleben
Venue:
ICANN'05 Proceedings of the 15th international conference on Artificial Neural Networks: biological Inspirations - Volume Part I
Year:
2005

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Abstract

Multidimensional Scaling (MDS) is a powerful dimension reduction technique for embedding high-dimensional data into a low-dimensional target space. Thereby, the distance relationships in the source are reconstructed in the target space as best as possible according to a given embedding criterion. Here, a new stress function with intuitive properties and a very good convergence behavior is presented. Optimization is combined with an efficient implementation for calculating dynamic distance matrix correlations, and the implementation can be transferred to other related algorithms. The suitability of the proposed MDS for high-throughput data (HiT-MDS) is studied in applications to macroarray analysis for up to 12,000 genes.