In this work we present a contrast pattern kernel for strings. In this kernel, the feature extraction is based on contrast patterns, that are substrings (patterns) common for the positive class but rare for the negative one. The presented idea can be also illustrated as the extension of a spectrum kernel, investigated in previous work [11]. This extension consists on incorporating feature selection based on contrast patterns to the spectrum kernel. Therefore, presentation of contrast pattern kernel was referenced to the spectrum kernel and the results of tests done were compared with those obtained for the spectrum kernel. Kernels were tested on the data sets obtained from the Phospho.ELM database. These data incoroporate amino acids sequences to which specified enzymes (protein kinases) were assigned. The enzymes catalyze reaction of phosphorylation for these sequences.

Date Published: 6 October 2011
PDF: 8 pages
Proc. SPIE 8008, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2011, 80080T (6 October 2011); doi: 10.1117/12.906689

Published in SPIE Proceedings Vol. 8008:
Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2011
Ryszard S. Romaniuk, Editor(s)