IEICE Electronics Express
Online ISSN : 1349-2543
ISSN-L : 1349-2543
LETTER
The prediction of membrane protein types with NPE
Lipeng WangZhanting YuanXuhui ChenZhifang Zhou
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JOURNALS FREE ACCESS

2010 Volume 7 Issue 6 Pages 397-402

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Abstract

The first step in membrane protein type prediction is how to represent the sample of a protein. In this work, a protein can be represented by a high-dimension feature vector by using the DC (Dipeptide Composition) method. This extremely high dimensionality of the protein data may increase the computing time and classifier complexity. Thus, a linear dimensionality reduction algorithm NPE (Neighborhood Preserving Embedding) is introduced to extract the indispensable features from the high-dimensional DC space. Based on the reduced low-dimensional features, K-NN (K-nearest neighbor) classifier is introduced to identify the types of membrane proteins. Finally, a very encouraging experimental result is obtained.

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© 2010 by The Institute of Electronics, Information and Communication Engineers
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