Contrast pattern kernel for strings

Jakub Węcławski; Stanisław Jankowski

doi:10.1117/12.906689

6 October 2011 Contrast pattern kernel for strings

Jakub Węcławski, Stanisław Jankowski

Proceedings Volume 8008, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2011; 80080T (2011) https://doi.org/10.1117/12.906689
Event: Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2011, 2011, Wilga, Poland

Abstract

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.

Citation Download Citation

Jakub Węcławski and Stanisław Jankowski "Contrast pattern kernel for strings", Proc. SPIE 8008, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2011, 80080T (6 October 2011); https://doi.org/10.1117/12.906689

ACCESS THE FULL ARTICLE

INSTITUTIONAL
Select your institution to access the SPIE Digital Library.

SELECT YOUR INSTITUTION

PERSONAL
Sign in with your SPIE account to access your personal subscriptions or to use specific features such as save to my library, sign up for alerts, save searches, etc.

PERSONAL SIGN IN

No SPIE Account? Create one

PURCHASE THIS CONTENT

SUBSCRIBE TO DIGITAL LIBRARY

50 downloads per 1-year subscription

Members: $195

Non-members: $335 ADD TO CART

25 downloads per 1 - year subscription

Members: $145

Non-members: $250 ADD TO CART

PURCHASE SINGLE ARTICLE

Includes PDF, HTML & Video, when available

Members: $17.00

Non-members: $21.00 ADD TO CART

PROCEEDINGS
8 PAGES

DOWNLOAD PAPER SAVE TO MY LIBRARY

GET CITATION

RIGHTS & PERMISSIONS

Get copyright permission Get copyright permission on Copyright Marketplace

KEYWORDS

Image classification

Databases

Proteins

Feature extraction

Performance modeling

Data modeling

Feature selection

Show All Keywords

Keywords/Phrases

Search In:

Publication Years