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JCP
2008
104views more  JCP 2008»
13 years 10 months ago
Analysis and Improved Recognition of Protein Names Using Transductive SVM
We first analyzed protein names using various dictionaries and databases and found five problems with protein names; i.e., the treatment of special characters, the treatment of hom...
Masaki Murata, Tomohiro Mitsumori, Kouichi Doi
BMCBI
2005
134views more  BMCBI 2005»
13 years 10 months ago
Systematic feature evaluation for gene name recognition
In task 1A of the BioCreAtIvE evaluation, systems had to be devised that recognize words and phrases forming gene or protein names in natural language sentences. We approach this ...
Jörg Hakenberg, Steffen Bickel, Conrad Plake,...
BMCBI
2008
178views more  BMCBI 2008»
13 years 11 months ago
A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic ana
Background: Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) ...
Bin Liu, Xiaolong Wang, Lei Lin, Qiwen Dong, Xuan ...
BMCBI
2005
251views more  BMCBI 2005»
13 years 10 months ago
Contextual weighting for Support Vector Machines in literature mining: an application to gene versus protein name disambiguation
Background: The ability to distinguish between genes and proteins is essential for understanding biological text. Support Vector Machines (SVMs) have been proven to be very effici...
Tapio Pahikkala, Filip Ginter, Jorma Boberg, Jouni...
BMCBI
2008
138views more  BMCBI 2008»
13 years 11 months ago
Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote ho
Background: Nonnegative matrix factorization (NMF) is a feature extraction method that has the property of intuitive part-based representation of the original features. This uniqu...
Inkyung Jung, Jaehyung Lee, Soo-Young Lee, Dongsup...