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» Support Vector Training of Protein Alignment Models
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BMCBI
2007
112views more  BMCBI 2007»
13 years 7 months ago
PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments
Background: By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to ...
Daniel R. Caffrey, Paul H. Dana, Vidhya Mathur, Ma...
BIBE
2007
IEEE
167views Bioinformatics» more  BIBE 2007»
13 years 11 months ago
Assessing the Performance of Macromolecular Sequence Classifiers
Machine learning approaches offer some of the most cost-effective approaches to building predictive models (e.g., classifiers) in a broad range of applications in computational bio...
Cornelia Caragea, Jivko Sinapov, Vasant Honavar, D...
KDD
2008
ACM
178views Data Mining» more  KDD 2008»
14 years 8 months ago
Training structural svms with kernels using sampled cuts
Discriminative training for structured outputs has found increasing applications in areas such as natural language processing, bioinformatics, information retrieval, and computer ...
Chun-Nam John Yu, Thorsten Joachims
BMCBI
2010
190views more  BMCBI 2010»
13 years 7 months ago
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility
Background: It is well known that most of the binding free energy of protein interaction is contributed by a few key hot spot residues. These residues are crucial for understandin...
Jun-Feng Xia, Xing-Ming Zhao, Jiangning Song, De-S...
ICML
2008
IEEE
14 years 8 months ago
Large scale manifold transduction
We show how the regularizer of Transductive Support Vector Machines (TSVM) can be trained by stochastic gradient descent for linear models and multi-layer architectures. The resul...
Michael Karlen, Jason Weston, Ayse Erkan, Ronan Co...