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» Optimizing Complex Loss Functions in Structured Prediction
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CORR
2010
Springer
110views Education» more  CORR 2010»
14 years 9 months ago
Detecting communities of triangles in complex networks using spectral optimization
The study of the sub-structure of complex networks is of major importance to relate topology and functionality. Many efforts have been devoted to the analysis of the modular struc...
Belkacem Serrour, Alex Arenas, Sergio Gómez
BMCBI
2006
116views more  BMCBI 2006»
14 years 9 months ago
Optimized mixed Markov models for motif identification
Background: Identifying functional elements, such as transcriptional factor binding sites, is a fundamental step in reconstructing gene regulatory networks and remains a challengi...
Weichun Huang, David M. Umbach, Uwe Ohler, Leping ...
RECOMB
2003
Springer
15 years 10 months ago
An integrated probabilistic model for functional prediction of proteins
We develop an integrated probabilistic model to combine protein physical interactions, genetic interactions, highly correlated gene expression network, protein complex data, and d...
Minghua Deng, Ting Chen, Fengzhu Sun
ISMB
1996
14 years 11 months ago
A Knowledge-Based Method for Protein Structure Refinement and Prediction
The native conformation of a protein, in a given environment, is determined entirely by the various interatomic interactions dictated by the amino acid sequence (1-3). We describe...
Shankar Subramaniam, David K. Tcheng, James M. Fen...
BMCBI
2008
145views more  BMCBI 2008»
14 years 9 months ago
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction
Background: Amino acids responsible for structure, core function or specificity may be inferred from multiple protein sequence alignments where a limited set of residue types are ...
Jonathan R. Manning, Emily R. Jefferson, Geoffrey ...