BioCRF is an implementation of Grammatical-Restrained Hidden Conditional Random Fields (GRHCRFs) , an extension of linear HCRF to include prior knowledge about the problem at hand by means of a regular grammar. This results very useful in several Bioinformatics problems where only solution that agree with a regular grammar rules are biologically meaningful.
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Piero Fariselli, Castrense Savojardo, Pier L Martelli and Rita Casadio
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications
Algorithms for Molecular Biology 2009, 4:13