Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso.
Morihiro HayashidaMayumi KamadaJiangning SongTatsuya AkutsuPublished in: BMC Syst. Biol. (2013)
Keyphrases
- conditional random fields
- contact map
- contact maps
- protein structure prediction
- amino acids
- protein structure
- crf model
- secondary structure
- long range
- random fields
- protein chains
- hidden markov models
- probabilistic model
- higher order
- maximum entropy
- graphical models
- subcellular localization
- markov random field
- protein sequences
- structured prediction
- information extraction
- image labeling
- pairwise
- generative model
- amino acid sequences
- semantic segmentation
- sequence analysis
- least squares
- superpixels
- natural images
- contextual features
- structural motifs
- genomic sequences
- protein folding
- max margin
- genome wide
- sparse representation
- computer vision
- feature selection
- multiscale
- natural language
- sequence alignment
- linear regression
- graph cuts