A method for peptide binding prediction includes receiving a peptide sequence descriptor and descriptors of contacting amino acids on major histocompatibility complex (MHC) protein-peptide interaction structure; generating a model with an ensemble of high order neural network; pre-training the model by high order semi-restricted Boltzmann machine (RBM) or high-order denoising autoencoder; and generating a prediction as a binary output or continuous output with initial model parameters pre-trained using binary output data if available. A systematic learning method for leveraging high-order interactions/associations among items for better collaborative filtering and item recommendation.
High-order semi-Restricted Boltzmann Machines and Deep Models for accurate peptide-MHC binding prediction