DeepMHC: Deep Convolutional Neural Networks for High-performance peptide-MHC Binding Affinity Prediction

[SiminaB]

https://doi.org/10.1101/239236 https://www.biorxiv.org/content/early/2017/12/24/239236

Convolutional neural networks (CNN) have been shown to outperform conventional methods in DNA-protien binding specificity prediction. However, whether we can transfer this success to protien-peptide binding affinity prediction depends on appropriate design of the CNN architecture that calls for thorough understanding how to match the architecture to the problem. Here we propose DeepMHC, a deep convolutional neural network (CNN) based protein-peptide binding prediction algorithm for achieving better performance in MHC-I peptide binding affinity prediction than conventional algorithms. Our model takes only raw binding peptide sequences as input without needing any human-designed features and other physichochemical or evolutionary information of the amino acids. Our CNN models are shown to be able to learn non-linear relationships among the amino acid positions of the peptides to achieve highly competitive performance on most of the IEDB benchmark datasets with a single model architecture and without using any consensus or composite ensemble classifier models. By systematically exploring the best CNN architecture, we identified critical design considerations in CNN architecture development for peptide-MHC binding prediction.

[zietzm]

This certainly seems in-scope for #638. @cgreene I don't know if the reviewing of that (#638) PR has yet started, but perhaps I should review this and think about adding it?

[agitter]

@zietzm I'm going to work on reviewing #638. We can independently decide whether to add this. If we merge #638 but want to include this later, you could make another small pull request.