Predicting protein-protein interactions through sequence-based deep learning

Motivation: High-throughput experimental techniques have produced a large amount of protein-protein interaction (PPI) data, but their coverage is still low and the PPI data is also very noisy. Computational prediction of PPIs can be used to discover new PPIs and identify errors in the experimental PPI data. Results: We present a novel deep learning framework, DPPI, to model and predict PPIs from sequence information alone. Our model efficiently applies a deep, Siamese-like convolutional neural network combined with random projection and data augmentation to predict PPIs, leveraging existing high-quality experimental PPI data and evolutionary information of a protein pair under prediction. Our experimental results show that DPPI outperforms the state-of-the-art methods on several benchmarks in terms of area under precision-recall curve (auPR), and computationally is more efficient. We also show that DPPI is able to predict homodimeric interactions where other methods fail to work accurately, and the effectiveness of DPPI in specific applications such as predicting cytokine-receptor binding affinities.