A multitask transfer learning framework for the prediction of virus-human protein-protein interactions

TL;DR

This paper introduces a multitask transfer learning framework that leverages large-scale protein data and domain knowledge to predict virus-human protein-protein interactions, addressing data scarcity and mutation challenges.

Contribution

The novel approach combines deep language models for protein representation with multitask learning to improve virus-human PPI prediction accuracy.

Findings

Achieved competitive results on 13 benchmark datasets.

Effective in predicting both virus-human and bacteria-human PPIs.

Utilizes domain knowledge as a regularizer to enhance model performance.

Abstract

Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection and pathogenesis. This could further help in the prevention and treatment of virus-related diseases. However, the task of predicting protein-protein interactions between a new virus and human cells is extremely challenging due to scarce data on virus-human interactions and fast mutation rates of most viruses. We developed a multitask transfer learning approach that exploits the information of around 24 million protein sequences and the interaction patterns from the human interactome to counter the problem of small training datasets. Instead of using hand-crafted protein features, we utilize statistically rich protein representations learned by a deep language modeling approach from a massive source of protein sequences. Additionally, we employ an additional objective which aims to maximize the probability of observing human protein-protein interactions. This additional task objective acts as a regularizer and also allows to incorporate domain knowledge to inform the virus-human protein-protein interaction prediction model. Our approach achieved competitive results on 13 benchmark datasets and the case study for the SAR-CoV-2 virus receptor. Experimental results show that our proposed model works effectively for both virus-human and bacteria-human protein-protein interaction prediction tasks. We share our code for reproducibility and future research at https://git.l3s.uni-hannover.de/dong/multitask-transfer.