Ocean archaea PPI prediction with pretraining models

Protein-Protein Interaction (PPI) provides important insights into the metabolic mechanisms of different biological processes. Although PPIs in some organisms have been investigated systematically, PPIs in the ocean archaea remain largely unexplored. But such species have special investigation value since their adaptation to extreme living conditions may generate unique PPIs. In this paper, we aim to characterize and predict PPIs in ocean archaea to advance understanding of their metabolic networks. First, we collect all ocean archaea PPIs with high confidence from STRING database and analyze the PPI network features, including centrality and enrichment analysis. The functional enrichment results of the largest connecting subgraph in the PPI network show most PPIs in our constructed dataset is related to the translation and transcription processes. Then, we generate an equal number of negative PPI pairs, whose members have either different subcellular locations or GO terms. We also use the generated dataset to test the performance of three pretraining methods and their ensemble methods in the binary PPI prediction task. Our results suggest the ensemble methods could be applied to further improve models’ performance. Fine-tuned models trained on the ocean archaea dataset are expected to predict the other ocean archaea PPIs that are not included in the STRING database and get more understanding about the ocean archaea PPI universe.