RT Journal Article
SR Electronic
T1 RAPPPID: Towards Generalisable Protein Interaction Prediction with AWD-LSTM Twin Networks
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.08.13.456309
DO 10.1101/2021.08.13.456309
A1 Szymborski, Joseph
A1 Emad, Amin
YR 2022
UL http://biorxiv.org/content/early/2022/04/18/2021.08.13.456309.abstract
AB Motivation Computational methods for the prediction of protein-protein interactions, while important tools for researchers, are plagued by challenges in generalising to unseen proteins. Datasets used for modelling protein-protein predictions are particularly predisposed to information leakage and sampling biases.Results In this study, we introduce RAPPPID, a method for the Regularised Automatic Prediction of Protein-Protein Interactions using Deep Learning. RAPPPID is a twin AWD-LSTM network which employs multiple regularisation methods during training time to learn generalised weights. Testing on stringent interaction datasets composed of proteins not seen during training, RAPPPID outperforms state-of-the-art methods. Further experiments show that RAPPPID’s performance holds regardless of the particular proteins in the testing set and its performance is higher for biologically supported edges. This study serves to demonstrate that appropriate regularisation is an important component of overcoming the challenges of creating models for protein-protein interaction prediction that generalise to unseen proteins. Additionally, as part of this study, we provide datasets corresponding to several data splits of various strictness, in order to facilitate assessment of PPI reconstruction methods by others in the future. Availability and Implementation: Code and datasets are freely available at https://github.com/jszym/rapppid.Contact amin.emad{at}mcgill.caSupplementary Information Online-only supplementary data is available at the journal’s website.Competing Interest StatementThe authors have declared no competing interest.