rapppid_dataset
Joseph Szymborski and Amin Emad

rapppid_dataset (3 files)
rapppid_dataset_meta.xml 2.11kB
rapppid_dataset_meta.sqlite 20.48kB
rapppid.zip 62.68MB
Type: Dataset
Tags: protein protein interaction, ppi, rapppid, string, szymborski, emad

Bibtex:
@article{,
title= {rapppid_dataset},
journal= {},
author= {Joseph Szymborski and Amin Emad},
year= {},
url= {https://www.biorxiv.org/content/10.1101/2021.08.13.456309v1},
abstract= {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.

Availability and Implementation 
Code and datasets are freely available at https://github.com/jszym/rapppid.

Contact
amin.emad{at}mcgill.ca

Supplementary Information 
Online-only supplementary data is available at the journal’s website.

Competing Interest Statement
The authors have declared no competing interest.},
keywords= {protein protein interaction, ppi, rapppid, string, szymborski, emad},
terms= {},
license= {GNU AFFERO GENERAL PUBLIC LICENSE Version 3},
superseded= {}
}


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