Multi-scale Convolutional Neural Networks for the Prediction of Human-virus Protein Interactions

Xiaodi Yang, Ziding Zhang, Stefan Wuchty, Stefan Wuchty

2021

Abstract

Allowing the prediction of human-virus protein-protein interactions (PPI), our algorithm is based on a Siamese Convolutional Neural Network architecture (CNN), accounting for pre-acquired protein evolutionary profiles (i.e. PSSM) as input. In combinations with a multilayer perceptron, we evaluate our model on a variety of human-virus PPI datasets and compare its results with traditional machine learning frameworks, a deep learning architecture and several other human-virus PPI prediction methods, showing superior performance. Furthermore, we propose two transfer learning methods, allowing the reliable prediction of interactions in cross-viral settings, where we train our system with PPIs in a source human-virus domain and predict interactions in a target human-virus domain. Notable, we observed that our transfer learning approaches allowed the reliable prediction of PPIs in relatively less investigated human-virus domains, such as Dengue, Zika and SARS-CoV-2.

Paper Citation

in Harvard Style

Yang X., Zhang Z. and Wuchty S. (2021). Multi-scale Convolutional Neural Networks for the Prediction of Human-virus Protein Interactions.In Proceedings of the 13th International Conference on Agents and Artificial Intelligence - Volume 2: ICAART, ISBN 978-989-758-484-8, pages 41-48. DOI: 10.5220/0010185300410048

in Bibtex Style

@conference{icaart21,
author={Xiaodi Yang and Ziding Zhang and Stefan Wuchty},
title={Multi-scale Convolutional Neural Networks for the Prediction of Human-virus Protein Interactions},
booktitle={Proceedings of the 13th International Conference on Agents and Artificial Intelligence - Volume 2: ICAART,},
year={2021},
pages={41-48},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0010185300410048},
isbn={978-989-758-484-8},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 13th International Conference on Agents and Artificial Intelligence - Volume 2: ICAART,
TI - Multi-scale Convolutional Neural Networks for the Prediction of Human-virus Protein Interactions
SN - 978-989-758-484-8
AU - Yang X.
AU - Zhang Z.
AU - Wuchty S.
PY - 2021
SP - 41
EP - 48
DO - 10.5220/0010185300410048