Classification of Influenza Hemagglutinin Protein Sequences using Convolutional Neural Networks

TL;DR

This study employs convolutional neural networks to classify influenza Hemagglutinin protein sequences by host type, achieving higher accuracy and more balanced results than previous methods, aiding in virus host prediction.

Contribution

The paper introduces a CNN-based approach using hydrophobicity index encoding for accurate influenza HA protein host classification, improving accuracy and balance over prior work.

Findings

Up to 10% higher accuracy for avian host classification.

More balanced accuracy across host classes.

Effective distinction of HA sequences for different hosts.

Abstract

The Influenza virus can be considered as one of the most severe viruses that can infect multiple species with often fatal consequences to the hosts. The Hemagglutinin (HA) gene of the virus can be a target for antiviral drug development realised through accurate identification of its sub-types and possible the targeted hosts. This paper focuses on accurately predicting if an Influenza type A virus can infect specific hosts, and more specifically, Human, Avian and Swine hosts, using only the protein sequence of the HA gene. In more detail, we propose encoding the protein sequences into numerical signals using the Hydrophobicity Index and subsequently utilising a Convolutional Neural Network-based predictive model. The Influenza HA protein sequences used in the proposed work are obtained from the Influenza Research Database (IRD). Specifically, complete and unique HA protein sequences were used for avian, human and swine hosts. The data obtained for this work was 17999 human-host proteins, 17667 avian-host proteins and 9278 swine-host proteins. Given this set of collected proteins, the proposed method yields as much as 10% higher accuracy for an individual class (namely, Avian) and 5% higher overall accuracy than in an earlier study. It is also observed that the accuracy for each class in this work is more balanced than what was presented in this earlier study. As the results show, the proposed model can distinguish HA protein sequences with high accuracy whenever the virus under investigation can infect Human, Avian or Swine hosts.