HostNet: improved sequence representation in deep neural networks for virus-host prediction

• Published in: BMC bioinformatics Vol. 24; no. 1; pp. 1 - 455
• Main Authors: Ming, Zhaoyan, Chen, Xiangjun, Wang, Shunlong, Liu, Hong, Yuan, Zhiming, Wu, Minghui, Xia, Han
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 01.12.2023; BioMed Central; BMC
• Subjects: Accuracy; Analysis; Artificial neural networks; Communicable diseases; Computer applications; Datasets; Deep learning; Deep Learning-based Sequence Modeling; Disease control; Genomes; Genomics; Host range; Host-virus relationships; Infectious diseases; Machine learning; Modules; Natural language; Neural networks; Predictions; Prevention; Public health; Rabies; Representations; Sequence Representation; Sequences; Software; Vaccine development; Vaccines; Vectorization; Virus-Host Prediction; Viruses; China
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-023-05582-9

The escalation of viruses over the past decade has highlighted the need to determine their respective hosts, particularly for emerging ones that pose a potential menace to the welfare of both human and animal life. Yet, the traditional means of ascertaining the host range of viruses, which involves field surveillance and laboratory experiments, is a laborious and demanding undertaking. A computational tool with the capability to reliably predict host ranges for novel viruses can provide timely responses in the prevention and control of emerging infectious diseases. The intricate nature of viral-host prediction involves issues such as data imbalance and deficiency. Therefore, developing highly accurate computational tools capable of predicting virus-host associations is a challenging and pressing demand. To overcome the challenges of virus-host prediction, we present HostNet, a deep learning framework that utilizes a Transformer-CNN-BiGRU architecture and two enhanced sequence representation modules. The first module, k-mer to vector, pre-trains a background vector representation of k-mers from a broad range of virus sequences to address the issue of data deficiency. The second module, an adaptive sliding window, truncates virus sequences of various lengths to create a uniform number of informative and distinct samples for each sequence to address the issue of data imbalance. We assess HostNet's performance on a benchmark dataset of "Rabies lyssavirus" and an in-house dataset of "Flavivirus". Our results show that HostNet surpasses the state-of-the-art deep learning-based method in host-prediction accuracies and F1 score. The enhanced sequence representation modules, significantly improve HostNet's training generalization, performance in challenging classes, and stability. HostNet is a promising framework for predicting virus hosts from genomic sequences, addressing challenges posed by sparse and varying-length virus sequence data. Our results demonstrate its potential as a valuable tool for virus-host prediction in various biological contexts. Virus-host prediction based on genomic sequences using deep neural networks is a promising approach to identifying their potential hosts accurately and efficiently, with significant impacts on public health, disease prevention, and vaccine development.