# Computational approaches for virus host prediction: A review of methods and applications

## TL;DR

This paper systematically reviews and benchmarks 27 computational tools for virus-host prediction, highlighting their performance variability and providing insights into their applicability across different scenarios.

## Contribution

It introduces a standardized benchmark framework and evaluates existing tools, guiding future research in virus-host interaction prediction.

## Key findings

- No single tool is universally best across all scenarios.
- Tools like CHERRY and iPHoP are broadly applicable.
- Trade-offs exist between accuracy, speed, and computational cost.

## Abstract

Accurate prediction of virus-host interactions is critical for understanding viral ecology and developing applications like phage therapy. However, the growing number of computational tools has created a complex landscape, making direct performance comparison challenging due to inconsistent benchmarks and varying usability. Here, we provide a systematic review and a rigorous benchmark of 27 virus-host prediction tools. We formulate the host prediction task into two primary frameworks, link prediction and multi-class classification, and construct two benchmark datasets to evaluate tool performance in distinct scenarios: a database-centric dataset (RefSeq-VHDB) and a metagenomic discovery dataset (MetaHiC-VHDB). Our results reveal that no single tool is universally optimal. Performance is highly context-dependent, with tools like CHERRY and iPHoP demonstrating robust, broad applicability, while others, such as RaFAH and PHIST, excel in specific contexts. We further identify a critical trade-off between predictive accuracy, prediction rate, and computational cost. This work serves as a practical guide for researchers and establishes a standardized benchmark to drive future innovation in deciphering complex virus-host interactions.