arXiv subjects

Dehan Cai

Publications and source records attributed to Dehan Cai.

3 recordsLinked to original sources

arXiv2026

SeekRBP: Leveraging Sequence-Structure Integration with Reinforcement Learning for Receptor-Binding Protein Identification

Motivation: Receptor-binding proteins (RBPs) initiate viral infection and determine host specificity, serving as key targets for phage engineering and therapy. However, the identification of RBPs is complicated by their extreme sequence divergence, which often renders traditional homology-based alignment methods ineffective. While machine learning offers a promising alternative, such approaches struggle with severe class imbalance and the difficulty of selecting informative negative samples from heterogeneous tail proteins. Existing methods often fail to balance learning from these ``hard negatives'' while maintaining generalization. Results: We present SeekRBP, a sequence--structure framework that models negative sampling as a sequential decision-making problem. By employing a multi-armed bandit strategy, SeekRBP dynamically prioritizes informative non-RBP sequences based on real-time training feedback, complemented by a multimodal fusion of protein language and structural embeddings. Benchmarking demonstrates that SeekRBP consistently outperforms static sampling strategies. Furthermore, a case study on Vibrio phages validates that SeekRBP effectively identifies RBPs to improve host prediction, highlighting its potential for large-scale annotation and synthetic biology applications.

q-bio.GN↗

arXiv2025

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

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.

q-bio.GN↗

arXiv2024

Accurate and efficient protein embedding using multi-teacher distillation learning

Motivation: Protein embedding, which represents proteins as numerical vectors, is a crucial step in various learning-based protein annotation/classification problems, including gene ontology prediction, protein-protein interaction prediction, and protein structure prediction. However, existing protein embedding methods are often computationally expensive due to their large number of parameters, which can reach millions or even billions. The growing availability of large-scale protein datasets and the need for efficient analysis tools have created a pressing demand for efficient protein embedding methods. Results: We propose a novel protein embedding approach based on multi-teacher distillation learning, which leverages the knowledge of multiple pre-trained protein embedding models to learn a compact and informative representation of proteins. Our method achieves comparable performance to state-of-the-art methods while significantly reducing computational costs and resource requirements. Specifically, our approach reduces computational time by ~70\% and maintains almost the same accuracy as the original large models. This makes our method well-suited for large-scale protein analysis and enables the bioinformatics community to perform protein embedding tasks more efficiently.

q-bio.GN↗