Jiaqing Xie

Last Name

Xie

Jiaqing

Publications 1 - 2 of 2

DeepProtein: deep learning library and benchmark for protein sequence learning
Xie, Jiaqing; Li, Yuqiang; Fu, Tianfan (2025)
Bioinformatics
Motivation: Deep learning has deeply influenced protein science, enabling breakthroughs in predicting protein properties, higher-order structures, and molecular interactions. Results: This article introduces DeepProtein, a comprehensive and user-friendly deep learning library tailored for protein-related tasks. It enables researchers to seamlessly address protein data with cutting-edge deep learning models. To assess model performance, we establish a benchmark that evaluates different deep learning architectures across multiple protein-related tasks, including protein function prediction, subcellular localization prediction, protein-protein interaction prediction, and protein structure prediction. Furthermore, we introduce DeepProt-T5, a series of fine-tuned Prot-T5-based models that achieve state-of-the-art performance on four benchmark tasks, while demonstrating competitive results on six of others. Comprehensive documentation and tutorials are available which could ensure accessibility and support reproducibility.
Comparing Sparse Autoencoder Representations and Mean Activation Difference for Language Model Steering
Xie, Jiaqing (2025)

Publications 1 - 2 of 2