Multi-level Protein Structure Pre-training via Prompt Learning

Zeyuan Wang, Qiang Zhang, Shuang-Wei HU, Haoran Yu, Xurui Jin, Zhichen Gong, Huajun Chen

Keywords: protein representation learning, prompt learning, multi-task learning, multi-level structure

Abstract: A protein can focus on different structure levels to implement its functions. Each structure has its own merit and driving forces in describing some specific characteristics, and they cannot replace each other. Most existing function prediction methods take the tertiary structure as input, unintentionally ignoring the other levels of protein structures. Considering protein sequences can determine multi-level structures, in this paper, we aim to realize the comprehensive potential of protein sequences for function prediction. Specifically, we propose a new prompt-guided multi-task pre-training and fine-tuning framework, and the resulting protein model is called PromptProtein. Through the prompt-guided multi-task pre-training, we learn multiple prompt signals to steer the model to focus on different structure levels. We also design a prompt fine-tuning module to provide downstream tasks the on-demand flexibility of utilizing respective levels of structure information. Extensive experiments on function prediction and protein engineering show that PromptProtein outperforms state-of-the-art methods by large margins.

Anonymous Url: I certify that there is no URL (e.g., github page) that could be used to find authors’ identity.

No Acknowledgement Section: I certify that there is no acknowledgement section in this submission for double blind review.

Code Of Ethics: I acknowledge that I and all co-authors of this work have read and commit to adhering to the ICLR Code of Ethics

Submission Guidelines: Yes

Please Choose The Closest Area That Your Submission Falls Into: Machine Learning for Sciences (eg biology, physics, health sciences, social sciences, climate/sustainability )