@inproceedings{
qiu2023tree,
title={Tree Search-Based Evolutionary Bandits for Protein Sequence Optimization},
author={Jiahao Qiu and Hui Yuan and Jinghong Zhang and Wentao Chen and Huazheng Wang and Mengdi Wang},
booktitle={NeurIPS 2023 Workshop on New Frontiers of AI for Drug Discovery and Development},
year={2023},
url={https://openreview.net/forum?id=9Zim5Lpsq3}
}
While modern biotechnologies allow synthesizing new proteins and function measurements at scale, efficiently exploring a protein sequence space and engineering it remains a daunting task due to the vast sequence space of any given protein. Protein engineering is typically conducted through an iterative process of adding mutations to the wild-type or lead sequences, recombination of mutations, and running new rounds of screening. To enhance the efficiency of such a process, we propose a tree search-based bandit learning method, which expands a tree starting from the initial sequence with the guidance of a bandit machine learning model. Under simplified assumptions and a Gaussian Process prior, we provide theoretical analysis and a Bayesian regret bound, demonstrating that the method can efficiently discover a near-optimal design. The full algorithm is compatible with a suite of randomized tree search heuristics, machine learning models, pre-trained embeddings, and bandit techniques. We test various instances of the algorithm across benchmark protein datasets using simulated screens. Experiment results demonstrate that the algorithm is both sample-efficient, diversity-promoting, and able to find top designs using reasonably small mutation counts.
Tree Search-Based Evolutionary Bandits for Protein Sequence Optimization
Jiahao Qiu Hui Yuan Jinghong Zhang Wentao Chen Huazheng Wang Mengdi Wang