2024/01/08 by Jiahao Qiu, Qiu, Jiahao, Hui Yuan +9 · 1 citation
Computer Science · Decision Sciences · #Advanced Bandit Algorithms Research #Advanced Multi-Objective Optimization Algorithms #Biomolecules (q-bio.BM) #Evolutionary Algorithms and Applications #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG)
paper · pdf · doi:10.48550/arxiv.2401.06173
openalex publication_date 2024/01/08 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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 combination of local search and bandit learning 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 and able to find top designs using reasonably small mutation counts.