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.

Attribute selection is considered as the most characteristic result in rough set theory to distinguish itself to other theories. However, existing attribute selection approaches can not handle partially labeled data. So far, few studies on attribute selection in partially labeled data have been conducted. In this paper, the concept of discernibility pair based on rough set theory is raised to construct a uniform measure for the attributes in both supervised framework and unsupervised framework. Based on discernibility pair, two kinds of semisupervised attribute selection algorithm based on rough set theory are developed to handle partially labeled categorical data. Experiments demonstrate the effectiveness of the proposed attribute selection algorithms.