Jinghong Zhang

Jiahao Qiu, Hui Yuan, Jinghong Zhang et al.

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.

Jinghong Zhang, Yidong Cui, Weiling Wang et al.

With the advancement of technology and changes in the market, the demand for the construction of domain-specific knowledge bases has been increasing, either to improve model performance or to promote enterprise innovation and competitiveness. The construction of domain-specific knowledge bases typically relies on web crawlers or existing industry databases, leading to problems with accuracy and consistency of the data. To address these challenges, we considered the characteristics of domain data, where internal knowledge is interconnected, and proposed the Self-Natural Language Inference Data Filtering (self-nli-TDF) framework. This framework compares trusted filtered knowledge with the data to be filtered, deducing the reasoning relationship between them, thus improving filtering performance. The framework uses plug-and-play large language models for trustworthiness assessment and employs the RoBERTa-MNLI model from the NLI domain for reasoning. We constructed three datasets in the domains of biology, radiation, and science, and conducted experiments using RoBERTa, GPT3.5, and the local Qwen2 model. The experimental results show that this framework improves filter quality, producing more consistent and reliable filtering results.