Generative Artificial Intelligence GPT‑4 Accelerates Knowledge Mining and Machine Learning for Synthetic Biology

Knowledge mining from synthetic biology journal articles for machine learning (ML) applications is a labor-intensive process. The development of natural language processing (NLP) tools, such as GPT-4, can accelerate the extraction of published information related to microbial performance under complex strain engineering and bioreactor conditions. As a proof of concept, we proposed prompt engineering for a GPT-4 workflow pipeline to extract knowledge from 176 publications on two oleaginous yeasts (Yarrowia lipolytica and Rhodosporidium toruloides). After human intervention, the pipeline obtained a total of 2037 data instances. The structured data sets and feature selections enabled ML approaches (e.g., a random forest model) to predict Yarrowia fermentation titers with decent accuracy (R2 of 0.86 for unseen test data). Via transfer learning, the trained model could assess the production potential of the engineered nonconventional yeast, R. toruloides, for which there are fewer published reports. This work demonstrated the potential of generative artificial intelligence to streamline information extraction from research articles, thereby facilitating fermentation predictions and biomanufacturing development