Extracting structured seed-mediated gold nanorod growth procedures from scientific text with LLMs

Although gold nanorods have been the subject of much research, the pathways for controlling their shape and thereby their optical properties remain largely heuristically understood. Although it is apparent that the simultaneous presence of and interaction between various reagents during synthesis control these properties, computational and experimental approaches for exploring the synthesis space can be either intractable or too time-consuming in practice. This motivates an alternative approach leveraging the wealth of synthesis information already embedded in the body of scientific literature by developing tools to extract relevant structured data in an automated, high-throughput manner. To that end, we present an approach using the powerful GPT-3 language model to extract structured multi-step seed-mediated growth procedures and outcomes for gold nanorods from unstructured scientific text. GPT-3 prompt completions are fine-tuned to predict synthesis templates in the form of JSON documents from unstructured text input with an overall accuracy of 86% aggregated by entities and 76% aggregated by papers. The performance is notable, considering the model is performing simultaneous entity recognition and relation extraction. We present a dataset of 11 644 entities extracted from 1137 papers, resulting in 268 papers with at least one complete seed-mediated gold nanorod growth procedure and outcome for a total of 332 complete procedures.