Fine-tuning large language models for chemical text mining

• Published in: Chemical science (Cambridge) Vol. 15; no. 27; pp. 16 - 1611
• Main Authors: Zhang, Wei, Wang, Qinggong, Kong, Xiangtai, Xiong, Jiacheng, Ni, Shengkun, Cao, Duanhua, Niu, Buying, Chen, Mingan, Li, Yameng, Zhang, Runze, Wang, Yitian, Zhang, Lehan, Li, Xutong, Xiong, Zhaoping, Shi, Qian, Huang, Ziming, Fu, Zunyun, Zheng, Mingyue
• Format: Journal Article
• Language: English
• Published: Cambridge Royal Society of Chemistry 10.07.2024; The Royal Society of Chemistry
• Subjects: Artificial intelligence; Chatbots; Chemistry; Data acquisition; Data mining; Information retrieval; Large language models; Metal-organic frameworks; NMR; NMR spectroscopy; Nuclear magnetic resonance; Prompt engineering; Task complexity
• ISSN: 2041-6520; 2041-6539
• DOI: 10.1039/d4sc00924j

Extracting knowledge from complex and diverse chemical texts is a pivotal task for both experimental and computational chemists. The task is still considered to be extremely challenging due to the complexity of the chemical language and scientific literature. This study explored the power of fine-tuned large language models (LLMs) on five intricate chemical text mining tasks: compound entity recognition, reaction role labelling, metal-organic framework (MOF) synthesis information extraction, nuclear magnetic resonance spectroscopy (NMR) data extraction, and the conversion of reaction paragraphs to action sequences. The fine-tuned LLMs demonstrated impressive performance, significantly reducing the need for repetitive and extensive prompt engineering experiments. For comparison, we guided ChatGPT (GPT-3.5-turbo) and GPT-4 with prompt engineering and fine-tuned GPT-3.5-turbo as well as other open-source LLMs such as Mistral, Llama3, Llama2, T5, and BART. The results showed that the fine-tuned ChatGPT models excelled in all tasks. They achieved exact accuracy levels ranging from 69% to 95% on these tasks with minimal annotated data. They even outperformed those task-adaptive pre-training and fine-tuning models that were based on a significantly larger amount of in-domain data. Notably, fine-tuned Mistral and Llama3 show competitive abilities. Given their versatility, robustness, and low-code capability, leveraging fine-tuned LLMs as flexible and effective toolkits for automated data acquisition could revolutionize chemical knowledge extraction. Extracting knowledge from complex chemical texts is essential for both experimental and computational chemists. Fine-tuned large language models (LLMs) can serve as flexible and effective extractors for automated data acquisition.