Comparative Analysis of LLaMA and ChatGPT Embeddings for Molecule Embedding

Purpose: LLMs like ChatGPT and LLaMA are increasingly recognized for their potential in the field of cheminformatics, particularly in interpreting Simplified Molecular Input Line Entry System (SMILES), a standard method for representing chemical structures. These LLMs can decode SMILES strings into vector representations, providing a novel approach to understanding chemical graphs. Methods: We investigate the performance of ChatGPT and LLaMA in embedding SMILES strings. Our evaluation focuses on two key applications: molecular property (MP) prediction and drug-drug interaction (DDI) prediction, both essential in drug development and healthcare. Results: We find that SMILES embeddings generated using LLaMA outperform those from ChatGPT in both MP and DDI prediction tasks. Notably, LLaMA-based SMILES embeddings show results comparable to existing methods in both prediction tasks. Conclusion: The application of LLMs in cheminformatics, particularly in utilizing SMILES embeddings, shows significant promise for advancing drug development. This includes improving the prediction of chemical properties and facilitating the drug discovery process. GitHub: https://github.com/sshaghayeghs/LLaMA-VS-ChatGPT