@inproceedings{zhang-etal-2025-automated,
    title = "Automated Molecular Concept Generation and Labeling with Large Language Models",
    author = "Zhang, Zimin  and
      Wu, Qianli  and
      Xia, Botao  and
      Sun, Fang  and
      Hu, Ziniu  and
      Sun, Yizhou  and
      Zhang, Shichang",
    editor = "Rambow, Owen  and
      Wanner, Leo  and
      Apidianaki, Marianna  and
      Al-Khalifa, Hend  and
      Eugenio, Barbara Di  and
      Schockaert, Steven",
    booktitle = "Proceedings of the 31st International Conference on Computational Linguistics",
    month = jan,
    year = "2025",
    address = "Abu Dhabi, UAE",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/jlcl-multiple-ingestion/2025.coling-main.462/",
    pages = "6918--6936",
    abstract = "Artificial intelligence (AI) is transforming scientific research, with explainable AI methods like concept-based models (CMs) showing promise for new discoveries. However, in molecular science, CMs are less common than black-box models like Graph Neural Networks (GNNs), due to their need for predefined concepts and manual labeling. This paper introduces the Automated Molecular Concept (AutoMolCo) framework, which leverages Large Language Models (LLMs) to automatically generate and label predictive molecular concepts. Through iterative concept refinement, AutoMolCo enables simple linear models to outperform GNNs and LLM in-context learning on several benchmarks. The framework operates without human knowledge input, overcoming limitations of existing CMs while maintaining explainability and allowing easy intervention. Experiments on MoleculeNet and High-Throughput Experimentation (HTE) datasets demonstrate that AutoMolCoinduced explainable CMs are beneficial for molecular science research."
}