arXiv:2603.01274cs.LGcs.AI2026-03KDD被引 2

用可解释概念提升分子性质预测,既准又看得懂。

GlassMol: Interpretable Molecular Property Prediction with Concept Bottleneck Models

  • 自动筛选化学相关概念,解决黑箱难题
  • 13个基准测试中性能媲美甚至超越黑盒模型
  • 适合药物研发中需可信解释的场景

机器学习加速分子性质预测,但主流大语言模型和图神经网络是黑箱。在药物研发中,安全至关重要,黑箱可能隐藏错误关联并排斥人类经验。现有可解释方法存在效果与可信度的权衡:解释可能不反映真实推理、降低性能或缺乏领域依据。概念瓶颈模型(CBMs)通过将输入映射到人类可理解的概念再输出,确保解释与决策过程一致。但将其应用于化学面临三大挑战:概念相关性差距(从大量描述符中选出任务相关概念)、标注差距(获取分子数据的概念标签)、容量差距(瓶颈限制导致性能下降)。我们提出GlassMol,一种模型无关的CBM,通过自动化概念筛选与大模型引导选择来应对这些挑战。在十三个基准测试中,GlassMol通常达到或超过黑盒基线性能,表明可解释性无需牺牲准确率,挑战了性能与可解释性不可兼得的普遍假设。代码已开源。

原文摘要 · Abstract (English)

Machine learning accelerates molecular property prediction, yet state-of-the-art Large Language Models and Graph Neural Networks operate as black boxes. In drug discovery, where safety is critical, this opacity risks masking false correlations and excluding human expertise. Existing interpretability methods suffer from the effectiveness-trustworthiness trade-off: explanations may fail to reflect a model's true reasoning, degrade performance, or lack domain grounding. Concept Bottleneck Models (CBMs) offer a solution by projecting inputs to human-interpretable concepts before readout, ensuring that explanations are inherently faithful to the decision process. However, adapting CBMs to chemistry faces three challenges: the Relevance Gap (selecting task-relevant concepts from a large descriptor space), the Annotation Gap (obtaining concept supervision for molecular data), and the Capacity Gap (degrading performance due to bottleneck constraints). We introduce GlassMol, a model-agnostic CBM that addresses these gaps through automated concept curation and LLM-guided concept selection. Experiments across thirteen benchmarks demonstrate that \method generally matches or exceeds black-box baselines, suggesting that interpretability does not sacrifice performance and challenging the commonly assumed trade-off. Code is available at https://github.com/walleio/GlassMol.

分子预测可解释性概念瓶颈药物发现

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