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    KG-MoLM3D:元素知识图谱增强的3维分子语言模型

    KG-MoLM3D: Element KG-Enhanced 3D Molecular Language Model

    • 摘要: 大语言模型(LLM)在多个领域展现出强大能力,推动了多模态分子语言模型的发展,使其能够联合处理分子结构、化学表征和自然语言描述。然而,现有基于3维图的分子模型大多依赖纯数据驱动的编码器,缺乏显式化学先验,如元素关系、周期性质和化学语义关联,因而限制了其在广阔化学空间中的泛化能力,也影响了对复杂结构-性质关系和分子-文本推理的建模效果。为解决上述问题,提出KG-MoLM3D,一种知识图谱增强的3维分子语言模型。该模型在统一框架中融合结构、关系和文本信息:通过知识图谱增强的 EGNN编码器,将3维分子几何与元素级化学知识结合;利用BLIP-2对齐分子图表示与文本描述,实现分子与语言之间的跨模态交互;并引入MixLoRA进行高效的多任务参数适配。KG-MoLM3D在分子表征、分子-文本检索、分子描述生成和性质问答任务上均取得稳定优势,例如在6个MoleculeNet回归数据集上取得最低 MAE,并在PubChem M2T检索和描述性性质问答任务中达到96.85% recall@20和53.89 METEOR。

       

      Abstract: Large Language Model (LLM) has demonstrated remarkable capabilities across a wide range of domains, inspiring the development of multimodal molecular language models that can jointly process molecular structures, chemical representations, and natural language descriptions. Despite recent progress, existing 3D graph-based molecular models still largely rely on purely data-driven molecular encoders. These models often neglect explicit chemical priors, such as element-level relationships, periodic properties, and chemically meaningful semantic associations, which limits their ability to generalize across the vast chemical space. As a result, they may struggle to accurately capture complex structure–property relationships and to support robust molecule-text reasoning. To address these limitations, we propose KG-MoLM3D, a Knowledge Graph (KG)-Enhanced 3D Molecular Language Model for comprehensive molecular understanding. KG-MoLM3D seamlessly integrates structural, relational, and textual information within a unified multimodal framework. Specifically, we design a KG-enhanced EGNN encoder to fuse 3D molecular geometries with element-level chemical knowledge derived from curated knowledge graphs. In addition, the BLIP-2 framework is employed to align molecular graph representations with textual descriptions, enabling effective cross-modal interaction between molecules and language. Furthermore, we introduce MixLoRA, an efficient parameter adaptation strategy for multitask learning. KG-MoLM3D achieves consistent advantages across molecular representa-tion, molecule-text retrieval, molecule captioning, and property QA tasks; for example, it obtains the lowest MAE on all six MoleculeNet regression datasets, and achieves 96.85% recall@20 in PubChem M2T retrieval and 53.89 METEOR in descriptive property QA.

       

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