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arXiv 2511.08080cs.LGcs.AI
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用于数据高效分子生成与编辑的分层结构-属性对齐

Hierarchical Structure-Property Alignment for Data-Efficient Molecular Generation and Editing

School of Computer Science and Engineering(计算机科学与工程学院);Central South University(中南大学);Institute for Infocomm Research Agency for Science, Technology and Research (A* STAR)(信息通信研究所(A* STAR))

Ziyu Fan, Zhijian Huang, Yahan Li, Xiaowen Hu, Siyuan Shen, Yunliang Wang, Zeyu Zhong, Shuhong Liu, Shuning Yang, Shangqian Wu, Min Wu, Lei Deng

AI总结:

针对属性约束分子生成与编辑中的结构-属性关系捕捉难和属性注释不足问题,提出HSPAG分层结构-属性对齐框架,通过多层面学习、样本选择策略提升数据效率,实现细粒度关系捕捉与多属性可控生成。

摘要:

属性约束的分子生成与编辑在AI驱动的药物发现中至关重要,但仍受两个因素阻碍:(i)捕捉分子结构与多种属性间的复杂关系具有挑战性;(ii)分子属性的覆盖范围窄且注释不完整,削弱了基于属性的模型的有效性。为解决这些局限,我们提出HSPAG,一个具有分层结构-属性对齐的高效数据框架。该模型将SMILES与分子属性视为互补模态,在原子、子结构和全分子层面学习它们的关系。此外,我们通过骨架聚类选择代表性样本,通过辅助变分自动编码器(VAE)选择难样本,大幅减少所需预训练数据。我们还引入属性相关性感知掩码机制和多样化扰动策略,以提升稀疏注释下的生成质量。实验表明,HSPAG捕捉到细粒度的结构-属性关系,支持多属性约束下的可控生成。两个真实世界案例研究进一步验证了HSPAG的编辑能力。

英文摘要:

Property-constrained molecular generation and editing are crucial in AI-driven drug discovery but remain hindered by two factors: (i) capturing the complex relationships between molecular structures and multiple properties remains challenging, and (ii) the narrow coverage and incomplete annotations of molecular properties weaken the effectiveness of property-based models. To tackle these limitations, we propose HSPAG, a data-efficient framework featuring hierarchical structure-property alignment. By treating SMILES and molecular properties as complementary modalities, the model learns their relationships at atom, substructure, and whole-molecule levels. Moreover, we select representative samples through scaffold clustering and hard samples via an auxiliary variational auto-encoder (VAE), substantially reducing the required pre-training data. In addition, we incorporate a property relevance-aware masking mechanism and diversified perturbation strategies to enhance generation quality under sparse annotations. Experiments demonstrate that HSPAG captures fine-grained structure-property relationships and supports controllable generation under multiple property constraints. Two real-world case studies further validate the editing capabilities of HSPAG.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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