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.
@article{arxiv.2511.08080,
title = {Hierarchical Structure-Property Alignment for Data-Efficient Molecular Generation and Editing},
author = {Ziyu Fan and Zhijian Huang and Yahan Li and Xiaowen Hu and Siyuan Shen and Yunliang Wang and Zeyu Zhong and Shuhong Liu and Shuning Yang and Shangqian Wu and Min Wu and Lei Deng},
journal= {arXiv preprint arXiv:2511.08080},
year = {2025}
}