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MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation
May 15, 2023
Molecular de novo design is a critical yet challenging task in scientific fields, aiming to design novel molecular structures with desired property profiles. Significant progress has been made by resorting to generative models for graphs. However, limited attention is paid to hierarchical generative models, which can exploit the inherent hierarchical structure (with rich semantic information) of the molecular graphs and generate complex molecules of larger size that we shall demonstrate to be difficult for most existing models. The primary challenge to hierarchical generation is the non-differentiable issue caused by the generation of intermediate discrete coarsened graph structures. To sidestep this issue, we cast the tricky hierarchical generation problem over discrete spaces as the reverse process of hierarchical representation learning and propose MolHF, a new hierarchical flow-based model that generates molecular graphs in a coarse-to-fine manner. Specifically, MolHF first generates bonds through a multi-scale architecture, then generates atoms based on the coarsened graph structure at each scale. We demonstrate that MolHF achieves state-of-the-art performance in random generation and property optimization, implying its high capacity to model data distribution. Furthermore, MolHF is the first flow-based model that can be applied to model larger molecules (polymer) with more than 100 heavy atoms. The code and models are available at https://github.com/violet-sto/MolHF.
DialMed: A Dataset for Dialogue-based Medication Recommendation
Feb 22, 2022
Medication recommendation is a crucial task for intelligent healthcare systems. Previous studies mainly recommend medications with electronic health records(EHRs). However, some details of interactions between doctors and patients may be ignored in EHRs, which are essential for automatic medication recommendation. Therefore, we make the first attempt to recommend medications with the conversations between doctors and patients. In this work, we construct DialMed, the first high-quality dataset for medical dialogue-based medication recommendation task. It contains 11,996 medical dialogues related to 16 common diseases from 3 departments and 70 corresponding common medications. Furthermore, we propose a Dialogue structure and Disease knowledge aware Network(DDN), where a graph attention network is utilized to model the dialogue structure and the knowledge graph is used to introduce external disease knowledge. The extensive experimental results demonstrate that the proposed method is a promising solution to recommend medications with medical dialogues. The dataset and code are available at https://github.com/Hhhhhhhzf/DialMed.