arXiv:2506.15725cs.LGcs.AI2025-06NeurIPS被引 5

提出可增删节点的图扩散模型,实现分子大小自适应生成。

Graph Diffusion that can Insert and Delete

  • 重构噪声与去噪过程,支持节点单调插入删除
  • 在分子属性定向生成任务中性能达或超过现有模型
  • 适合需要调整分子尺寸的药物设计场景

基于离散去噪扩散概率模型(DDPM)的图生成模型通过迭代原子和键的调整系统性地去除结构噪声,为分子生成提供了合理方法。然而,现有方法在扩散过程中无法动态调整图的大小(即原子数量),严重限制了其在属性驱动分子设计等条件生成场景中的有效性,因为目标属性常与分子尺寸相关。本文重新设计了噪声添加与去噪过程,支持节点的单调插入与删除。所提出的模型GrIDDD可在生成过程中动态增减化学图。尽管训练于更困难的问题,GrIDDD在分子属性目标生成任务上的表现仍匹配或超越现有图扩散模型。此外,在分子优化任务中,其性能也达到专业优化模型的水平。该工作为图扩散模型实现尺寸自适应分子生成开辟了新路径。

原文摘要 · Abstract (English)

Generative models of graphs based on discrete Denoising Diffusion Probabilistic Models (DDPMs) offer a principled approach to molecular generation by systematically removing structural noise through iterative atom and bond adjustments. However, existing formulations are fundamentally limited by their inability to adapt the graph size (that is, the number of atoms) during the diffusion process, severely restricting their effectiveness in conditional generation scenarios such as property-driven molecular design, where the targeted property often correlates with the molecular size. In this paper, we reformulate the noising and denoising processes to support monotonic insertion and deletion of nodes. The resulting model, which we call GrIDDD, dynamically grows or shrinks the chemical graph during generation. GrIDDD matches or exceeds the performance of existing graph diffusion models on molecular property targeting despite being trained on a more difficult problem. Furthermore, when applied to molecular optimization, GrIDDD exhibits competitive performance compared to specialized optimization models. This work paves the way for size-adaptive molecular generation with graph diffusion.

图生成扩散模型分子设计

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