用连续分布生成分子图,避免采样时的离散误差
Transport-Coupled Bayesian Flows for Molecular Graph Generation
- 直接在连续空间建模分子结构,避免训练与采样不一致
- 通过最优传输耦合学习图拓扑,生成结构更真实
- 可控制性质生成,无需重新训练模型
分子图生成(MGG)本质上是多类别生成任务,在严格的化学和结构约束下预测原子和键的类型。现有扩散方法通常学习回归数值嵌入,并在采样阶段依赖硬性离散规则恢复离散标签,导致训练与采样存在根本差异。模型虽追求点级数值精度,但采样过程却依赖跨越类别决策边界,迫使模型浪费精力于类别内部无关变化,最终影响多样性、结构统计特性和泛化性能。为此,我们提出TopBF框架:(i)在连续参数分布中直接进行MGG;(ii)通过测地线代价下的拟沃尔瑟斯坦最优传输耦合学习图拓扑理解;(iii)支持采样时无须重训练即可实现可控属性生成。TopBF创新性地利用累积分布函数(CDF)计算高斯信道诱导的类别概率,使训练目标与采样离散化操作统一。在QM9和ZINC250k数据集上的实验表明,该方法在结构保真度和生成效率方面均取得显著提升。
原文摘要 · Abstract (English)
Molecular graph generation (MGG) is essentially a multi-class generative task, aimed at predicting categories of atoms and bonds under strict chemical and structural constraints. However, many prevailing diffusion paradigms learn to regress numerical embeddings and rely on a hard discretization rule during sampling to recover discrete labels. This introduces a fundamental discrepancy between training and sampling. While models are trained for point-wise numerical fidelity, the sampling process fundamentally relies on crossing categorical decision boundaries. This discrepancy forces the model to expend efforts on intra-class variations that become irrelevant after discretization, ultimately compromising diversity, structural statistics, and generalization performance. Therefore, we propose TopBF, a unified framework that (i) performs MGG directly in continuous parameter distributions, (ii) learns graph-topological understanding through a Quasi-Wasserstein optimal-transport coupling under geodesic costs, and (iii) supports controllable, property-conditioned generation during sampling without retraining the base model. TopBF innovatively employs cumulative distribution function (CDF) to compute category probabilities induced by the Gaussian channel, thereby unifying the training objective with the sampling discretization operation. Experiments on QM9 and ZINC250k demonstrate superior structural fidelity and efficient generation with improved performance.
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