用连续场建模分子构象,支持生成与属性预测。
HyperDiffusionFields (HyDiF): Diffusion-Guided Hypernetworks for Learning Implicit Molecular Neural Fields
- 以向量场表示分子空间方向,通过神经隐式网络建模
- 超网络+扩散模型实现跨分子生成,支持结构补全任务
- 适合分子生成、性质预测及大分子建模研究者
我们提出HyperDiffusionFields(HyDiF),将3D分子构象建模为连续场而非离散原子坐标或图结构。核心是分子方向场(MDF),将空间任意点映射到最近特定类型原子的方向。使用分子特异的神经隐式场(MNF)表示MDF。为实现跨分子学习和泛化,采用共享超网络,根据分子条件生成对应MNF的权重。通过将超网络训练为去噪扩散模型,实现分子场函数空间中的采样。设计自然扩展至掩码扩散机制,支持结构条件生成任务如分子补全。此外,MDF的局部连续特性支持精细空间特征提取,用于分子属性预测,优于图或点云方法。我们还证明该方法可扩展至较大生物分子,展示了基于场的分子建模的前景。
原文摘要 · Abstract (English)
We introduce HyperDiffusionFields (HyDiF), a framework that models 3D molecular conformers as continuous fields rather than discrete atomic coordinates or graphs. At the core of our approach is the Molecular Directional Field (MDF), a vector field that maps any point in space to the direction of the nearest atom of a particular type. We represent MDFs using molecule-specific neural implicit fields, which we call Molecular Neural Fields (MNFs). To enable learning across molecules and facilitate generalization, we adopt an approach where a shared hypernetwork, conditioned on a molecule, generates the weights of the given molecule's MNF. To endow the model with generative capabilities, we train the hypernetwork as a denoising diffusion model, enabling sampling in the function space of molecular fields. Our design naturally extends to a masked diffusion mechanism to support structure-conditioned generation tasks, such as molecular inpainting, by selectively noising regions of the field. Beyond generation, the localized and continuous nature of MDFs enables spatially fine-grained feature extraction for molecular property prediction, something not easily achievable with graph or point cloud based methods. Furthermore, we demonstrate that our approach scales to larger biomolecules, illustrating a promising direction for field-based molecular modeling.
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