# Learning Neural Generative Dynamics for Molecular Conformation Generation

arXiv: https://arxiv.org/abs/2102.10240 · HTML: https://mlsanity.com/paper/2102.10240/

## Key facts

- Cited by 88 papers in the map (data through 14 Oct 2026).
- Builds on 17 of its 44 references that are in the map.
- First posted on arXiv 20 Feb 2021.

## Builds on (most cited first, 17 of 17)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Neural Ordinary Differential Equations](https://mlsanity.com/paper/1806.07366/) (2018)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Variational Inference with Normalizing Flows](https://mlsanity.com/paper/1505.05770/) (2015)
- [NICE: Non-linear Independent Components Estimation](https://mlsanity.com/paper/1410.8516/) (2014)
- [FFJORD: Free-form Continuous Dynamics for Scalable Reversible Generative Models](https://mlsanity.com/paper/1810.01367/) (2018)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation](https://mlsanity.com/paper/1806.02473/) (2018)
- [GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation](https://mlsanity.com/paper/2001.09382/) (2020)
- [GEOM: Energy-annotated molecular conformations for property prediction and molecular generation](https://mlsanity.com/paper/2006.05531/) (2020)
- [A Theory of Generative ConvNet](https://mlsanity.com/paper/1602.03264/) (2016)
- [Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules](https://mlsanity.com/paper/1906.00957/) (2019)
- [Generalized Denoising Auto-Encoders as Generative Models](https://mlsanity.com/paper/1305.6663/) (2013)
- [Molecular geometry prediction using a deep generative graph neural network](https://mlsanity.com/paper/1904.00314/) (2019)
- [A Generative Model for Molecular Distance Geometry](https://mlsanity.com/paper/1909.11459/) (2019)
- [Generating valid Euclidean distance matrices](https://mlsanity.com/paper/1910.03131/) (2019)
- [Discriminator Contrastive Divergence: Semi-Amortized Generative Modeling by Exploring Energy of the Discriminator](https://mlsanity.com/paper/2004.01704/) (2020)

## Built on by (most cited first, 30 of 88)

- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Crystal Diffusion Variational Autoencoder for Periodic Material Generation](https://mlsanity.com/paper/2110.06197/) (2021)
- [Torsional Diffusion for Molecular Conformer Generation](https://mlsanity.com/paper/2206.01729/) (2022)
- [Long Range Graph Benchmark](https://mlsanity.com/paper/2206.08164/) (2022)
- [E(n) Equivariant Normalizing Flows](https://mlsanity.com/paper/2105.09016/) (2021)
- [Learning Gradient Fields for Molecular Conformation Generation](https://mlsanity.com/paper/2105.03902/) (2021)
- [3D Infomax improves GNNs for Molecular Property Prediction](https://mlsanity.com/paper/2110.04126/) (2021)
- [EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction](https://mlsanity.com/paper/2202.05146/) (2022)
- [Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design](https://mlsanity.com/paper/2210.05274/) (2022)
- [GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles](https://mlsanity.com/paper/2106.07802/) (2021)
- [Diffusion-based Molecule Generation with Informative Prior Bridges](https://mlsanity.com/paper/2209.00865/) (2022)
- [Inverse design of 3d molecular structures with conditional generative neural networks](https://mlsanity.com/paper/2109.04824/) (2021)
- [SE(3) Equivariant Graph Neural Networks with Complete Local Frames](https://mlsanity.com/paper/2110.14811/) (2021)
- [An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming](https://mlsanity.com/paper/2105.07246/) (2021)
- [DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding](https://mlsanity.com/paper/2211.11214/) (2022)
- [Swallowing the Bitter Pill: Simplified Scalable Conformer Generation](https://mlsanity.com/paper/2311.17932/) (2023)
- [Smooth Normalizing Flows](https://mlsanity.com/paper/2110.00351/) (2021)
- [ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation](https://mlsanity.com/paper/2410.22388/) (2024)
- [Efficient and Equivariant Graph Networks for Predicting Quantum Hamiltonian](https://mlsanity.com/paper/2306.04922/) (2023)
- [A Survey on Graph Diffusion Models: Generative AI in Science for Molecule, Protein and Material](https://mlsanity.com/paper/2304.01565/) (2023)
- [3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design](https://mlsanity.com/paper/2205.07309/) (2022)
- [Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs](https://mlsanity.com/paper/2110.01717/) (2021)
- [Direct Molecular Conformation Generation](https://mlsanity.com/paper/2202.01356/) (2022)
- [Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration](https://mlsanity.com/paper/2306.13769/) (2023)
- [Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations](https://mlsanity.com/paper/2110.04383/) (2021)
- [A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation](https://mlsanity.com/paper/2402.08703/) (2024)
- [A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications](https://mlsanity.com/paper/2403.00485/) (2024)
- [Rigid Body Flows for Sampling Molecular Crystal Structures](https://mlsanity.com/paper/2301.11355/) (2023)
- [Towards Symmetry-Aware Generation of Periodic Materials](https://mlsanity.com/paper/2307.02707/) (2023)
- [DiffMD: A Geometric Diffusion Model for Molecular Dynamics Simulations](https://mlsanity.com/paper/2204.08672/) (2022)

## Abstract (arXiv)

We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning methods have shown great potential by training on a large collection of conformation data. Challenges arise from the limited model capacity for capturing complex distributions of conformations and the difficulty in modeling long-range dependencies between atoms. Inspired by the recent progress in deep generative models, in this paper, we propose a novel probabilistic framework to generate valid and diverse conformations given a molecular graph. We propose a method combining the advantages of both flow-based and energy-based models, enjoying: (1) a high model capacity to estimate the multimodal conformation distribution; (2) explicitly capturing the complex long-range dependencies between atoms in the observation space. Extensive experiments demonstrate the superior performance of the proposed method on several benchmarks, including conformation generation and distance modeling tasks, with a significant improvement over existing generative models for molecular conformation sampling.