# Latent Diffusion Pretraining for Crystal Property Prediction

arXiv: https://arxiv.org/abs/2606.00776 · HTML: https://mlsanity.com/paper/2606.00776/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Flow matching, time series and science, one of 14 directions in Diffusion models.
- Builds on 35 of its 71 references that are in the map.
- First posted on arXiv 30 May 2026.

## Placed in

- Diffusion models / [Flow matching, time series and science](https://mlsanity.com/diffusion/flow-matching-time-series-and-science/)

## Builds on (most cited first, 30 of 35)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [High-Resolution Image Synthesis with Latent Diffusion Models](https://mlsanity.com/paper/2112.10752/) (2021)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Diffusion Models Beat GANs on Image Synthesis](https://mlsanity.com/paper/2105.05233/) (2021)
- [Deep Unsupervised Learning using Nonequilibrium Thermodynamics](https://mlsanity.com/paper/1503.03585/) (2015)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Generative Modeling by Estimating Gradients of the Data Distribution](https://mlsanity.com/paper/1907.05600/) (2019)
- [Structured Denoising Diffusion Models in Discrete State-Spaces](https://mlsanity.com/paper/2107.03006/) (2021)
- [Learning deep representations by mutual information estimation and maximization](https://mlsanity.com/paper/1808.06670/) (2018)
- [Improved Techniques for Training Score-Based Generative Models](https://mlsanity.com/paper/2006.09011/) (2020)
- [Diffusion-LM Improves Controllable Text Generation](https://mlsanity.com/paper/2205.14217/) (2022)
- [Score-based Generative Modeling in Latent Space](https://mlsanity.com/paper/2106.05931/) (2021)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (2020)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [GemNet: Universal Directional Graph Neural Networks for Molecules](https://mlsanity.com/paper/2106.08903/) (2021)
- [Crystal Diffusion Variational Autoencoder for Periodic Material Generation](https://mlsanity.com/paper/2110.06197/) (2021)
- [Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs](https://mlsanity.com/paper/2206.11990/) (2022)
- [Riemannian Score-Based Generative Modelling](https://mlsanity.com/paper/2202.02763/) (2022)
- [Learning Gradient Fields for Molecular Conformation Generation](https://mlsanity.com/paper/2105.03902/) (2021)
- [Crystal Structure Prediction by Joint Equivariant Diffusion](https://mlsanity.com/paper/2309.04475/) (2023)
- [Periodic Graph Transformers for Crystal Material Property Prediction](https://mlsanity.com/paper/2209.11807/) (2022)
- [GraphEBM: Molecular Graph Generation with Energy-Based Models](https://mlsanity.com/paper/2102.00546/) (2021)
- [All-atom Diffusion Transformers: Unified generative modelling of molecules and materials](https://mlsanity.com/paper/2503.03965/) (2025)
- [Space Group Constrained Crystal Generation](https://mlsanity.com/paper/2402.03992/) (2024)
- [Scalable Diffusion for Materials Generation](https://mlsanity.com/paper/2311.09235/) (2023)
- [An invertible crystallographic representation for general inverse design of inorganic crystals with targeted properties](https://mlsanity.com/paper/2005.07609/) (2020)
- [Efficient Approximations of Complete Interatomic Potentials for Crystal Property Prediction](https://mlsanity.com/paper/2306.10045/) (2023)
- [Data-Driven Approach to Encoding and Decoding 3-D Crystal Structures](https://mlsanity.com/paper/1909.00949/) (2019)
- [Complete and Efficient Graph Transformers for Crystal Material Property Prediction](https://mlsanity.com/paper/2403.11857/) (2024)

## Built on by (most cited first, 1 of 1)

- [Model Agnostic Graph Prompt Learning for Crystal Property Prediction](https://mlsanity.com/paper/2607.08996/) (2026)

## Abstract (arXiv)

Fast and accurate prediction of crystal properties is a central challenge in new materials design. Graph neural networks and Transformer-based models have emerged as powerful tools for this task due to their ability to encode the local structural environment of atoms within a crystal. However, these models are data-hungry, and in practice, labeled data for crystal properties are scarce. Pretraining-finetuning strategies, particularly those based on diffusion models, have shown promise in addressing these limitations. In this work, we introduce a novel latent diffusion based pretraining framework, CrysLDNet, designed to mitigate data scarcity. Our approach integrates a Variational Autoencoder (VAE) with a diffusion model during the pretraining stage. The VAE encoder maps 3D crystal structures into a smooth latent space within which the diffusion process is applied. This latent diffusion pretraining enables the graph encoder to effectively capture structural and chemical semantics from large-scale unlabeled data, which can then be finetuned for specific property prediction tasks. Comprehensive experiments on popular DFT datasets for property prediction reveal that CrysLDNet significantly outperforms both training-from-scratch and pretrained baselines, with improvements of 4.26% and 4.90% on the JARVIS and MP datasets, respectively. Additionally, the learned representations remain robust in sparse-data conditions and are expressive enough to correct DFT errors when finetuned with limited experimental data. Code is available at: https://github.com/shrimonmuke0202/CrysLDNet.git.