# Crystalite: A Lightweight Transformer for Efficient Crystal Modeling

arXiv: https://arxiv.org/abs/2604.02270 · HTML: https://mlsanity.com/paper/2604.02270/

## Key facts

- Cited by 10 papers in the map (data through 14 Oct 2026).
- Builds on 28 of its 46 references that are in the map.
- First posted on arXiv 2 Apr 2026.

## Builds on (most cited first, 28 of 28)

- [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)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Generative Modeling by Estimating Gradients of the Data Distribution](https://mlsanity.com/paper/1907.05600/) (2019)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Stochastic Interpolants: A Unifying Framework for Flows and Diffusions](https://mlsanity.com/paper/2303.08797/) (2023)
- [E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials](https://mlsanity.com/paper/2101.03164/) (2021)
- [GemNet: Universal Directional Graph Neural Networks for Molecules](https://mlsanity.com/paper/2106.08903/) (2021)
- [Do Transformers Really Perform Bad for Graph Representation?](https://mlsanity.com/paper/2106.05234/) (2021)
- [Crystal Diffusion Variational Autoencoder for Periodic Material Generation](https://mlsanity.com/paper/2110.06197/) (2021)
- [Flow Matching on General Geometries](https://mlsanity.com/paper/2302.03660/) (2023)
- [Crystal Structure Prediction by Joint Equivariant Diffusion](https://mlsanity.com/paper/2309.04475/) (2023)
- [FlowMM: Generating Materials with Riemannian Flow Matching](https://mlsanity.com/paper/2406.04713/) (2024)
- [Fine-Tuned Language Models Generate Stable Inorganic Materials as Text](https://mlsanity.com/paper/2402.04379/) (2024)
- [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)
- [FlowLLM: Flow Matching for Material Generation with Large Language Models as Base Distributions](https://mlsanity.com/paper/2410.23405/) (2024)
- [SymmCD: Symmetry-Preserving Crystal Generation with Diffusion Models](https://mlsanity.com/paper/2502.03638/) (2025)
- [Space Group Informed Transformer for Crystalline Materials Generation](https://mlsanity.com/paper/2403.15734/) (2024)
- [Wyckoff Transformer: Generation of Symmetric Crystals](https://mlsanity.com/paper/2503.02407/) (2025)
- [LeMat-GenBench: A Unified Evaluation Framework for Crystal Generative Models](https://mlsanity.com/paper/2512.04562/) (2025)
- [PLaID++: A Preference Aligned Language Model for Targeted Inorganic Materials Design](https://mlsanity.com/paper/2509.07150/) (2025)
- [LLM Meets Diffusion: A Hybrid Framework for Crystal Material Generation](https://mlsanity.com/paper/2510.23040/) (2025)
- [Kinetic Langevin Diffusion for Crystalline Materials Generation](https://mlsanity.com/paper/2507.03602/) (2025)
- [CrystalDiT: A Diffusion Transformer for Crystal Generation](https://mlsanity.com/paper/2508.16614/) (2025)
- [OXtal: An All-Atom Diffusion Model for Organic Crystal Structure Prediction](https://mlsanity.com/paper/2512.06987/) (2025)

## Built on by (most cited first, 10 of 10)

- [Substitution-Based Analysis of Structural Novelty for Generative Models of Materials](https://mlsanity.com/paper/2606.23166/) (2026)
- [Discovering Crystal Structure Prediction Algorithms with an AI Co-Scientist](https://mlsanity.com/paper/2606.22866/) (2026)
- [OMatG-flash: An All-Atom Flow Map with Reinforce Adjoint Matching for Scalable Materials Discovery](https://mlsanity.com/paper/2609.26402/) (2026)
- [Representations from Pretrained Machine-Learning Interatomic Potentials as Coarse Coordinates for Material Generation and Evaluation](https://mlsanity.com/paper/2607.28776/) (2026)
- [Packora: Systematic Design for Generative Molecular Crystal Structure Prediction](https://mlsanity.com/paper/2608.26962/) (2026)
- [Let CSP Be Your ANCHOR: Adaptive Crystal Search over Frozen Structure Priors](https://mlsanity.com/paper/2609.33407/) (2026)
- [GLASS: Global Latent Aggregation with Slot-based Set Decoding for Scalable All-Atom Crystal Generation](https://mlsanity.com/paper/2609.37158/) (2026)
- [Riemannian Flow Models with Reinforcement Learning for Molecular Crystal Structure Prediction](https://mlsanity.com/paper/2609.39773/) (2026)
- [OxiGen: Oxidation-State-Aware Crystal Generation](https://mlsanity.com/paper/2610.08296/) (2026)
- [Zatom-2: Multitask Pretraining on Atomistic Data for Generative Modeling across Domains](https://mlsanity.com/paper/2610.11454/) (2026)

## Abstract (arXiv)

Generative models for crystalline materials often rely on equivariant graph neural networks, which capture geometric structure well but are costly to train and slow to sample. We present Crystalite, a lightweight diffusion Transformer for crystal modeling built around two simple inductive biases. The first is Subatomic Tokenization, a compact chemically structured atom representation that replaces high-dimensional one-hot encodings and is better suited to continuous diffusion. The second is the Geometry Enhancement Module (GEM), which injects periodic minimum-image pair geometry directly into attention through additive geometric biases. Together, these components preserve the simplicity and efficiency of a standard Transformer while making it better matched to the structure of crystalline materials. Crystalite achieves state-of-the-art results on crystal structure prediction benchmarks, and de novo generation performance, attaining the best S.U.N. discovery score among the evaluated baselines while sampling substantially faster than geometry-heavy alternatives.