# EDBench: Large-Scale Electron Density Data for Molecular Modeling

arXiv: https://arxiv.org/abs/2505.09262 · HTML: https://mlsanity.com/paper/2505.09262/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 28 of its 90 references that are in the map.
- First posted on arXiv 14 May 2025.

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

- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Unsupervised Learning of Visual Features by Contrasting Cluster Assignments](https://mlsanity.com/paper/2006.09882/) (2020)
- [Unsupervised Feature Learning via Non-Parametric Instance-level Discrimination](https://mlsanity.com/paper/1805.01978/) (2018)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Point-BERT: Pre-training 3D Point Cloud Transformers with Masked Point Modeling](https://mlsanity.com/paper/2111.14819/) (2021)
- [SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks](https://mlsanity.com/paper/2006.10503/) (2020)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [GemNet: Universal Directional Graph Neural Networks for Molecules](https://mlsanity.com/paper/2106.08903/) (2021)
- [OGB-LSC: A Large-Scale Challenge for Machine Learning on Graphs](https://mlsanity.com/paper/2103.09430/) (2021)
- [Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules](https://mlsanity.com/paper/2011.14115/) (2020)
- [Parametric Contrastive Learning](https://mlsanity.com/paper/2107.12028/) (2021)
- [Structure-based Drug Design with Equivariant Diffusion Models](https://mlsanity.com/paper/2210.13695/) (2022)
- [ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction](https://mlsanity.com/paper/2106.06130/) (2021)
- [EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations](https://mlsanity.com/paper/2306.12059/) (2023)
- [Spherical Message Passing for 3D Graph Networks](https://mlsanity.com/paper/2102.05013/) (2021)
- [GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles](https://mlsanity.com/paper/2106.07802/) (2021)
- [Inverse design of 3d molecular structures with conditional generative neural networks](https://mlsanity.com/paper/2109.04824/) (2021)
- [Mean-Shifted Contrastive Loss for Anomaly Detection](https://mlsanity.com/paper/2106.03844/) (2021)
- [Temperature Schedules for Self-Supervised Contrastive Methods on Long-Tail Data](https://mlsanity.com/paper/2303.13664/) (2023)
- [QH9: A Quantum Hamiltonian Prediction Benchmark for QM9 Molecules](https://mlsanity.com/paper/2306.09549/) (2023)
- [Equivariant graph neural networks for fast electron density estimation of molecules, liquids, and solids](https://mlsanity.com/paper/2112.00652/) (2021)
- [Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials](https://mlsanity.com/paper/2306.09375/) (2023)
- [PointVector: A Vector Representation In Point Cloud Analysis](https://mlsanity.com/paper/2205.10528/) (2022)
- [PubChemQC B3LYP/6-31G*//PM6 dataset: the Electronic Structures of 86 Million Molecules using B3LYP/6-31G* calculations](https://mlsanity.com/paper/2305.18454/) (2023)
- [X-3D: Explicit 3D Structure Modeling for Point Cloud Recognition](https://mlsanity.com/paper/2404.15010/) (2024)
- [Data-Driven Parametrization of Molecular Mechanics Force Fields for Expansive Chemical Space Coverage](https://mlsanity.com/paper/2408.12817/) (2024)

## Built on by (most cited first, 2 of 2)

- [ED-DiT: Physics-Guided Diffusion Pretraining for Transferable Molecular Representations from Electron Density](https://mlsanity.com/paper/2608.03260/) (2026)
- [A Systematic Evaluation of Molecule Generation Models for De Novo Drug Design: From Benchmarks to Practical Insights](https://mlsanity.com/paper/2609.10099/) (2026)

## Abstract (arXiv)

Existing molecular machine learning force fields (MLFFs) generally focus on the learning of atoms, molecules, and simple quantum chemical properties (such as energy and force), but ignore the importance of electron density (ED) ρ(r) in accurately understanding molecular force fields (MFFs). ED describes the probability of finding electrons at specific locations around atoms or molecules, which uniquely determines all ground state properties (such as energy, molecular structure, etc.) of interactive multi-particle systems according to the Hohenberg-Kohn theorem. However, the calculation of ED relies on the time-consuming first-principles density functional theory (DFT) which leads to the lack of large-scale ED data and limits its application in MLFFs. In this paper, we introduce EDBench, a large-scale, high-quality dataset of ED designed to advance learning-based research at the electronic scale. Built upon the PCQM4Mv2, EDBench provides accurate ED data, covering 3.3 million molecules. To comprehensively evaluate the ability of models to understand and utilize electronic information, we design a suite of ED-centric benchmark tasks spanning prediction, retrieval, and generation. Our evaluation on several state-of-the-art methods demonstrates that learning from EDBench is not only feasible but also achieves high accuracy. Moreover, we show that learning-based method can efficiently calculate ED with comparable precision while significantly reducing the computational cost relative to traditional DFT calculations. All data and benchmarks from EDBench will be freely available, laying a robust foundation for ED-driven drug discovery and materials science.