# Sliced Denoising: A Physics-Informed Molecular Pre-Training Method

arXiv: https://arxiv.org/abs/2311.02124 · HTML: https://mlsanity.com/paper/2311.02124/

## Key facts

- Cited by 18 papers in the map (data through 14 Oct 2026).
- Builds on 22 of its 52 references that are in the map.
- First posted on arXiv 3 Nov 2023.

## Builds on (most cited first, 22 of 22)

- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [On the Bottleneck of Graph Neural Networks and its Practical Implications](https://mlsanity.com/paper/2006.05205/) (2020)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (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)
- [Torsional Diffusion for Molecular Conformer Generation](https://mlsanity.com/paper/2206.01729/) (2022)
- [Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules](https://mlsanity.com/paper/2011.14115/) (2020)
- [ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction](https://mlsanity.com/paper/2106.06130/) (2021)
- [TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials](https://mlsanity.com/paper/2202.02541/) (2022)
- [Spherical Message Passing for 3D Graph Networks](https://mlsanity.com/paper/2102.05013/) (2021)
- [3D Infomax improves GNNs for Molecular Property Prediction](https://mlsanity.com/paper/2110.04126/) (2021)
- [Pre-training via Denoising for Molecular Property Prediction](https://mlsanity.com/paper/2206.00133/) (2022)
- [One Transformer Can Understand Both 2D & 3D Molecular Data](https://mlsanity.com/paper/2210.01765/) (2022)
- [Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching](https://mlsanity.com/paper/2206.13602/) (2022)
- [GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction](https://mlsanity.com/paper/2109.11730/) (2021)
- [Molecular Contrastive Learning with Chemical Element Knowledge Graph](https://mlsanity.com/paper/2112.00544/) (2021)
- [Unified 2D and 3D Pre-Training of Molecular Representations](https://mlsanity.com/paper/2207.08806/) (2022)
- [Energy-Motivated Equivariant Pretraining for 3D Molecular Graphs](https://mlsanity.com/paper/2207.08824/) (2022)
- [Fractional Denoising for 3D Molecular Pre-training](https://mlsanity.com/paper/2307.10683/) (2023)
- [A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining](https://mlsanity.com/paper/2305.18407/) (2023)
- [Automated 3D Pre-Training for Molecular Property Prediction](https://mlsanity.com/paper/2306.07812/) (2023)
- [Denoise Pretraining on Nonequilibrium Molecules for Accurate and Transferable Neural Potentials](https://mlsanity.com/paper/2303.02216/) (2023)

## Built on by (most cited first, 18 of 18)

- [A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications](https://mlsanity.com/paper/2403.00485/) (2024)
- [Dual Cone Gradient Descent for Training Physics-Informed Neural Networks](https://mlsanity.com/paper/2409.18426/) (2024)
- [UniGEM: A Unified Approach to Generation and Property Prediction for Molecules](https://mlsanity.com/paper/2410.10516/) (2024)
- [UniCorn: A Unified Contrastive Learning Approach for Multi-view Molecular Representation Learning](https://mlsanity.com/paper/2405.10343/) (2024)
- [A Survey of Graph Transformers: Architectures, Theories and Applications](https://mlsanity.com/paper/2502.16533/) (2025)
- [MolSpectra: Pre-training 3D Molecular Representation with Multi-modal Energy Spectra](https://mlsanity.com/paper/2502.16284/) (2025)
- [Graph-structured Small Molecule Drug Discovery Through Deep Learning: Progress, Challenges, and Opportunities](https://mlsanity.com/paper/2502.08975/) (2025)
- [Self-Conditioned Denoising for Atomistic Representation Learning](https://mlsanity.com/paper/2603.17196/) (2026)
- [Pushing the Limits of All-Atom Geometric Graph Neural Networks: Pre-Training, Scaling and Zero-Shot Transfer](https://mlsanity.com/paper/2410.21683/) (2024)
- [GeoRecon: Graph-Level Representation Learning for 3D Molecules via Reconstruction-Based Pretraining](https://mlsanity.com/paper/2506.13174/) (2025)
- [Physics-Informed Weakly Supervised Learning for Interatomic Potentials](https://mlsanity.com/paper/2408.05215/) (2024)
- [REBIND: Enhancing ground-state molecular conformation via force-based graph rewiring](https://mlsanity.com/paper/2410.14696/) (2024)
- [Augmenting Molecular Graphs with Geometries via Machine Learning Interatomic Potentials](https://mlsanity.com/paper/2507.00407/) (2025)
- [MoleculeCLA: Rethinking Molecular Benchmark via Computational Ligand-Target Binding Analysis](https://mlsanity.com/paper/2406.17797/) (2024)
- [3D Interaction Geometric Pre-training for Molecular Relational Learning](https://mlsanity.com/paper/2412.02957/) (2024)
- [3D-GSRD: 3D Molecular Graph Auto-Encoder with Selective Re-mask Decoding](https://mlsanity.com/paper/2510.16780/) (2025)
- [Learning 3D Anisotropic Noise Distributions Improves Molecular Force Field Modeling](https://mlsanity.com/paper/2510.22123/) (2025)
- [Hessian-Informed Conformation Augmentation for Potential Energy Surface Curvature in Machine Learning Interatomic Potentials](https://mlsanity.com/paper/2609.05233/) (2026)

## Abstract (arXiv)

While molecular pre-training has shown great potential in enhancing drug discovery, the lack of a solid physical interpretation in current methods raises concerns about whether the learned representation truly captures the underlying explanatory factors in observed data, ultimately resulting in limited generalization and robustness. Although denoising methods offer a physical interpretation, their accuracy is often compromised by ad-hoc noise design, leading to inaccurate learned force fields. To address this limitation, this paper proposes a new method for molecular pre-training, called sliced denoising (SliDe), which is based on the classical mechanical intramolecular potential theory. SliDe utilizes a novel noise strategy that perturbs bond lengths, angles, and torsion angles to achieve better sampling over conformations. Additionally, it introduces a random slicing approach that circumvents the computationally expensive calculation of the Jacobian matrix, which is otherwise essential for estimating the force field. By aligning with physical principles, SliDe shows a 42% improvement in the accuracy of estimated force fields compared to current state-of-the-art denoising methods, and thus outperforms traditional baselines on various molecular property prediction tasks.