# Neural Atoms: Propagating Long-range Interaction in Molecular Graphs through Efficient Communication Channel

arXiv: https://arxiv.org/abs/2311.01276 · HTML: https://mlsanity.com/paper/2311.01276/

## Key facts

- Cited by 10 papers in the map (data through 14 Oct 2026).
- Builds on 48 of its 72 references that are in the map.
- First posted on arXiv 2 Nov 2023.

## Builds on (most cited first, 30 of 48)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Big Bird: Transformers for Longer Sequences](https://mlsanity.com/paper/2007.14062/) (2020)
- [Rethinking Attention with Performers](https://mlsanity.com/paper/2009.14794/) (2020)
- [WILDS: A Benchmark of in-the-Wild Distribution Shifts](https://mlsanity.com/paper/2012.07421/) (2020)
- [Pitfalls of Graph Neural Network Evaluation](https://mlsanity.com/paper/1811.05868/) (2018)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Simple and Deep Graph Convolutional Networks](https://mlsanity.com/paper/2007.02133/) (2020)
- [Hierarchical Graph Representation Learning with Differentiable Pooling](https://mlsanity.com/paper/1806.08804/) (2018)
- [TUDataset: A collection of benchmark datasets for learning with graphs](https://mlsanity.com/paper/2007.08663/) (2020)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [DropEdge: Towards Deep Graph Convolutional Networks on Node Classification](https://mlsanity.com/paper/1907.10903/) (2019)
- [On the Bottleneck of Graph Neural Networks and its Practical Implications](https://mlsanity.com/paper/2006.05205/) (2020)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [Understanding over-squashing and bottlenecks on graphs via curvature](https://mlsanity.com/paper/2111.14522/) (2021)
- [Rethinking Graph Transformers with Spectral Attention](https://mlsanity.com/paper/2106.03893/) (2021)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [Diffusion Improves Graph Learning](https://mlsanity.com/paper/1911.05485/) (2019)
- [Residual Gated Graph ConvNets](https://mlsanity.com/paper/1711.07553/) (2017)
- [Graph Neural Networks with Learnable Structural and Positional Representations](https://mlsanity.com/paper/2110.07875/) (2021)
- [Long Range Graph Benchmark](https://mlsanity.com/paper/2206.08164/) (2022)
- [Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules](https://mlsanity.com/paper/2011.14115/) (2020)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [ASAP: Adaptive Structure Aware Pooling for Learning Hierarchical Graph Representations](https://mlsanity.com/paper/1911.07979/) (2019)
- [3D Infomax improves GNNs for Molecular Property Prediction](https://mlsanity.com/paper/2110.04126/) (2021)

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

- [From Passive to Active Reasoning: Can Large Language Models Ask the Right Questions under Incomplete Information?](https://mlsanity.com/paper/2506.08295/) (2025)
- [E(n) Equivariant Topological Neural Networks](https://mlsanity.com/paper/2405.15429/) (2024)
- [Model Inversion Attacks: A Survey of Approaches and Countermeasures](https://mlsanity.com/paper/2411.10023/) (2024)
- [Reference-guided Policy Optimization for Molecular Optimization via LLM Reasoning](https://mlsanity.com/paper/2603.05900/) (2026)
- [DualEquiNet: A Dual-Space Hierarchical Equivariant Network for Large Biomolecules](https://mlsanity.com/paper/2506.19862/) (2025)
- [Natural Language-Assisted Multi-modal Medication Recommendation](https://mlsanity.com/paper/2501.07166/) (2025)
- [XIMP: Cross Graph Inter-Message Passing for Molecular Property Prediction](https://mlsanity.com/paper/2601.19037/) (2026)
- [ReHub: Linear Complexity Graph Transformers with Adaptive Hub-Spoke Reassignment](https://mlsanity.com/paper/2412.01519/) (2024)
- [MCGM: Multi-stage Clustered Global Modeling for Long-range Interactions in Molecules](https://mlsanity.com/paper/2509.22028/) (2025)
- [MEGA-CL: A Molecular Foundation Model for Generalizable ADMET Prediction through Graph External Attention and Contrastive Learning](https://mlsanity.com/paper/2607.24314/) (2026)

## Abstract (arXiv)

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs mainly excel in leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method to abstract the collective information of atomic groups into a few textitNeural Atoms by implicitly projecting the atoms of a molecular. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection to the traditional LRI calculation method, Ewald Summation. The Neural Atom can enhance GNNs to capture LRI by approximating the potential LRI of the molecular. We conduct extensive experiments on four long-range graph benchmarks, covering graph-level and link-level tasks on molecular graphs. We achieve up to a 27.32% and 38.27% improvement in the 2D and 3D scenarios, respectively. Empirically, our method can be equipped with an arbitrary GNN to help capture LRI. Code and datasets are publicly available in https://github.com/tmlr-group/NeuralAtom.