# Atomic and Subgraph-aware Bilateral Aggregation for Molecular Representation Learning

arXiv: https://arxiv.org/abs/2305.12618 · HTML: https://mlsanity.com/paper/2305.12618/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 27 of its 43 references that are in the map.
- First posted on arXiv 22 May 2023.

## Builds on (most cited first, 27 of 27)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [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)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (2020)
- [GraphMAE: Self-Supervised Masked Graph Autoencoders](https://mlsanity.com/paper/2205.10803/) (2022)
- [InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization](https://mlsanity.com/paper/1908.01000/) (2019)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [GPT-GNN: Generative Pre-Training of Graph Neural Networks](https://mlsanity.com/paper/2006.15437/) (2020)
- [Graph Contrastive Learning Automated](https://mlsanity.com/paper/2106.07594/) (2021)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [Adversarial Graph Augmentation to Improve Graph Contrastive Learning](https://mlsanity.com/paper/2106.05819/) (2021)
- [SimGRACE: A Simple Framework for Graph Contrastive Learning without Data Augmentation](https://mlsanity.com/paper/2202.03104/) (2022)
- [Motif-based Graph Self-Supervised Learning for Molecular Property Prediction](https://mlsanity.com/paper/2110.00987/) (2021)
- [3D Infomax improves GNNs for Molecular Property Prediction](https://mlsanity.com/paper/2110.04126/) (2021)
- [Self-supervised Graph-level Representation Learning with Local and Global Structure](https://mlsanity.com/paper/2106.04113/) (2021)
- [Molecular Property Prediction: A Multilevel Quantum Interactions Modeling Perspective](https://mlsanity.com/paper/1906.11081/) (2019)
- [Let Invariant Rationale Discovery Inspire Graph Contrastive Learning](https://mlsanity.com/paper/2206.07869/) (2022)
- [Molecule Generation by Principal Subgraph Mining and Assembling](https://mlsanity.com/paper/2106.15098/) (2021)
- [PotentialNet for Molecular Property Prediction](https://mlsanity.com/paper/1803.04465/) (2018)
- [Molformer: Motif-based Transformer on 3D Heterogeneous Molecular Graphs](https://mlsanity.com/paper/2110.01191/) (2021)
- [KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction](https://mlsanity.com/paper/2206.03364/) (2022)

## Abstract (arXiv)

Molecular representation learning is a crucial task in predicting molecular properties. Molecules are often modeled as graphs where atoms and chemical bonds are represented as nodes and edges, respectively, and Graph Neural Networks (GNNs) have been commonly utilized to predict atom-related properties, such as reactivity and solubility. However, functional groups (subgraphs) are closely related to some chemical properties of molecules, such as efficacy, and metabolic properties, which cannot be solely determined by individual atoms. In this paper, we introduce a new model for molecular representation learning called the Atomic and Subgraph-aware Bilateral Aggregation (ASBA), which addresses the limitations of previous atom-wise and subgraph-wise models by incorporating both types of information. ASBA consists of two branches, one for atom-wise information and the other for subgraph-wise information. Considering existing atom-wise GNNs cannot properly extract invariant subgraph features, we propose a decomposition-polymerization GNN architecture for the subgraph-wise branch. Furthermore, we propose cooperative node-level and graph-level self-supervised learning strategies for ASBA to improve its generalization. Our method offers a more comprehensive way to learn representations for molecular property prediction and has broad potential in drug and material discovery applications. Extensive experiments have demonstrated the effectiveness of our method.