# HiGNN: Hierarchical Informative Graph Neural Networks for Molecular Property Prediction Equipped with Feature-Wise Attention

arXiv: https://arxiv.org/abs/2208.13994 · HTML: https://mlsanity.com/paper/2208.13994/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 60 references that are in the map.
- First posted on arXiv 30 Aug 2022.

## Builds on (most cited first, 18 of 18)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [XGBoost: A Scalable Tree Boosting System](https://mlsanity.com/paper/1603.02754/) (2016)
- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [CBAM: Convolutional Block Attention Module](https://mlsanity.com/paper/1807.06521/) (2018)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [Drug discovery with explainable artificial intelligence](https://mlsanity.com/paper/2007.00523/) (2020)
- [Hi-Transformer: Hierarchical Interactive Transformer for Efficient and Effective Long Document Modeling](https://mlsanity.com/paper/2106.01040/) (2021)
- [KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images](https://mlsanity.com/paper/1811.09036/) (2018)

## Built on by (most cited first, 1 of 1)

- [Learn to Jump: Adaptive Random Walks for Long-Range Propagation through Graph Hierarchies](https://mlsanity.com/paper/2509.01381/) (2025)

## Abstract (arXiv)

Elucidating and accurately predicting the druggability and bioactivities of molecules plays a pivotal role in drug design and discovery and remains an open challenge. Recently, graph neural networks (GNN) have made remarkable advancements in graph-based molecular property prediction. However, current graph-based deep learning methods neglect the hierarchical information of molecules and the relationships between feature channels. In this study, we propose a well-designed hierarchical informative graph neural networks framework (termed HiGNN) for predicting molecular property by utilizing a co-representation learning of molecular graphs and chemically synthesizable BRICS fragments. Furthermore, a plug-and-play feature-wise attention block is first designed in HiGNN architecture to adaptively recalibrate atomic features after the message passing phase. Extensive experiments demonstrate that HiGNN achieves state-of-the-art predictive performance on many challenging drug discovery-associated benchmark datasets. In addition, we devise a molecule-fragment similarity mechanism to comprehensively investigate the interpretability of HiGNN model at the subgraph level, indicating that HiGNN as a powerful deep learning tool can help chemists and pharmacists identify the key components of molecules for designing better molecules with desired properties or functions. The source code is publicly available at https://github.com/idruglab/hignn.