# Heterophily-informed Message Passing

arXiv: https://arxiv.org/abs/2504.19785 · HTML: https://mlsanity.com/paper/2504.19785/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 47 of its 66 references that are in the map.
- First posted on arXiv 28 Apr 2025.

## Builds on (most cited first, 30 of 47)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [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)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Glow: Generative Flow with Invertible 1x1 Convolutions](https://mlsanity.com/paper/1807.03039/) (2018)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [NICE: Non-linear Independent Components Estimation](https://mlsanity.com/paper/1410.8516/) (2014)
- [Pitfalls of Graph Neural Network Evaluation](https://mlsanity.com/paper/1811.05868/) (2018)
- [Revisiting Semi-Supervised Learning with Graph Embeddings](https://mlsanity.com/paper/1603.08861/) (2016)
- [Representation Learning on Graphs with Jumping Knowledge Networks](https://mlsanity.com/paper/1806.03536/) (2018)
- [Geom-GCN: Geometric Graph Convolutional Networks](https://mlsanity.com/paper/2002.05287/) (2020)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [Adaptive Universal Generalized PageRank Graph Neural Network](https://mlsanity.com/paper/2006.07988/) (2020)
- [Multi-scale Attributed Node Embedding](https://mlsanity.com/paper/1909.13021/) (2019)
- [MixHop: Higher-Order Graph Convolutional Architectures via Sparsified Neighborhood Mixing](https://mlsanity.com/paper/1905.00067/) (2019)
- [MolGAN: An implicit generative model for small molecular graphs](https://mlsanity.com/paper/1805.11973/) (2018)
- [Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation](https://mlsanity.com/paper/1806.02473/) (2018)
- [A critical look at the evaluation of GNNs under heterophily: Are we really making progress?](https://mlsanity.com/paper/2302.11640/) (2023)
- [Large Scale Learning on Non-Homophilous Graphs: New Benchmarks and Strong Simple Methods](https://mlsanity.com/paper/2110.14446/) (2021)
- [GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation](https://mlsanity.com/paper/2001.09382/) (2020)
- [Grammar Variational Autoencoder](https://mlsanity.com/paper/1703.01925/) (2017)
- [Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models](https://mlsanity.com/paper/1811.12823/) (2018)
- [Generalization and Representational Limits of Graph Neural Networks](https://mlsanity.com/paper/2002.06157/) (2020)
- [Neural Sheaf Diffusion: A Topological Perspective on Heterophily and Oversmoothing in GNNs](https://mlsanity.com/paper/2202.04579/) (2022)
- [Graph Neural Networks with Heterophily](https://mlsanity.com/paper/2009.13566/) (2020)
- [Geometric Latent Diffusion Models for 3D Molecule Generation](https://mlsanity.com/paper/2305.01140/) (2023)

## Abstract (arXiv)

Graph neural networks (GNNs) are known to be vulnerable to oversmoothing due to their implicit homophily assumption. We mitigate this problem with a novel scheme that regulates the aggregation of messages, modulating the type and extent of message passing locally thereby preserving both the low and high-frequency components of information. Our approach relies solely on learnt embeddings, obviating the need for auxiliary labels, thus extending the benefits of heterophily-aware embeddings to broader applications, e.g., generative modelling. Our experiments, conducted across various data sets and GNN architectures, demonstrate performance enhancements and reveal heterophily patterns across standard classification benchmarks. Furthermore, application to molecular generation showcases notable performance improvements on chemoinformatics benchmarks.