# How do Probabilistic Graphical Models and Graph Neural Networks Look at Network Data?

arXiv: https://arxiv.org/abs/2506.11869 · HTML: https://mlsanity.com/paper/2506.11869/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 60 of its 91 references that are in the map.
- First posted on arXiv 13 Jun 2025.

## Builds on (most cited first, 30 of 60)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [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)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering](https://mlsanity.com/paper/1606.09375/) (2016)
- [Modeling Relational Data with Graph Convolutional Networks](https://mlsanity.com/paper/1703.06103/) (2017)
- [Revisiting Semi-Supervised Learning with Graph Embeddings](https://mlsanity.com/paper/1603.08861/) (2016)
- [Link Prediction Based on Graph Neural Networks](https://mlsanity.com/paper/1802.09691/) (2018)
- [Geom-GCN: Geometric Graph Convolutional Networks](https://mlsanity.com/paper/2002.05287/) (2020)
- [On the Bottleneck of Graph Neural Networks and its Practical Implications](https://mlsanity.com/paper/2006.05205/) (2020)
- [Geometric deep learning on graphs and manifolds using mixture model CNNs](https://mlsanity.com/paper/1611.08402/) (2016)
- [Community Detection and Stochastic Block Models](https://mlsanity.com/paper/1703.10146/) (2017)
- [Long Range Graph Benchmark](https://mlsanity.com/paper/2206.08164/) (2022)
- [Revisiting Graph Neural Networks: All We Have is Low-Pass Filters](https://mlsanity.com/paper/1905.09550/) (2019)
- [A Note on Over-Smoothing for Graph Neural Networks](https://mlsanity.com/paper/2006.13318/) (2020)
- [A Survey on Oversmoothing in Graph Neural Networks](https://mlsanity.com/paper/2303.10993/) (2023)
- [A Fair Comparison of Graph Neural Networks for Graph Classification](https://mlsanity.com/paper/1912.09893/) (2019)
- [GraphLIME: Local Interpretable Model Explanations for Graph Neural Networks](https://mlsanity.com/paper/2001.06216/) (2020)
- [Is Homophily a Necessity for Graph Neural Networks?](https://mlsanity.com/paper/2106.06134/) (2021)
- [Finding Global Homophily in Graph Neural Networks When Meeting Heterophily](https://mlsanity.com/paper/2205.07308/) (2022)
- [How Powerful are Spectral Graph Neural Networks](https://mlsanity.com/paper/2205.11172/) (2022)
- [Revisiting Heterophily For Graph Neural Networks](https://mlsanity.com/paper/2210.07606/) (2022)
- [Graph Clustering with Graph Neural Networks](https://mlsanity.com/paper/2006.16904/) (2020)
- [Attributed Graph Clustering: A Deep Attentional Embedding Approach](https://mlsanity.com/paper/1906.06532/) (2019)
- [Predicting multicellular function through multi-layer tissue networks](https://mlsanity.com/paper/1707.04638/) (2017)
- [Interpretable Deep Learning: Interpretation, Interpretability, Trustworthiness, and Beyond](https://mlsanity.com/paper/2103.10689/) (2021)
- [Edge Directionality Improves Learning on Heterophilic Graphs](https://mlsanity.com/paper/2305.10498/) (2023)
- [Automated Concatenation of Embeddings for Structured Prediction](https://mlsanity.com/paper/2010.05006/) (2020)

## Abstract (arXiv)

Graphs are a powerful data structure for representing relational data and are widely used to describe complex real-world systems. Probabilistic Graphical Models (PGMs) and Graph Neural Networks (GNNs) can both leverage graph-structured data, but their inherent functioning is different. The question is how do they compare in capturing the information contained in networked datasets? We address this objective by solving a link prediction task and we conduct three main experiments, on both synthetic and real networks: one focuses on how PGMs and GNNs handle input features, while the other two investigate their robustness to noisy features and increasing heterophily of the graph. PGMs do not necessarily require features on nodes, while GNNs cannot exploit the network edges alone, and the choice of input features matters. We find that GNNs are outperformed by PGMs when input features are low-dimensional or noisy, mimicking many real scenarios where node attributes might be scalar or noisy. Then, we find that PGMs are more robust than GNNs when the heterophily of the graph is increased. Finally, to assess performance beyond prediction tasks, we also compare the two frameworks in terms of their computational complexity and interpretability.