# CI-GNN: A Granger Causality-Inspired Graph Neural Network for Interpretable Brain Network-Based Psychiatric Diagnosis

arXiv: https://arxiv.org/abs/2301.01642 · HTML: https://mlsanity.com/paper/2301.01642/

## Key facts

- Cited by 16 papers in the map (data through 14 Oct 2026).
- Builds on 37 of its 85 references that are in the map.
- First posted on arXiv 4 Jan 2023.

## Builds on (most cited first, 30 of 37)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [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)
- [Modeling Relational Data with Graph Convolutional Networks](https://mlsanity.com/paper/1703.06103/) (2017)
- [Hierarchical Graph Representation Learning with Differentiable Pooling](https://mlsanity.com/paper/1806.08804/) (2018)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [MINE: Mutual Information Neural Estimation](https://mlsanity.com/paper/1801.04062/) (2018)
- [Parameterized Explainer for Graph Neural Network](https://mlsanity.com/paper/2011.04573/) (2020)
- [Explainability in Graph Neural Networks: A Taxonomic Survey](https://mlsanity.com/paper/2012.15445/) (2020)
- [GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders](https://mlsanity.com/paper/1802.03480/) (2018)
- [Beyond Low-frequency Information in Graph Convolutional Networks](https://mlsanity.com/paper/2101.00797/) (2021)
- [On Explainability of Graph Neural Networks via Subgraph Explorations](https://mlsanity.com/paper/2102.05152/) (2021)
- [XGNN: Towards Model-Level Explanations of Graph Neural Networks](https://mlsanity.com/paper/2006.02587/) (2020)
- [PGM-Explainer: Probabilistic Graphical Model Explanations for Graph Neural Networks](https://mlsanity.com/paper/2010.05788/) (2020)
- [Discovering Invariant Rationales for Graph Neural Networks](https://mlsanity.com/paper/2201.12872/) (2022)
- [Interpretable and Generalizable Graph Learning via Stochastic Attention Mechanism](https://mlsanity.com/paper/2201.12987/) (2022)
- [Explainability Techniques for Graph Convolutional Networks](https://mlsanity.com/paper/1905.13686/) (2019)
- [Generative Causal Explanations for Graph Neural Networks](https://mlsanity.com/paper/2104.06643/) (2021)
- [ProtGNN: Towards Self-Explaining Graph Neural Networks](https://mlsanity.com/paper/2112.00911/) (2021)
- [Generalizing Graph Neural Networks on Out-Of-Distribution Graphs](https://mlsanity.com/paper/2111.10657/) (2021)
- [Interpretable Graph Neural Networks for Connectome-Based Brain Disorder Analysis](https://mlsanity.com/paper/2207.00813/) (2022)
- [Improving Subgraph Recognition with Variational Graph Information Bottleneck](https://mlsanity.com/paper/2112.09899/) (2021)
- [Generative causal explanations of black-box classifiers](https://mlsanity.com/paper/2006.13913/) (2020)
- [Stop Explaining Black Box Machine Learning Models for High Stakes Decisions and Use Interpretable Models Instead](https://mlsanity.com/paper/1811.10154/) (2018)
- [Reinforced Causal Explainer for Graph Neural Networks](https://mlsanity.com/paper/2204.11028/) (2022)
- [OrphicX: A Causality-Inspired Latent Variable Model for Interpreting Graph Neural Networks](https://mlsanity.com/paper/2203.15209/) (2022)
- [Recognizing Predictive Substructures with Subgraph Information Bottleneck](https://mlsanity.com/paper/2103.11155/) (2021)
- [BrainIB: Interpretable Brain Network-based Psychiatric Diagnosis with Graph Information Bottleneck](https://mlsanity.com/paper/2205.03612/) (2022)

## Built on by (most cited first, 16 of 16)

- [A Comprehensive Survey of Foundation Models in Medicine](https://mlsanity.com/paper/2406.10729/) (2024)
- [Explaining Graph Neural Networks via Structure-aware Interaction Index](https://mlsanity.com/paper/2405.14352/) (2024)
- [Exploring Causal Learning through Graph Neural Networks: An In-depth Review](https://mlsanity.com/paper/2311.14994/) (2023)
- [LOGIN: A Large Language Model Consulted Graph Neural Network Training Framework](https://mlsanity.com/paper/2405.13902/) (2024)
- [BACE: Behavior-Adaptive Connectivity Estimation for Interpretable Graphs of Neural Dynamics](https://mlsanity.com/paper/2510.20831/) (2025)
- [Causal Spherical Hypergraph Networks for Modelling Social Uncertainty](https://mlsanity.com/paper/2506.17840/) (2025)
- [When Graph Neural Network Meets Causality: Opportunities, Methodologies and An Outlook](https://mlsanity.com/paper/2312.12477/) (2023)
- [MHNet: Multi-view High-order Network for Diagnosing Neurodevelopmental Disorders Using Resting-state fMRI](https://mlsanity.com/paper/2407.03217/) (2024)
- [A Survey of Out-of-distribution Generalization for Graph Machine Learning from a Causal View](https://mlsanity.com/paper/2409.09858/) (2024)
- [Discovering robust biomarkers of psychiatric disorders from resting-state functional MRI via graph neural networks: A systematic review](https://mlsanity.com/paper/2405.00577/) (2024)
- [Beyond Pairwise Connections: Extracting High-Order Functional Brain Network Structures under Global Constraints](https://mlsanity.com/paper/2510.09175/) (2025)
- [Causal Graph Neural Networks for Healthcare](https://mlsanity.com/paper/2511.02531/) (2025)
- [SphUnc: Hyperspherical Uncertainty Decomposition and Causal Identification via Information Geometry](https://mlsanity.com/paper/2603.01168/) (2026)
- [Neurocircuitry-Inspired Hierarchical Graph Causal Attention Networks for Explainable Depression Identification](https://mlsanity.com/paper/2511.17622/) (2025)
- [ARM-Explainer -- Explaining and improving graph neural network predictions for the maximum clique problem using node features and association rule mining](https://mlsanity.com/paper/2511.22866/) (2025)
- [Artemis: Anatomy-Resolved inTervention for Eliminating Multimodal NeuroImage confounderS](https://mlsanity.com/paper/2606.18287/) (2026)

## Abstract (arXiv)

There is a recent trend to leverage the power of graph neural networks (GNNs) for brain-network based psychiatric diagnosis, which,in turn, also motivates an urgent need for psychiatrists to fully understand the decision behavior of the used GNNs. However, most of the existing GNN explainers are either post-hoc in which another interpretive model needs to be created to explain a well-trained GNN, or do not consider the causal relationship between the extracted explanation and the decision, such that the explanation itself contains spurious correlations and suffers from weak faithfulness. In this work, we propose a granger causality-inspired graph neural network (CI-GNN), a built-in interpretable model that is able to identify the most influential subgraph (i.e., functional connectivity within brain regions) that is causally related to the decision (e.g., major depressive disorder patients or healthy controls), without the training of an auxillary interpretive network. CI-GNN learns disentangled subgraph-level representations α and beta that encode, respectively, the causal and noncausal aspects of original graph under a graph variational autoencoder framework, regularized by a conditional mutual information (CMI) constraint. We theoretically justify the validity of the CMI regulation in capturing the causal relationship. We also empirically evaluate the performance of CI-GNN against three baseline GNNs and four state-of-the-art GNN explainers on synthetic data and three large-scale brain disease datasets. We observe that CI-GNN achieves the best performance in a wide range of metrics and provides more reliable and concise explanations which have clinical evidence.The source code and implementation details of CI-GNN are freely available at GitHub repository (https://github.com/ZKZ-Brain/CI-GNN/).