# Adaptive Node Feature Selection For Graph Neural Networks

arXiv: https://arxiv.org/abs/2510.03096 · HTML: https://mlsanity.com/paper/2510.03096/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 38 of its 73 references that are in the map.
- First posted on arXiv 3 Oct 2025.

## Builds on (most cited first, 30 of 38)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- ["Why Should I Trust You?": Explaining the Predictions of Any Classifier](https://mlsanity.com/paper/1602.04938/) (2016)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Geometric deep learning: going beyond Euclidean data](https://mlsanity.com/paper/1611.08097/) (2016)
- [Pitfalls of Graph Neural Network Evaluation](https://mlsanity.com/paper/1811.05868/) (2018)
- [Predict then Propagate: Graph Neural Networks meet Personalized PageRank](https://mlsanity.com/paper/1810.05997/) (2018)
- [Geom-GCN: Geometric Graph Convolutional Networks](https://mlsanity.com/paper/2002.05287/) (2020)
- [Image-based Recommendations on Styles and Substitutes](https://mlsanity.com/paper/1506.04757/) (2015)
- [Distribution-Free Predictive Inference For Regression](https://mlsanity.com/paper/1604.04173/) (2016)
- [Explainability in Graph Neural Networks: A Taxonomic Survey](https://mlsanity.com/paper/2012.15445/) (2020)
- [All Models are Wrong, but Many are Useful: Learning a Variable's Importance by Studying an Entire Class of Prediction Models Simultaneously](https://mlsanity.com/paper/1801.01489/) (2018)
- [Consistent Individualized Feature Attribution for Tree Ensembles](https://mlsanity.com/paper/1802.03888/) (2018)
- [Explaining by Removing: A Unified Framework for Model Explanation](https://mlsanity.com/paper/2011.14878/) (2020)
- [GraphLIME: Local Interpretable Model Explanations for Graph Neural Networks](https://mlsanity.com/paper/2001.06216/) (2020)
- [Topology Adaptive Graph Convolutional Networks](https://mlsanity.com/paper/1710.10370/) (2017)
- [L-Shapley and C-Shapley: Efficient Model Interpretation for Structured Data](https://mlsanity.com/paper/1808.02610/) (2018)
- [Unrestricted Permutation forces Extrapolation: Variable Importance Requires at least One More Model, or There Is No Free Variable Importance](https://mlsanity.com/paper/1905.03151/) (2019)
- [Simplifying approach to Node Classification in Graph Neural Networks](https://mlsanity.com/paper/2111.06748/) (2021)
- [Are Powerful Graph Neural Nets Necessary? A Dissection on Graph Classification](https://mlsanity.com/paper/1905.04579/) (2019)
- [On Generalized Degree Fairness in Graph Neural Networks](https://mlsanity.com/paper/2302.03881/) (2023)
- [RawlsGCN: Towards Rawlsian Difference Principle on Graph Convolutional Network](https://mlsanity.com/paper/2202.13547/) (2022)
- [RAW-GNN: RAndom Walk Aggregation based Graph Neural Network](https://mlsanity.com/paper/2206.13953/) (2022)
- [On Structural Explanation of Bias in Graph Neural Networks](https://mlsanity.com/paper/2206.12104/) (2022)
- [LSGNN: Towards General Graph Neural Network in Node Classification by Local Similarity](https://mlsanity.com/paper/2305.04225/) (2023)
- [Graph Neural Networks Including Sparse Interpretability](https://mlsanity.com/paper/2007.00119/) (2020)
- [GNNShap: Scalable and Accurate GNN Explanation using Shapley Values](https://mlsanity.com/paper/2401.04829/) (2024)
- [Motif Graph Neural Network](https://mlsanity.com/paper/2112.14900/) (2021)

## Abstract (arXiv)

We propose an adaptive node feature selection approach for graph neural networks (GNNs) that identifies and removes unnecessary features during training. The ability to measure how features contribute to model output is key for interpreting decisions and reducing dimensionality by eliminating unhelpful variables. However, graph-structured data introduces complex dependencies that may be unsuited to classical feature importance metrics. Inspired by this, we present a data-, model-, and task-agnostic method that determines relevant features during training based on changes in validation performance upon permuting feature values. We theoretically motivate our approach by characterizing how the relationships between node data and graph structure influences GNN performance. Empirically, we show that (i) our highly general approach rivals the performance of tailored feature selection approaches that exploit prior assumptions; (ii) we return meaningful feature importance scores well before the GNN is fully trained; and (iii) our scores demonstrably extract relevant properties that inform feature importance for various graph learning settings.