TMLR 2026

AIMing for Standardised Explainability Evaluation in GNNs: A Framework and Case Study on Graph Kernel Networks

Magdalena Proszewska, N. Siddharth

Main figure for AIMing for Standardised Explainability Evaluation in GNNs: A Framework and Case Study on Graph Kernel Networks

Abstract

Graph Neural Networks (GNNs) have advanced significantly in handling graph-structured data, but a comprehensive framework for evaluating explainability remains lacking. Existing evaluation frameworks primarily involve post-hoc explanations, and operate in the setting where multiple methods generate a suite of explanations for a single model. This makes comparison of explanations across models difficult. Evaluation of inherently interpretable models often targets a specific aspect of interpretability relevant to the model, but remains underdeveloped in terms of generating insight across a suite of measures. We introduce AIM, a comprehensive framework that addresses these limitations by measuring Accuracy, Instance-level explanations, and Model-level explanations. AIM is formulated with minimal constraints to enhance flexibility and facilitate broad applicability. Here, we use AIM in a pipeline, extracting explanations from inherently interpretable GNNs such as graph kernel networks (GKNs) and prototype networks (PNs), evaluating these explanations with AIM, identifying their limitations and obtaining insights to their characteristics. Taking GKNs as a case study, we show how the insights obtained from AIM can be used to develop an updated model, xGKN, that maintains high accuracy while demonstrating improved explainability. Our approach aims to advance the field of Explainable AI (XAI) for GNNs, providing more robust and practical solutions for understanding and improving complex models.

Benchmark Results

Tested on 1 dataset

Tables show presented results in global context (best 3 papers + GCN + MLP).

TU Dortmund

#ModelAccuracy ↑Paper
1
MSH-GNN
0.9910 ±0.0030
2
ID-GNN+BEC
0.9830 ±0.0360
3
SupCosine
0.9830 ±0.0250
39
GIN
actual #39 vs paper #580 541 places worse
0.9330 ±0.0290
best reported
actual #39 vs paper #580 541 places worse
paper 0.8150 ±0.0980

Difference within reported uncertainty; not counted as underperformance.

paper 0.8150 ±0.0980 Δ at pub 0.1180
63
GCN
0.9220 ±0.0440
81
ProtGNN
actual #81 vs paper #237 156 places worse
0.9170 ±0.0290
best reported
actual #81 vs paper #237 156 places worse
paper 0.8940 ±0.0720

Difference within reported uncertainty; not counted as underperformance.

paper 0.8940 ±0.0720 Δ at pub 0.0230
183
GAT
actual #183 vs paper #614 431 places worse
0.9010 ±0.0580
best reported
actual #183 vs paper #614 431 places worse
paper 0.8000 ±0.0990

Difference within reported uncertainty; not counted as underperformance.

paper 0.8000 ±0.0990 Δ at pub 0.1010 Δ today 0.1010
403
MLP
0.8660 ±0.0495
480
XGKN
0.8420 ±0.0690
This paper
571
KerGNN
0.8190 ±0.0600
This paper
702
GKNN
0.7570 ±0.0690
This paper
SOTA performance (not significantly different from the best) Baseline / comparison (this paper) Global context (other papers)