Papers › Towards Mechanistic Interpretability of Graph Transformers via Attention Graphs
Towards Mechanistic Interpretability of Graph Transformers via Attention Graphs
Batu El, Deepro Choudhury, Pietro Liò, Chaitanya K. Joshi
We introduce Attention Graphs, a new tool for mechanistic interpretability of Graph Neural Networks (GNNs) and Graph Transformers based on the mathematical equivalence between message passing in GNNs and the self-attention mechanism in Transformers. Attention Graphs aggregate attention matrices across Transformer layers and heads to describe how information flows among input nodes. Through experiments on homophilous and heterophilous node classification tasks, we analyze Attention Graphs from a network science perspective and find that: (1) When Graph Transformers are allowed to learn the optimal graph structure using all-to-all attention among input nodes, the Attention Graphs learned by the model do not tend to correlate with the input/original graph structure; and (2) For heterophilous graphs, different Graph Transformer variants can achieve similar performance while utilising distinct information flow patterns. Open source code: https://github.com/batu-el/understanding-inductive-biases-of-gnns
In Syntology Open this paper in Syntology's Atlas, the map of the papers in Syntology's graph and their citations.
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Tasks
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Methods
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections