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Life sciences · Preprint
arXiv · September 28, 2026
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Graph Transformers produce, for each attention head, a dense $n\times n$ matrix of learned pairwise interactions. We ask a fundamental question: do these attention-induced graphs converge to a stable limit object as $n$ grows, or does the learned interaction pattern remain unstructured and size-dependent? We answer this using dense graph limit theory, treating each attention matrix as a finite sample from an underlying kernel---an \emph{attention graphon}---and studying concentration around this limit under the cut-distance. We derive a worst-case variance bound requiring no assumptions on the graphon, and a sharper regularity-aware bound based on nonparametric estimation theory. To operationalize the theory, we propose a canonicalize-then-block-average pipeline for estimating dataset-level attention graphons, and a variance-based diagnostic for testing whether attention admits a stable continuum description. Experiments across multiple graph benchmarks show that learned attention stabilizes to dataset-specific graphon structure on several datasets; that empirical cut-distance and cut-norm variance decreases with $n$ consistent with our bounds; and that attention graphons transfer to larger graph sizes with error decreasing in $n$.