Approximating SPR Distance Between Phylogenetic Trees with Graph Neural Networks

Abstract

Comparing phylogenetic tree topologies is essential for understanding epidemic dynamics, yet biologically meaningful distances such as the Subtree Prune and Regraft (SPR) distance are NP-hard to compute and intractable on large datasets. We investigate whether a Graph Neural Network (GNN) can approximate SPR distances in near-constant time per comparison after training. Our contributions are fourfold. First, we build and publicly release a dataset of 864 phylogenetic trees inferred with UPGMA and Neighbor-Joining over four bacterial species, spanning up to 9{,}500 isolates, together with 388 labelled tree pairs. Second, we establish a reproducible pre-processing pipeline including midpoint re-rooting, which reduces tree depth and supplies the rooting required for exact distance computation and for the model's root-based features. Third, we validate the supervision target: on small trees, where exact SPR is tractable, the unrooted phangorn::SPR.dist heuristic correlates almost perfectly with the exact rooted distance computed by rspr (Pearson $0.98$--$0.99$), making it an excellent monotonic surrogate. Lastly, we train a Siamese Graph Isomorphism Network (GIN) regressor. In-distribution, i.e., held-out trees from the same species and size range as training, it explains roughly 87--90% of the variance ($R^2 \approx 0.87$ on a held-out split; $0.90 \pm 0.19$ under stratified cross-validation), with about four times lower error than a mean-predictor baseline, and shows partial transfer to unseen species ($R^2 \approx 0.37$). Its main limitation is extrapolation to trees larger than those seen in training, where accuracy collapses. The released dataset and the validated heuristic versus exact relationship provide a reproducible basis for scaling learned SPR approximation.