Year: 2026
Type: article
Abstract: In this work, we introduce a Tropical Axial Attention neural reasoning architecture that replaces vanilla softmax dot-product attention with max-plus operators, inducing a piecewise-linear structure aligned with dynamic programming formulations. From multi-species sequence alignments, our model learns all possible pairwise distances and is trained using a combination of ℓ 1 and tropical symmetric distance metric losses with an ultrametric violation penalty. We leverage the well known isomorphic relationship between the space of all phylogenetic trees with n species and tropical Grassmannian to show that tropical attention provides a natural geometric framework for phylogenetic inference. On empirical D S 1 − D S 11 alignments, where true trees are unknown, the tropical model achieves the lowest MAE to its FastME-induced tree metric on every dataset, with a MAE reductions averaging 81.5% relative to Phyloformer and 98.4% relative than Phyloformer 2. These results suggest that tropical attention is a useful geometric inductive bias for neural phylogenetic inference, especially under distribution shift and when tree-metric consistency is important.
Source: Frontiers in Systems Biology
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,353
Funder: National Science Foundation
Award: Tropical Neural Networks
OpenAlex ID: W7161296277