Phylogenetic Tree Inference with Tropical Axial Attention
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 $\ell_1$ 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 infe...
| Authors | Chris Teska, Kurt Pasque, Ruriko Yoshida et al. |
|---|---|
| Primary category | q-bio.PE |
| Published | 12 May 2026 |
| Last updated at source | 6 August 2026 |
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