# On the Approximation of Phylogenetic Distance Functions by Artificial Neural Networks

arXiv: https://arxiv.org/abs/2512.02223 · HTML: https://mlsanity.com/paper/2512.02223/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 15 of its 50 references that are in the map.
- First posted on arXiv 1 Dec 2025.

## Builds on (most cited first, 15 of 15)

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## Abstract (arXiv)

Inferring the phylogenetic relationships among a sample of organisms is a fundamental problem in modern biology. While distance-based hierarchical clustering algorithms achieved early success on this task, these have been supplanted by Bayesian and maximum likelihood search procedures based on complex models of molecular evolution. In this work we describe minimal neural network architectures that can approximate classic phylogenetic distance functions and the properties required to learn distances under a variety of molecular evolutionary models. In contrast to model-based inference (and recently proposed model-free convolutional and transformer networks), these architectures have a small computational footprint and are scalable to large numbers of taxa and molecular characters. The learned distance functions generalize well and, given an appropriate training dataset, achieve results comparable to state-of-the art inference methods.