Abstract
Neural networks are widely used in bioinformatics to extract features from morphological, structural, and sequence data of different taxa. A key question is whether such features are compatible with a known phylogenetic tree describing the evolutionary relationships among the taxa. We address this question with a machine learning approach that takes taxon-specific data and a reference tree as input, and trains a neural network to produce a latent feature space whose pairwise distances are consistent with the tree topology. Our approach builds on the established role of quartets in distance-based phylogeny, leading to a quartet-based loss function for neural network training. In a proof-of-concept study using bacterial ribosomal RNA sequences, we show that the learned feature distances closely match the reference phylogeny. This framework can be applied to diverse biological data types, providing a principled way to incorporate phylogenetic constraints into neural network-based feature extraction.