Enformer-Based Phylogenetic Tree Reconstruction (opens in new tab)

Enformer is a deep learning model trained on human and mouse genomes to predict regulatory activity from 196,608 bp DNA windows. Its trunk embeddings capture long-range cis-regulatory interactions, but whether this signal generalises across the tree of life has not been assessed. We embed universal single-copy orthologous groups (OGs) from OrthoDB v12 across three taxonomic scales and evaluate reconstructed trees against TimeTree5 using Mantel r and Normalised Robinson-Foulds (NRF). On 702 OG...