Hyb-Adam-UM: hybrid ultrametric-aware mtDNA phylogeny reconstruction
Abstract
Motivation: mtDNA distance matrices are standard inputs for distance-based phylogeny, but computing all pairwise alignments is costly. Missing entries can degrade inferred topology and branch lengths, and generic matrix-completion methods may disrupt tree-like (ultrametric) structure. Results: We propose Hyb-Adam-UM, which starts from an alignment-limited Needleman-Wunsch distance backbone and completes the matrix by minimizing a robust triplet ultrametric-violation functional. An Adam-style finite-difference optimizer updates only missing entries while enforcing symmetry, non-negativity, and a zero diagonal. From one complete reference matrix, we generate 20 masked instances at 30%, 50%, 65%, and 85% missingness. Hyb-Adam-UM consistently reduces ultrametric violations and achieves competitive reconstruction error, with improved topological accuracy and branch-length agreement relative to MW*/NJ* projection baselines (which exactly preserve observed distances) and Soft-Impute; gains are most pronounced at 85% missingness. Availability and implementation: https://github.com/mitichya/hyb-adam-um/; Zenodo: https://doi.org/10.5281/zenodo.18609748 Supplementary information: Supplementary data available online.
Keywords
Cite
@article{arxiv.2602.12854,
title = {Hyb-Adam-UM: hybrid ultrametric-aware mtDNA phylogeny reconstruction},
author = {Dmitrii Chaikovskii and Weilai Qu and Boris Melnikov and Ye Zhang and Yuehong Zhao},
journal= {arXiv preprint arXiv:2602.12854},
year = {2026}
}