Hyb-Adam-UM: hybrid ultrametric-aware mtDNA phylogeny reconstruction

TL;DR

Hyb-Adam-UM is a novel method for reconstructing mtDNA phylogenies from incomplete distance matrices, effectively reducing ultrametric violations and improving accuracy even with high levels of missing data.

Contribution

It introduces a hybrid matrix completion approach that enforces ultrametric structure using an Adam-style optimizer, outperforming existing methods at high missingness levels.

Findings

Reduces ultrametric violations across missing data levels.

Achieves better topological accuracy and branch-length agreement.

Most significant improvements at 85% missing data.

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.