Hyb-Adam-UM: hybrid ultrametric-aware mtDNA phylogeny reconstruction
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arXiv
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| Autori principali: | , , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2026
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| _version_ | 1866912903023558656 |
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| author | Chaikovskii, Dmitrii Qu, Weilai Melnikov, Boris Zhang, Ye Zhao, Yuehong |
| author_facet | Chaikovskii, Dmitrii Qu, Weilai Melnikov, Boris Zhang, Ye Zhao, Yuehong |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2602_12854 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | Hyb-Adam-UM: hybrid ultrametric-aware mtDNA phylogeny reconstruction Chaikovskii, Dmitrii Qu, Weilai Melnikov, Boris Zhang, Ye Zhao, Yuehong Populations and Evolution Numerical Analysis 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. |
| title | Hyb-Adam-UM: hybrid ultrametric-aware mtDNA phylogeny reconstruction |
| topic | Populations and Evolution Numerical Analysis |
| url | https://arxiv.org/abs/2602.12854 |