Graph construction in QUBO-based recursive phylogenetic tree reconstruction

arXiv:2609.16640 · q-bio.PE, quant-ph · Submitted 2026-09-15 · Read on arXiv

q-bio.PE, quant-ph

Submitted: 2026-09-15

Updated: 2026-09-23

Comments: 23 pages, 6 figures, plus a graphical abstract; revised manuscript; author list updated

Code: https://github.com/Keio-University-Bio2Q/graph-construction-in-qubo-based-recursi

License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/

Terminology

• Accuracy — 16× in this paper · explained in 1 episode
• Alignment — 10× in this paper · explained in 1 episode
• Graph Construction — 7× in this paper · explained in 3 episodes
• Clustering — 5× in this paper · explained in 2 episodes
• Simulated Bifurcation — 4× in this paper
• Adam — 2× in this paper · explained in 2 episodes
• Combinatorial Optimization — 2× in this paper · explained in 2 episodes
• Consistency — 2× in this paper · explained in 3 episodes
• Spectral clustering — 2× in this paper · explained in 2 episodes
• Core — 1× in this paper · explained in 2 episodes
• Exchangeability — 1× in this paper · explained in 2 episodes
• Parsimony — 1× in this paper · explained in 2 episodes
• QUBO Formulation — 1× in this paper · explained in 3 episodes

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