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

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

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

Related papers

• Drivers of periodicity in population dynamic models of long-lived, large mammals
• Constraints on the perfect phylogeny mixture model and their effect on reducing degeneracy
• Interplay between evolutionary and epidemic time scales challenges the outcome of control policies
• Evolutionary foraging in grids: Intermittent search dynamics emerge in finite, depletable landscapes
• Life Finds A Way: Emergence of Cooperative Structures in Adaptive Threshold Networks
• Fluctuating growth rate and spatial diffusion shape plankton diversity