arXiv subjects

Manuela Profir

Publications and source records attributed to Manuela Profir.

2 recordsLinked to original sources

arXiv2026

A Block Decomposed QUBO Workflow for Chromosome-Y Phylogeny Reconstruction

This paper sets out a computational workflow that reconstructs the phylogeny of human Y-chromosome populations from a Variant Call Format (VCF) file of biallelic Single Nucleotide Polymorphisms (SNP). The two classical phylogenetic decisions - topology selection and root placement - are cast as Quadratic Unconstrained Binary Optimisation (QUBO) problems. The workflow combines two QUBO formulations with an Alternating Direction Method of Multipliers (ADMM) decomposition strategy and a plug-in Digitized Counter-Diabatic Quantum Optimization (DCQO) solver, enabling large phylogenetic optimization problems to be executed across multiple classical or quantum computing resources. The DCQO gate-based optimizer drives each ADMM-block QUBO with short-depth counter-diabatic circuits in the impulse regime, without the necessity for an outer variational loop. The combination of ADMM decomposition and the DCQO block solver facilitates problem sizes that surpass the qubit budget of any individual digital quantum processing unit call, while maintaining the integrity of the original objective. The workflow extracts genotype information from VCF files, reconstructs topology and rooting through two QUBO formulations, and annotates the resulting tree using PhyloTree. The resultant data set comprises a Nexus-annotated rooted tree, in addition to diagnostic figures. The workflow demonstrates the potential of modest-scale QUBO formulations combined with ADMM decomposition to serve as a scalable alternative to greedy heuristics in the domain of population genomics.

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arXiv2026

Managing Iterative Hybrid Quantum-Classical Optimization as a First-Class Scientific Workflow

Today's Quantum Processing Units (QPUs) are too small and too noisy to solve large combinatorial optimization problems directly, so practical hybrid solvers split a problem into pieces and iterate a decompose-solve-aggregate loop over whatever backends are available: classical heuristics, simulators, emulators, or a QPU. In practice, the loop is a driver script. It sits on top of the quantum-HPC middleware, handling task generation, provenance, recovery, and portability. Instead, we treat the loop as a scientific workflow and ask what a workflow layer adds to a generic workflow management system and QPU-sharing middleware. Two decomposition patterns from real applications, iterative consensus (ADMM) and hierarchical partitioning, turn out to stress the orchestration layer very differently: over 120 managed runs, orchestration took 78.4% of end-to-end time for the iterative pattern, almost all of it in a per-round barrier, but only 6.2% for the hierarchical one. Our workflow model adds four things a generic engine does not have: a termination predicate residing in the task graph that reads the previous round's residuals, subproblem-level recovery with warm-start and quorum-deferred aggregation, failover from a QPU to a classical replica within a round, and a provenance schema that describes CPUs, simulators and QPUs with the same fields, including the shot budget included. We report the cost of each layer on our engine, show that speculative re-execution enable runs to complete under injected failures that stall an unmanaged driver. We also use the same provenance to give per-device latency tails across simulators, emulators and IQM QPUs.

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