Reliability Limits and Decoding for Partial Nanopore Protein Rereads With Persistent State
arXiv:2608.24819
Abstract
Repeated observations of one physical object need not constitute independent channel uses. We model partial nanopore protein rereads as a finite-alphabet channel with canonical content, persistent readout, and pass-local coverage and synchronization. For exact compound-pass data, matched inference approaches the equivalence-class canonical posterior, and sitewise excess Bayes risk admits an action-aware achievable exponent. In an aligned specialization, observation-local redraw can cause linear-in- growth in true-label negative log-likelihood (NLL). We derive order- projection-stability bounds and an exact passwise-fusion diagnostic. On a PASTOR-informed semi-synthetic hard-symbol channel, label-blind deterministic-mixture importance sampling (LB-IS) agrees with exact enumeration at . At , LB-IS meets every prespecified aggregate absolute marginal-posterior and score-agreement criterion against a fixed high-allocation reference in three selected conditions. Joint agreement holds for the representative and high-NLL conditions, while the near-zero condition remains inconclusive. Exact benchmarks identify order 4 as the smallest tested common cap. At target scale, the reference supports selected unprojected functionals, while neither order 4 nor 5 attains joint agreement, defining a tested finite-memory boundary. Across 16 cells, the order-4 shared branch lowers NLL by 0.033-0.224 nats per residue relative to pass-local.
12 pages, 6 figures