omicau Benchmark Protocol Record: Prospective Evaluation of Leakage-Aware Multi-Omics Auditing and Fusion Benchmarking

Prospectively registered protocol for the omicau publication benchmark. omicau is a leakage-safe multi-omics audit tool that couples fusion benchmarking to explicit tests of the conditions under which its own results would be untrustworthy: value-level provenance hashing, missingness-bias and batch-confounding diagnostics, group-aware cross-validation with strictly fold-internal preprocessing, corrupted-input control baselines, and a modality-utility ledger in which a layer is credited with independent contribution only when its leave-one-out gain clears both an effect-size floor and a variance-corrected paired test. This record specifies, in advance of any definitive analysis: the hypotheses and their refutation rules; the generative simulation design with ground-truth modality roles; the leakage, batch-confounding, missingness and small-sample stress tests, each with a clean control condition; the real multi-omics cohorts and their eligibility rules; the comparator set and eligibility audit; the resampling scheme and split-freezing procedure; the statistical analysis plan; the exclusion criteria; the failure-reporting and deviation policies; the compute plan; and the decision gates that must hold before the benchmark is called publication-ready. The record contains no benchmark results. The declaration is machine-checked rather than asserted: the freeze tooling refuses to produce the freeze manifest while any result, split or simulation directory is non-empty, while the audit thresholds mirrored in the protocol disagree with the constants in the installed software, while any protocol document is still marked as undrafted, or while the reserved DOI is absent. Development analyses performed before the protocol was written are enumerated explicitly and are excluded from confirmatory evidence. A second Zenodo record will carry the frozen result tables, per-fold and per-seed outputs, failed runs, the deviation log, the figures and a protocol-compliance report, and will reference this record as the protocol it derives from.