Experiments
Every experiment directory in the repository contains its configuration, seeds, environment, results file and README. The entries below summarise the major ones; benchmarks list the measured numbers.
Studies
V9: consensus V2 and adaptive computational coverage
Five pre-registered hypotheses on decoding under a nanopore-like stress channel: a native consensus kernel, the oracle gap, a better consensus (candidate E), adaptive coverage, and a latent-class channel model. Four accepted, one rejected.
Simulated 2026-10-08V7: indel-aware consensus at low coverage
Full-template consensus confirmed on fresh pre-registered seeds; a low-coverage parity profile reaches 5-read coverage at +42 % strands; below 5 reads the architecture was not sufficient.
Simulated 2026-10-07V8: fitting a nanopore channel model to public data
A channel model fitted to the public D13 nanopore dataset reproduces per-base rates and indel run lengths but fails read-level structure tests. Reported as INADEQUATE; held-out data never opened.
Public data 2026-10-07
Measured results
| Benchmark | Class | Result | Version |
|---|---|---|---|
| Clean-channel encode and decode, 20 KB to 1 GiB | Verified (software) | 1 GiB: encode 105.8 s, decode 195.4 s, byte-exact; 9.78 nt per byte | V9 |
| Consensus V2 selection: candidate E vs the V8 decoder | Simulated | EXACT 283 / 600 vs 240 / 600; pooled ORE 0.575 vs 0.488; Holm-adjusted exact McNemar p = 5.2e-12; 0 false success | V9 |
| Native C11 consensus-polish kernel | Simulated | 60 / 60 decodes byte-identical to the NumPy reference; median speed-up 2.46× (bootstrap 95 % 2.41-2.51) | V9 |
| Adaptive computational coverage (stopping rule) | Simulated | 200 / 200 EXACT at the stopping point; 0 false terminations; 41.7 % (v4-balanced) and 31.2 % (v7-lowcov) fewer reads than the smallest fixed coverage with equal EXACT | V9 |
| Whole-archive recovery vs archive size under a stress channel | Simulated | 20 KB: 28 / 30 EXACT; 1 MiB: 2 / 30 EXACT; 0 false success at both sizes | V9 |
| Public-data nanopore channel model G1 (adequacy test) | Public data | INADEQUATE: fails the pre-registered FIT-only pre-check on M6r and M8 | V9 |
| V9 release verification | Verified (software) | 3,337 tests passed, 0 failed, 6 skipped; sanitizers PASS; 0 fuzz crashes; 29 / 29 reproduction rows | V9 |
| VNX-Secure simulated attack scenarios | Simulated | 10 / 10 included scenarios detected and contained; 0 findings over 270 benign requests; median detection 4.2 ms, recovery 12.1 ms | V9 |
| Outer code under i.i.d. strand loss (V6 product code) | Simulated | 20 / 20 seeds decoded up to 16 % strand loss (V5 code: 7 %), at redundant-strand overhead 0.249 vs 0.251 | V6 |