{
  "date": "2026-09-24",
  "scope": "Method metadata from original hash-verified reports; no new fit or outcome analysis.",
  "methods": [
    {
      "case": "flip2",
      "source_report_uri": "https://raw.githubusercontent.com/rewire-bio/rewire-benchmarks/ca73fa47136d182f2d4ddb083d084712198fc0e2/research/local-runs-2026-09-20/flip2-composition/report.json",
      "source_report_sha256": "abd08d3f493428d06f43740c94e268575d755560e72120c73b294127acb395e6",
      "dataset_id": "flip2-rhomax-by-wild-type",
      "model": {
        "name": "Amino-acid composition + fixed ridge (Rewire control)",
        "training_overlap": "No pretraining; fitted only on this protocol training split. Split is not a claim of homology separation."
      },
      "model_configuration": {
        "alpha": 10,
        "features": "40 amino-acid fractions; second component zero for Rhomax",
        "fit_intercept": true,
        "target_scaling": "training-only StandardScaler",
        "validation_used": false
      },
      "note": "Saved baseline predictions replayed during pilot; composition was not refitted in the pilot."
    },
    {
      "case": "mrnabench",
      "source_report_uri": "https://raw.githubusercontent.com/rewire-bio/rewire-benchmarks/ca73fa47136d182f2d4ddb083d084712198fc0e2/research/local-runs-2026-09-20/mrnabench-composition/report.json",
      "source_report_sha256": "8b68dfe5725bf5d8c108265039e3787f4b3b55986eab8a430082c4d446a4f960",
      "dataset_id": "mrnabench-sample-mrl-designed-target_mrl_designed",
      "model": {
        "name": "Sequence composition + RidgeCV (Rewire control)",
        "training_overlap": "No pretraining; fitted only on this protocol training split. Split is not a claim of homology separation."
      },
      "model_configuration": {
        "alphas": [
          0.001,
          0.01,
          0.1,
          1,
          10
        ],
        "features": "log1p length, A/C/G/T fractions, unknown fraction",
        "normalization": "none",
        "selection": "RidgeCV within training only",
        "split_seed": 2541,
        "validation_used": false
      },
      "note": "Saved baseline predictions replayed during pilot; composition was not refitted in the pilot."
    }
  ]
}