{
  "schema": "astropome-biology-evidence.v1",
  "curated_date": "2026-10-22",
  "study_ids": [
    "dna-population-inference-20261022"
  ],
  "provenance": "Newly curated from retained local computational study records; not sourced from a public repository main branch.",
  "publication_status": "Independent research record; not peer reviewed.",
  "curation_scope": "Selected aggregate values, declared assumptions, source hashes and saved verification outcomes. No new simulations or biological experiments were performed for this article.",
  "reproducibility_limit": "This is a portable evidence summary, not a complete reproducibility release. Hashes identify retained source artifacts and do not establish independent timestamps or external replication.",
  "source_artifacts": [
    {
      "study_id": "dna-population-inference-20261022",
      "artifact": "protocol.json",
      "sha256": "14dda94b9f0ecefa291eae13c5bbc7948c6024f0c5559be3315e70ac0bff7b37",
      "bytes": 6331,
      "availability": "Retained original study artifact; not included in this public summary."
    },
    {
      "study_id": "dna-population-inference-20261022",
      "artifact": "runs/population-v1/summary.json",
      "sha256": "afe6efd21b0cf1886992e1e202ed6fb5c996b5b40a5ebc9ee25375c7bcacca52",
      "bytes": 13771245,
      "availability": "Retained original study artifact; not included in this public summary."
    },
    {
      "study_id": "dna-population-inference-20261022",
      "artifact": "runs/population-v1/numerical-audit.json",
      "sha256": "2d2de02322f050fc285c5d1596af0a8d30d9490406f56f266d3de8a1878ee904",
      "bytes": 51289,
      "availability": "Retained original study artifact; not included in this public summary."
    },
    {
      "study_id": "dna-population-inference-20261022",
      "artifact": "runs/population-v1/main-manifest.json",
      "sha256": "221501aa096971bc27e718a98eb1abb9cce08a8e0adf78580b3efcfd7f1e66ba",
      "bytes": 3729,
      "availability": "Retained original study artifact; not included in this public summary."
    },
    {
      "study_id": "dna-population-inference-20261022",
      "artifact": "verification.json",
      "sha256": "63d1122876f88575f762f86dd1573b45496b76fab8d6ffa335ce2808718b65c0",
      "bytes": 102874,
      "availability": "Retained original study artifact; not included in this public summary."
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  ],
  "protocol": {
    "purpose": "Synthetic acquisition-design and inference validation; not empirical evidence for a biological mechanism or a new occupancy assay.",
    "models": {
      "A": "P pauses; H slows during pause, then immediately returns to full speed. A persistent separation remains. O=1.",
      "B": "Same P pause; H remains slow until P catches up. O=1.",
      "C": "Same H/P trajectories as B; O=0 during the P pause and 1 otherwise."
    },
    "physical_parameters": {
      "v_nt_s": 510,
      "u_nt_s": 84
    },
    "observation": {
      "window_s": 60,
      "exposure_s": 0.4,
      "sample_centers": "0.2 + k * cadence, with the whole exposure inside [0,60]",
      "position_noise_sd_nt_assumed": 100,
      "occupancy_noise_sd_assumed": 0.35,
      "position_offset": "Unknown independent constant offset in H and P, removed by orthogonal contrast; the same operation is applied to observations and predictions.",
      "occupancy_scale": "Known and calibrated off=0/on=1 baseline; no bleaching or intensity drift.",
      "noise": "Independent Gaussian errors across frames/channels/molecules before position contrast; no smoothing.",
      "cadence_control": "Same exposure and per-frame noise across cadences; observation time is fixed, total frames and total light dose are not matched."
    },
    "latent_prior_and_generation": {
      "pause_onset_s": "Uniform(8,12), independently per molecule; the same coarse localization is available to inference.",
      "pause_duration_s": "Exponential with known mean 2 s (primary), or known mean 12 s (sensitivity). No truncation; right-censored long pauses retained.",
      "mean_duration_role": "Known population hyperparameter; not estimated from these simulated datasets.",
      "unit": "One independent molecule with one prespecified candidate pause window. Not a search over unselected movies, not independent repeated events from the same molecule."
    },
    "inference": {
      "molecule_likelihood": "Integrate Gaussian observation likelihood over s and D with their normalized common priors. Never maximize nuisance likelihood to choose a class.",
      "numerical_resolution": "Resolution is a convergence control, not a random biological parameter; standard and fine quadrature must be compared on identical data.",
      "pair_prior": "Equal prior model probabilities; AB uses HP and BC uses HPO.",
      "population": "Within each homogeneous pair test, all molecules share one hypothesis; add independent per-molecule log Bayes factors.",
      "confidence_threshold": 0.95,
      "mixture": "Conditional on no A: one common theta with Beta(1,1) prior; product over molecules of (1-theta)*L_B + theta*L_C. Numerical theta integration on 1001 nodes with trapezoidal weights.",
      "theta_interpretation": "Population fraction of C among independent molecules each with one prespecified candidate pause, not time occupancy, not a cell-wide detachment rate."
    },
    "interpretation_limits": [
      "The P-only 1/3 and HP 2/3 ceilings follow from the definitions; pipeline controls, not discoveries.",
      "Matched-model posterior calibration and coverage are computational checks, not experimental validation.",
      "Known speed, pause distribution, localization, observation model, and independent molecules are favorable assumptions.",
      "Misestimated noise is one illustrative model-misspecification stress, not a realistic calibrated microscope model.",
      "No biological parameters are inferred from real images in this run.",
      "Existing fluorescence occupancy experiments do not automatically supply independent H, P and O channels; real-data feasibility remains conditional."
    ]
  },
  "design": {
    "n_trajectories": 105000,
    "n_conditions": 7,
    "n_hypotheses": 3,
    "replicates_per_true_class": 100,
    "molecules_per_replicate": 50,
    "confidence_threshold": 0.95,
    "sample_sizes": [
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      2,
      5,
      10,
      20,
      50
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  ],
  "uncertainty": "Wilson intervals describe finite Monte Carlo frequencies under the stated model; Bayesian mixture intervals have a separately measured repeated-sample coverage. Reused prefixes correlate sample-size comparisons.",
  "verification": [
    {
      "artifact": "dna-population-inference-20261022/verification.json",
      "saved_status": "passed",
      "saved_check_count": 493,
      "interpretation": "Numerical/artifact verification, not independent biological experiments. The saved verifier was not rerun for this publication."
    }
  ],
  "numerical_sensitivity": {
    "saved_status": "passed",
    "scope": "Same first 50 simulated trajectories per truth/condition at two quadrature accuracies; finite sensitivity check, not a proof of exact convergence.",
    "tolerances": {
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      "max_abs_sum_delta_log_bf_n50": 0.5,
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      "confidence_decisions_changed": 0,
      "population_decision_changed": false,
      "max_mixture_mean_shift": 0.005,
      "max_mixture_ci_endpoint_shift": 0.01
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    "n_observations_compared": 1050
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}