{
  "title": "Discover, Falsify, Revise: Auditing Input-Use Claims from Source Code to Predictive Contribution in Agent-Discovered Cell Models",
  "project": "CellAudit",
  "authors": [
    {
      "name": "Mengran Li",
      "affiliation": "Sun Yat-sen University"
    },
    {
      "name": "Bo Li",
      "affiliation": "University of Macau"
    },
    {
      "name": "Chengyang Zhang",
      "affiliation": "Sichuan University"
    },
    {
      "name": "Yang Yan",
      "affiliation": "Zhejiang University"
    },
    {
      "name": "Jinfeng Xu",
      "affiliation": "University of British Columbia"
    },
    {
      "name": "Zhenchao Tang",
      "affiliation": "Tencent AI Lab"
    }
  ],
  "scope": {
    "three_questions": [
      {
        "id": "source",
        "label": "Source consumption",
        "question": "Can the input enter the cited computation?",
        "test": "Inspect the registered input-use claim and its cited source path.",
        "status": [
          "Implemented",
          "Implementation-contradicted",
          "Unresolved"
        ]
      },
      {
        "id": "dependence",
        "label": "Fitted dependence",
        "question": "Do fitted predictions change when the input changes?",
        "test": "Replace one registered input at a frozen checkpoint; measure prediction distance."
      },
      {
        "id": "contribution",
        "label": "Predictive contribution",
        "question": "Does the original input help predict the observed response?",
        "test": "Compare target loss and predictive score under correct and replacement inputs."
      }
    ],
    "source": {
      "path": "arxiv-source/CellAudit_arXiv.tex",
      "line": 71
    },
    "interpretation": "Replacement effects are predictive evidence relative to registered replacements, not causal effects of biological interventions."
  },
  "flagship": {
    "cohort": "BBBC047",
    "evaluation": "Fold 5 held-out replication",
    "n": 5,
    "unit": "paired fitting seeds",
    "full_pcc": 0.3153,
    "control_only_pcc": 0.3142,
    "full_minus_control_pcc": 0.0011,
    "paired_95ci": [
      -0.0005,
      0.0027
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    "compound_factorial_pcc_effect": 0.0,
    "compound_prediction_distance": 0.0,
    "control_factorial_pcc_effect": 0.2004,
    "source_path_result": "The cited compound-query attention has a single key-value pair and therefore a constant normalized weight.",
    "source": {
      "path": "arxiv-source/CellAudit_arXiv.tex",
      "line": 166
    },
    "selection_scope": "Sources were selected within policy on Fold 3, then a prespecified across-policy rule used Fold 4. Fold 5 did not choose the source. Each Fold-5 source was independently refit using Folds 1–2 and checkpoint selection on Fold 3.",
    "selection_source": {
      "path": "arxiv-source/CellAudit_arXiv.tex",
      "line": 311
    },
    "disjoint_control_check": {
      "score_selected_pcc_fold4": 0.3085,
      "score_selected_pcc_fold5": 0.3193,
      "control_only_pcc_fold4": 0.3082,
      "control_only_pcc_fold5": 0.3185,
      "compound_invariant_every_refit": true,
      "source": {
        "path": "arxiv-source/CellAudit_arXiv.tex",
        "line": 177
      }
    }
  },
  "candidate_audit": {
    "count": 48,
    "cohorts": [
      "BBBC036",
      "BBBC047"
    ],
    "same_checkpoint_boundaries": 96,
    "sensitive_both_folds": 47,
    "target_loss_ci_positive_both_folds": 20,
    "invariant_both_folds": 1,
    "sensitive_without_positive_interval_on_at_least_one_fold": 27,
    "source_implemented": 43,
    "source_unresolved": 5,
    "sampling": "Dataset–policy-balanced and source-structure-stratified sample of 48 real candidate sources; these counts describe this sampled set.",
    "interval": "95% source-group intervals condition on selected checkpoints, donor pools and 128 registered replacement maps; unadjusted descriptive intervals.",
    "source": {
      "path": "arxiv-source/results/appendix_tables/generated_existing_audit_checks.tex",
      "line": 93
    },
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        "invariant": 0,
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        "positive_both": 0
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        "cohort": "LINCS-Pilot1",
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          "line": 8
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      },
      {
        "cohort": "LINCS-Pilot1",
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        "mean": 0.046704902134370056,
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      },
      {
        "cohort": "LINCS-Pilot1",
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        "component": "chemical_dose_interaction",
        "mean": 0.004218809963203967,
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      },
      {
        "cohort": "LINCS-Pilot1",
        "fold": 5,
        "metric": "global_pcc",
        "component": "double_shuffled_over_anchor",
        "mean": -0.035949021666310726,
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          "line": 11
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      },
      {
        "cohort": "LKCP Batch 2",
        "fold": 4,
        "metric": "global_pcc",
        "component": "full_over_anchor",
        "mean": 0.01044620007276535,
        "std": 0.00015812571618072896,
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      },
      {
        "cohort": "LKCP Batch 2",
        "fold": 4,
        "metric": "global_pcc",
        "component": "chemical_shapley",
        "mean": -6.999990437179804e-05,
        "std": 0.0003075053118916192,
        "ci95_low": -0.0002899759370253539,
        "ci95_high": 0.00014997612828175784,
        "n": 10,
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          "line": 13
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      },
      {
        "cohort": "LKCP Batch 2",
        "fold": 4,
        "metric": "global_pcc",
        "component": "dose_shapley",
        "mean": 0.023744017551653087,
        "std": 0.0013168494077885954,
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        "cohort": "LKCP Batch 2",
        "fold": 4,
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        "mean": 4.048758186399937e-05,
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        "cohort": "LKCP Batch 2",
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          "line": 16
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      },
      {
        "cohort": "LKCP Batch 2",
        "fold": 5,
        "metric": "global_pcc",
        "component": "full_over_anchor",
        "mean": 0.021079646050930025,
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      },
      {
        "cohort": "LKCP Batch 2",
        "fold": 5,
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        "mean": 0.0033403171133249998,
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        "ci95_high": 0.00393296327625663,
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          "path": "paper/results/figure_panels/coordinate_effects.csv",
          "line": 18
        }
      },
      {
        "cohort": "LKCP Batch 2",
        "fold": 5,
        "metric": "global_pcc",
        "component": "dose_shapley",
        "mean": 0.03408454868942499,
        "std": 0.0013270360335669612,
        "ci95_low": 0.0331352443666585,
        "ci95_high": 0.035033853012191474,
        "n": 10,
        "source": {
          "path": "paper/results/figure_panels/coordinate_effects.csv",
          "line": 19
        }
      },
      {
        "cohort": "LKCP Batch 2",
        "fold": 5,
        "metric": "global_pcc",
        "component": "chemical_dose_interaction",
        "mean": 0.00023824987933039664,
        "std": 0.00012752746798044,
        "ci95_low": 0.00014702223097491754,
        "ci95_high": 0.00032947752768587574,
        "n": 10,
        "source": {
          "path": "paper/results/figure_panels/coordinate_effects.csv",
          "line": 20
        }
      },
      {
        "cohort": "LKCP Batch 2",
        "fold": 5,
        "metric": "global_pcc",
        "component": "double_shuffled_over_anchor",
        "mean": -0.01634521975181997,
        "std": 0.0009504032354817902,
        "ci95_low": -0.017025097220850726,
        "ci95_high": -0.01566534228278921,
        "n": 10,
        "source": {
          "path": "paper/results/figure_panels/coordinate_effects.csv",
          "line": 21
        }
      }
    ],
    "effect_definition": "Compound and dose are two-player Shapley allocations relative to both inputs replaced. The both-shuffled residual completes Full−control-only; interaction is already allocated and must not be added again.",
    "reference_pass_counts": [
      {
        "cohort": "LINCS–Pilot1",
        "fold": 4,
        "compound": 35,
        "dose": 50,
        "n_refits": 50
      },
      {
        "cohort": "LINCS–Pilot1",
        "fold": 5,
        "compound": 10,
        "dose": 50,
        "n_refits": 50
      },
      {
        "cohort": "LKCP Batch 2",
        "fold": 4,
        "compound": 0,
        "dose": 50,
        "n_refits": 50
      },
      {
        "cohort": "LKCP Batch 2",
        "fold": 5,
        "compound": 0,
        "dose": 50,
        "n_refits": 50
      }
    ],
    "counts_source": {
      "path": "arxiv-source/CellAudit_arXiv.tex",
      "line": 228
    },
    "interpretation": "Dose contribution and predictive gains persist. Compound identity does not pass the reference-relative criterion on LKCP, even though its Fold-5 mean Shapley allocation is positive. Positive mean contribution and per-refit qualification are distinct."
  },
  "rendering_notes": [
    "The schema includes internal relative provenance strings; replace source links with actual repository paths before public linking.",
    "Do not label Figure 2 candidate target-loss intervals as across-seed confidence intervals.",
    "Do not turn the three evidence questions into a guaranteed nested success funnel: implemented, unresolved and fitted outcomes do not form an implication chain.",
    "Do not pool the two linked BBBC cohorts as independent studies or two held-out sci-Plex folds as ten trajectories.",
    "Retain per-panel statistical units and distinguish SD error bars from paired-effect confidence intervals.",
    "The abstract-style claim of no compound support on LKCP is criterion-relative, not proof of zero biological compound effect."
  ]
}