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  "Title": "Leakage-Safe Modeling and Auditing for Genomic and Clinical Data",
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  "Authors@R": "c(\nperson(\"Selcuk\", \"Korkmaz\", role = c(\"aut\",\"cre\"), email = \"selcukorkmaz@gmail.com\",\ncomment = c(ORCID = \"0000-0003-4632-6850\"))\n)",
  "Description": "Prevents and detects information leakage in biomedical\nmachine learning. Provides leakage-resistant split policies\n(subject-grouped, batch-blocked, study leave-out,\ntime-ordered), guarded preprocessing (train-only imputation,\nnormalization, filtering, feature selection), cross-validated\nfitting with common learners, permutation-gap auditing, batch\nand fold association tests, and duplicate detection.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/selcukorkmaz/bioLeak",
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  "Repository": "https://selcukorkmaz.r-universe.dev",
  "Date/Publication": "2026-05-21 18:15:03 UTC",
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  "_exports": [
    "as_leaksplits",
    "as_rsample",
    "audit_batch_assoc",
    "audit_duplicates",
    "audit_info",
    "audit_leakage",
    "audit_leakage_by_learner",
    "audit_perm_gap",
    "audit_report",
    "audit_target_assoc",
    "benchmark_leakage_suite",
    "calibration_summary",
    "check_split_overlap",
    "confounder_sensitivity",
    "cv_ci",
    "delta_lsi",
    "dlsi_ci",
    "dlsi_metric",
    "dlsi_p_value",
    "dlsi_R_eff",
    "dlsi_repeats",
    "dlsi_robust",
    "dlsi_tier",
    "fit_metrics",
    "fit_resample",
    "guard_ensure_levels",
    "guard_fit",
    "guard_to_recipe",
    "impute_guarded",
    "make_split_plan",
    "plot",
    "plot_calibration",
    "plot_confounder_sensitivity",
    "plot_dlsi_repeats",
    "plot_fold_balance",
    "plot_overlap_checks",
    "plot_perm_distribution",
    "plot_time_acf",
    "predict_guard",
    "show",
    "simulate_leakage_suite",
    "tune_resample"
  ],
  "_help": [
    {
      "page": "as_leaksplits",
      "title": "Convert a splitGraph split_spec into bioLeak splits",
      "topics": [
        "as_leaksplits"
      ]
    },
    {
      "page": "as_rsample",
      "title": "Convert LeakSplits to an rsample resample set",
      "topics": [
        "as_rsample"
      ]
    },
    {
      "page": "audit_batch_assoc",
      "title": "Batch / study association results from a LeakAudit",
      "topics": [
        "audit_batch_assoc",
        "audit_batch_assoc,LeakAudit-method"
      ]
    },
    {
      "page": "audit_duplicates",
      "title": "Near-duplicate pairs from a LeakAudit",
      "topics": [
        "audit_duplicates",
        "audit_duplicates,LeakAudit-method"
      ]
    },
    {
      "page": "audit_info",
      "title": "Auxiliary information from a LeakAudit",
      "topics": [
        "audit_info",
        "audit_info,LeakAudit-method"
      ]
    },
    {
      "page": "audit_leakage",
      "title": "Audit leakage and confounding",
      "topics": [
        "audit_leakage"
      ]
    },
    {
      "page": "audit_leakage_by_learner",
      "title": "Audit leakage per learner",
      "topics": [
        "audit_leakage_by_learner"
      ]
    },
    {
      "page": "audit_perm_gap",
      "title": "Permutation-gap test results from a LeakAudit",
      "topics": [
        "audit_perm_gap",
        "audit_perm_gap,LeakAudit-method"
      ]
    },
    {
      "page": "audit_report",
      "title": "Render an HTML audit report",
      "topics": [
        "audit_report"
      ]
    },
    {
      "page": "audit_target_assoc",
      "title": "Target-leakage scan results from a LeakAudit",
      "topics": [
        "audit_target_assoc",
        "audit_target_assoc,LeakAudit-method"
      ]
    },
    {
      "page": "benchmark_leakage_suite",
      "title": "Simulation benchmark matrix for leakage diagnostics",
      "topics": [
        "benchmark_leakage_suite"
      ]
    },
    {
      "page": "calibration_summary",
      "title": "Calibration diagnostics for binomial predictions",
      "topics": [
        "calibration_summary"
      ]
    },
    {
      "page": "check_split_overlap",
      "title": "Check split overlap invariants",
      "topics": [
        "check_split_overlap"
      ]
    },
    {
      "page": "confounder_sensitivity",
      "title": "Confounder sensitivity summaries",
      "topics": [
        "confounder_sensitivity"
      ]
    },
    {
      "page": "cv_ci",
      "title": "Confidence intervals for cross-validated metrics",
      "topics": [
        "cv_ci"
      ]
    },
    {
      "page": "delta_lsi",
      "title": "Delta Leakage Sensitivity Index (Delta LSI)",
      "topics": [
        "delta_lsi"
      ]
    },
    {
      "page": "dlsi_ci",
      "title": "BCa confidence interval from a LeakDeltaLSI",
      "topics": [
        "dlsi_ci",
        "dlsi_ci,LeakDeltaLSI-method"
      ]
    },
    {
      "page": "dlsi_metric",
      "title": "Raw delta-metric estimate from a LeakDeltaLSI",
      "topics": [
        "dlsi_metric",
        "dlsi_metric,LeakDeltaLSI-method"
      ]
    },
    {
      "page": "dlsi_p_value",
      "title": "Sign-flip p-value from a LeakDeltaLSI",
      "topics": [
        "dlsi_p_value",
        "dlsi_p_value,LeakDeltaLSI-method"
      ]
    },
    {
      "page": "dlsi_R_eff",
      "title": "Effective number of paired repeats from a LeakDeltaLSI",
      "topics": [
        "dlsi_R_eff",
        "dlsi_R_eff,LeakDeltaLSI-method"
      ]
    },
    {
      "page": "dlsi_repeats",
      "title": "Per-repeat metric data frames from a LeakDeltaLSI",
      "topics": [
        "dlsi_repeats",
        "dlsi_repeats,LeakDeltaLSI-method"
      ]
    },
    {
      "page": "dlsi_robust",
      "title": "Huber-robust delta_lsi point estimate from a LeakDeltaLSI",
      "topics": [
        "dlsi_robust",
        "dlsi_robust,LeakDeltaLSI-method"
      ]
    },
    {
      "page": "dlsi_tier",
      "title": "Inference tier from a LeakDeltaLSI",
      "topics": [
        "dlsi_tier",
        "dlsi_tier,LeakDeltaLSI-method"
      ]
    },
    {
      "page": "fit_metrics",
      "title": "Per-fold metric data frame from a LeakFit",
      "topics": [
        "fit_metrics",
        "fit_metrics,LeakFit-method"
      ]
    },
    {
      "page": "fit_resample",
      "title": "Fit and evaluate with leakage guards over predefined splits",
      "topics": [
        "fit_resample"
      ]
    },
    {
      "page": "guard_ensure_levels",
      "title": "Ensure consistent categorical levels for guarded preprocessing",
      "topics": [
        "guard_ensure_levels"
      ]
    },
    {
      "page": "guard_fit",
      "title": "Fit leakage-safe preprocessing pipeline",
      "topics": [
        "guard_fit"
      ]
    },
    {
      "page": "guard_to_recipe",
      "title": "Convert guard preprocessing steps to a recipes recipe",
      "topics": [
        "guard_to_recipe"
      ]
    },
    {
      "page": "impute_guarded",
      "title": "Leakage-safe data imputation via guarded preprocessing",
      "topics": [
        "impute_guarded"
      ]
    },
    {
      "page": "LeakClasses",
      "title": "S4 Classes for bioLeak Pipeline",
      "topics": [
        "LeakAudit-class",
        "LeakClasses",
        "LeakDeltaLSI-class",
        "LeakFit-class",
        "LeakSplits-class",
        "show,LeakDeltaLSI-method"
      ]
    },
    {
      "page": "make_split_plan",
      "title": "Create leakage-resistant splits",
      "topics": [
        "make_split_plan"
      ]
    },
    {
      "page": "plot_calibration",
      "title": "Plot calibration curve for binomial predictions",
      "topics": [
        "plot_calibration"
      ]
    },
    {
      "page": "plot_confounder_sensitivity",
      "title": "Plot confounder sensitivity",
      "topics": [
        "plot_confounder_sensitivity"
      ]
    },
    {
      "page": "plot_dlsi_repeats",
      "title": "Plot per-repeat Delta_r values from a LeakDeltaLSI object",
      "topics": [
        "plot_dlsi_repeats"
      ]
    },
    {
      "page": "plot_fold_balance",
      "title": "Plot fold balance of class counts per fold",
      "topics": [
        "plot_fold_balance"
      ]
    },
    {
      "page": "plot_overlap_checks",
      "title": "Plot overlap diagnostics between train/test groups",
      "topics": [
        "plot_overlap_checks"
      ]
    },
    {
      "page": "plot_perm_distribution",
      "title": "Plot permutation distribution for a LeakAudit object",
      "topics": [
        "plot_perm_distribution"
      ]
    },
    {
      "page": "plot_time_acf",
      "title": "Plot ACF of test predictions for time-series leakage checks",
      "topics": [
        "plot_time_acf"
      ]
    },
    {
      "page": "plot-LeakAudit-missing-method",
      "title": "Plot method for LeakAudit",
      "topics": [
        "plot,LeakAudit,missing-method",
        "plot,LeakAudit-method"
      ]
    },
    {
      "page": "plot-LeakDeltaLSI-missing-method",
      "title": "Plot method for LeakDeltaLSI",
      "topics": [
        "plot,LeakDeltaLSI,missing-method",
        "plot,LeakDeltaLSI-method"
      ]
    },
    {
      "page": "plot-LeakFit-missing-method",
      "title": "Plot method for LeakFit",
      "topics": [
        "plot,LeakFit,missing-method",
        "plot,LeakFit-method"
      ]
    },
    {
      "page": "predict.GuardFit",
      "title": "Apply a fitted GuardFit transformer to new data",
      "topics": [
        "predict.GuardFit",
        "predict_guard"
      ]
    },
    {
      "page": "print.LeakTune",
      "title": "Print a LeakTune object",
      "topics": [
        "print.LeakTune"
      ]
    },
    {
      "page": "show-LeakAudit-method",
      "title": "Display summary for LeakAudit objects",
      "topics": [
        "show,LeakAudit-method"
      ]
    },
    {
      "page": "show-LeakFit-method",
      "title": "Display summary for LeakFit objects",
      "topics": [
        "show,LeakFit-method"
      ]
    },
    {
      "page": "show-LeakSplits-method",
      "title": "Display summary for LeakSplits objects",
      "topics": [
        "show,LeakSplits-method"
      ]
    },
    {
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      "source": "bioLeak-intro.Rmd",
      "filename": "bioLeak-intro.html",
      "title": "bioLeak: Leakage-Aware Biomedical Modeling",
      "author": "Selçuk Korkmaz",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Why bioLeak",
        "Guided workflow",
        "Example data",
        "Create leakage-aware splits with make_split_plan()",
        "Validating splits with check_split_overlap()",
        "Scalability",
        "Strict leakage mode",
        "Guarded preprocessing and imputation",
        "Fit and resample with fit_resample()",
        "Tidymodels interoperability",
        "Nested tuning with tune_resample()",
        "Advanced: Using Gradient Boosting with Parsnip",
        "Advanced: Custom learners",
        "Visual diagnostics",
        "Audit leakage with audit_leakage()",
        "Time-series leakage checks",
        "Cross-validation uncertainty with cv_ci()",
        "Delta Leakage Sensitivity Index: Quantifying Performance Inflation",
        "Motivation",
        "Mathematical framework",
        "Notation",
        "Stage 1: Within-repeat aggregation",
        "Stage 2: Per-repeat inflation score",
        "Point estimates",
        "Setting up a two-pipeline comparison",
        "Running delta_lsi()",
        "Designing for a target inference tier",
        "Statistical inference",
        "Sign-flip randomization test",
        "Huber M-estimator and robustness properties",
        "BCa bootstrap confidence interval",
        "Pairing condition and the inference tier system",
        "Paired vs. unpaired designs",
        "Metric direction with higher_is_better",
        "Accessing the LeakDeltaLSI object",
        "Connection to audit_leakage()",
        "Parallel Processing",
        "Simulation suite",
        "Objects and summaries"
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      "created": "2025-12-28 21:57:35",
      "modified": "2026-05-21 18:15:03",
      "commits": 26
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