REPOSITORY_MANIFEST.csv

path,role
".github/workflows/validate-frozen-package.yml","GitHub Actions integrity check for the public frozen aggregate package"
".gitignore","Git ignore rules for generated, local-environment, and non-redistributed data artifacts"
"CITATION.cff","Citation metadata for the repository and associated manuscript"
"README.md","Repository overview, study summary, results map, and reproduction entry point"
"REPOSITORY_MANIFEST.csv","Exhaustive file-level repository manifest"
"config/experiment.yaml","Frozen documentary experiment configuration"
"data/README.md","Data retrieval and local-placement instructions"
"data/checksums.csv","SHA-256 checksums for frozen third-party source files"
"data/manifests/dataset_audit.csv","Frozen dataset audit counts"
"data/sources.md","Public dataset sources, citations, and provenance notes"
"docs/DATA_PROVENANCE.md","Dataset provenance and redistribution notes"
"docs/EXPERIMENT_PROTOCOL.md","Frozen experimental protocol and evaluation-scope documentation"
"docs/FROZEN_RESULTS.md","Inventory and interpretation notes for frozen aggregate results"
"docs/LICENSE_AND_USAGE.md","License, code-provenance, and third-party usage notes"
"docs/REPRODUCIBILITY.md","Reproduction, rerun, and exact-replay scope documentation"
"docs/assets/agrr-workflow-animated.svg","Animated high-contrast AGRR workflow graphic"
"docs/assets/agrr-workflow.svg","Static high-contrast AGRR workflow graphic"
"docs/assets/repository-banner.svg","README repository banner artwork"
"environment.yml","Conda environment specification including the pinned B3DB dependency"
"requirements.txt","Pinned pip dependency specification"
"results/frozen/ablations/gate_diagnostics.csv","Frozen ablation or no-rule sensitivity output"
"results/frozen/ablations/no_rule_sensitivity.csv","Frozen ablation or no-rule sensitivity output"
"results/frozen/external_validation/external_b3db_results.csv","Frozen external B3DB transfer output"
"results/frozen/main_metrics/bbbp_auroc_summary.csv","Frozen primary benchmark aggregate metric output"
"results/frozen/main_metrics/esol_rmse_summary.csv","Frozen primary benchmark aggregate metric output"
"results/frozen/statistical_outputs/attribution_stability_recomputation.csv","Frozen statistical comparison or audit output"
"results/frozen/statistical_outputs/external_proposed_metric_recomputation.csv","Frozen statistical comparison or audit output"
"results/frozen/statistical_outputs/failure_diagnostics_summary.csv","Frozen statistical comparison or audit output"
"results/frozen/statistical_outputs/paired_bootstrap_recomputation.csv","Frozen statistical comparison or audit output"
"results/frozen/statistical_outputs/paired_comparisons.csv","Frozen statistical comparison or audit output"
"results/frozen/statistical_outputs/split_sizes.csv","Frozen statistical comparison or audit output"
"results/frozen/uncertainty/explanation_stability.csv","Frozen uncertainty, calibration, or explanation-stability output"
"results/frozen/uncertainty/uncertainty_summary.csv","Frozen uncertainty, calibration, or explanation-stability output"
"scripts/regenerate_manuscript_artifacts.py","Manuscript artifact-regeneration entry helper"
"scripts/validate_frozen_package.py","Public frozen-output integrity validator"
"src/__init__.py","Research pipeline package marker"
"src/classical_models.py","Classical descriptor and fingerprint baselines"
"src/data_pipeline.py","Molecular standardization, feature generation, dataset loading, and scientific-rule scores"
"src/explanation_analysis.py","Descriptor-pathway attribution-stability analysis"
"src/external_comparators.py","External B3DB transfer comparators"
"src/generate_artifacts.py","Primary manuscript table and figure generation source"
"src/generate_case_figure.py","Molecular audit-case figure source"
"src/generate_review_figures.py","Review/final figure generation source"
"src/graph_models.py","Graph, descriptor-fusion, residual, gated, and AGRR model components"
"src/metrics.py","Regression, classification, calibration, and selective-risk metrics"
"src/rule_failure_diagnostics.py","Independent train-only rule-failure diagnosis"
"src/run_experiments.py","Primary frozen-protocol experiment orchestration"
"src/splits.py","Random, scaffold, and Butina split construction"
"tables/README.md","Guide to table-ready machine-readable sources"
"tables/bbbp_auroc_summary.csv","Machine-readable manuscript table source"
"tables/esol_rmse_summary.csv","Machine-readable manuscript table source"
"tables/explanation_stability.csv","Machine-readable manuscript table source"
"tables/external_b3db_results.csv","Machine-readable manuscript table source"
"tables/failure_diagnostics_summary.csv","Machine-readable manuscript table source"
"tables/gate_diagnostics.csv","Machine-readable manuscript table source"
"tables/no_rule_sensitivity.csv","Machine-readable manuscript table source"
"tables/paired_comparisons.csv","Machine-readable manuscript table source"
"tables/uncertainty_summary.csv","Machine-readable manuscript table source"