jang1563/agentic-drug-discovery-system

Agentic Drug Discovery System

This card describes the approved public 0.3.0.dev2 exact-source mirror for the Agentic Drug Discovery System. It contains the executable control plane, tests, documentation, schemas, aggregate evidence, release metadata, safety boundaries, and the ctdbench scorer. It is not a row dataset or model release and does not contain raw source bundles, real provider review jobs, ingestion runs, raw clinical/regulatory source snapshots, hidden labels, real curator manifests, real clinical decision, cohort, outcome-evaluation, uncertainty, design/stress-scenario, or closed-loop policies/manifests/submissions/catalogs/batches/receipts/packages/unit results, real scenario elicitation or hidden-dependence working records, unit-to-cluster assignments, replicate- or cluster-level results, locked episodes, generated trajectories, scheduler logs, local paths, credentials, or unpublished working notes. Every future update requires a new exact-package review and explicit approval.

At a Glance

• Surface: Hugging Face Dataset repository.
• Public state: 0.3.0.dev2 exact-source mirror, published after explicit approval.
• Release lineage: 0.2.0 remains the latest tagged stable release.
• Contents: Bounded planner, typed execution core, deterministic policy replanning and hash-bound checkpoint resume, cross-stage disease/target/assay/model-system/intervention/trial/design identity ledgers, atomic multi-trial portfolio extraction, reviewer-approved endpoint mapping, mapping-gated source-disjoint non-pooled benefit-risk synthesis, bounded source-preserving ClinicalTrials.gov harmonization, ten-dimension provenance-preserving clinical evidence tensor compilation and bounded VOI action planning, accepted-state-bindable cohort diagnostics with matched policy sensitivity and provenance-overlap reporting, preregistered package-bound clinical outcome forecasts with aggregate calibration and paired policy evaluation, dependence-audited CR1 uncertainty for additive outcome metrics, deterministic aggregate prospective clustered-board design simulation, informative-evaluability and residual-dependence stress comparison over population/evaluable targets and nominal/dependence-closed clustering, bounded selected-action execution with compact receipts, reviewer-only refresh and exact source-rejoined transition validation, source capture and payload-free manifest compiler, semantic mappings, dependency-free pinned-evidence adapter and binding, stage and multi-stage program runners, matched and sealed evaluators, preregistered held-out curation contracts, stage-stratified uncertainty, synthetic evaluation tests, aggregate external evaluation evidence, manifests, audit code, and the ctdbench scorer.
• Excludes: Raw source data, real sealed or held-out boards, curator identities/attestations/votes/adjudications, curation manifests, real clinical decision policies/action catalogs/evidence tensors/packages, real clinical cohort manifests/accepted-state bindings/package diagnostics/reports, real clinical prediction submissions/outcome or dependence manifests/unit labels/source assessments/unit-to-cluster assignments/cluster-level or per-unit scores, real closed-loop policies/execution batches/provider requests or outcomes/receipts/reviewer refresh records/transitions, cached episode packets, label vaults, policy submissions, per-episode evaluations, hidden labels, generated trajectories, logs, credentials, local paths, or model weights.
• Source: Exact commit and tree are recorded in upload_manifest.json.

Intended Use

• Review the public system architecture and release boundary.
• Read the caveats-first SCD vertical slice before citing benchmark numbers.
• Read the small-N target-identification results card and aggregate claim ledger.
• Inspect schema and verifier-contract documentation.
• Run the illustrative, non-benchmark eight-stage control-plane demo.
• Run the dependency-free adds-bounded-agent-demo planner-to-transition fixture.
• Inspect tests/test_program_runner.py for cumulative-ledger multi-stage stopping and exact replay.
• Inspect tests/test_semantic_mappings.py for the explicit unmet-need and functional-effect non-implication boundaries.
• Inspect tests/test_pinned_evidence_adapter.py for composite pinned-source gates, matched independent/same-source cases, eight-stage provider-backed execution through clinical endpoint/safety design and regulatory review, and exact replay.
• Inspect docs/14_target_identity_continuity.md and tests/test_target_identity_continuity.py for the canonical Ensembl-to-ChEMBL target ledger, namespace invariants, candidate links, and matched target-symbol success/failure pair.
• Inspect docs/15_discovery_context_identity.md and tests/test_context_identity_continuity.py for the disease, assay, and model-system ledgers, evidence links, stage requirements, rebinding/collision attacks, and fail-closed behavior.
• Inspect docs/16_clinical_intervention_identity.md and tests/test_clinical_identity_continuity.py for candidate-to-intervention-to-trial-design continuity, source identity checks, regulatory extension, and fail-closed attacks.
• Inspect docs/17_pinned_source_ingestion.md and tests/test_pinned_evidence_ingestion.py for exact source receipts, external bundle integrity, payload-free compilation, review gates, and matched bounded-stage integration.
• Inspect docs/18_cdc_mmwr_ingestion.md and tests/test_cdc_mmwr_ingestion.py for the CDC provider-specific article, section, value, unit, context, excerpt-removal, and matched independent-source/same-document controls.
• Inspect docs/19_ncbi_pubmed_ingestion.md and tests/test_ncbi_pubmed_ingestion.py for strict EFetch request and article identity, structured abstract evidence, typed treatment-gap values, excerpt removal, matched-context advance, and cross-population defer behavior.
• Inspect docs/20_preclinical_provider_ingestion.md, tests/test_chembl_activity_ingestion.py, tests/test_ncbi_pubmed_disease_model_ingestion.py, and tests/test_preclinical_provider_pair.py for release-bound ChEMBL activity, typed PubMed in-vivo evidence, candidate aliases, publication lineage, and matched advance/shared-lineage defer behavior.
• Inspect docs/preclinical_provider_validation_snapshot.json for the payload-free machine record of external source ids, typed values, hashes, matched outcomes, and limitations.
• Inspect docs/21_clinical_provider_ingestion.md, docs/clinical_provider_validation_snapshot.json, and tests/test_clinicaltrials_gov_ingestion.py for exact ClinicalTrials.gov receipt, NCT, arm, population, endpoint, posted serious-adverse-event aggregate, atomic promotion, external hashes, and matched missing-safety behavior.
• Inspect docs/22_clinical_benefit_risk_synthesis.md and tests/test_clinical_benefit_risk_synthesis.py for explicit multi-trial endpoint/safety selections, retained trial values and hashes, non-pooling boundaries, exact replay, and tamper controls.
• Inspect docs/23_clinical_portfolio_endpoint_mapping.md and tests/test_clinical_portfolio.py for exact-set multi-job/bundle preflight, payload-free output, reviewer-approved ontology identity, append-only mapping continuity, and atomic failure controls.
• Inspect docs/24_policy_replanning_and_resume.md and tests/test_policy_replanning.py for typed observations, bounded rule application, append-only queue revisions, hash-bound checkpoints, and deterministic resume.
• Inspect docs/25_cutoff_safe_policy_evaluation.md, docs/retrospective_policy_evaluation_snapshot.json, and tests/test_sealed_evaluation.py for role-neutral board sealing, externally separated labels, commitment opening, strict JSON round-trip, exact submission binding, aggregate policy comparison, and leakage controls.
• Inspect docs/26_independent_heldout_evaluation.md and tests/test_heldout_evaluation.py for preregistered cohort/label/curator contracts, strict-majority and independent-adjudication validation, stage minima, Wilson intervals, action coverage, selective risk, and the explicit no-real-result boundary.
• Inspect docs/27_clinical_evidence_tensor_and_voi.md, agentic_drug_discovery/clinical_decision.py, and tests/test_clinical_benefit_risk_synthesis.py for committed-synthesis tensor compilation, provenance-linked gaps, deterministic bounded VOI ranking, budget failure, safety-signal hold, integrity checks, and the evidence-workflow-only decision boundary.
• Inspect docs/28_clinical_evidence_closed_loop.md, agentic_drug_discovery/clinical_closed_loop.py, and the adjacent transition schema/example for exact selected-action execution, compact payload-free receipts, bounded reviewer-verifier refresh, single-use actions, exact source rejoin, and two-state transition replay.
• Inspect docs/29_clinical_cohort_diagnostics.md, agentic_drug_discovery/clinical_cohort.py, and the adjacent manifest/report schemas and compiler-generated examples for accepted-state binding, evidence-unit identity, matched policy sensitivity, exact gap/action denominators, cross-unit provenance overlap, and the explicit no-outcome/no-calibration boundary.
• Inspect docs/30_preregistered_clinical_outcome_evaluation.md, agentic_drug_discovery/clinical_outcome_evaluation.py, and the adjacent protocol/submission/ manifest/report schemas for cutoff-safe package-bound forecasts, endpoint/safety provenance, aggregate calibration, paired policy comparisons, and the evaluator-only unit-label boundary.
• Inspect docs/31_cluster_robust_clinical_outcome_uncertainty.md, agentic_drug_discovery/clinical_outcome_uncertainty.py, and the adjacent dependence/protocol/ report schemas for exact assignment coverage, known-overlap closure, aggregate CR1 intervals, fixed stage-by-endpoint strata, explicit no-interval states, and the private assignment boundary.
• Inspect docs/32_prospective_clinical_outcome_design_simulation.md, agentic_drug_discovery/clinical_outcome_design_simulation.py, and the adjacent design protocol/report schemas for beta-binomial known-truth simulation, production CR1 parity, IID diagnostic comparison, Monte Carlo target checks, and the no-automatic-selection boundary.
• Inspect docs/33_informative_evaluability_and_dependence_stress.md, agentic_drug_discovery/clinical_outcome_stress_simulation.py, and the adjacent stress protocol/report schemas for analytic estimand shifts, exact dependence blocks, nominal/oracle-closure CR1 comparison, combined stress signatures, and the no-automatic-correction boundary.
• Inspect rl_env/specs/pinned_evidence_manifest.schema.json and its synthetic example before constructing a source manifest.
• Inspect rl_env/specs/target_identity_record.schema.json and its synthetic example before producing or consuming serialized target records.
• Inspect rl_env/specs/discovery_context_identity.schema.json and its synthetic example before producing or consuming serialized disease, assay, or model-system records.
• Inspect rl_env/specs/clinical_intervention_identity.schema.json and its synthetic example before producing or consuming serialized clinical intervention, trial, or atomic design records.
• Inspect rl_env/specs/clinical_benefit_risk_synthesis.schema.json and its synthetic example before selecting source-ledger trials for cross-trial harmonization.
• Inspect rl_env/specs/clinical_evidence_decision_package.schema.json and its compiler-generated synthetic example before producing or consuming policy-bound evidence tensors or action plans.
• Inspect rl_env/specs/clinical_evidence_decision_config.schema.json and its synthetic example, then use adds-clinical-evidence to compile, validate, or summarize a package without importing internal dataclasses.
• Use adds-clinical-evidence cohort, validate-cohort, and summarize-cohort with the cohort manifest/report contracts to compare exact package rosters without treating policy variants as independent clinical observations.
• Use adds-clinical-evidence evaluate-outcomes, validate-outcomes, and summarize-outcomes with frozen package forecasts and an evaluator-controlled outcome manifest. The checked-in one-unit example verifies contract execution only and is not calibration evidence.
• Inspect rl_env/specs/clinical_endpoint_mapping.schema.json and rl_env/specs/clinicaltrials_gov_portfolio_job.schema.json before approving an endpoint family or assembling an exact multi-trial source bundle.
• Inspect rl_env/specs/source_receipt.schema.json and rl_env/specs/pinned_evidence_ingestion_job.schema.json before capturing or compiling a source.
• Inspect rl_env/specs/cdc_mmwr_ingestion_job.schema.json before authoring a CDC MMWR review job.
• Inspect rl_env/specs/ncbi_pubmed_ingestion_job.schema.json before authoring an NCBI PubMed treatment-gap review job.
• Inspect rl_env/specs/chembl_activity_ingestion_job.schema.json and rl_env/specs/ncbi_pubmed_disease_model_ingestion_job.schema.json before authoring preclinical provider review jobs.
• Inspect rl_env/specs/clinicaltrials_gov_ingestion_job.schema.json before authoring a reviewed registry study, selected-arm, population, endpoint, analysis, and serious-adverse-event contract.
• Inspect strict replay bundles and run the machine-readable adds-replay-bundle CLI.
• Use benchmark/ to score the separately hosted clinical-trial decision dataset.
• Track provenance for the public artifact surface.
• Inspect the mirrored GitHub release surface and source-commit provenance.

Sealed Retrospective Evaluation

The external evaluator executed four matched pairs and eight cutoff-safe episodes built from the real senicapoc continuous program and PALOMA-2/PALOMA-3 clinical portfolio. Only the payload-free aggregate and artifact hashes are included here.

Policy	Exact	Success arm	Failure arm	Both correct	Unsafe advance
Deterministic gated stage output	8/8	4/4	4/4	4/4	0/7
Always advance counterfactual	1/8	1/4	0/4	0/4	7/7
Defer-safe counterfactual	4/8	0/4	4/4	0/4	0/7

This is a small contract diagnostic. It does not establish drug-discovery performance, prospective clinical utility, policy optimality, or confidence calibration. The complete board, cached real packets, label vault, commitment nonces, submissions, and per-episode evaluations stay outside both public release surfaces.

Artifact Map

Path	Purpose
README.md	This Hugging Face Dataset card.
github/README.md	GitHub README preserved inside the Hub mirror.
release_manifest.json	Cross-surface release manifest.
release_decision_packet.json	Machine-readable launch decision packet.
huggingface/release_manifest.json	Hugging Face-specific include/exclude manifest.
upload_manifest.json	Exact uploaded file list and source commit.
docs/release_boundary.md	Public-release boundary and exclusion rules.
docs/release_trust_report.md	Trust claims, machine anchors, and interpretation warnings.
docs/12_scd_vertical_slice.md	Audited SCD vertical slice, with small-N caveats.
docs/13_target_id_governance_node.md	Upstream target-identification results card.
docs/14_target_identity_continuity.md	Executable target ledger, stage namespace requirements, and fail-closed identity rules.
docs/15_discovery_context_identity.md	Disease, assay, and model-system ledgers, evidence links, stage gates, and matched failure contract.
docs/16_clinical_intervention_identity.md	Candidate-to-intervention-to-trial-design continuity, source checks, regulatory extension, and failure contract.
docs/17_pinned_source_ingestion.md	Exact external source capture, payload-free compilation, review gates, and control-plane integration.
docs/18_cdc_mmwr_ingestion.md	CDC MMWR article binding, evidence-location checks, payload-free extraction, and matched stage behavior.
docs/19_ncbi_pubmed_ingestion.md	NCBI PubMed XML identity, structured abstract anchors, payload-free extraction, and context-mismatch behavior.
docs/20_preclinical_provider_ingestion.md	ChEMBL functional-activity and PubMed disease-model contracts, payload-free external validation snapshot, and lineage-independence failure control.
docs/preclinical_provider_validation_snapshot.json	Payload-free machine record of provider ids, typed values, hashes, matched outcomes, and limitations.
docs/21_clinical_provider_ingestion.md	ClinicalTrials.gov source receipt, endpoint/safety design identities, bounded promotion, and matched failure contract.
docs/clinical_provider_validation_snapshot.json	Payload-free NCT/design/safety identities, artifact hashes, live stage outcome, matched control, and limitations.
docs/22_clinical_benefit_risk_synthesis.md	Explicit reviewed selection, retained trial values, source-disjoint provenance, non-pooling boundary, and fail-closed synthesis behavior.
docs/23_clinical_portfolio_endpoint_mapping.md	Exact multi-bundle portfolio transaction, reviewer-approved endpoint mapping ledger, synthesis dependency, and release boundary.
docs/24_policy_replanning_and_resume.md	Typed policy observations, bounded replans, checkpoint integrity, and deterministic resume.
docs/25_cutoff_safe_policy_evaluation.md	Cutoff-safe sealing, submission, scoring, real aggregate results, and interpretation limits.
docs/26_independent_heldout_evaluation.md	Preregistered held-out protocol, evaluator-only curator manifest, stage uncertainty, and release boundary.
docs/27_clinical_evidence_tensor_and_voi.md	Exact evidence cells, typed workflow gaps, bounded VOI ranking, budget behavior, provenance replay, and interpretation boundaries.
docs/29_clinical_cohort_diagnostics.md	Exact package/state rosters, evidence-unit identity, matched policy sensitivity, provenance overlap, and calibration boundaries.
docs/30_preregistered_clinical_outcome_evaluation.md	Package-bound probability forecasts, cutoff-safe endpoint/safety outcomes, aggregate calibration, paired policy metrics, and evaluator-only boundaries.
docs/31_cluster_robust_clinical_outcome_uncertainty.md	Dependence commitments, known-overlap closure, aggregate CR1 intervals, fixed strata, fail-closed diagnostics, and interpretation boundaries.
docs/32_prospective_clinical_outcome_design_simulation.md	Beta-binomial design scenarios, analytic truths, CR1/IID coverage comparison, Monte Carlo target checks, and gate-selection boundaries.
docs/33_informative_evaluability_and_dependence_stress.md	Outcome-dependent evaluability, analytic population/evaluable shifts, residual dependence blocks, nominal/oracle-closure CR1 comparison, and correction boundaries.
docs/retrospective_policy_evaluation_snapshot.json	Payload-free machine aggregate with policy metrics, artifact hashes, gate outcomes, and withheld-data boundary.
docs/public_evidence_summary.json	Machine-readable aggregate claims and limitations.
agentic_drug_discovery/	Bounded planning, typed tool execution, semantic promotion, stage and program orchestration, matched evaluation, replay, and fail-closed transitions.
agentic_drug_discovery/sealed_evaluation.py	Role-neutral board sealing, external label vaults, commitments, strict envelope readers, submission validation, and aggregate scoring.
agentic_drug_discovery/heldout_evaluation.py	Preregistered protocol binding, independent curation validation, Wilson intervals, action coverage, selective risk, and strict aggregate reporting.
agentic_drug_discovery/ingestion.py	Immutable source receipts, external bundle verification, payload-free manifest compilation, and review reports.
agentic_drug_discovery/cdc_mmwr.py	CDC MMWR article and reviewer-selected evidence verification with excerpt removal.
agentic_drug_discovery/ncbi_pubmed.py	NCBI PubMed EFetch article and treatment-gap evidence verification with excerpt and anchor removal.
agentic_drug_discovery/chembl_activity.py	ChEMBL release/resource reconciliation and typed functional-activity verification with assay-text removal.
agentic_drug_discovery/clinicaltrials_gov.py	ClinicalTrials.gov study, arm, population, endpoint, statistical-analysis, and serious-adverse-event verification with payload removal.
agentic_drug_discovery/clinical_portfolio.py	Atomic exact-set multi-trial extraction with source-hash disjointness and payload-free output.
agentic_drug_discovery/clinical_endpoint_mapping.py	Strict approved-mapping parser, endpoint/safety fingerprint compiler, approval chronology, and replay validation.
agentic_drug_discovery/clinical_synthesis.py	Deterministic source-ledger compiler for trial-level hazard ratios and serious-event risk differences without pooling.
agentic_drug_discovery/clinical_decision.py	Committed-synthesis tensor compiler, typed gaps, deterministic budget-aware bounded VOI planner, integrity envelopes, and state replay.
agentic_drug_discovery/clinical_cohort.py	Accepted-state-bindable package rosters, deterministic cohort aggregation, matched policy comparisons, strict readers, and cross-unit provenance overlap.
agentic_drug_discovery/clinical_outcome_evaluation.py	Preregistered protocol and submission binding, post-deadline outcome provenance, aggregate Brier/calibration/threshold metrics, paired policy comparisons, and full replay.
agentic_drug_discovery/clinical_outcome_uncertainty.py	Frozen dependence commitments, exact assignment coverage, known-overlap closure, CR1 policy/stratum/paired intervals, strict readers, and full replay.
agentic_drug_discovery/clinical_outcome_design_simulation.py	Bounded deterministic beta-binomial simulation, analytic truths, production CR1 parity, IID diagnostics, candidate-gate evaluation, strict readers, and replay.
agentic_drug_discovery/clinical_outcome_stress_simulation.py	Bounded block-Polya stress simulation, analytic population/evaluable truths, nominal/dependence-closed CR1 comparison, strict boundaries, readers, summaries, and replay.
adapters/pinned_evidence_adapter.py	Dependency-free validation and lookup for source-pinned, payload-free evidence manifests.
adapters/clinical_synthesis_adapter.py	Local normalization of approved endpoint mappings and reviewed synthesis selections without supplied source measurements.
adapters/execution_registry.py	Typed contracts for the pinned adapter and caller-supplied GitHub adapter instances.
rl_env/specs/pinned_evidence_manifest.schema.json	Machine-readable pinned-record schema; the adjacent example is synthetic.
rl_env/specs/target_identity_record.schema.json	Machine-readable cross-stage target record; the adjacent example is synthetic.
rl_env/specs/discovery_context_identity.schema.json	Machine-readable disease, assay, and model-system records; the adjacent example is synthetic.
rl_env/specs/clinical_intervention_identity.schema.json	Machine-readable clinical intervention, trial, endpoint, safety, and atomic design records; the adjacent example is synthetic.
rl_env/specs/clinical_endpoint_mapping.schema.json	Machine-readable approved reviewer, ontology identity, and exact endpoint/safety binding contract; the adjacent example is synthetic.
rl_env/specs/clinical_benefit_risk_synthesis.schema.json	Machine-readable reviewed multi-trial selection contract; the adjacent example is synthetic.
rl_env/specs/clinical_evidence_decision_package.schema.json	Integrity-bound policy, exact tensor, gaps, action catalog, budget, and bounded-VOI plan contract; the adjacent example is synthetic.
rl_env/specs/clinical_evidence_decision_package.relaxed.example.json	Compiler-generated synthetic ADVANCE package over the same evidence unit for reproducible matched-policy sensitivity.
rl_env/specs/clinical_evidence_cohort_manifest.schema.json	Exact package roster and optional all-or-none accepted-state SHA-256 binding contract; the adjacent example is synthetic.
rl_env/specs/clinical_evidence_cohort_report.schema.json	Package/policy strata, matched transitions, gap/action diagnostics, provenance overlap, and explicit no-outcome calibration-status contract; the adjacent example is synthetic.
rl_env/specs/clinical_evidence_cohort_summary.schema.json	Compact cohort summary and optional validation-status contract.
rl_env/specs/clinical_outcome_evaluation_protocol.schema.json	Public cohort/cutoff/outcome/harmonization/curation/metric preregistration contract; the adjacent example is synthetic.
rl_env/specs/clinical_prediction_submission.schema.json	Exact package/evidence-unit-bound favorable-outcome probability contract; adjacent examples are synthetic.
rl_env/specs/clinical_outcome_manifest.schema.json	Evaluator-only endpoint/safety assessment and post-deadline source-provenance contract; the adjacent example is synthetic.
rl_env/specs/clinical_outcome_evaluation_report.schema.json	Aggregate attrition, Wilson, Brier/calibration/threshold, paired-policy, and provenance-overlap contract; the adjacent example is synthetic.
rl_env/specs/clinical_outcome_dependence_manifest.schema.json	Evaluator-only exact unit-to-cluster assignment and dependence-basis contract; the adjacent example is synthetic.
rl_env/specs/clinical_outcome_uncertainty_protocol.schema.json	Public dependence-construction, confidence, cluster-floor, dominance, strata, and metric preregistration contract; the adjacent example is synthetic.
rl_env/specs/clinical_outcome_uncertainty_report.schema.json	Aggregate cluster diagnostics and CR1 policy, stratum, and paired-policy interval contract; the adjacent example is synthetic.
rl_env/specs/clinical_outcome_uncertainty_summary.schema.json	Compact dependence-aware uncertainty and optional validation-status contract.
rl_env/specs/clinical_outcome_design_simulation_protocol.schema.json	Seeded cluster-size, prevalence, ICC, evaluability, prediction-pattern, gate, and Monte Carlo design contract; the adjacent example is synthetic.
rl_env/specs/clinical_outcome_design_simulation_report.schema.json	Aggregate analytic truth, replicate diagnostic, IID/CR1 performance, gate status, and privacy-boundary contract; the adjacent example is synthetic.
rl_env/specs/clinical_outcome_design_simulation_summary.schema.json	Compact scenario/gate coverage, yield, width, error, status, and optional replay-validation contract.
rl_env/specs/clinical_outcome_stress_simulation_protocol.schema.json	Exact dependence partitions, outcome-specific evaluability, fixed estimand/mode comparison, gate, RNG, and Monte Carlo commitments; the adjacent example is synthetic.
rl_env/specs/clinical_outcome_stress_simulation_report.schema.json	Aggregate analytic shifts, mode diagnostics, target performance, and fixed claim-boundary contract; the adjacent example is synthetic.
rl_env/specs/clinical_outcome_stress_simulation_summary.schema.json	Compact evaluable-only target passage and dependence-closure recovery contract.
rl_env/specs/sealed_evaluation_board.schema.json	Policy-visible, role-neutral cutoff episode and matched-pair board contract.
rl_env/specs/sealed_evaluation_vault.schema.json	Evaluator-only label, failure-cause, arm-role, and commitment-opening contract.
rl_env/specs/policy_evaluation_submission.schema.json	Exact board-bound policy prediction and confidence contract.
rl_env/specs/policy_evaluation_report.schema.json	Aggregate and evaluator-only per-episode scoring report contract.
rl_env/specs/heldout_evaluation_protocol.schema.json	Public preregistration contract for cohort, labels, opaque roster, stages, and metrics; the adjacent example is synthetic.
rl_env/specs/heldout_curation_manifest.schema.json	Evaluator-only opaque declarations, votes, consensus, and adjudication contract.
rl_env/specs/stage_stratified_evaluation_report.schema.json	Aggregate exact counts, Wilson intervals, sufficiency flags, action coverage, and selective-risk contract; the adjacent example is synthetic.
rl_env/specs/source_receipt.schema.json	Machine-readable exact source version, locator, hash, size, retrieval time, and transport.
rl_env/specs/pinned_evidence_ingestion_job.schema.json	Machine-readable reviewer-authored summaries linked to external source receipts.
rl_env/specs/cdc_mmwr_ingestion_job.schema.json	Machine-readable CDC MMWR article, context, value, unit, and excerpt review contract.
rl_env/specs/ncbi_pubmed_ingestion_job.schema.json	Machine-readable PubMed article, METHODS/RESULTS, typed treatment-gap value, and context-anchor contract.
rl_env/specs/chembl_activity_ingestion_job.schema.json	Machine-readable ChEMBL release, linked resource, typed endpoint, candidate alias, target, and lineage contract.
rl_env/specs/ncbi_pubmed_disease_model_ingestion_job.schema.json	Machine-readable PubMed in-vivo exposure, endpoint, model, candidate, and lineage contract.
rl_env/specs/clinicaltrials_gov_ingestion_job.schema.json	Machine-readable exact study, arm, population, endpoint, measurement, analysis, and serious-adverse-event contract.
rl_env/specs/clinicaltrials_gov_portfolio_job.schema.json	Machine-readable exact set of single-trial jobs, receipts, identities, and approved mapping bindings.
rl_env/specs/clinical_evidence_decision_config.schema.json	Machine-readable accepted-synthesis, policy, action-catalog, and output-identity compiler contract; the adjacent example is synthetic.
rl_env/specs/clinical_evidence_decision_summary.schema.json	Machine-readable compact package summary and optional state-replay validation-report contract.
tests/test_target_identity_continuity.py	Namespace rebinding/collision, broken candidate link, and matched target-symbol coverage.
tests/test_context_identity_continuity.py	Disease/model rebinding, assay collision, unknown-candidate evidence, and strict example parsing.
tests/test_clinical_identity_continuity.py	Intervention rebinding, trial collision, unknown-intervention linkage, support removal, and strict example parsing.
tests/test_pinned_evidence_ingestion.py	Receipt/job parsing, source tamper checks, compiler boundaries, CLI capture, and matched source-independence coverage.
tests/test_cdc_mmwr_ingestion.py	Provider identity, location, value, unit, excerpt removal, stage transition, and matched-pair coverage.
tests/test_ncbi_pubmed_ingestion.py	PubMed identity, request, XML/retraction, section, value, anchor, stage transition, and matched-pair coverage.
tests/test_chembl_activity_ingestion.py	ChEMBL release/resource identity, endpoint, target, alias, lineage, text-removal, and CLI-hash coverage.
tests/test_ncbi_pubmed_disease_model_ingestion.py	PubMed article, exposure, endpoint, model/candidate anchor, text-removal, and CLI-hash coverage.
tests/test_preclinical_provider_pair.py	Matched independent-lineage advance and shared-lineage defer integration coverage.
tests/test_clinicaltrials_gov_ingestion.py	Strict registry extraction, payload removal, atomic promotion, continuity attacks, and matched mismatch coverage.
tests/test_clinical_benefit_risk_synthesis.py	Two-source tool-to-replay synthesis plus mismatch, overlap, pooling, forgery, unbound-support, direct-commit, and removal controls.
tests/test_clinical_portfolio.py	Exact-set portfolio extraction, source chronology/disjointness, strict schemas, payload removal, and atomic CLI failure controls.
tests/test_clinical_decision_cli.py	Exact package reproduction, accepted-packet provenance, strict config parsing, atomic CLI output, replay validation, and compact summary coverage.
tests/test_clinical_cohort.py	State-bound roster replay, matched policy sensitivity, provenance overlap, strict readers/schemas, tamper rejection, and atomic cohort CLI coverage.
tests/test_clinical_outcome_evaluation.py	Cutoff/source/package/roster controls, attrition, calibration math, paired comparison, strict schemas/readers, and atomic outcome CLI coverage.
tests/test_clinical_outcome_uncertainty.py	CR1 math, paired covariance, fixed strata, chronology, known-overlap closure, non-estimable states, privacy, strict readers, and atomic CLI coverage.
tests/test_clinical_outcome_design_simulation.py	Analytic truths, seeded replay, ICC undercoverage stress, floor/dominance/attrition states, strict bounds/readers, privacy, schemas, and atomic CLI coverage.
tests/test_clinical_outcome_stress_simulation.py	Analytic estimand shifts, informative-selection bias, hidden-linkage undercoverage, oracle-closure recovery, combined stress, exact partitions, strict readers, privacy, schemas, and atomic CLI coverage.
tests/test_sealed_evaluation.py	Synthetic board determinism, commitment, submission, confidence, schema, leakage, and baseline-policy coverage.
tests/	Dependency-free planning, multi-stage stopping, mapping, evaluation, execution, replay, and transition regression tests.
benchmark/	Installable ctdbench scorer and tests.
docs/public_launch_checklist.md	Human launch checklist before any visibility change.
scripts/audit/*.py	Local release audits and reproducible Hub package builder.

Not Included

• Raw source snapshots or full case banks.
• Raw source bundles, real provider review jobs, ingestion runs, multi-trial portfolio selections, endpoint-family reviewer approvals, ontology-authority resolutions, or reviewer working files.
• Hidden/evaluator labels or locked episode records.
• Real sealed evaluation boards, cached episode packets, label vaults, commitment nonces, policy submissions, or per-episode evaluations.
• Generated reward/verifier outputs or run logs.
• Credentials, local machine paths, or private infrastructure details.
• Model weights or a complete autonomous discovery or wet-lab system.
• Live adapter implementations, endpoint configuration, or raw execution ledgers.
• A real matched success/failure episode corpus or a claim of discovery performance.
• A pooled meta-analysis, benefit-risk score, clinical acceptability judgment, or treatment recommendation; the synthesis path is descriptive and trial-preserving only.
• Real disease-burden, treatment-gap, functional-assay, or disease-model source payloads. The included pinned manifest example is synthetic and demonstrates the contract only.
• Source-pinned clinical registry payloads or reviewer jobs. Typed synthetic design records and one payload-free external validation snapshot are included.
• Provider-specific reviewed disease/preclinical ingestion jobs or real compiled manifests.
• Croissant metadata for jang1563/clinical-trial-decision-benchmark; that metadata belongs to the separate external dataset, not this artifact mirror.

Linked External Dataset

The scorer in benchmark/ targets https://huggingface.co/datasets/jang1563/clinical-trial-decision-benchmark. That dataset has its own card, rows, and Croissant metadata. This repository's Hub package intentionally does not duplicate those data or metadata.

Validation Before Upload

Run these checks from the GitHub repository root before creating or updating the Hugging Face repository:

python3 -m pip install -e . -e ./benchmark pytest build ruff
python3 scripts/audit/github_release_file_audit.py
python3 scripts/audit/validate_hf_release_package.py
python3 scripts/audit/validate_public_launch_packet.py
python3 scripts/audit/validate_vertical_slice_doc.py
python3 scripts/audit/validate_policy_evaluation_snapshot.py
python3 -m unittest discover -s tests -v
python3 -m ruff check agentic_drug_discovery tests adapters/boltz_adapter.py adapters/chembl_adapter.py adapters/opentargets_adapter.py adapters/execution_registry.py adapters/pinned_evidence_adapter.py adapters/clinical_synthesis_adapter.py scripts/audit
python3 -m pytest -q benchmark/tests
python3 -m build --wheel . --outdir /tmp/agentic-core-dist
python3 scripts/audit/smoke_test_core_wheel.py --wheel-dir /tmp/agentic-core-dist
python3 scripts/audit/build_hf_release_package.py --output /tmp/agentic-hf-release-package --force
python3 scripts/audit/validate_hf_release_package.py --package /tmp/agentic-hf-release-package
git diff --check
python3 -m compileall agentic_drug_discovery adapters chains benchmark/src scripts/audit tests

Hub Placement

• Repository type: Dataset
• Repo id: jang1563/agentic-drug-discovery-system
• Current visibility: public and ungated
• Current public update: 0.3.0.dev2, published after explicit approval
• Future updates require a new exact-package review and approval

Source

Primary source repository:

https://github.com/jang1563/agentic-drug-discovery-system