{ "acceptance_criteria": [ "Every r in R_cal finishes or is explicit HOLD", "Diagnosis remains sealed", "PTSD nuclei remain excluded", "Original ENSG row order unchanged", "No AST_MEMBERSHIP_FREEZE", "No single privileged resolution declared as biological truth", "Admissible set size is not 0 or 1, or the report is HOLD", "IMPLEMENTATION_CHECK records Pegasus with registered kwargs (no Scanpy substitute, no live library defaults)", "If r=0.4 or r=2.4 is admissible, report RANGE_BOUNDARY_NOT_BRACKETED and do not claim a complete range", "If any required grid point is unfinished, calibration is HOLD/INCOMPLETE and does not claim a complete range", "marker_separability is HOLD_NOT_RUN unless a frozen public panel identity/hash was resolved before freeze" ], "approval_requirement": { "authorized_scientific_step": "P2_RESOLUTION_CALIBRATION", "channel": "existing trusted approval envelope; not this webpage", "required": true }, "contract_body_sha256": "8353201ade216c8ef00c103c596f87889e67a1392780977fbf5c6d029b1467b9", "contract_frozen_at": "2026-09-22T15:48:03.338125Z", "excluded_scope": "Do not run clustering GO, annotation, unblind, DE, pathway, PTSD inclusion, P1 C2 copy, OPEN_01 auto-approval, production ENSG remapping, or scientific GO change. Do not use diagnosis, AST count-max, Channel balance, P1 concordance, 241/DEG, or Hwang ST2 AST fraction as selection targets. Do not use P1 8-gene panel. Do not open the restricted diagnosis asset. UMAP is sanity only and does not define identity. Do not execute archived frozen contracts.", "execution_location": "cloud", "expected_outputs": [ "calibration_metrics.tsv (r, seed, n_clusters, size stats, modularity, Channel entropy, technical Cramer's V, over-fragmentation/collapse flags)", "pairwise_ari.tsv (seed ARI and adjacent-r ARI)", "marker_separability.tsv = HOLD_NOT_RUN (no frozen public panel identity in Record Core)", "IMPLEMENTATION_CHECK.json (Pegasus required; n_top=2000, batch=Channel, n_components=50, Harmony Channel, K=100)", "UNIVERSE_CHECK.json (n=625220, n_channels=70, PTSD=false, diagnosis_columns=none)", "CALIBRATION_REPORT.md (admissible range only if complete and bracketed; else HOLD/INCOMPLETE and/or RANGE_BOUNDARY_NOT_BRACKETED; no AST membership; no final r)" ], "frozen_contract_hash": "8353201ade216c8ef00c103c596f87889e67a1392780977fbf5c6d029b1467b9", "holds": [ "OPEN_01 UNION_REMOVE remains unapproved; this task does not decide Round-1 merge", "Public class-marker panel has no frozen Record Core identity/hash; marker_separability = HOLD_NOT_RUN; do not search or substitute P1 panels", "G2 specimen HOLD remains; this task is nucleus-level geometry only; 70 Channels are not 70 verified specimens", "RNA gene identity ledger is audit-only; no remap", "CALIBRATION/CLUSTERING/ANNOTATION Record Core flags remain NOT_AUTHORIZED until a later approved execution actually records them", "CSR matrix is CLOUD_AUTHORITATIVE; execution must be on the registered cloud host after approval", "Previous frozen calibration contracts are archived and not executable on this runtime" ], "kind": "PRE_EXECUTION_REVIEW", "loop": "0.3.2-rc4", "not_a_commit": true, "not_a_scientific_result": true, "objective": "Determine a phenotype-blind Leiden resolution range and selection basis for later P2 clustering. This freeze is not execution approval.", "output_assets": [ { "asset_id": "P2_CALIBRATION_METRICS", "filename": "calibration_metrics.tsv", "required": true, "role": "calibration_metrics" }, { "asset_id": "P2_CALIBRATION_PAIRWISE_ARI", "filename": "pairwise_ari.tsv", "required": true, "role": "pairwise_ari" }, { "asset_id": "P2_CALIBRATION_IMPLEMENTATION_CHECK", "filename": "IMPLEMENTATION_CHECK.json", "required": true, "role": "implementation_check" }, { "asset_id": "P2_CALIBRATION_UNIVERSE_CHECK", "filename": "UNIVERSE_CHECK.json", "required": true, "role": "universe_check" }, { "asset_id": "P2_CALIBRATION_REPORT", "filename": "CALIBRATION_REPORT.md", "required": true, "role": "calibration_report" }, { "asset_id": "P2_CALIBRATION_MARKER_SEPARABILITY", "filename": "marker_separability.tsv", "required": false, "role": "marker_separability" } ], "policy_summary": "execution_location=cloud; network=cloud_registered_ssh_only; tools=python, pegasus", "project_id": "P2_HWANG", "recording_effects": { "minimum": [ "task_receipt" ], "on_failure": [ "task_receipt" ], "on_success": [ "task_receipt", "asset_registry" ] }, "resolved_logical_assets": [ { "access_mode": "cloud_live_hash", "alias_zh": "P2 MDD+CON 聚类队列（625,220 / 70 Channels）", "asset_id": "P2_MDD_CON_CLUSTERING_COHORT_625220", "bytes": 21882716, "execution_location": "cloud", "execution_site": "SSH_CLOUD", "object_identity": null, "object_identity_status": "not_applicable", "path_withheld": true, "restricted": false, "restricted_class": "none", "role": "analysis_cohort", "selected_replica": "SSH_CLOUD", "sha256": "ffc9dcc707452e5b49ebd12132d3b2bff2143b1871bb59bbb1f45536bcd1e3f4", "status": "MATCH" }, { "access_mode": "cloud_live_hash", "alias_zh": "P2 计数矩阵（只公布逻辑名与哈希）", "asset_id": "P2_CSR_COUNT_MATRIX", "bytes": 5948837770, "execution_location": "cloud", "execution_site": "SSH_CLOUD", "object_identity": null, "object_identity_status": "not_applicable", "path_withheld": true, "restricted": false, "restricted_class": "none", "role": "count_matrix_csr", "selected_replica": "SSH_CLOUD", "sha256": "79876eda346f3a6c325a2cb33de9f35cfc2d276018b79462bd749a957b279922", "status": "MATCH" }, { "access_mode": "cloud_live_hash", "alias_zh": "P2_RNA_CELLNAMES", "asset_id": "P2_RNA_CELLNAMES", "bytes": 24319646, "execution_location": "cloud", "execution_site": "SSH_CLOUD", "object_identity": null, "object_identity_status": "not_applicable", "path_withheld": true, "restricted": false, "restricted_class": "none", "role": "cell_id_order", "selected_replica": "SSH_CLOUD", "sha256": "3d274bcc16ef0d57014e4c2a47bf47e7f83bdf579f2fc8d8be349c17a9b7a9ba", "status": "MATCH" }, { "access_mode": "cloud_live_hash", "alias_zh": "P2_RNA_GENENAMES", "asset_id": "P2_RNA_GENENAMES", "bytes": 3271355, "execution_location": "cloud", "execution_site": "SSH_CLOUD", "object_identity": null, "object_identity_status": "not_applicable", "path_withheld": true, "restricted": false, "restricted_class": "none", "role": "gene_id_order", "selected_replica": "SSH_CLOUD", "sha256": "ba827830af502d16a9aa4dbc80a31bb61bc5b7ec440698171d78bfc5af1fee62", "status": "MATCH" } ], "review_snapshot_id": "rev-0e53d62a-aadd-4bd0-bfeb-a4d10aab656c-8353201ade21", "review_state": "APPROVED", "reviewed_contract_hash": "8353201ade216c8ef00c103c596f87889e67a1392780977fbf5c6d029b1467b9", "schema": "p2.contract_review_projection.v1", "scientific_go": false, "scientific_scope": "Accepted clustering universe = 625220 MDD+CON nuclei / 70 Channels. Canonical clustering implementation is Pegasus only; Worker may not substitute Scanpy. Registered Pegasus kwargs: robust genes; log-norm with counts retained; HVG n_top=2000 batch=Channel; pca n_components=50; Harmony attrs=Channel; neighbors K=100; Leiden r from R_cal only. UMAP is sanity only. Grid R_cal = [0.4, 0.6, 1.0, 1.2, 1.6, 1.8, 2.4] with seeds [0, 1, 2]. G3b operational set {0.6, 1.2, 1.8} is included; author Leiden resolution remains NOT_FOUND. Admissible range uses operational guardrails (collapse n_clusters<7; over-fragment n_clusters>80 or >25% clusters size<50 or seed-ARI median<0.70). If lowest r=0.4 or highest r=2.4 remains admissible, mark RANGE_BOUNDARY_NOT_BRACKETED and do not claim a complete admissible range; recommend a later grid-extension contract. If any required grid point is unfinished, report completed diagnostics only and mark the calibration HOLD/INCOMPLETE; do not claim a complete admissible range. Do not declare one biological true resolution. Do not assign class labels. Marker-panel gaps are diagnostic distributions only (no GAP_WEAK cutoff) and run only if a frozen public panel identity/hash is resolved; otherwise HOLD_NOT_RUN.", "scientific_step": "P2_RESOLUTION_CALIBRATION", "task_id": "0e53d62a-aadd-4bd0-bfeb-a4d10aab656c", "task_title": "P2 resolution calibration (phenotype-blind, MDD+CON 625220)", "test_only": false, "webpage_is_not_scientific_authorization": true }