{ "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 registered kwargs (no live library defaults)" ], "canonical_stop": "WAITING_FOR_INVESTIGATOR_REVIEW", "cloud_environment_manifest_sha256": "0fe8e83f3513bd9766faae0b7175fb393bfbe160272798b7089fbf4890c2de7c", "contract_body_sha256": "4792109f456ac7a8e30742f115148b28f973198bb436a80075b72a01d91865d0", "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 contract a5aebb33… on this runtime.", "execution_runtime_release_id": "0.3.2-rc4-reviewpub-v2", "holds": [ "OPEN_01 UNION_REMOVE remains unapproved; this task does not decide Round-1 merge", "Marker Hodge/Lake/Ma JSON not frozen; unpublished JSON is not scored; public class panel gaps are diagnostic-only", "G2 specimen HOLD remains; this task is nucleus-level geometry only; 70 Channels are not 70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", "Archived frozen contract b90b5917-… / a5aebb33… is immutable and not executable on this runtime" ], "method_identity": "p2-task-contract/0.3.2-rc4", "objective": "Determine a phenotype-blind Leiden resolution range and selection basis for later P2 clustering. This freeze is not execution approval.", "output_assets": [], "project_id": "P2_HWANG", "record_checkpoint_id": "ckpt-1d9b0900-de09-4037-aaad-36d77ce380b9", "resolved_inputs": [ { "access_mode": "local_read", "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": "local", "execution_site": "LOCAL", "object_identity": null, "object_identity_status": "not_applicable", "path_withheld": true, "restricted": false, "restricted_class": "none", "role": "analysis_cohort", "selected_replica": "LOCAL", "sha256": "ffc9dcc707452e5b49ebd12132d3b2bff2143b1871bb59bbb1f45536bcd1e3f4", "status": "MATCH" }, { "access_mode": "metadata_only", "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" } ], "review_schema": "p2.contract_review_projection.v1", "runtime_manifest_sha256": "db6674929f862ff6df3134ca04ca74e6dea84e21a001a4b04e120f0bee9fff34", "schema": "p2.review_public_contract.v1", "schema_version": "p2-task-contract/0.3.2-rc4", "scientific_go": false, "scientific_parameters": { "calibration_spec": { "author_leiden_resolution": "NOT_FOUND", "design_reference": "archived TASK_CONTRACT_DRAFT_V0_2_RICHER_METRICS.md used as planner input only; not executable", "forbidden_selection_targets": [ "diagnosis", "AST_count_max", "channel_balance_optimization", "P1_C2_concordance", "DEG_241", "Hwang_ST2_AST_fraction", "UMAP_aesthetics" ], "g3b_operational_subset": [ 0.6, 1.2, 1.8 ], "grid": [ 0.4, 0.6, 1.0, 1.2, 1.6, 1.8, 2.4 ], "guardrails": { "GAP_WEAK": "DELETED", "admissible_set_size_0_or_1": "HOLD", "collapse_if_n_clusters_lt": 7, "marker_separability": "diagnostic distribution only; no pass/fail cutoff", "overfragment_if_frac_clusters_size_lt_50_gt": 0.25, "overfragment_if_n_clusters_gt": 80, "overfragment_if_seed_ari_median_lt": 0.7 }, "harmony_covariate": "Channel", "hvg_batch": "Channel", "hvg_n_top": 2000, "implementation": { "family": "Pegasus or equivalent registered kwargs", "harmony": { "batch": "Channel" }, "hvg": { "batch": "Channel", "fn": "highly_variable_features", "n_top": 2000 }, "log_norm": "pg.log_norm; raw counts retained in a separate layer", "neighbors": { "K": 100, "use_cache": false }, "no_live_library_defaults": true, "pca": { "n_components": 50 }, "robust_genes": "pg.identify_robust_genes; keep var.robust" }, "k_neighbors": 100, "n_pcs": 50, "ptsd_included": false, "seeds": [ 0, 1, 2 ], "universe_asset_id": "P2_MDD_CON_CLUSTERING_COHORT_625220", "universe_n_channels": 70, "universe_n_nuclei": 625220 }, "csr_axis_semantics": null }, "scientific_scope": "Accepted clustering universe = 625220 MDD+CON nuclei / 70 Channels. Canonical calls register 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). Do not declare one biological true resolution. Do not assign class labels. Marker-panel gaps are diagnostic distributions only (no GAP_WEAK cutoff).", "task_id": "f4979fd9-0a3a-42ab-a187-88b778e1b307", "test_only": false, "title": "P2 resolution calibration (phenotype-blind, MDD+CON 625220)", "webpage_is_not_scientific_authorization": true }