Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261004T003810Z-behcet-pair-recovery/diffusion/dataset/server_1/model8/plans/behcet_pair_recovery_20261004/out/RULE.json

@@ -0,0 +1,40 @@
+{
+ "identity_genes": "identity_genes_all4.csv top 50",
+ "genes": "G50",
+ "stat": "r_best",
+ "threshold": 0.6581375985244046,
+ "rule": "mutual best and r_best >= threshold",
+ "selected_by": "highest sensitivity on ye2026_sepsis at <= 1 % wrong calls per sc column (all 9 statistic x gene-set combinations in calibration_summary.csv)",
+ "sepsis": {
+  "cohort": "ye2026_sepsis",
+  "genes": "G50",
+  "stat": "r_best",
+  "threshold": 0.6581375985244046,
+  "sensitivity": 0.5506666666666666,
+  "wrong_call_rate": 0.01,
+  "draws_with_any_wrong_call": 0.078,
+  "top1_true_rate_shared": 0.836,
+  "mutual_true_rate_shared": 0.823,
+  "all_3_called_rate": 0.192,
+  "draws": 1000
+ },
+ "liu2021_replication": {
+  "cohort": "liu2021",
+  "genes": "G50",
+  "stat": "r_best",
+  "threshold": 0.6252459681052224,
+  "sensitivity": 0.7326666666666667,
+  "wrong_call_rate": 0.009875,
+  "draws_with_any_wrong_call": 0.079,
+  "top1_true_rate_shared": 0.9506666666666667,
+  "mutual_true_rate_shared": 0.9306666666666666,
+  "all_3_called_rate": 0.412,
+  "draws": 1000
+ },
+ "false_call_max_per_sc_column": 0.01,
+ "draws": 1000,
+ "seed": 20261004,
+ "frozen_before_final_behcet_scoring": true,
+ "ages_used": false,
+ "note": "margin_z / G100 was the first rule; the first 50-draw test of v2 also printed Beh\u00e7et scores. r_best and dc_margin were added afterwards; the choice is made on the controls only."
+}

paper-releases/pbisc-diffusion/updates/20261004T003810Z-behcet-pair-recovery/diffusion/dataset/server_1/model8/plans/behcet_pair_recovery_20261004/out/SUMMARY.json

@@ -0,0 +1,188 @@
+{
+ "rule": {
+  "identity_genes": "identity_genes_all4.csv top 50",
+  "genes": "G50",
+  "stat": "r_best",
+  "threshold": 0.6581375985244046,
+  "rule": "mutual best and r_best >= threshold",
+  "selected_by": "highest sensitivity on ye2026_sepsis at <= 1 % wrong calls per sc column (all 9 statistic x gene-set combinations in calibration_summary.csv)",
+  "sepsis": {
+   "cohort": "ye2026_sepsis",
+   "genes": "G50",
+   "stat": "r_best",
+   "threshold": 0.6581375985244046,
+   "sensitivity": 0.5506666666666666,
+   "wrong_call_rate": 0.01,
+   "draws_with_any_wrong_call": 0.078,
+   "top1_true_rate_shared": 0.836,
+   "mutual_true_rate_shared": 0.823,
+   "all_3_called_rate": 0.192,
+   "draws": 1000
+  },
+  "liu2021_replication": {
+   "cohort": "liu2021",
+   "genes": "G50",
+   "stat": "r_best",
+   "threshold": 0.6252459681052224,
+   "sensitivity": 0.7326666666666667,
+   "wrong_call_rate": 0.009875,
+   "draws_with_any_wrong_call": 0.079,
+   "top1_true_rate_shared": 0.9506666666666667,
+   "mutual_true_rate_shared": 0.9306666666666666,
+   "all_3_called_rate": 0.412,
+   "draws": 1000
+  },
+  "false_call_max_per_sc_column": 0.01,
+  "draws": 1000,
+  "seed": 20261004,
+  "frozen_before_final_behcet_scoring": true,
+  "ages_used": false,
+  "note": "margin_z / G100 was the first rule; the first 50-draw test of v2 also printed Beh\u00e7et scores. r_best and dc_margin were added afterwards; the choice is made on the controls only."
+ },
+ "behcet_calls_primary": [
+  {
+   "genes": "G50",
+   "stat": "r_best",
+   "primary": true,
+   "sc_sample": "PBMC_BD_1",
+   "best_bulk": "HC3",
+   "r_best": 0.33480143235686677,
+   "r_second": 0.18484391378329088,
+   "mutual": false,
+   "value": 0.33480143235686677,
+   "threshold": 0.6581375985244046,
+   "called": false,
+   "sc_chrY_cpm": 1072.2533251383536
+  },
+  {
+   "genes": "G50",
+   "stat": "r_best",
+   "primary": true,
+   "sc_sample": "PBMC_BD_2",
+   "best_bulk": "BDV4",
+   "r_best": 0.7842087546676991,
+   "r_second": 0.37591454589207096,
+   "mutual": true,
+   "value": 0.7842087546676991,
+   "threshold": 0.6581375985244046,
+   "called": true,
+   "sc_chrY_cpm": 1010.5252431743482
+  },
+  {
+   "genes": "G50",
+   "stat": "r_best",
+   "primary": true,
+   "sc_sample": "PBMC_BD_3",
+   "best_bulk": "BDV5",
+   "r_best": 0.555423006090796,
+   "r_second": 0.2583440898534389,
+   "mutual": true,
+   "value": 0.555423006090796,
+   "threshold": 0.6581375985244046,
+   "called": false,
+   "sc_chrY_cpm": 885.5437573448836
+  },
+  {
+   "genes": "G50",
+   "stat": "r_best",
+   "primary": true,
+   "sc_sample": "PBMC_BD_4",
+   "best_bulk": "BDV6",
+   "r_best": 0.7455896536503368,
+   "r_second": 0.35592449667581927,
+   "mutual": true,
+   "value": 0.7455896536503368,
+   "threshold": 0.6581375985244046,
+   "called": true,
+   "sc_chrY_cpm": 943.4389424015894
+  },
+  {
+   "genes": "G50",
+   "stat": "r_best",
+   "primary": true,
+   "sc_sample": "PBMC_HC_1",
+   "best_bulk": "HC6",
+   "r_best": 0.5109677763618931,
+   "r_second": 0.22648868696849972,
+   "mutual": true,
+   "value": 0.5109677763618931,
+   "threshold": 0.6581375985244046,
+   "called": false,
+   "sc_chrY_cpm": 0.35083152333503254
+  },
+  {
+   "genes": "G50",
+   "stat": "r_best",
+   "primary": true,
+   "sc_sample": "PBMC_HC_2",
+   "best_bulk": "HC2",
+   "r_best": 0.3795763066007761,
+   "r_second": 0.36140861630172444,
+   "mutual": true,
+   "value": 0.3795763066007761,
+   "threshold": 0.6581375985244046,
+   "called": false,
+   "sc_chrY_cpm": 0.802656579235515
+  },
+  {
+   "genes": "G50",
+   "stat": "r_best",
+   "primary": true,
+   "sc_sample": "PBMC_HC_3",
+   "best_bulk": "BDV1",
+   "r_best": 0.24992765157037453,
+   "r_second": 0.24930659693358473,
+   "mutual": true,
+   "value": 0.24992765157037453,
+   "threshold": 0.6581375985244046,
+   "called": false,
+   "sc_chrY_cpm": 969.4879641434213
+  },
+  {
+   "genes": "G50",
+   "stat": "r_best",
+   "primary": true,
+   "sc_sample": "PBMC_HC_4",
+   "best_bulk": "HC8",
+   "r_best": 0.41700971208793053,
+   "r_second": 0.2641597878054443,
+   "mutual": true,
+   "value": 0.41700971208793053,
+   "threshold": 0.6581375985244046,
+   "called": false,
+   "sc_chrY_cpm": 997.0481058509805
+  }
+ ],
+ "behcet_negative_control": "sc samples with chrY CPM < 10 (female) must not be called: [{\"sc_sample\": \"PBMC_HC_1\", \"called\": false}, {\"sc_sample\": \"PBMC_HC_2\", \"called\": false}]",
+ "inputs": {
+  "behcet_bulk": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/bulk/GSE198533_count/harmonized.h5ad",
+  "behcet_bulk_sha256": "61a9fca887964bba2502209b6c6e9c71086b90c0e967ee6a2f7d5004430b3939",
+  "behcet_sc": {
+   "PBMC_BD_1": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953767",
+   "PBMC_BD_2": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953768",
+   "PBMC_BD_3": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953769",
+   "PBMC_BD_4": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953770",
+   "PBMC_HC_1": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953771",
+   "PBMC_HC_2": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953772",
+   "PBMC_HC_3": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953773",
+   "PBMC_HC_4": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953774"
+  },
+  "pairs": {
+   "imperial_eskd": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv",
+   "liu2021": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/liu2021/pairs.csv",
+   "ji2025_chili": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv",
+   "giroux2022": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/pairs.csv",
+   "ye2026_sepsis": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv"
+  },
+  "sex_linked_exclusion": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sex_linked_genes_exclude.csv"
+ },
+ "n_pairs_identity_pass": {
+  "imperial_eskd": 158,
+  "liu2021": 61,
+  "ji2025_chili": 33,
+  "giroux2022": 24,
+  "ye2026_sepsis": 82
+ },
+ "code_sha256": "4dec1f955d1874bac0f485a9e327c7e768690705ab45f78ba317a7ce250ecd2f",
+ "ages_used": false
+}

paper-releases/pbisc-diffusion/updates/20261004T003810Z-behcet-pair-recovery/diffusion/dataset/server_1/model8/plans/behcet_pair_recovery_20261004/out/UNBLIND.json

@@ -0,0 +1,41 @@
+{
+ "p_same_age_by_chance": 0.0005831753899985419,
+ "pairs": [
+  {
+   "sc_sample": "PBMC_BD_2",
+   "sc_gsm": "GSM5953768",
+   "bulk_sample": "BDV4",
+   "bulk_gsm": "GSM5951805",
+   "age": 31,
+   "rules_calling_it": 8,
+   "rules": 9,
+   "primary_rule_called": true,
+   "primary_r_best": 0.7842087546676991,
+   "tier": "expression_identity_called_by_primary_rule+age_equal"
+  },
+  {
+   "sc_sample": "PBMC_BD_3",
+   "sc_gsm": "GSM5953769",
+   "bulk_sample": "BDV5",
+   "bulk_gsm": "GSM5951806",
+   "age": 58,
+   "rules_calling_it": 6,
+   "rules": 9,
+   "primary_rule_called": false,
+   "primary_r_best": 0.555423006090796,
+   "tier": "expression_best_and_mutual_in_all_rules+age_equal"
+  },
+  {
+   "sc_sample": "PBMC_BD_4",
+   "sc_gsm": "GSM5953770",
+   "bulk_sample": "BDV6",
+   "bulk_gsm": "GSM5951807",
+   "age": 41,
+   "rules_calling_it": 8,
+   "rules": 9,
+   "primary_rule_called": true,
+   "primary_r_best": 0.7455896536503368,
+   "tier": "expression_identity_called_by_primary_rule+age_equal"
+  }
+ ]
+}

paper-releases/pbisc-diffusion/updates/20261004T003810Z-behcet-pair-recovery/diffusion/dataset/server_1/model8/plans/behcet_pair_recovery_20261004/out/_v1_resid_test/RULE.json

@@ -0,0 +1,26 @@
+{
+ "primary_method": "resid_k3",
+ "threshold": 1.3144402334737855,
+ "chosen_on": "ye2026_sepsis: highest sensitivity at <= 1 % wrong calls per sc column",
+ "secondary_method": "onoff",
+ "secondary_threshold": 1.4397104875288682,
+ "false_call_max": 0.01,
+ "draws": 20,
+ "seed": 20261004,
+ "top_n": 2000,
+ "liu2021_at_this_rule": [
+  {
+   "cohort": "liu2021",
+   "method": "resid_k3",
+   "threshold": 1.5582282806423087,
+   "sensitivity": 0.13333333333333333,
+   "wrong_call_rate": 0.00625,
+   "top1_true_rate_shared": 0.7,
+   "mutual_true_rate_shared": 0.6333333333333333,
+   "nonshared_mutual_rate": 0.46,
+   "all_3_called_rate": 0.0,
+   "draws": 20
+  }
+ ],
+ "frozen_before_behcet": true
+}