Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw0_cibersortx/contrast.csv

@@ -0,0 +1,17 @@
+genes,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast
+zero_filled,T cell,mean_cp10k,2863,,0.4659672798536223,,
+zero_filled,T cell,pseudobulk_log1p_cpm,2863,,0.5669062142141347,,
+zero_filled,B cell,mean_cp10k,3005,,0.3989038406365887,,
+zero_filled,B cell,pseudobulk_log1p_cpm,3005,,0.4804240789506083,,
+zero_filled,Monocyte,mean_cp10k,3028,0.043169836902222695,0.6141260231172326,0.033616720303144165,0.02711007793624428
+zero_filled,Monocyte,pseudobulk_log1p_cpm,3028,0.04454977741191298,0.6247044807439144,0.025028568806486993,0.04005353183807079
+zero_filled,NK cell,mean_cp10k,2910,,0.40486451543783863,,
+zero_filled,NK cell,pseudobulk_log1p_cpm,2910,,0.47190028654240307,,
+covered,T cell,mean_cp10k,0,,,,
+covered,T cell,pseudobulk_log1p_cpm,0,,,,
+covered,B cell,mean_cp10k,0,,,,
+covered,B cell,pseudobulk_log1p_cpm,0,,,,
+covered,Monocyte,mean_cp10k,422,0.11204850205858954,0.6007393502931081,0.049820621838729755,0.12070269389731475
+covered,Monocyte,pseudobulk_log1p_cpm,422,0.168134303770332,0.5371276579221712,0.09740848038499386,0.1620779206543591
+covered,NK cell,mean_cp10k,0,,,,
+covered,NK cell,pseudobulk_log1p_cpm,0,,,,

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw0_cibersortx/per_donor.csv

@@ -0,0 +1,12 @@
+donor,group,bp_comp_l1_final_cells,bp_comp_l1_first_cells,bp_comp_l1_final_mrna,bp_comp_l1_first_mrna,lora_comp_l1,bp_first_T cell,bp_final_T cell,obs_T cell,bp_first_B cell,bp_final_B cell,obs_B cell,bp_first_Monocyte,bp_final_Monocyte,obs_Monocyte,bp_first_NK cell,bp_final_NK cell,obs_NK cell,bp_first_DC,bp_final_DC,obs_DC,bp_first_Other,bp_final_Other,obs_Other
+450905_d0,mild,0.9359422324480268,0.9359422324480268,0.7190758106414383,0.7190758106414383,0.2412030210799234,0.04586723546820452,0.04586723546820452,0.30943523841731485,0.0,0.0,0.036185322962461956,0.3297794844378918,0.3297794844378918,0.4293202570172472,0.062198869990959,0.062198869990959,0.12089956036523504,0.0,0.0,0.009976327358809604,0.5621544101029448,0.5621544101029448,0.09418329387893135
+450905_d14,mild,1.1851297603259647,1.1851297603259647,0.7413638629739969,0.7413638629739969,0.3741714594302686,0.09282429341926661,0.09282429341926661,0.4422843256379101,0.024720978715043092,0.024720978715043092,0.02929661131362225,0.12610352195017244,0.12610352195017244,0.27420008100445525,0.0825684674202862,0.0825684674202862,0.15782368030241664,0.01465919760590934,0.01465919760590934,0.02983664101525584,0.6591235408893222,0.6591235408893222,0.06655866072633995
+2AD75E_d0,mild,0.7040716436253494,0.7040716436253494,0.4324983757924855,0.4324983757924855,0.2003147450062828,0.399636382951114,0.399636382951114,0.6034056934875861,0.07461665182938818,0.07461665182938818,0.06408423241908229,0.06469942891651932,0.06469942891651932,0.14064734173924348,0.11252476564375288,0.11252476564375288,0.15949564539191471,0.0,0.0,0.025347718705316522,0.34852277065922577,0.34852277065922577,0.007019368256856883
+2AD75E_d7,mild,0.8095624477598989,0.8095624477598989,0.4948630294403784,0.4948630294403784,0.1966216465060165,0.3570277646664299,0.3570277646664299,0.5808172206876845,0.09616491692531406,0.09616491692531406,0.14372797409277074,0.0613717251647656,0.0613717251647656,0.10277169254214687,0.06884372073033777,0.06884372073033777,0.14715687208305553,0.0,0.0,0.013715591961139155,0.4165918725131526,0.4165918725131526,0.011810648633203162
+2AD75E_d14,mild,0.7836929827349306,0.7836929827349306,0.5450125270819403,0.5450125270819403,0.2692947706690038,0.35742884056208424,0.35742884056208424,0.5811422728600643,0.08538771410158554,0.08538771410158554,0.12503651767455448,0.10301797489195019,0.10301797489195019,0.14198071866783524,0.05202099485255004,0.05202099485255004,0.12496348232544552,0.0,0.0,0.016579024247735902,0.4021444755918299,0.4021444755918299,0.010297984224364592
+82CCF5_d0,severe,0.8825964378065364,0.8825964378065364,0.6363632110612917,0.6363632110612917,0.3435555555555555,0.24687045153721598,0.24687045153721598,0.5422222222222223,0.09390778169320316,0.09390778169320316,0.11832098765432099,0.11151007603485656,0.11151007603485656,0.1539753086419753,0.025424677280034988,0.025424677280034988,0.09303703703703704,0.0052357081316680605,0.0052357081316680605,0.016691358024691356,0.5170513053230212,0.5170513053230212,0.07575308641975309
+82CCF5_d7,severe,1.190443656348468,1.190443656348468,0.8072064174884148,0.8072064174884148,0.2525451197053406,0.22635006206816644,0.22635006206816644,0.619060773480663,0.03477009706432165,0.03477009706432165,0.09972375690607735,0.06997159617882355,0.06997159617882355,0.14152854511970533,0.04173429865073439,0.04173429865073439,0.09410681399631676,0.0,0.0,0.013627992633517496,0.627173946037954,0.627173946037954,0.03195211786372008
+82CCF5_d14,severe,0.8324325697335235,0.8324325697335235,0.6309614796595555,0.6309614796595555,0.1954423540762179,0.3837603731521846,0.3837603731521846,0.6330499276410999,0.03177557459316829,0.03177557459316829,0.10121201157742403,0.09905456912449895,0.09905456912449895,0.11369392185238784,0.0,0.0,0.06828871201157742,0.0,0.0,0.014562228654124458,0.48540948313014803,0.48540948313014803,0.0691931982633864
+0BF51C_d0,severe,0.7084701793068707,0.7084701793068707,0.5407787027020405,0.5407787027020405,0.3686513056835637,0.22510820859129665,0.22510820859129665,0.4012288786482335,0.00836778030886852,0.00836778030886852,0.01674347158218126,0.35599179176406015,0.35599179176406015,0.4609831029185868,0.018316631393450872,0.018316631393450872,0.07726574500768049,0.00034608968673786726,0.00034608968673786726,0.006144393241167435,0.39186949825558587,0.39186949825558587,0.03763440860215054
+0BF51C_d7,severe,0.6115494625199089,0.6115494625199089,0.3128267435802498,0.3128267435802498,0.2886135576447303,0.451788959924333,0.451788959924333,0.612370113805047,0.06696273493711088,0.06696273493711088,0.05700148441365661,0.07578613563411928,0.07578613563411928,0.1607125185551707,0.0,0.0,0.05294408708560119,0.0,0.0,0.0073231073725878275,0.40546216950443675,0.40546216950443675,0.10964868876793667
+0BF51C_d14,severe,0.7207592175996038,0.7207592175996038,0.43017142095444794,0.43017142095444794,0.2608470093703476,0.45164960374754143,0.45164960374754143,0.6330676941938874,0.07696126373986181,0.07696126373986181,0.07960416849111131,0.057781986404047664,0.057781986404047664,0.151589456169542,0.007076385719291166,0.007076385719291166,0.07907872843506436,0.0,0.0,0.010508801120938787,0.4065307603892581,0.4065307603892581,0.04615115158945617

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw0_cibersortx/summary.json

@@ -0,0 +1,157 @@
+{
+ "dataset": "giroux2022",
+ "comparison": "fewshot",
+ "draw": 0,
+ "gene_mode": "cibersortx",
+ "stored_scores": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5/draw0",
+ "lora_arm": "lora5",
+ "n_donors": 11,
+ "contrast": true,
+ "genes_scoring": 5563,
+ "genes_covered_by_Z_all_donors": 436,
+ "bayesprism": {
+  "comp_l1": 0.8513318718371892,
+  "comp_l1_by_variant": {
+   "final_cells": 0.8513318718371892,
+   "first_cells": 0.8513318718371892,
+   "final_mrna": 0.5719201437614763,
+   "first_mrna": 0.5719201437614763
+  },
+  "mean_fraction": {
+   "final_cells": {
+    "T cell": 0.2944,
+    "B cell": 0.054,
+    "Monocyte": 0.1323,
+    "NK cell": 0.0428,
+    "DC": 0.0018,
+    "Other": 0.4747
+   },
+   "first_cells": {
+    "T cell": 0.2944,
+    "B cell": 0.054,
+    "Monocyte": 0.1323,
+    "NK cell": 0.0428,
+    "DC": 0.0018,
+    "Other": 0.4747
+   },
+   "final_mrna": {
+    "T cell": 0.3339,
+    "B cell": 0.0781,
+    "Monocyte": 0.2639,
+    "NK cell": 0.056,
+    "DC": 0.007,
+    "Other": 0.2612
+   },
+   "first_mrna": {
+    "T cell": 0.3339,
+    "B cell": 0.0781,
+    "Monocyte": 0.2639,
+    "NK cell": 0.056,
+    "DC": 0.007,
+    "Other": 0.2612
+   }
+  },
+  "logfc_r_mean_cp10k": 0.043169836902222695,
+  "partial_r_mean_cp10k": 0.033616720303144165,
+  "logfc_r_mean_cp10k_covered_genes": 0.11204850205858954,
+  "deg_top50_sum": 0,
+  "deg_top50_sum_covered_genes": 0,
+  "per_type_logfc_r": {
+   "T cell": NaN,
+   "B cell": NaN,
+   "Monocyte": 0.0432,
+   "NK cell": NaN
+  }
+ },
+ "observed_mean_fraction": {
+  "T cell": 0.5416,
+  "B cell": 0.0792,
+  "Monocyte": 0.2065,
+  "NK cell": 0.1068,
+  "DC": 0.0149,
+  "Other": 0.0509
+ },
+ "lora": {
+  "comp_l1": 0.27193277679338645,
+  "coverage": 0.96,
+  "logfc_r_mean_cp10k": 0.243392212681724,
+  "deg_top50_sum": 0,
+  "partial_r_mean_cp10k": 0.15035969319388034
+ },
+ "broadcast": {
+  "logfc_r_mean_cp10k": 0.4709654147613206,
+  "logfc_r_mean_cp10k_covered_genes": 0.6007393502931081,
+  "deg_top50_sum": 0
+ },
+ "other_arms": {
+  "zs_raw": {
+   "comp_l1": 0.3551759564415273,
+   "logfc_r_mean_cp10k": 0.14641874658292783,
+   "deg_top50_sum": 0
+  },
+  "zs_pseudo": {
+   "comp_l1": 0.3125921721151519,
+   "logfc_r_mean_cp10k": 0.34770957181723616,
+   "deg_top50_sum": 0
+  },
+  "zs_cal": {
+   "comp_l1": 0.27177224639619263,
+   "logfc_r_mean_cp10k": 0.11201111078574608,
+   "deg_top50_sum": 0
+  }
+ },
+ "gates": {
+  "observed_composition_equal": true,
+  "broadcast_r_equal": true,
+  "broadcast_deg_equal": true
+ },
+ "method": "cibersortx",
+ "has_cell_type_expression": true,
+ "n_case": 6,
+ "n_control": 5,
+ "deg_per_type": {
+  "zero_filled": {
+   "bp": {
+    "T cell": 0,
+    "B cell": 0,
+    "Monocyte": 0,
+    "NK cell": 0,
+    "DC": 0
+   },
+   "broadcast": {
+    "T cell": 0,
+    "B cell": 0,
+    "Monocyte": 0,
+    "NK cell": 0,
+    "DC": 0
+   }
+  },
+  "covered": {
+   "bp": {
+    "T cell": null,
+    "B cell": null,
+    "Monocyte": 0,
+    "NK cell": null,
+    "DC": null
+   },
+   "broadcast": {
+    "T cell": null,
+    "B cell": null,
+    "Monocyte": 0,
+    "NK cell": null,
+    "DC": null
+   }
+  }
+ },
+ "hires_imputed_genes": {
+  "fewshot0|T cell": 0,
+  "fewshot0|B cell": 0,
+  "fewshot0|Monocyte": 436,
+  "fewshot0|NK cell": 0,
+  "fewshot0|DC": 0,
+  "fewshot0|Other": 0
+ },
+ "tool_sha256": "b541f68dc286497e8347d487af58ff3550a383d126eeabe347c0726e4fb28799",
+ "score_ft_sha256": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+ "seconds": 1.2
+}

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw0_full/contrast.csv

@@ -0,0 +1,17 @@
+genes,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast
+zero_filled,T cell,mean_cp10k,2863,0.4450342443049589,0.4659672798536223,0.009908301396054291,0.9491531243203285
+zero_filled,T cell,pseudobulk_log1p_cpm,2863,0.49915806198996104,0.5669062142141347,-0.06685080073642811,0.9188320105149228
+zero_filled,B cell,mean_cp10k,3005,0.21048028869219484,0.3989038406365887,0.02246521083521104,0.4824105859530561
+zero_filled,B cell,pseudobulk_log1p_cpm,3005,0.1725309302058749,0.4804240789506083,0.011778294050314587,0.33889270468287586
+zero_filled,Monocyte,mean_cp10k,3028,0.451718818929678,0.6141260231172326,0.09191276389983874,0.6453165995326846
+zero_filled,Monocyte,pseudobulk_log1p_cpm,3028,0.2665806253575015,0.6247044807439144,0.0011560926381755227,0.42542298237481724
+zero_filled,NK cell,mean_cp10k,2910,0.1729799258525644,0.40486451543783863,0.0434208477812698,0.3348500751705107
+zero_filled,NK cell,pseudobulk_log1p_cpm,2910,0.11356617042819667,0.47190028654240307,0.00392105973189747,0.23353397894298705
+covered,T cell,mean_cp10k,2787,0.4490005840494196,0.4653295771207368,0.01461751590006361,0.956826996425422
+covered,T cell,pseudobulk_log1p_cpm,2787,0.5044845274872,0.5676373657246707,-0.07196771465810874,0.9277094415540562
+covered,B cell,mean_cp10k,2928,0.2117350832569316,0.3994621586880924,0.02197104094417252,0.48598259936429156
+covered,B cell,pseudobulk_log1p_cpm,2928,0.1748687400646824,0.48266271341558614,0.01132480580495454,0.3429974632238547
+covered,Monocyte,mean_cp10k,2964,0.4533068817467863,0.614250373738069,0.09055049594047745,0.649536288189083
+covered,Monocyte,pseudobulk_log1p_cpm,2964,0.26852733496616726,0.6242546538181976,0.001440174454213203,0.42852829148500776
+covered,NK cell,mean_cp10k,2841,0.17437782389694467,0.4025106919183804,0.04503470389429981,0.33678791527345736
+covered,NK cell,pseudobulk_log1p_cpm,2841,0.11609952946854808,0.47148335302906846,0.006045727916726192,0.23525239442982984