Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/scores/imperial_eskd/draw4/contrast.csv

@@ -0,0 +1,27 @@
+arm,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast,n_case_donors_obs,n_control_donors_obs,n_case_donors_gen,n_control_donors_gen,n_cells_obs,n_cells_gen,deg_scored,top50_overlap,top50_jaccard,obs_top_list_size,gen_top_list_size,n_sig_obs,n_sig_gen,top50_overlap_broadcast,top50_jaccard_broadcast,broadcast_top_list_size,n_sig_broadcast
+lora5,T cell,mean_cp10k,3032,0.8059045624765077,0.6232824935145761,0.6830373773657741,0.6219371457769157,104,31,104,31,244943,101603,,,,,,,,,,,
+lora5,T cell,pseudobulk_log1p_cpm,3032,0.6465446680830627,0.6213005296240948,0.42503711636245656,0.6200804115945403,104,31,104,31,244943,101603,,,,,,,,,,,
+lora5,B cell,mean_cp10k,3180,0.7163924713709098,0.6315018114438883,0.555801647558496,0.5771115200863269,104,31,104,31,46230,29368,,,,,,,,,,,
+lora5,B cell,pseudobulk_log1p_cpm,3180,0.4296036374452691,0.49592343727839516,0.2827171287861692,0.4161268120271373,104,31,104,31,46230,29368,,,,,,,,,,,
+lora5,Monocyte,mean_cp10k,2878,0.7373071097010572,0.7121111596726496,0.5073758042263012,0.65925946583927,103,31,104,31,77634,35093,,,,,,,,,,,
+lora5,Monocyte,pseudobulk_log1p_cpm,2878,0.6337093986912523,0.7117946294640722,0.38405503048441375,0.582159574712861,103,31,104,31,77634,35093,,,,,,,,,,,
+lora5,NK cell,mean_cp10k,2963,0.7373692348845863,0.6592751152623284,0.5547085636439567,0.6241843468321499,104,31,104,31,65766,27118,,,,,,,,,,,
+lora5,NK cell,pseudobulk_log1p_cpm,2963,0.4978441929415583,0.5939124968903833,0.2848434236777936,0.5052645958331808,104,31,104,31,65766,27118,,,,,,,,,,,
+lora5,T cell,welch_top50_deg,5927,,,,,104,31,104,31,244943,101603,True,31,0.4492753623188406,50,50,1194,764,15,0.17647058823529413,50,2055
+lora5,B cell,welch_top50_deg,5927,,,,,104,31,104,31,46230,29368,True,21,0.26582278481012656,50,50,310,411,12,0.13636363636363635,50,2055
+lora5,Monocyte,welch_top50_deg,5927,,,,,103,31,104,31,77634,35093,True,26,0.35135135135135137,50,50,305,651,21,0.26582278481012656,50,2055
+lora5,NK cell,welch_top50_deg,5927,,,,,104,31,104,31,65766,27118,True,22,0.28205128205128205,50,50,431,395,14,0.16279069767441862,50,2055
+lora5,DC,welch_top50_deg,5927,,,,,104,31,104,31,12690,4696,True,13,0.14942528735632185,50,50,295,234,14,0.16279069767441862,50,2055
+lora5_k4000,T cell,mean_cp10k,3032,0.8045657833068549,0.6232824935145761,0.6817348645604332,0.6192494505353141,104,31,104,31,244943,99739,,,,,,,,,,,
+lora5_k4000,T cell,pseudobulk_log1p_cpm,3032,0.6411605700592031,0.6213005296240948,0.410861761352564,0.629234894138444,104,31,104,31,244943,99739,,,,,,,,,,,
+lora5_k4000,B cell,mean_cp10k,3180,0.7048747466915234,0.6315018114438883,0.5369045913202616,0.5784425447173432,104,31,104,31,46230,30702,,,,,,,,,,,
+lora5_k4000,B cell,pseudobulk_log1p_cpm,3180,0.4148982663496203,0.49592343727839516,0.2572985305967253,0.42982724934455846,104,31,104,31,46230,30702,,,,,,,,,,,
+lora5_k4000,Monocyte,mean_cp10k,2878,0.7132016461634106,0.7121111596726496,0.4889140740405178,0.6254174562688941,103,31,104,31,77634,35240,,,,,,,,,,,
+lora5_k4000,Monocyte,pseudobulk_log1p_cpm,2878,0.6354673266064814,0.7117946294640722,0.4224028267624155,0.5426579171329636,103,31,104,31,77634,35240,,,,,,,,,,,
+lora5_k4000,NK cell,mean_cp10k,2963,0.7444289366610192,0.6592751152623284,0.5760563176336144,0.607102167665815,104,31,104,31,65766,27868,,,,,,,,,,,
+lora5_k4000,NK cell,pseudobulk_log1p_cpm,2963,0.525291654263538,0.5939124968903833,0.3227999619365533,0.5077455389202454,104,31,104,31,65766,27868,,,,,,,,,,,
+lora5_k4000,T cell,welch_top50_deg,5927,,,,,104,31,104,31,244943,99739,True,32,0.47058823529411764,50,50,1194,731,15,0.17647058823529413,50,2055
+lora5_k4000,B cell,welch_top50_deg,5927,,,,,104,31,104,31,46230,30702,True,15,0.17647058823529413,50,50,310,575,12,0.13636363636363635,50,2055
+lora5_k4000,Monocyte,welch_top50_deg,5927,,,,,103,31,104,31,77634,35240,True,22,0.28205128205128205,50,50,305,781,21,0.26582278481012656,50,2055
+lora5_k4000,NK cell,welch_top50_deg,5927,,,,,104,31,104,31,65766,27868,True,21,0.26582278481012656,50,50,431,372,14,0.16279069767441862,50,2055
+lora5_k4000,DC,welch_top50_deg,5927,,,,,104,31,104,31,12690,4891,True,16,0.19047619047619047,50,50,295,203,14,0.16279069767441862,50,2055

paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/scores/imperial_eskd/draw4/summary.json

@@ -0,0 +1,1292 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "imperial_eskd",
+ "written_utc": "2026-10-06T02:35:41.000823+00:00",
+ "command": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
+  "--dataset",
+  "imperial_eskd",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/scores/imperial_eskd/draw4",
+  "--threads",
+  "6",
+  "--donors",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/fewshot_n5/draw4/test_samples.txt",
+  "--case-groups",
+  "covid_positive",
+  "--control-groups",
+  "covid_negative",
+  "--arm",
+  "lora5=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/ref_k1000/imperial_eskd/draw4/lora__raw.npz",
+  "--arm",
+  "lora5_k4000=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/generated/imperial_eskd/draw4/paired_test_K4000.npz"
+ ],
+ "arms": [
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+ "code_sha256": {
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+ },
+ "seconds": 83.9
+}

paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/scores/ye2026_sepsis/draw0/contrast.csv

@@ -0,0 +1,27 @@
+arm,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast,n_case_donors_obs,n_control_donors_obs,n_case_donors_gen,n_control_donors_gen,n_cells_obs,n_cells_gen,deg_scored,top50_overlap,top50_jaccard,obs_top_list_size,gen_top_list_size,n_sig_obs,n_sig_gen,top50_overlap_broadcast,top50_jaccard_broadcast,broadcast_top_list_size,n_sig_broadcast
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+lora5,DC,welch_top50_deg,5975,,,,,54,20,37,16,3096,435,True,0,0.0,50,0,1229,0,1,0.010101010101010102,50,1101
+lora5_k4000,T cell,mean_cp10k,3259,0.45797329829704647,0.28779071017741836,0.44299688654656333,0.12959344546093954,57,20,57,20,281037,69792,,,,,,,,,,,
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+lora5_k4000,B cell,pseudobulk_log1p_cpm,3304,0.5119371414683642,0.2824129554276003,0.48316575519105204,0.20710354990214794,57,20,57,20,94421,22918,,,,,,,,,,,
+lora5_k4000,Monocyte,mean_cp10k,3285,0.2624613948737378,0.5511838088445075,0.20713741480015213,0.16701664009729666,57,20,54,20,106918,11088,,,,,,,,,,,
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+lora5_k4000,T cell,welch_top50_deg,5975,,,,,57,20,57,20,281037,69792,True,1,0.01282051282051282,50,29,1558,29,4,0.041666666666666664,50,1101
+lora5_k4000,B cell,welch_top50_deg,5975,,,,,57,20,57,20,94421,22918,True,2,0.02040816326530612,50,50,1022,211,3,0.030927835051546393,50,1101
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+lora5_k4000,DC,welch_top50_deg,5975,,,,,54,20,35,15,3096,379,True,0,0.0,50,0,1229,0,1,0.010101010101010102,50,1101