Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261004T141237Z-c1q-crossdisease/diffusion/dataset/server_1/model8/plans/c1q_crossdisease_20261004/out/group_means.csv

@@ -0,0 +1,15 @@
+arm,group,obs_mono_pct,gen_mono_pct,obsthin_c1q_ge1_pct,gen_c1q_ge1_pct,obsthin_c1q_ge2_pct,gen_c1q_ge2_pct
+dress_zs_s13,DRESS|bacterial_stim,10.824742268041238,10.52,84.12698412698413,30.038022813688215,80.15873015873017,5.513307984790875
+dress_zs_s13,DRESS|none,18.282402528977872,14.1,6.772334293948126,9.645390070921986,3.7463976945244957,2.127659574468085
+dress_zs_s13,DRESS|tofacitinib,5.520833333333333,5.46,55.9748427672956,18.315018315018314,42.138364779874216,3.296703296703297
+dress_zs_s13,healthy|none,22.694457382394038,22.96,4.976911236531555,6.620209059233449,1.6931759876859929,0.9581881533101044
+dress_zs_s13,unspecified|bacterial_stim,15.267947421638018,16.22,73.17880794701986,26.880394574599258,59.60264900662252,4.562268803945746
+dress_zs_s13,unspecified|control,5.328200972447326,4.02,55.13307984790875,17.412935323383085,33.840304182509506,3.482587064676617
+dress_zs_s13,unspecified|none,4.5330088226346215,2.58,8.389261744966444,3.875968992248062,3.691275167785235,1.550387596899225
+kawasaki_zs_s13,HC,6.853252295779886,5.32,12.494060744131284,3.2688858489132087,4.110992674337189,0.12919896640826875
+kawasaki_zs_s13,KD_after,8.866570526298453,8.93,7.1633632959541425,5.5450313626179195,3.98611245741157,0.8372597070796718
+kawasaki_zs_s13,KD_before,17.266907147716243,14.833333333333334,11.663083224491515,4.8482422452800265,7.034004119249997,0.47869559232578557
+sle_zs_s13,aHD,17.26807285044304,11.1,4.854622534651557,5.82295499386,1.8359606080597195,0.7264368510629727
+sle_zs_s13,aSLE,27.57720379771101,16.142857142857142,9.933118234605274,5.836752600065445,3.3398652985605772,0.6235967083522613
+sle_zs_s13,cHD,10.480836742711288,5.548484848484848,6.33215108407067,4.562420495814535,1.6747320162197576,0.4268703567150181
+sle_zs_s13,cSLE,23.447362362333802,15.097979797979798,6.623481914197014,5.262227566957699,2.2648228091336655,0.5407014552349638

paper-releases/pbisc-diffusion/updates/20261004T141237Z-c1q-crossdisease/diffusion/dataset/server_1/model8/plans/c1q_crossdisease_20261004/out/per_sample.csv

@@ -0,0 +1,79 @@
+arm,dataset,sample_id,obs_cells,obs_monocytes,obs_mono_pct,obs_c1q_ge1_pct,obs_c1q_ge2_pct,obs_n_ge2,obs_c1q_umi_mean,obsthin_cells,obsthin_monocytes,obsthin_mono_pct,obsthin_c1q_ge1_pct,obsthin_c1q_ge2_pct,obsthin_n_ge2,obsthin_c1q_umi_mean,gen_cells,gen_monocytes,gen_mono_pct,gen_c1q_ge1_pct,gen_c1q_ge2_pct,gen_n_ge2,gen_c1q_umi_mean,group
+dress_zs_s13,dress,PBMC_DRESS1,7592,1388,18.282402528977872,7.564841498559077,4.034582132564841,56,2.042507204610951,7592,1388,18.282402528977872,6.772334293948126,3.7463976945244957,52,1.255763688760807,5000,705,14.1,9.645390070921986,2.127659574468085,15,0.15602836879432624,DRESS|none
+dress_zs_s13,dress,PBMC_HV,8588,1949,22.694457382394038,5.951770138532581,1.8984094407388403,37,0.4422780913288866,8588,1949,22.694457382394038,4.976911236531555,1.6931759876859929,33,0.2606464853771165,5000,1148,22.96,6.620209059233449,0.9581881533101044,11,0.10714285714285714,healthy|none
+dress_zs_s13,dress,PBMC_T4_CTRL,4936,263,5.328200972447326,62.737642585551335,41.44486692015209,109,4.798479087452471,4936,263,5.328200972447326,55.13307984790875,33.840304182509506,89,2.893536121673004,5000,201,4.02,17.412935323383085,3.482587064676617,7,0.21890547263681592,unspecified|control
+dress_zs_s13,dress,PBMC_T4_BACT,1978,302,15.267947421638018,75.16556291390728,64.90066225165563,196,24.55960264900662,1978,302,15.267947421638018,73.17880794701986,59.60264900662252,180,14.956953642384105,5000,811,16.22,26.880394574599258,4.562268803945746,37,0.36128236744759556,unspecified|bacterial_stim
+dress_zs_s13,dress,DRESS_Day4_BACT,1164,126,10.824742268041238,84.92063492063492,81.74603174603175,103,88.65079365079364,1164,126,10.824742268041238,84.12698412698413,80.15873015873017,101,53.801587301587304,5000,526,10.52,30.038022813688215,5.513307984790875,29,0.4220532319391635,DRESS|bacterial_stim
+dress_zs_s13,dress,DRESS_Day4_TOFA,2880,159,5.520833333333333,58.490566037735846,45.911949685534594,73,18.849056603773583,2880,159,5.520833333333333,55.9748427672956,42.138364779874216,67,11.559748427672956,5000,273,5.46,18.315018315018314,3.296703296703297,9,0.24175824175824176,DRESS|tofacitinib
+dress_zs_s13,dress,PBMC_POST2W,6574,298,4.5330088226346215,9.060402684563758,4.026845637583892,12,0.5234899328859061,6574,298,4.5330088226346215,8.389261744966444,3.691275167785235,11,0.31543624161073824,5000,129,2.58,3.875968992248062,1.550387596899225,2,0.05426356589147287,unspecified|none
+kawasaki_zs_s13,kawasaki,P1_before,5953,518,8.70149504451537,22.00772200772201,14.478764478764477,75,3.088803088803089,5953,518,8.70149504451537,22.00772200772201,14.478764478764477,75,3.088803088803089,5000,255,5.1,6.666666666666667,1.1764705882352942,3,0.11372549019607843,KD_before
+kawasaki_zs_s13,kawasaki,P1_after,7239,2024,27.959662936869734,14.130434782608695,8.053359683794467,163,4.101778656126482,7239,2024,27.959662936869734,14.130434782608695,8.053359683794467,163,4.101778656126482,5000,817,16.34,9.424724602203183,1.346389228886169,11,0.1554467564259486,KD_after
+kawasaki_zs_s13,kawasaki,P2_before,5973,641,10.73162564875272,13.72854914196568,7.644305772230889,49,10.2402496099844,5973,641,10.73162564875272,13.72854914196568,7.644305772230889,49,10.2402496099844,5000,326,6.52,5.214723926380368,0.0,0,0.05828220858895705,KD_before
+kawasaki_zs_s13,kawasaki,P2_after,9872,174,1.7625607779578607,10.919540229885058,6.896551724137931,12,3.942528735632184,9872,174,1.7625607779578607,10.919540229885058,6.896551724137931,12,3.942528735632184,5000,166,3.32,6.626506024096386,0.6024096385542169,1,0.08433734939759036,KD_after
+kawasaki_zs_s13,kawasaki,P3_before,6185,674,10.89733225545675,10.534124629080118,6.379821958456973,43,3.0756676557863503,6185,674,10.89733225545675,10.534124629080118,6.379821958456973,43,3.0756676557863503,5000,302,6.04,4.635761589403973,0.33112582781456956,1,0.06622516556291391,KD_before
+kawasaki_zs_s13,kawasaki,P3_after,7215,236,3.270963270963271,3.8135593220338984,1.694915254237288,4,0.5508474576271186,7215,236,3.270963270963271,3.8135593220338984,1.694915254237288,4,0.5508474576271186,5000,105,2.1,9.523809523809524,1.9047619047619049,2,0.13333333333333333,KD_after
+kawasaki_zs_s13,kawasaki,P4_before,5658,1169,20.661010957935666,12.489307100085544,7.698887938408896,90,5.166809238665526,5658,1169,20.661010957935666,12.489307100085544,7.698887938408896,90,5.166809238665526,5000,687,13.74,4.512372634643377,0.5822416302765648,4,0.0611353711790393,KD_before
+kawasaki_zs_s13,kawasaki,P4_after,10305,246,2.3871906841339157,4.878048780487805,2.8455284552845526,7,0.45934959349593496,10305,246,2.3871906841339157,4.878048780487805,2.8455284552845526,7,0.45934959349593496,5000,236,4.72,2.5423728813559325,0.423728813559322,1,0.038135593220338986,KD_after
+kawasaki_zs_s13,kawasaki,P5_before,8783,1388,15.803256290561311,6.195965417867435,3.45821325648415,48,1.4956772334293948,8783,1388,15.803256290561311,6.195965417867435,3.45821325648415,48,1.4956772334293948,5000,757,15.14,3.302509907529723,0.26420079260237783,2,0.04491413474240423,KD_before
+kawasaki_zs_s13,kawasaki,P5_after,10203,721,7.066549054199745,1.9417475728155338,1.1095700416088765,8,0.18169209431345354,10203,721,7.066549054199745,1.9417475728155338,1.1095700416088765,8,0.18169209431345354,5000,551,11.02,2.540834845735027,0.0,0,0.030852994555353903,KD_after
+kawasaki_zs_s13,kawasaki,P6_before,4165,1533,36.80672268907563,5.0228310502283104,2.5440313111545985,39,1.8734507501630788,4165,1533,36.80672268907563,5.0228310502283104,2.5440313111545985,39,1.8734507501630788,5000,2123,42.46,4.757418747056052,0.5181347150259068,11,0.07018370230805464,KD_before
+kawasaki_zs_s13,kawasaki,P6_after,5608,603,10.752496433666192,7.2968490878938645,3.316749585406302,20,0.6268656716417911,5608,603,10.752496433666192,7.2968490878938645,3.316749585406302,20,0.6268656716417911,5000,804,16.08,2.6119402985074625,0.7462686567164178,6,0.0472636815920398,KD_after
+kawasaki_zs_s13,kawasaki,H1_health,5687,501,8.809565676103393,11.177644710578843,4.191616766467066,21,1.1357285429141717,5687,501,8.809565676103393,11.177644710578843,4.191616766467066,21,1.1357285429141717,5000,340,6.8,4.705882352941177,0.0,0,0.08823529411764706,HC
+kawasaki_zs_s13,kawasaki,H2_health,5076,240,4.7281323877068555,15.833333333333332,5.0,12,1.3666666666666667,5076,240,4.7281323877068555,15.833333333333332,5.0,12,1.3666666666666667,5000,200,4.0,2.0,0.0,0,0.02,HC
+kawasaki_zs_s13,kawasaki,H3_health,5440,382,7.022058823529412,10.471204188481675,3.1413612565445024,12,0.6780104712041884,5440,382,7.022058823529412,10.471204188481675,3.1413612565445024,12,0.6780104712041884,5000,258,5.16,3.10077519379845,0.3875968992248062,1,0.04263565891472868,HC
+sle_zs_s13,sle,cSLE1,4640,1396,30.086206896551722,4.369627507163324,1.002865329512894,14,0.3209169054441261,4640,1396,30.086206896551722,4.226361031518625,1.002865329512894,14,0.3022922636103152,3000,711,23.7,4.219409282700422,0.5625879043600562,4,0.07172995780590717,cSLE
+sle_zs_s13,sle,cSLE2,5192,1322,25.462249614791986,9.606656580937972,3.1013615733736764,41,0.9455370650529501,5192,1322,25.462249614791986,9.304084720121027,3.1013615733736764,41,0.8978819969742814,3000,625,20.833333333333332,3.6799999999999997,0.16,1,0.0432,cSLE
+sle_zs_s13,sle,cSLE3,3893,1438,36.93809401489854,9.666203059805285,2.5730180806675937,37,0.7927677329624478,3893,1438,36.93809401489854,9.388038942976356,2.364394993045897,34,0.7552155771905424,3000,1064,35.46666666666667,6.203007518796992,0.4699248120300752,5,0.09210526315789473,cSLE
+sle_zs_s13,sle,cSLE4,6171,2201,35.666828714957056,7.223989095865516,1.4993184915947297,33,0.38164470695138575,6171,2201,35.666828714957056,7.042253521126761,1.4538845979100408,32,0.36665152203543844,3000,864,28.8,2.430555555555556,0.11574074074074073,1,0.04282407407407408,cSLE
+sle_zs_s13,sle,cSLE5,4213,1240,29.43270828388322,4.112903225806452,0.24193548387096775,3,0.11048387096774194,4213,1240,29.43270828388322,3.951612903225806,0.16129032258064516,2,0.10564516129032259,3000,704,23.466666666666665,2.9829545454545454,0.0,0,0.03835227272727273,cSLE
+sle_zs_s13,sle,cSLE6,5433,2389,43.97202282348611,1.9673503557974048,0.9627459187944746,23,0.16031812473838425,5433,2389,43.97202282348611,1.9673503557974048,0.9627459187944746,23,0.15613227291753873,3000,960,32.0,2.2916666666666665,0.20833333333333334,2,0.03333333333333333,cSLE
+sle_zs_s13,sle,cSLE7,3897,887,22.761098280728767,8.455467869222097,2.705749718151071,24,0.7384441939120632,3897,887,22.761098280728767,8.342728297632469,2.705749718151071,24,0.7034949267192785,3000,445,14.833333333333334,5.842696629213483,0.44943820224719105,2,0.08764044943820225,cSLE
+sle_zs_s13,sle,cSLE8,6245,366,5.860688550840672,19.12568306010929,9.289617486338798,34,4.907103825136612,6245,366,5.860688550840672,18.852459016393443,9.289617486338798,34,4.715846994535519,3000,43,1.4333333333333333,6.976744186046512,0.0,0,0.11627906976744186,cSLE
+sle_zs_s13,sle,cSLE10,13448,4205,31.26859012492564,0.713436385255648,0.1426872770511296,6,0.04328180737217598,13448,4205,31.26859012492564,0.713436385255648,0.1426872770511296,6,0.040903686087990485,3000,559,18.633333333333333,3.041144901610018,0.17889087656529518,1,0.03935599284436494,cSLE
+sle_zs_s13,sle,cSLE11,10155,4452,43.84047267355982,35.87151841868823,13.656783468104223,608,7.215408805031447,10155,4452,43.84047267355982,35.17520215633424,13.387241689128482,596,6.90251572327044,3000,992,33.06666666666667,9.475806451612904,1.310483870967742,13,0.14112903225806453,cSLE
+sle_zs_s13,sle,cSLE9,13561,2691,19.843669345918443,5.2396878483835,1.2263099219620959,33,0.3612040133779264,13561,2691,19.843669345918443,5.202526941657377,1.2263099219620959,33,0.3433667781493868,3000,378,12.6,7.4074074074074066,1.0582010582010581,4,0.13227513227513227,cSLE
+sle_zs_s13,sle,cHD1,13437,2116,15.747562700007443,4.300567107750473,0.8506616257088847,18,0.21880907372400757,13437,2116,15.747562700007443,4.206049149338374,0.8506616257088847,18,0.2112476370510397,3000,354,11.8,2.824858757062147,0.0,0,0.031073446327683617,cHD
+sle_zs_s13,sle,cSLE12,5400,1614,29.88888888888889,1.6728624535315983,0.7434944237918215,12,0.21561338289962825,5400,1614,29.88888888888889,1.6109045848822798,0.7434944237918215,12,0.20755885997521686,3000,455,15.166666666666666,3.5164835164835164,0.21978021978021978,1,0.05274725274725275,cSLE
+sle_zs_s13,sle,cSLE13,5313,1157,21.776773950686994,5.963699222126189,1.5557476231633534,18,0.32497839239412274,5313,1157,21.776773950686994,5.877268798617114,1.5557476231633534,18,0.31287813310285223,3000,419,13.966666666666667,2.386634844868735,0.23866348448687352,1,0.031026252983293555,cSLE
+sle_zs_s13,sle,cSLE14,4458,1850,41.49842978914312,2.810810810810811,1.027027027027027,19,0.4464864864864865,4458,1850,41.49842978914312,2.6486486486486487,1.027027027027027,19,0.4221621621621622,3000,674,22.466666666666665,7.121661721068249,0.741839762611276,5,0.1083086053412463,cSLE
+sle_zs_s13,sle,cSLE15,6427,413,6.426015248171775,1.694915254237288,0.9685230024213075,4,1.2760290556900726,6427,413,6.426015248171775,1.694915254237288,0.9685230024213075,4,1.2203389830508475,3000,61,2.033333333333333,1.639344262295082,0.0,0,0.03278688524590164,cSLE
+sle_zs_s13,sle,cSLE16,5560,468,8.417266187050359,7.905982905982905,4.700854700854701,22,1.0277777777777777,5560,468,8.417266187050359,7.6923076923076925,4.700854700854701,22,0.9850427350427351,3000,63,2.1,3.1746031746031744,1.5873015873015872,1,0.06349206349206349,cSLE
+sle_zs_s13,sle,cSLE17,6135,1371,22.34718826405868,4.011670313639679,1.0940919037199124,15,0.36469730123997085,6135,1371,22.34718826405868,3.8657913931436907,1.0940919037199124,15,0.3486506199854121,3000,411,13.7,5.109489051094891,0.48661800486618007,2,0.0681265206812652,cSLE
+sle_zs_s13,sle,cHD2,8857,570,6.435587670768883,5.964912280701754,1.5789473684210527,9,0.443859649122807,8857,570,6.435587670768883,5.964912280701754,1.5789473684210527,9,0.4245614035087719,3000,119,3.966666666666667,2.5210084033613445,0.0,0,0.03361344537815126,cHD
+sle_zs_s13,sle,cHD3,8999,977,10.856761862429158,1.4329580348004094,0.2047082906857728,2,0.033776867963152504,8999,977,10.856761862429158,1.4329580348004094,0.2047082906857728,2,0.032753326509723645,3000,239,7.966666666666667,2.928870292887029,0.0,0,0.04602510460251046,cHD
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paper-releases/pbisc-diffusion/updates/20261004T141237Z-c1q-crossdisease/diffusion/dataset/server_1/model8/plans/c1q_crossdisease_20261004/out/summary.csv

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paper-releases/pbisc-diffusion/updates/20261004T141237Z-c1q-crossdisease/diffusion/metadata/request.json

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+      "note": "Poisson read-out h5ad moved to server_2 (sha-checked)",
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/c1q_crossdisease_20261004/work/dress_zs_s13_poisson.h5ad",
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+      "note": "Poisson read-out h5ad moved to server_2 (sha-checked)",
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/c1q_crossdisease_20261004/work/sle_zs_s13_poisson.h5ad",
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+  "project_id": "pbisc-diffusion",
+  "summary": "Cross-disease C1Q-high test (plans/c1q_crossdisease_20261004, 2026-10-04): final model zero-shot on each sample's sc pseudobulk (K = 1000) for DRESS GSE132802 (in the pretraining corpus), Kawasaki GSE168732 and SLE GSE135779 (not in the corpus). Generated / observed (depth-matched) rate of monocytes with >= 2 C1Q genes: DRESS 0.24 (uncultured PBMC 0.53, Spearman over samples 0.96), Kawasaki 0.10 (0.17), SLE 0.20 (0.42); disease direction reversed in Kawasaki and adult SLE. Code, README, conditions, labels, tables; NPZs and read-out h5ads on server_2."
+}