Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/fewshot4/out_fractions/.run.log

@@ -0,0 +1,126 @@
+>Running CIBERSORTxFractions...
+>[Options] username: [REDACTED]
+>[Options] token: [REDACTED]
+>[Options] single_cell: TRUE
+>[Options] refsample: refsample.txt
+>[Options] mixture: mixture.txt
+>[Options] rmbatchSmode: TRUE
+>[Options] fraction: 0
+>[Options] replicates: 5
+>[Options] sampling: 0.5
+>[Options] G.min: 300
+>[Options] G.max: 500
+>[Options] q.value: 0.01
+>[Options] perm: 0
+>[Options] QN: FALSE
+>[Options] verbose: TRUE
+>Making reference sample file.
+>Making phenotype class file.
+>==========Signature Matrix Settings============
+>Pure samples file: /src/outdir//CIBERSORTx_refsample_inferred_refsample.txt
+>Phenotype classes file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.txt
+>Minimum number of DEGs to consider from each phenotype for signature matrix set to: 300
+>Maximum number of DEGs to consider from each phenotype for signature matrix set to: 500
+>Q-value for signature matrix construction set to: 0.01
+>Quantile normalization of input samples is disabled
+>===============================================
+>C++14
+>Loaded 30 columns and 19864 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>50778 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 15.5855068095546
+>Best kappa: 15.5855068095546 
+>SVD UpperRightDiag: 65780.3
+>SVD LowerRightDiag: 4220.6
+>=============CIBERSORTx Settings===============
+>Mixture file: /src/data/mixture.txt
+>Signature matrix file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.CIBERSORTx_refsample_inferred_refsample.bm.K999.txt
+>Enable verbose output
+>Do S-mode batch correction
+>==================CIBERSORTx===================
+>Adjusting mixtures with S-mode batch correction.
+>Running CIBERSORTx on unadjusted mixtures with S-mode adjusted signature matrix.
+>=============CIBERSORTx Settings===============
+>Mixture file: /src/data/mixture.txt
+>Signature matrix file: /src/outdir//CIBERSORTx_sigmatrix_Adjusted.txt
+>Enable verbose output
+>==================CIBERSORTx===================
+column B cell DC Monocyte NK cell Other T cell P-value Correlation RMSE %Completed
+1 0.0582662 0.166702 0.642664 0.00661117 0.0823318 0.0434248 9999 1.2987
+2 0.302508 0.0733307 0.1654 0.0294465 0.278064 0.151252 9999 2.5974
+3 0 0.124268 0.0132825 0.342868 0.0191645 0.500416 9999 3.8961
+4 0.0496025 0.24656 0.171967 0.0483529 0.0913121 0.392205 9999 5.19481
+5 0.599231 0 0 0 0 0.400769 9999 6.49351
+6 0.244084 0 0.129801 0 0.366744 0.25937 9999 7.79221
+7 0.00159031 0.0964812 0.0538411 0 0.0578444 0.790243 9999 9.09091
+8 0.0503381 0.0932943 0.0977678 0 0.376403 0.382197 9999 10.3896
+9 0.0598338 0.125579 0.38705 0.0996633 0.0645161 0.263357 9999 11.6883
+10 0.0649834 0.137704 0.413046 0.134956 0.12893 0.12038 9999 12.987
+11 0.0158628 0.142689 0.486219 0.0709509 0.10765 0.176628 9999 14.2857
+12 0.0574784 0.0678412 0.485018 0.0854547 0.147169 0.157039 9999 15.5844
+13 0.0220006 0.121441 0.184326 0.258849 0.0774895 0.335895 9999 16.8831
+14 0.231041 0 0.0252108 0 0.0141318 0.729616 9999 18.1818
+15 0.238911 0.164838 0.280968 0.11193 0.0848634 0.11849 9999 19.4805
+16 0.100405 0.166632 0.149603 0.345461 0.0673462 0.170552 9999 20.7792
+17 0 0.153616 0.252146 0.0886655 0.131723 0.373849 9999 22.0779
+18 0.126256 0.119006 0.360909 0.211521 0.0794065 0.102901 9999 23.3766
+19 0.152949 0.060468 0.42281 0.0520989 0.0476423 0.264031 9999 24.6753
+20 0 0.133591 0.525052 0.0299526 0.311404 0 9999 25.974
+21 0 0.130247 0.464484 0.139308 0.134754 0.131207 9999 27.2727
+22 0.0621891 0.329744 0.063453 0.110621 0.0161493 0.417843 9999 28.5714
+23 0.0921302 0.138436 0.0213269 0.261884 0.00446007 0.481763 9999 29.8701
+24 0 0.335676 0.0610145 0.366257 0.010068 0.226985 9999 31.1688
+25 0.028714 0.221914 0.0609431 0.23808 0 0.450349 9999 32.4675
+26 0.0192485 0.18913 0.0630379 0.287831 0.0305106 0.410242 9999 33.7662
+27 0.0530537 0.174542 0.0258502 0.278067 0.0239746 0.444512 9999 35.0649
+28 0 0.178929 0 0.532519 0.00886414 0.279688 9999 36.3636
+29 0.077115 0.105294 0.0602585 0.147947 0.117496 0.491888 9999 37.6623
+30 0.0316092 0.265364 0.0782195 0.2033 0.011163 0.410344 9999 38.961
+31 0.145287 0.0526288 0.434404 0.141461 0.0735101 0.152709 9999 40.2597
+32 0.0313192 0.293734 0.280135 0.0085009 0.124891 0.26142 9999 41.5584
+33 0 0.283959 0.358868 0.0641568 0.0790432 0.213973 9999 42.8571
+34 0.10996 0.214241 0 0.104519 0.0214815 0.549798 9999 44.1558
+35 0.21016 0.200221 0.0219016 0.0188525 0.0159517 0.532913 9999 45.4545
+36 0.181123 0.132867 0 0.0257733 0 0.660236 9999 46.7532
+37 0.0863218 0.215894 0.0545178 0.0664293 0.0283904 0.548446 9999 48.0519
+38 0.0570863 0.0875069 0.0335836 0.022602 0.0446135 0.754608 9999 49.3506
+39 0.382156 0.147337 0.00995575 0.0203175 0.0280702 0.412163 9999 50.6494
+40 0.0949604 0.118328 0.381268 0 0.0348814 0.370562 9999 51.9481
+41 0.179387 0.172518 0.130903 0 0.0124657 0.504726 9999 53.2468
+42 0.165647 0.0128334 0.134909 0 0.0395115 0.6471 9999 54.5455
+43 0.243591 0.247567 0.222384 0 0.0487347 0.237723 9999 55.8442
+44 0.286497 0 0.277321 0 0.0197982 0.416384 9999 57.1429
+45 0.206651 0.0342885 0 0 0.00764597 0.751415 9999 58.4416
+46 0.0891273 0.0718037 0.297864 0.120319 0.155533 0.265353 9999 59.7403
+47 0.443969 0.020882 0.0672486 0 0.000160816 0.46774 9999 61.039
+48 0.179554 0 0.0873814 0 0 0.733064 9999 62.3377
+49 0 0.000191785 0.0666248 0 0.24167 0.691513 9999 63.6364
+50 0.171748 0 0.223549 0.169438 0.00550055 0.429765 9999 64.9351
+51 0 0.283412 0.338987 0.0515946 0.0700183 0.255987 9999 66.2338
+52 0 0.248494 0.436406 0 0.0166842 0.298415 9999 67.5325
+53 0 0.141495 0.371222 0.3202 0 0.167083 9999 68.8312
+54 0.0843562 0.106667 0.332977 0.00611685 0.0226302 0.447253 9999 70.1299
+55 0.0571767 0.204798 0.320262 0.145171 0.0299208 0.242672 9999 71.4286
+56 0.0941968 0.229276 0.35514 0.109025 0.19414 0.0182225 9999 72.7273
+57 0.0850422 0.188801 0.0551375 0.105706 0.0235864 0.541727 9999 74.026
+58 0.220523 0.0471077 0.357934 0.0659356 0.0202085 0.288291 9999 75.3247
+59 0.0515481 0.17063 0.0607913 0.0485625 0.114808 0.55366 9999 76.6234
+60 0.22575 0.066886 0.0621272 0.106213 0 0.539024 9999 77.9221
+61 0.0187079 0.0399523 0.343442 0.177721 0.0594998 0.360677 9999 79.2208
+62 0.0116106 0.0784218 0.14212 0.171907 0.241029 0.354912 9999 80.5195
+63 0.0763532 0.0185243 0.277712 0.12725 0.11962 0.38054 9999 81.8182
+64 0.0609356 0.184225 0.15973 0.0444274 0.0817144 0.468968 9999 83.1169
+65 0.102388 0.075768 0.35118 0 0.149111 0.321554 9999 84.4156
+66 0 0.30166 0.233574 0.134292 0.156639 0.173836 9999 85.7143
+67 0.194809 0.0070307 0.395823 0.0331227 0.13284 0.236374 9999 87.013
+68 0 0.301494 0.211226 0.0866825 0.00333344 0.397264 9999 88.3117
+69 0.070911 0.0466859 0.116281 0.0449677 0.022422 0.698732 9999 89.6104
+70 0 0.108525 0.0880334 0 0.198224 0.605217 9999 90.9091
+71 0.116991 0.00138185 0.0654282 0 0.306059 0.51014 9999 92.2078
+72 0 0.0331709 0 0.267023 0.0132804 0.686526 9999 93.5065
+73 0.0181794 0.220367 0.310484 0.0610545 0.0843189 0.305596 9999 94.8052
+74 0.156602 0.133796 0.0911782 0.0193956 0.0153484 0.58368 9999 96.1039
+75 0.24431 0.177735 0.186476 0.0816581 0.0165535 0.293268 9999 97.4026
+76 0.00538573 0.128483 0.270283 0.000259945 0.15223 0.443358 9999 98.7013
+77 0.10432 0.153996 0.159908 0 0.394424 0.187353 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold0/arms/scsemi__raw/deg_top50_lists.csv

@@ -0,0 +1 @@
+celltype,source,rank,gene_id

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold0/arms/scsemi__raw/generated_cells.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d3b857048e3812512c8266676ae69ae7167ddf266548e810ef40e27c963e74ad
+size 46781

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold0/arms/scsemi__raw/labels/labels.manifest.json

@@ -0,0 +1,152 @@
+{
+  "dataset_id": "Giroux2022",
+  "split": "generated",
+  "input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold0/arms/scsemi__raw/query.h5ad",
+  "method": "scsemi__raw",
+  "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold0/arms/scsemi__raw/labels/labels.parquet",
+  "training_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/reference/aifi_reference_f01common.h5ad",
+  "target_truth_used_for_fitting": false,
+  "classifier": "aifi_scanvi_rebuild_20260916_frozen_predict[aifi_scanvi_f01common_v1]",
+  "labels": [
+    "T cell",
+    "B cell",
+    "Monocyte",
+    "NK cell",
+    "DC",
+    "Other"
+  ],
+  "l2_labels": [
+    "ASDC",
+    "CD14 monocyte",
+    "CD16 monocyte",
+    "CD56bright NK cell",
+    "CD56dim NK cell",
+    "CD8aa",
+    "DN T cell",
+    "Effector B cell",
+    "Erythrocyte",
+    "ILC",
+    "Intermediate monocyte",
+    "MAIT",
+    "Memory B cell",
+    "Memory CD4 T cell",
+    "Memory CD8 T cell",
+    "Naive B cell",
+    "Naive CD4 T cell",
+    "Naive CD8 T cell",
+    "Plasma cell",
+    "Platelet",
+    "Progenitor cell",
+    "Proliferating NK cell",
+    "Proliferating T cell",
+    "Transitional B cell",
+    "Treg",
+    "cDC1",
+    "cDC2",
+    "gdT",
+    "pDC"
+  ],
+  "n_cells": 6000,
+  "n_genes": 1005,
+  "note": "Evaluation-only annotation with a frozen AIFI scANVI (zero query-training epochs); L1 outside PBMC5 -> Other, never dropped.",
+  "label_source_column": "AIFI_L2 (reference) -> AIFI_L2_TO_L1 -> PBMC5 + Other",
+  "query_train_epochs": 0,
+  "confidence_threshold": 0.0,
+  "subset": false,
+  "evaluator_aligned": true,
+  "gene_space": {
+    "join_key": "ensembl_id",
+    "model_genes": 1005,
+    "query_genes": 1006,
+    "model_genes_missing_from_query_zero_padded": 0,
+    "query_genes_outside_model_dropped": 1,
+    "rule": "query is subset/reordered to the model's gene list; zero-padding of absent model genes is refused unless --allow-missing-genes"
+  },
+  "readout": null,
+  "query_build": {
+    "kind": "generated_npz",
+    "poisson_note": "one draw over the whole NPZ, then the scored donors' rows",
+    "readout": "poisson",
+    "seed": 20260916,
+    "set": "scsemi__raw",
+    "source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/fold0/scsemi__raw.npz",
+    "source_sha256": "2048421545bf1bb1b4efee2e82d79ec904f1c36ff1a424cde6976863266d5a6f"
+  },
+  "model": {
+    "scanvi_model_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_model",
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "model_manifest": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/MODEL_MANIFEST.json",
+    "held_out_summary": {
+      "l2_accuracy": 0.8692869740488788,
+      "l2_macro_f1": 0.8500925599737216,
+      "l1_accuracy": 0.9918367346938776,
+      "l1_macro_f1": 0.9715232379009036,
+      "pbmc5_other_accuracy": 0.9920886873267826,
+      "pbmc5_other_macro_f1": 0.9812088972148597
+    }
+  },
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 2877,
+      "Monocyte": 1960,
+      "NK cell": 827,
+      "B cell": 211,
+      "Other": 73,
+      "DC": 52
+    },
+    "aifi_l1": {
+      "T cell": 2877,
+      "Monocyte": 1960,
+      "NK cell": 827,
+      "B cell": 211,
+      "Platelet": 57,
+      "DC": 52,
+      "Erythrocyte": 10,
+      "ILC": 6
+    },
+    "aifi_l2": {
+      "Intermediate monocyte": 1126,
+      "CD8aa": 871,
+      "Memory CD4 T cell": 850,
+      "CD56dim NK cell": 609,
+      "CD16 monocyte": 531,
+      "Memory CD8 T cell": 333,
+      "MAIT": 312,
+      "CD14 monocyte": 303,
+      "Proliferating NK cell": 199,
+      "gdT": 159,
+      "Proliferating T cell": 145,
+      "Transitional B cell": 100,
+      "Naive CD8 T cell": 95,
+      "DN T cell": 83,
+      "Naive B cell": 75,
+      "Platelet": 57,
+      "cDC2": 32,
+      "Effector B cell": 30,
+      "Naive CD4 T cell": 20,
+      "CD56bright NK cell": 19,
+      "pDC": 18,
+      "Erythrocyte": 10,
+      "Treg": 9,
+      "ILC": 6,
+      "Plasma cell": 6,
+      "cDC1": 2
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.8589728014046947,
+    "mean_l1_mass": 0.9767552018165588,
+    "frac_l2_max_prob_ge_0.5": 0.9425
+  },
+  "timings_s": {
+    "predict": 0.0,
+    "total": 0.2
+  },
+  "versions": {
+    "scvi-tools": "1.4.1",
+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-08T01:55:43.053207+00:00"
+}