Archive 4 checkpoints (1-4)
Browse files- .gitattributes +1 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/strict_20261012/source_data/fig1_corpus_aggregates.json +81 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/strict_20261012/source_data/fig2_historical_rank_full.csv +5 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/strict_20261012/source_data/fig4_historical_5fold.csv +17 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/supplementary.pdf +3 -0
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/figures/fig04_full_deg_edger_robustness.pdf filter=lfs diff=lfs merge=lfs -text
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/figures/fig04_full_deg_welch_paper.pdf filter=lfs diff=lfs merge=lfs -text
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/main.pdf filter=lfs diff=lfs merge=lfs -text
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/figures/fig04_full_deg_edger_robustness.pdf filter=lfs diff=lfs merge=lfs -text
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/figures/fig04_full_deg_welch_paper.pdf filter=lfs diff=lfs merge=lfs -text
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/main.pdf filter=lfs diff=lfs merge=lfs -text
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/supplementary.pdf filter=lfs diff=lfs merge=lfs -text
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/strict_20261012/source_data/fig1_corpus_aggregates.json
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{
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"schema": "pbisc.figure1.corpus.v1",
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"denominator": "all 41,395,184 corpus cells; proportions are cell shares, not donor shares",
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"sources": [
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{
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{
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/protocol/PROTOCOL.json",
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}
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/strict_20261012/source_data/fig2_historical_rank_full.csv
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design,arm,label,precision,coverage,comp_l1,trainable_parameters,source,source_sha256
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historical_real_bulk_5fold_pooled107,real_full__raw,Full FT,0.8895327102803738,0.6953894080996885,0.1572206245036138,54185184,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,6d168fc230f5afe2d0a7395dad811aea615cae1778200694ce740b7cd0765068
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historical_real_bulk_5fold_pooled107,lora_r4__raw,LoRA r=4,0.9333333333333333,0.7123364485981308,0.18577808236758375,324056,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/lora_rank_20261001/pooled/summary.json,3d8f7f9b20e147bb92978ca0e638bf03c7834a7c3dec3b88683dc11a99254fc4
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historical_real_bulk_5fold_pooled107,real_lora__raw,LoRA r=16,0.9241121495327103,0.7842990654205607,0.16172890350786212,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,6d168fc230f5afe2d0a7395dad811aea615cae1778200694ce740b7cd0765068
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historical_real_bulk_5fold_pooled107,lora_r64__raw,LoRA r=64,0.9044236760124611,0.8158878504672897,0.1609507558094419,5184896,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/lora_rank_20261001/pooled/summary.json,3d8f7f9b20e147bb92978ca0e638bf03c7834a7c3dec3b88683dc11a99254fc4
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/strict_20261012/source_data/fig4_historical_5fold.csv
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cohort,design,arm,source_arm,pb_r_median,comp_l1_mean,logfc_pearson_legacy_mean,partial_r_legacy_mean,deg_welch_legacy_sum,statistical_scope,n_test_samples,reference_sha256,gene_exclusion_sha256,source,source_sha256
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| 2 |
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ye2026_sepsis,historical_5fold_separate,lora,real_lora__raw,0.890814724779387,0.3618246783833512,0.5267612711229187,0.46874787884206276,,historical sample-level estimators; not donor-corrected strict primary,82,bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json,8b3a62e4a2784d93a5986fd3a1d938d4bc660fa482c9fc30d1c7a3bf71610270
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| 3 |
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ye2026_sepsis,historical_5fold_separate,scsemi,scsemi__raw,0.6129241550465101,0.5022299158951089,0.43526410070392063,0.3581975013221415,6,historical sample-level estimators; not donor-corrected strict primary,82,bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_cv_20261002/pooled/summary.json,121b390f69630c025c6155caf68b013fa34ebe1f4563cc78e3cc4df3488ce819
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| 4 |
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ye2026_sepsis,historical_5fold_separate,raw,zs__raw,0.8780210921882927,0.5108261993151957,-0.011802666469938336,-0.09476408639430833,,historical sample-level estimators; not donor-corrected strict primary,82,bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json,8b3a62e4a2784d93a5986fd3a1d938d4bc660fa482c9fc30d1c7a3bf71610270
|
| 5 |
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ye2026_sepsis,historical_5fold_separate,legacy_cal,zs__cal,0.8611254347365214,0.40065324062398555,0.12267970089558222,0.03938214909552812,,historical sample-level estimators; not donor-corrected strict primary,82,bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json,8b3a62e4a2784d93a5986fd3a1d938d4bc660fa482c9fc30d1c7a3bf71610270
|
| 6 |
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imperial_eskd,historical_5fold_separate,lora,real_lora__raw,0.8801149509776351,0.37638560875745664,0.8187448084273437,0.6899314750539278,143,historical sample-level estimators; not donor-corrected strict primary,157,34b4caa3f8a60b46d5faf58f09cdaa5622bcce19e4c45d9902a711fead96375e,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/pooled/summary.json,b302d03ecf5631785a2d59766f79163d390f89cc94214a1b5f5782fe33ed4848
|
| 7 |
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imperial_eskd,historical_5fold_separate,scsemi,scsemi__raw,0.617057169470448,0.5203155086290455,0.7053598964433999,0.538089704477334,87,historical sample-level estimators; not donor-corrected strict primary,157,34b4caa3f8a60b46d5faf58f09cdaa5622bcce19e4c45d9902a711fead96375e,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/pooled/summary.json,01fc078b3d9257248034654b1853456b0fc2b4d43ccbcd6f08eeb40a9e7d664b
|
| 8 |
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imperial_eskd,historical_5fold_separate,raw,zs__raw,0.8833799591322163,0.8077907232980434,0.6439837621001347,0.43172144888499,106,historical sample-level estimators; not donor-corrected strict primary,157,34b4caa3f8a60b46d5faf58f09cdaa5622bcce19e4c45d9902a711fead96375e,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/pooled/summary.json,b302d03ecf5631785a2d59766f79163d390f89cc94214a1b5f5782fe33ed4848
|
| 9 |
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imperial_eskd,historical_5fold_separate,legacy_cal,zs__cal,0.8669239796274295,0.4943429956255003,0.6787028713891314,0.41180392471305144,111,historical sample-level estimators; not donor-corrected strict primary,157,34b4caa3f8a60b46d5faf58f09cdaa5622bcce19e4c45d9902a711fead96375e,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/pooled/summary.json,b302d03ecf5631785a2d59766f79163d390f89cc94214a1b5f5782fe33ed4848
|
| 10 |
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giroux2022,historical_5fold_separate,lora,real_lora__raw,0.8654960479659805,0.2580442754044374,0.46094848304079133,0.3230347269696575,5,historical sample-level estimators; not donor-corrected strict primary,24,dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593,e3a0f3f225d94d7c193d94ea020b1ab097fa657c0601fce4301b9a09a9c243de,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json,5deaaf60370f4868e02859ed4bc06dfab29227ed25397e153efe74ae62e7f709
|
| 11 |
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giroux2022,historical_5fold_separate,scsemi,scsemi__raw,0.6255991076366978,0.24307690277174857,0.5372927269740906,0.38821939203903755,0,historical sample-level estimators; not donor-corrected strict primary,24,dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593,e3a0f3f225d94d7c193d94ea020b1ab097fa657c0601fce4301b9a09a9c243de,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/scsemi_cv_20261002/pooled/summary.json,a9aceb5ba082c625923496f45bd317d91b45cf7b888a1c262b979cbb60f58595
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| 12 |
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giroux2022,historical_5fold_separate,raw,zs__raw,0.8892820136254734,0.32538517903623476,0.33402890838128363,0.19038234933406017,1,historical sample-level estimators; not donor-corrected strict primary,24,dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593,e3a0f3f225d94d7c193d94ea020b1ab097fa657c0601fce4301b9a09a9c243de,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json,5deaaf60370f4868e02859ed4bc06dfab29227ed25397e153efe74ae62e7f709
|
| 13 |
+
giroux2022,historical_5fold_separate,legacy_cal,zs__cal,0.865104686301811,0.2663183045196587,0.26862025176520443,0.13339193412452294,0,historical sample-level estimators; not donor-corrected strict primary,24,dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593,e3a0f3f225d94d7c193d94ea020b1ab097fa657c0601fce4301b9a09a9c243de,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json,5deaaf60370f4868e02859ed4bc06dfab29227ed25397e153efe74ae62e7f709
|
| 14 |
+
ji2025_chili,historical_5fold_separate,lora,real_lora__raw,0.8728442542892082,0.5044992874562503,0.47928798340225065,0.45204372964017614,15,historical sample-level estimators; not donor-corrected strict primary,33,19c30f56db699eb4f5a642927c1cd6e173212b877c29ff20d84e60a5ecccef6d,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled/summary.json,c5affd46bccadfd4ca31a8a75f8b0047e691ca8f1ca3f56a04db53df53e743d9
|
| 15 |
+
ji2025_chili,historical_5fold_separate,scsemi,scsemi__raw,0.5735524798532866,0.575388570715078,0.2730887293849816,0.22877233904234578,0,historical sample-level estimators; not donor-corrected strict primary,33,19c30f56db699eb4f5a642927c1cd6e173212b877c29ff20d84e60a5ecccef6d,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/scsemi_cv_20261002/pooled/summary.json,4fea2c1a53a4b5324fbd0b2a9ba541ed8eb3fb4d83fe6fa7c0e21dc241132071
|
| 16 |
+
ji2025_chili,historical_5fold_separate,raw,zs__raw,0.8339363944349169,0.7378376387839275,0.08352233208682591,0.03286103285000008,0,historical sample-level estimators; not donor-corrected strict primary,33,19c30f56db699eb4f5a642927c1cd6e173212b877c29ff20d84e60a5ecccef6d,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled/summary.json,c5affd46bccadfd4ca31a8a75f8b0047e691ca8f1ca3f56a04db53df53e743d9
|
| 17 |
+
ji2025_chili,historical_5fold_separate,legacy_cal,zs__cal,0.8385862483484186,0.5005691181619872,0.14191696206220386,0.11277544159311834,0,historical sample-level estimators; not donor-corrected strict primary,33,19c30f56db699eb4f5a642927c1cd6e173212b877c29ff20d84e60a5ecccef6d,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled/summary.json,c5affd46bccadfd4ca31a8a75f8b0047e691ca8f1ca3f56a04db53df53e743d9
|
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/supplementary.pdf
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version https://git-lfs.github.com/spec/v1
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oid sha256:dfe7a9a9c5e5791c38cbd01b0fe874eac0f2580ae816f11ef22176c75fa3546e
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size 1524696
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