Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/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/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/source_data/fig2_historical_rank_full_provenance.json +186 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/source_data/fig2_strict_curve.csv +6 -0
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/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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"condition_handling_overlap": "healthy and in vitro are overlapping attributes",
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"aggregates": {
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"assay": {
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"10x": 30967465,
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"Parse": 9697974,
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"ScaleBio + Seq-Well": 729745
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"condition": {
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"Healthy": 36639276,
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"Autoimmune": 2927959,
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"Infection": 1396029,
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"Other": 431920
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},
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"cell_type": {
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"T cell": 24772208,
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"Monocyte": 7373579,
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"B cell": 3744614,
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"NK cell": 3369999,
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"Other / unlabeled": 2134784
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}
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},
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"totals": {
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"cells": 41395184,
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"datasets": 22,
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"samples": 6507,
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"donors": 3199,
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"split_cells": {
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"test": 3892772,
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"train": 33141380,
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"val": 4361032
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},
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"family_cells": {
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"Autoimmune": 2927959,
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"Drug reaction": 25272,
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"Healthy": 36639276,
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"Hematologic": 406648,
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"Infection": 1396029
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},
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"handling_cells": {
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"ex vivo": 31621421,
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"in vitro": 9773763
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}
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},
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"sources": [
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{
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"path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_summary.json",
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"sha256": "cbccff88a6872bc67dd80c0dfde7d4741733274194f5fd10e002fe0a633a6fa3"
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{
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"path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_assay_condition.csv",
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"sha256": "d3adc5349083175d0a9e0f196cdf03b2eb28001b345e6e5b8f8b7149c90586a6"
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{
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"path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_celltypes.csv",
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"sha256": "5b29e8373ad2597f02a2a7535405106f1a2ed0c9a966d828e89d43c1c59e89d1"
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{
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"path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/corpus_datasets.csv",
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"sha256": "f4314d4e43d0ee3fa2d8c6fcabb616a7fb5cc3e06dd6dbe38a00e389190d0cea"
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},
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| 64 |
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{
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"path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/source_data/corpus/README.md",
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"sha256": "ae5ec49b2c2d2c16d065a95165142ba7809a6cb70ed399a884d094bb8f81154a"
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},
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{
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"path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/sections/methods_model.tex",
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"sha256": "059a3e627d5fce2333a4e84af7b6b2ecd918bc88711b4d3efd52ef87a5e112a8"
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},
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{
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"path": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/sections/methods_paired.tex",
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"sha256": "d3414e46865e9d5b2b5ac7b19179801808e105b0f91a1c06c445d0cc98249396"
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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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| 78 |
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"sha256": "0ec308ab9867d4421c57db54611b67576f73f66fab6744c40288c74897c15a74"
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}
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]
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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/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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| 5 |
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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/source_data/fig2_historical_rank_full_provenance.json
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| 1 |
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{
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| 2 |
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"schema": "pbisc.fig2.rank-realbulk.v1",
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| 3 |
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"selection": "quality-size balance; not best on every metric",
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| 4 |
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"arms": [
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{
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"arm": "real_full__raw",
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| 7 |
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"folds": [
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| 8 |
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{
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| 9 |
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"fold": 0,
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| 10 |
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"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold0/real_full/RUN.json",
|
| 11 |
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"sha256": "3a24013d5cccb3f5e27b6eaeccb352b2037c7bd816d45121cf65452bef8741c3",
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| 12 |
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"train_samples": 78,
|
| 13 |
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"validation_samples": 7,
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"test_samples": 22
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},
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{
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"fold": 1,
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"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold1/real_full/RUN.json",
|
| 19 |
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"sha256": "9b785b5b007c98a529b794939c9d76a1b3314370049a57a82a2d54f5e2257417",
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| 20 |
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"train_samples": 78,
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| 21 |
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"validation_samples": 7,
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"test_samples": 22
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},
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{
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"fold": 2,
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| 26 |
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"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold2/real_full/RUN.json",
|
| 27 |
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"sha256": "cbe286d62b9f88ce6e2ed948ccfb79c66a0f470a0e9665a09b96f8b3dcba9882",
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| 29 |
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"validation_samples": 7,
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"test_samples": 21
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{
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"fold": 3,
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| 34 |
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"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold3/real_full/RUN.json",
|
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"sha256": "9b97af2eb93f06bb0bc1e196dce4a5bf1c8f1183b83b9aface44ed066b2b4a55",
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"test_samples": 21
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},
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{
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"fold": 4,
|
| 42 |
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"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/real_full/RUN.json",
|
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"sha256": "cc6b00dfb5eb58c12d0fe59d53a48931aa041fc01292ca5519d904edeebf7ece",
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| 46 |
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"test_samples": 21
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| 47 |
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}
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| 48 |
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]
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| 49 |
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},
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| 50 |
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{
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| 51 |
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"arm": "lora_r4__raw",
|
| 52 |
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"folds": [
|
| 53 |
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{
|
| 54 |
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"fold": 0,
|
| 55 |
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"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold0/lora_r4/RUN.json",
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| 56 |
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"sha256": "48d4d0504750e0a3c2ee755834e5a438340088e28f55455a4bec32d86d2a09f3",
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| 57 |
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"train_samples": 78,
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| 58 |
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"validation_samples": 7,
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| 59 |
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"test_samples": 22
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| 60 |
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},
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| 61 |
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{
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| 62 |
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"fold": 1,
|
| 63 |
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"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold1/lora_r4/RUN.json",
|
| 64 |
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"sha256": "0e6a1225f5216be5bed567a5fb62d2537b7b8def82f5b35ff5b853e547e6823d",
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| 65 |
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"train_samples": 78,
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| 66 |
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"validation_samples": 7,
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| 67 |
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"test_samples": 22
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},
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| 69 |
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{
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| 70 |
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"fold": 2,
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| 71 |
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"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold2/lora_r4/RUN.json",
|
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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/source_data/fig2_strict_curve.csv
ADDED
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| 1 |
+
design,fold,n_pairs,target_pairs_used,arm,precision,coverage,comp_l1,support_sha256,summary,summary_sha256
|
| 2 |
+
strict_exact_n,fold0,5,5,lora,0.9945454545454545,0.9075757575757576,0.18047144313256866,85c04462a9c768c205fc0adfcb0a40e5f94f504a93d6d822944387bc055b65d4,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/immicro/healthy/fold0/n5/score/summary.json,277150474c9950ea7af327e2a7dec0cf76788078245145555e2640b02c8b3d46
|
| 3 |
+
strict_exact_n,fold0,5,5,pairedcal,0.9887878787878788,0.7245454545454545,0.22241275521199746,85c04462a9c768c205fc0adfcb0a40e5f94f504a93d6d822944387bc055b65d4,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/immicro/healthy/fold0/n5/score/summary.json,277150474c9950ea7af327e2a7dec0cf76788078245145555e2640b02c8b3d46
|
| 4 |
+
strict_exact_n,fold0,5,5,scsemi,0.7363636363636363,0.08666666666666667,0.2568256469172848,85c04462a9c768c205fc0adfcb0a40e5f94f504a93d6d822944387bc055b65d4,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/immicro/healthy/fold0/n5/score/summary.json,277150474c9950ea7af327e2a7dec0cf76788078245145555e2640b02c8b3d46
|
| 5 |
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strict_exact_n,fold0,5,0,raw,0.9103030303030303,0.403030303030303,0.47238641254571206,85c04462a9c768c205fc0adfcb0a40e5f94f504a93d6d822944387bc055b65d4,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/immicro/healthy/fold0/n5/score/summary.json,277150474c9950ea7af327e2a7dec0cf76788078245145555e2640b02c8b3d46
|
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strict_exact_n,fold0,5,0,refcal,0.8821212121212121,0.16303030303030303,0.15475386729011903,85c04462a9c768c205fc0adfcb0a40e5f94f504a93d6d822944387bc055b65d4,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/immicro/healthy/fold0/n5/score/summary.json,277150474c9950ea7af327e2a7dec0cf76788078245145555e2640b02c8b3d46
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