Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/healthy_additions.json +594 -0
- paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/legacy_rare/PROVENANCE.json +133 -0
- paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/legacy_rare/fig5_rare_states.csv +449 -0
- paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/legacy_rare/fig5_rare_states_slide_text.json +69 -0
paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/healthy_additions.json
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| 1 |
+
{
|
| 2 |
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"slides": [
|
| 3 |
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{
|
| 4 |
+
"kind": "content",
|
| 5 |
+
"key": "healthy_stored_real_reference_umap",
|
| 6 |
+
"after_original": 19,
|
| 7 |
+
"title": "Input corrections on one real-reference UMAP",
|
| 8 |
+
"section_label": "Control evidence",
|
| 9 |
+
"layout": "full",
|
| 10 |
+
"figures": [
|
| 11 |
+
"figures/expanded_master_20261013/healthy/stored_real_reference_umap.png"
|
| 12 |
+
],
|
| 13 |
+
"keywords": [],
|
| 14 |
+
"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
|
| 15 |
+
"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nReplots only the stored interactive coordinates: 3,000 displayed cells per set. The reference PCA/UMAP was previously fitted to real R1. UMAP overlap is illustrative, not a score. Cell-type colors are preserved; no new labels or embedding were computed. Shared display bounds cover all saved coordinates plus 2.5% padding; the narrower old illustrative extent is not reused.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/interactive/cells_5arm.json",
|
| 16 |
+
"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/interactive/cells_5arm.json",
|
| 17 |
+
"palette": "preserved"
|
| 18 |
+
},
|
| 19 |
+
{
|
| 20 |
+
"kind": "content",
|
| 21 |
+
"key": "healthy_saved_density_difference",
|
| 22 |
+
"after_original": 19,
|
| 23 |
+
"title": "Where generated-cell density differs from real cells",
|
| 24 |
+
"section_label": "Control evidence",
|
| 25 |
+
"layout": "full",
|
| 26 |
+
"figures": [
|
| 27 |
+
"figures/expanded_master_20261013/healthy/saved_density_difference.png"
|
| 28 |
+
],
|
| 29 |
+
"keywords": [],
|
| 30 |
+
"footnote": "Original high-resolution density map; zoom for panel labels. Quantitative colors preserved. Historical native-depth controls.",
|
| 31 |
+
"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nThe original high-resolution PNG is copied byte-for-byte, with no crop, pixel recoloring, density-grid recomputation, or fresh embedding. Its diverging colors encode signed density differences, not PBISC/scSemiProfiler identities. Retained as a full-width working-master reference; zoom may be needed for small panel labels. UMAP-space density is a qualitative localization diagnostic, not a calibrated biological score. \n\nSource files:\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/figures/fig2_density_difference.png",
|
| 32 |
+
"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/figures/fig2_density_difference.png",
|
| 33 |
+
"palette": "preserved"
|
| 34 |
+
},
|
| 35 |
+
{
|
| 36 |
+
"kind": "content",
|
| 37 |
+
"key": "healthy_input_control_composition",
|
| 38 |
+
"after_original": 19,
|
| 39 |
+
"title": "Input calibration changes cell-type composition",
|
| 40 |
+
"section_label": "Control evidence",
|
| 41 |
+
"layout": "full",
|
| 42 |
+
"figures": [
|
| 43 |
+
"figures/expanded_master_20261013/healthy/input_control_composition.png"
|
| 44 |
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| 45 |
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"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
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| 47 |
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"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nSaved fractions from 150 cells/donor; displayed as percent. Color identifies biological cell type, not method. Do not interpret reference calibration's composition agreement as proof of within-type state recovery.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/b_composition_l1.csv",
|
| 48 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/b_composition_l1.csv",
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"title": "Same noise, different input: matched-cell shifts",
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| 56 |
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"layout": "full",
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|
| 60 |
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],
|
| 61 |
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"keywords": [],
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| 62 |
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"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
|
| 63 |
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"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nDisplay subset: first 12 stored pair IDs within each pseudobulk-predicted type, at most 72 pairs/arm, selected deterministically from the previously stored display sample. No embedding or labels recalculated. Lines connect generated samples sharing noise; they are not longitudinal biological transitions. Exact displayed pairs are saved. Shared display bounds cover all saved coordinates plus 2.5% padding.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/interactive/cells_5arm.json",
|
| 64 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/interactive/cells_5arm.json",
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|
| 70 |
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| 71 |
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"title": "Matched noise separates cell state from cell identity",
|
| 72 |
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"section_label": "Control evidence",
|
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"layout": "full",
|
| 74 |
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"figures": [
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| 75 |
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"figures/expanded_master_20261013/healthy/matched_similarity.png"
|
| 76 |
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],
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| 77 |
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"keywords": [],
|
| 78 |
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"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
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| 79 |
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"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nOriginal model-output comparisons over 160,500 paired generated cells. Expression-correlation whiskers show saved 25th–75th percentiles, not confidence intervals. All comparisons are against the pseudobulk-conditioned twin, not observed individual cells.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_matched_cells.csv",
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| 80 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_matched_cells.csv",
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{
|
| 84 |
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"kind": "content",
|
| 85 |
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"key": "healthy_label_transitions",
|
| 86 |
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|
| 87 |
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"title": "Input changes can switch the generated cell label",
|
| 88 |
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"section_label": "Control evidence",
|
| 89 |
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"layout": "full",
|
| 90 |
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"figures": [
|
| 91 |
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"figures/expanded_master_20261013/healthy/label_transitions.png"
|
| 92 |
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],
|
| 93 |
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"keywords": [],
|
| 94 |
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"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
|
| 95 |
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"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nExisting matched-cell transition counts, normalized within each pseudobulk-label row for display. Numbers are percentages. Frozen model labels, not proof of biological transdifferentiation. Greyscale represents a quantitative transition fraction.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_label_transition_pseudo_to_cal_counts.csv\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_label_transition_pseudo_to_raw_counts.csv\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_label_transition_pseudo_to_refcal_counts.csv\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_label_transition_pseudo_to_tpm_counts.csv",
|
| 96 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_label_transition_pseudo_to_cal_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_label_transition_pseudo_to_raw_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_label_transition_pseudo_to_refcal_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_label_transition_pseudo_to_tpm_counts.csv",
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{
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|
| 101 |
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"key": "healthy_nearest_real_by_type",
|
| 102 |
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"after_original": 19,
|
| 103 |
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"title": "Nearest real cells: distance and label agreement",
|
| 104 |
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"section_label": "Control evidence",
|
| 105 |
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"layout": "full",
|
| 106 |
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"figures": [
|
| 107 |
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"figures/expanded_master_20261013/healthy/nearest_real_by_type.png"
|
| 108 |
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],
|
| 109 |
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"keywords": [],
|
| 110 |
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"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
|
| 111 |
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"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nSaved PCA50 nearest-reference-cell metrics from 150 cells/donor. Different cell types have different geometry; distances are not calibrated probabilities or donor-level effect estimates.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/f7_nearest_real_by_type.csv",
|
| 112 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/f7_nearest_real_by_type.csv",
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|
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{
|
| 116 |
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"kind": "content",
|
| 117 |
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"key": "healthy_within_type_centroids",
|
| 118 |
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"after_original": 19,
|
| 119 |
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"title": "Composition agreement does not ensure state agreement",
|
| 120 |
+
"section_label": "Control evidence",
|
| 121 |
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"layout": "full",
|
| 122 |
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"figures": [
|
| 123 |
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"figures/expanded_master_20261013/healthy/within_type_centroids.png"
|
| 124 |
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],
|
| 125 |
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"keywords": [],
|
| 126 |
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"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
|
| 127 |
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"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nCentroids and real within-type RMS normalization are previously computed. No new embedding, centroids or annotation are fitted. Six broad types; small Other/DC groups require caution.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/b_type_centroid_shift_l1.csv",
|
| 128 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/b_type_centroid_shift_l1.csv",
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|
| 131 |
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{
|
| 132 |
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"kind": "content",
|
| 133 |
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"key": "healthy_depth_matched_quality",
|
| 134 |
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"after_original": 24,
|
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"title": "Depth matching changes precision and coverage",
|
| 136 |
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"section_label": "Control evidence",
|
| 137 |
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"layout": "full",
|
| 138 |
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"figures": [
|
| 139 |
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"figures/expanded_master_20261013/healthy/depth_matched_quality.png"
|
| 140 |
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],
|
| 141 |
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"keywords": [],
|
| 142 |
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"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
|
| 143 |
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"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nBoth tables already exist. The matched-depth procedure thins all seven source sets to common detected-gene depth, as documented in the original analysis. Real R2 is a held-out real-real control; neighborhood k=10 only. Display hatching, not a new sensitivity run.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/a_precision_coverage_pca50.csv\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/e_depth_matched_precision_coverage_pca50.csv",
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| 144 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/a_precision_coverage_pca50.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/e_depth_matched_precision_coverage_pca50.csv",
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| 146 |
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| 147 |
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{
|
| 148 |
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"kind": "content",
|
| 149 |
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"key": "healthy_gene_length_input",
|
| 150 |
+
"after_original": 19,
|
| 151 |
+
"title": "Gene-length effects in the bulk input",
|
| 152 |
+
"section_label": "Control evidence",
|
| 153 |
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"layout": "full",
|
| 154 |
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"figures": [
|
| 155 |
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"figures/expanded_master_20261013/healthy/gene_length_input.png"
|
| 156 |
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],
|
| 157 |
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"keywords": [],
|
| 158 |
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"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
|
| 159 |
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"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nOnly log10 axis conversion and plotting of saved per-gene shifts. The displayed Spearman values come directly from g_length_stats.csv; no correlation or regression is recomputed. Y values are input cpm_log1p differences. Gene length accounts for only part of assay mismatch; these are diagnostic associations.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_gene_shift_vs_length.csv\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_length_stats.csv",
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| 160 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_gene_shift_vs_length.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_length_stats.csv",
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{
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| 164 |
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| 165 |
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|
| 166 |
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"after_original": 19,
|
| 167 |
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"title": "Gene-length effects within label-stable cells",
|
| 168 |
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"section_label": "Control evidence",
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| 169 |
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"layout": "full",
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| 170 |
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| 171 |
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],
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| 173 |
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"keywords": [],
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| 174 |
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"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
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| 175 |
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"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nOnly log10 axis conversion and plotting of saved per-gene shifts. The displayed Spearman values come directly from g_length_stats.csv; no correlation or regression is recomputed. Label-stable means the frozen broad label agrees between generated twins; it does not establish identical biological state. Y values are generated log1p CP10K differences.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_gene_shift_vs_length.csv\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_length_stats.csv",
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| 176 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_gene_shift_vs_length.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_length_stats.csv",
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{
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| 180 |
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"kind": "content",
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| 181 |
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"key": "healthy_raw_tpm_top_genes",
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"after_original": 19,
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| 183 |
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"title": "Raw and TPM shifts persist within cell labels",
|
| 184 |
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| 185 |
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"layout": "full",
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| 186 |
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"figures": [
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"figures/expanded_master_20261013/healthy/raw_tpm_top_genes.png"
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| 188 |
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],
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| 189 |
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"keywords": [],
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| 190 |
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"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
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| 191 |
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"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nExisting ranked gene lists only; no DEG testing. Displayed ranks are original saved ranks within direction and label-stable cells. Immediate-early/stress differences may reflect handling or cohort state; that interpretation is untested. Input and output shifts use different normalization and should not be interpreted as an identical quantitative scale.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_top_genes_raw_tpm.csv",
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| 192 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_top_genes_raw_tpm.csv",
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| 194 |
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| 195 |
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{
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| 196 |
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"kind": "content",
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| 197 |
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"key": "healthy_refcal_top_genes",
|
| 198 |
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"after_original": 19,
|
| 199 |
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"title": "Reference calibration leaves specific gene-state shifts",
|
| 200 |
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"section_label": "Control evidence",
|
| 201 |
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"layout": "full",
|
| 202 |
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"figures": [
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| 203 |
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"figures/expanded_master_20261013/healthy/refcal_top_genes.png"
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],
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"keywords": [],
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| 206 |
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"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
|
| 207 |
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"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nExisting ranked gene lists only; no DEG testing. Displayed ranks are original saved ranks within direction and label-stable cells. Immediate-early/stress differences may reflect handling or cohort state; that interpretation is untested. Input and output shifts use different normalization and should not be interpreted as an identical quantitative scale.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_top_genes_refcal.csv",
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| 208 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/g_top_genes_refcal.csv",
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|
| 210 |
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},
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| 211 |
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{
|
| 212 |
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"kind": "content",
|
| 213 |
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"key": "healthy_donor_axes",
|
| 214 |
+
"after_original": 19,
|
| 215 |
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"title": "Donor trait axes and donor identification differ",
|
| 216 |
+
"section_label": "Control evidence",
|
| 217 |
+
"layout": "full",
|
| 218 |
+
"figures": [
|
| 219 |
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"figures/expanded_master_20261013/healthy/donor_axes.png"
|
| 220 |
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],
|
| 221 |
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"keywords": [],
|
| 222 |
+
"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
|
| 223 |
+
"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nAll Spearman and retrieval values are copied from the saved summary. Y-gene/sex calls and IFN/KLRC2 axes are expression-derived proxies, not independent clinical-label validation. Top-1 chance line is 1/107. High trait-axis agreement does not establish donor identity recovery.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/scorer_summary_5arm.csv",
|
| 224 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/scorer_summary_5arm.csv",
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|
| 227 |
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{
|
| 228 |
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"kind": "content",
|
| 229 |
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"key": "healthy_reference_choice",
|
| 230 |
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"after_original": 19,
|
| 231 |
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"title": "Reference choice changes different quality endpoints",
|
| 232 |
+
"section_label": "Control evidence",
|
| 233 |
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"layout": "full",
|
| 234 |
+
"figures": [
|
| 235 |
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"figures/expanded_master_20261013/healthy/reference_choice.png"
|
| 236 |
+
],
|
| 237 |
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"keywords": [],
|
| 238 |
+
"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
|
| 239 |
+
"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nAll eight generated arms are already scored in immicro_table.csv. No generation or rescore. AIDA and the training-mixture reference have their own pretraining overlap; this is not a held-out reference experiment. The composition dashed line is the observed donor-mean leave-one-out null, NOT a real-R2 composition error. No method-independent win claim is made across different endpoints.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md",
|
| 240 |
+
"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md",
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|
| 242 |
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|
| 243 |
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{
|
| 244 |
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"kind": "content",
|
| 245 |
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"key": "healthy_detection_and_library",
|
| 246 |
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"after_original": 24,
|
| 247 |
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"title": "Detection and library size are separate diagnostics",
|
| 248 |
+
"section_label": "Control evidence",
|
| 249 |
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"layout": "full",
|
| 250 |
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"figures": [
|
| 251 |
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"figures/expanded_master_20261013/healthy/detection_and_library.png"
|
| 252 |
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],
|
| 253 |
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"keywords": [],
|
| 254 |
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"footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
|
| 255 |
+
"footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nObserved counts and the previously computed Poisson readout of generated cells. Whiskers are saved 10th–90th cell percentiles, not donor confidence intervals. Scoring-gene libraries are not full-transcriptome UMI totals.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/e_detected_genes.csv",
|
| 256 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/e_detected_genes.csv",
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| 259 |
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{
|
| 260 |
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"kind": "content",
|
| 261 |
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"key": "healthy_sle_conditioning_interventions",
|
| 262 |
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"after_original": 14,
|
| 263 |
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"title": "Does the model follow its bulk conditioning?",
|
| 264 |
+
"section_label": "Control evidence",
|
| 265 |
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"layout": "full",
|
| 266 |
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"figures": [
|
| 267 |
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"figures/expanded_master_20261013/healthy/sle_conditioning_interventions.png"
|
| 268 |
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],
|
| 269 |
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"keywords": [],
|
| 270 |
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"footnote": "Existing SLE pseudobulk controls: same noise, 42 donors, 2,279 genes. This is a conditioning intervention, not real-bulk validation.",
|
| 271 |
+
"footnote_full": "SLE development benchmark: 42 donors, 2,279 genes, f01 6k E16 EMA, 1,500 generated cells/donor, 50 DDIM steps, seed20260913. Only conditioning differs; noise is matched. These are pseudobulk inputs, not an independent paired real-bulk validation. Donor-source caption uses saved uncentered nearest-match counts; centered flip retrieval is 27/42, permutation42/42. Displayed benchmark metrics use the common six-type gate. The pre-registered condition-use criterion and earlier-model tolerance context are in source RESULTS.md.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/conditioning_2279/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/conditioning_2279/paired_cells.csv\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_2279/summary_tidy.csv",
|
| 272 |
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"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/conditioning_2279/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/conditioning_2279/paired_cells.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_2279/summary_tidy.csv",
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|
| 274 |
+
},
|
| 275 |
+
{
|
| 276 |
+
"kind": "content",
|
| 277 |
+
"key": "healthy_sle_disjoint_truth_control",
|
| 278 |
+
"after_original": 43,
|
| 279 |
+
"title": "Disjoint-cell controls test the bulk-broadcast baseline",
|
| 280 |
+
"section_label": "Control evidence",
|
| 281 |
+
"layout": "full",
|
| 282 |
+
"figures": [
|
| 283 |
+
"figures/expanded_master_20261013/healthy/sle_disjoint_truth_control.png"
|
| 284 |
+
],
|
| 285 |
+
"keywords": [],
|
| 286 |
+
"footnote": "SLE pseudobulk benchmark; five existing half-cell splits. Error bars are saved split SDs. No new cell splitting or scoring.",
|
| 287 |
+
"footnote_full": "Existing five random half-A/half-B splits of the same 42 held-out SLE donors. Bulk A is formed from cells disjoint from per-type half-B truth. The full-bulk control includes B. The observed type-specific half-A predictor is a split-half reference. Bars and SDs are saved summary values; no split, expression analysis, or hypothesis test is rerun. PBISC values summarize its five existing sampling seeds.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle_broadcast/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle_broadcast/tables/splithalf_summary.csv",
|
| 288 |
+
"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle_broadcast/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle_broadcast/tables/splithalf_summary.csv",
|
| 289 |
+
"palette": "native"
|
| 290 |
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},
|
| 291 |
+
{
|
| 292 |
+
"kind": "content",
|
| 293 |
+
"key": "healthy_immicro_replicate_controls",
|
| 294 |
+
"after_original": 22,
|
| 295 |
+
"title": "Technical repeats and follow-up are different controls",
|
| 296 |
+
"section_label": "Control evidence",
|
| 297 |
+
"layout": "full",
|
| 298 |
+
"figures": [
|
| 299 |
+
"figures/expanded_master_20261013/healthy/immicro_replicate_controls.png"
|
| 300 |
+
],
|
| 301 |
+
"keywords": [],
|
| 302 |
+
"footnote": "Observed ImMicro controls. Technical remeasurement and follow-up: 16 donors each. Follow-up is not a technical replicate.",
|
| 303 |
+
"footnote_full": "Previously processed ImMicro observations. Technical remeasurement and follow-up have 16 donors; capture-half control has its own recorded sample count. Follow-up is biological longitudinal variation, not a technical replicate. Correlation and top-1 retrieval are saved aggregates; no new subsampling, correlation or retrieval analysis. Use the recorded follow-up gene-support rule in observed_summary.json.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/build_manifest.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/observed_summary.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/replicate_pseudobulk_per_donor.csv",
|
| 304 |
+
"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/build_manifest.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/observed_summary.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/replicate_pseudobulk_per_donor.csv",
|
| 305 |
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"palette": "preserved"
|
| 306 |
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},
|
| 307 |
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{
|
| 308 |
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"kind": "content",
|
| 309 |
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"key": "healthy_annotation_agreement",
|
| 310 |
+
"after_original": 22,
|
| 311 |
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"title": "Annotation agreement and difficult categories",
|
| 312 |
+
"section_label": "Control evidence",
|
| 313 |
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"layout": "full",
|
| 314 |
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"figures": [
|
| 315 |
+
"figures/expanded_master_20261013/healthy/annotation_agreement.png"
|
| 316 |
+
],
|
| 317 |
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"keywords": [],
|
| 318 |
+
"footnote": "Observed cells only. Overall agreement uses the supported six-type gate; author mixed/unlabelled cells are separate. Other is difficult.",
|
| 319 |
+
"footnote_full": "Saved observed-cell comparison, not generated-cell model performance. Overall 97.17% agreement uses 365,404 author-labelled cells in the supported six-type gate; mixed/unlabelled categories are displayed in the matrix but excluded from that agreement figure. Other has weak correspondence between taxonomies. The frozen annotation's comparison to author labels is not an independent gold-standard validation. Heatmap is a count-row normalization for display; precision/recall are saved summary metrics.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/build_manifest.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/confusion_author_vs_frozen_baseline.csv\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/observed_summary.json",
|
| 320 |
+
"sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/build_manifest.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/confusion_author_vs_frozen_baseline.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/observed_summary.json",
|
| 321 |
+
"palette": "preserved"
|
| 322 |
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}
|
| 323 |
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],
|
| 324 |
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"assets": [
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ADDED
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| 132 |
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"original_stdout": "56 state x cohort pairs\n{\n \"5 donors\": {\n \"n\": 56,\n \"frac_closer\": 51,\n \"within2_lora\": 19,\n \"within2_sc\": 5,\n \"not_generated_lora\": 0,\n \"not_generated_sc\": 6,\n \"rho_better\": 43,\n \"rho_median_lora\": 0.2381686657463106,\n \"rho_median_sc\": 0.17609850402537303,\n \"dir_lora\": 0.7321428571428571,\n \"dir_sc\": 0.6071428571428571\n },\n \"5-fold\": {\n \"n\": 56,\n \"frac_closer\": 47,\n \"within2_lora\": 25,\n \"within2_sc\": 9,\n \"not_generated_lora\": 0,\n \"not_generated_sc\": 5,\n \"rho_better\": 38,\n \"rho_median_lora\": 0.31696815102004133,\n \"rho_median_sc\": 0.2431928042007824,\n \"dir_lora\": 0.8035714285714286,\n \"dir_sc\": 0.6785714285714286\n }\n}\nRare states with 5 pairs: how many cells | Within 2-fold: LoRA-5 19/56, scSemiProfiler-5 5/56 | Closer to the observed fraction than scSemiProfiler-5: 51/56 | Rare states kept, not averaged away\nRare states with 5 pairs: in the right donors | Donor ranking: median \u03c1 0.24 vs 0.18 (scSemiProfiler-5) | Better donor ranking than scSemiProfiler-5: 43/56 | Disease direction kept: 73% vs 61% of draws\n5-fold CV: rare states | Within 2-fold: LoRA 25/56, scSemiProfiler 9/56 | Donor ranking: median \u03c1 0.32 vs 0.24 | Better donor ranking: 38/56\n"
|
| 133 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/legacy_rare/fig5_rare_states.csv
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|
| 1 |
+
dataset,state,arm,log2_ratio,spearman,auroc,direction,design
|
| 2 |
+
giroux2022,C1Q-high monocyte (reference),lora5,-2.6404,-0.012152,0.48311,0.6,5 donors (mean of 5 draws)
|
| 3 |
+
giroux2022,C1Q-high monocyte (reference),scsemi5,-3.6501,-0.14423,0.42467,0,5 donors (mean of 5 draws)
|
| 4 |
+
giroux2022,C1Q-high monocyte (reference),zs_cal,-2.563,-0.09803,0.436,0.4,5 donors (mean of 5 draws)
|
| 5 |
+
giroux2022,C1Q-high monocyte (reference),zs_raw,-2.2749,-0.23164,0.39867,0,5 donors (mean of 5 draws)
|
| 6 |
+
giroux2022,Cycling T/NK,lora5,-1.3087,0.43795,0.694,1,5 donors (mean of 5 draws)
|
| 7 |
+
giroux2022,Cycling T/NK,scsemi5,-3.5999,0.33924,0.58278,0.8,5 donors (mean of 5 draws)
|
| 8 |
+
giroux2022,Cycling T/NK,zs_cal,-1.9449,0.27444,0.62644,0.8,5 donors (mean of 5 draws)
|
| 9 |
+
giroux2022,Cycling T/NK,zs_raw,-1.2512,0.38518,0.62867,1,5 donors (mean of 5 draws)
|
| 10 |
+
giroux2022,Cycling activated T (CD38/HLA-DR),lora5,-2.5882,0.38932,0.684,0.8,5 donors (mean of 5 draws)
|
| 11 |
+
giroux2022,Cycling activated T (CD38/HLA-DR),scsemi5,-1.854,0.48112,0.68578,1,5 donors (mean of 5 draws)
|
| 12 |
+
giroux2022,Cycling activated T (CD38/HLA-DR),zs_cal,-3.3551,0.057451,0.44389,1,5 donors (mean of 5 draws)
|
| 13 |
+
giroux2022,Cycling activated T (CD38/HLA-DR),zs_raw,-2.638,0.3025,0.65878,1,5 donors (mean of 5 draws)
|
| 14 |
+
giroux2022,Cycling monocyte (Ye 2026),lora5,-3.2484,0.12073,0.54922,0.6,5 donors (mean of 5 draws)
|
| 15 |
+
giroux2022,Cycling monocyte (Ye 2026),scsemi5,-3.2112,-0.20694,0.43467,0.4,5 donors (mean of 5 draws)
|
| 16 |
+
giroux2022,Cycling monocyte (Ye 2026),zs_cal,-4.5199,0.0029991,0.46089,0.4,5 donors (mean of 5 draws)
|
| 17 |
+
giroux2022,Cycling monocyte (Ye 2026),zs_raw,-5.0497,0.049639,0.51078,0.4,5 donors (mean of 5 draws)
|
| 18 |
+
giroux2022,Cytotoxic CD4 T,lora5,-0.49456,0.4228,0.77222,1,5 donors (mean of 5 draws)
|
| 19 |
+
giroux2022,Cytotoxic CD4 T,scsemi5,3.7826,0.4332,0.77467,1,5 donors (mean of 5 draws)
|
| 20 |
+
giroux2022,Cytotoxic CD4 T,zs_cal,0.93121,0.33488,0.71467,0.6,5 donors (mean of 5 draws)
|
| 21 |
+
giroux2022,Cytotoxic CD4 T,zs_raw,-0.80043,0.25661,0.67978,0.6,5 donors (mean of 5 draws)
|
| 22 |
+
giroux2022,DN2 / ABC B,lora5,-1.9314,-0.0076739,0.46556,1,5 donors (mean of 5 draws)
|
| 23 |
+
giroux2022,DN2 / ABC B,scsemi5,,,0.5,0,5 donors (mean of 5 draws)
|
| 24 |
+
giroux2022,DN2 / ABC B,zs_cal,-1.712,-0.020185,0.44967,0,5 donors (mean of 5 draws)
|
| 25 |
+
giroux2022,DN2 / ABC B,zs_raw,-0.71825,0.31321,0.72667,0.6,5 donors (mean of 5 draws)
|
| 26 |
+
giroux2022,Granulocyte-like (LDG),lora5,-6.0304,0.2767,0.6,0.6,5 donors (mean of 5 draws)
|
| 27 |
+
giroux2022,Granulocyte-like (LDG),scsemi5,,,0.5,0,5 donors (mean of 5 draws)
|
| 28 |
+
giroux2022,Granulocyte-like (LDG),zs_cal,-3.6865,0.42869,0.658,0.6,5 donors (mean of 5 draws)
|
| 29 |
+
giroux2022,Granulocyte-like (LDG),zs_raw,-2.2949,0.61894,0.745,0.8,5 donors (mean of 5 draws)
|
| 30 |
+
giroux2022,HSPC,lora5,-1.6448,0.06297,0.54411,0.6,5 donors (mean of 5 draws)
|
| 31 |
+
giroux2022,HSPC,scsemi5,-3.4927,-0.17408,0.48,0,5 donors (mean of 5 draws)
|
| 32 |
+
giroux2022,HSPC,zs_cal,-1.2527,-0.16205,0.41189,0.4,5 donors (mean of 5 draws)
|
| 33 |
+
giroux2022,HSPC,zs_raw,-0.061678,-0.21312,0.39689,0.8,5 donors (mean of 5 draws)
|
| 34 |
+
giroux2022,ISG-high T,lora5,-0.86852,0.8469,0.92911,1,5 donors (mean of 5 draws)
|
| 35 |
+
giroux2022,ISG-high T,scsemi5,2.6225,0.76724,0.77,1,5 donors (mean of 5 draws)
|
| 36 |
+
giroux2022,ISG-high T,zs_cal,0.1885,0.83427,0.912,1,5 donors (mean of 5 draws)
|
| 37 |
+
giroux2022,ISG-high T,zs_raw,-0.5941,0.73226,0.90089,1,5 donors (mean of 5 draws)
|
| 38 |
+
giroux2022,ISG-high monocyte (positive control),lora5,-0.15917,0.72998,0.85089,1,5 donors (mean of 5 draws)
|
| 39 |
+
giroux2022,ISG-high monocyte (positive control),scsemi5,0.75684,0.65568,0.69333,0.8,5 donors (mean of 5 draws)
|
| 40 |
+
giroux2022,ISG-high monocyte (positive control),zs_cal,0.71977,0.72443,0.82511,1,5 donors (mean of 5 draws)
|
| 41 |
+
giroux2022,ISG-high monocyte (positive control),zs_raw,0.3143,0.80601,0.86511,0.8,5 donors (mean of 5 draws)
|
| 42 |
+
giroux2022,MS1 monocyte (IL1R2+),lora5,-2.2748,0.1478,0.50333,0.8,5 donors (mean of 5 draws)
|
| 43 |
+
giroux2022,MS1 monocyte (IL1R2+),scsemi5,,,0.5,0,5 donors (mean of 5 draws)
|
| 44 |
+
giroux2022,MS1 monocyte (IL1R2+),zs_cal,2.2914,0.039838,0.528,0.8,5 donors (mean of 5 draws)
|
| 45 |
+
giroux2022,MS1 monocyte (IL1R2+),zs_raw,0.31939,0.025603,0.50267,0.6,5 donors (mean of 5 draws)
|
| 46 |
+
giroux2022,Plasmablast (label),lora5,-0.91864,0.4396,0.79211,0.6,5 donors (mean of 5 draws)
|
| 47 |
+
giroux2022,Plasmablast (label),scsemi5,-3.7311,-0.06005,0.50789,1,5 donors (mean of 5 draws)
|
| 48 |
+
giroux2022,Plasmablast (label),zs_cal,-0.9373,0.36945,0.72756,0.4,5 donors (mean of 5 draws)
|
| 49 |
+
giroux2022,Plasmablast (label),zs_raw,-0.93464,-0.14304,0.48678,0.2,5 donors (mean of 5 draws)
|
| 50 |
+
giroux2022,Plasmablast (markers),lora5,-2.6619,0.17186,0.63278,0.4,5 donors (mean of 5 draws)
|
| 51 |
+
giroux2022,Plasmablast (markers),scsemi5,0.43243,0.43393,0.73467,1,5 donors (mean of 5 draws)
|
| 52 |
+
giroux2022,Plasmablast (markers),zs_cal,-2.6116,0.20474,0.64667,0.4,5 donors (mean of 5 draws)
|
| 53 |
+
giroux2022,Plasmablast (markers),zs_raw,-1.9185,0.15029,0.589,0,5 donors (mean of 5 draws)
|
| 54 |
+
giroux2022,Proliferating T (label),lora5,-0.41192,0.61193,0.74933,0.8,5 donors (mean of 5 draws)
|
| 55 |
+
giroux2022,Proliferating T (label),scsemi5,2.5503,0.622,0.74444,1,5 donors (mean of 5 draws)
|
| 56 |
+
giroux2022,Proliferating T (label),zs_cal,-0.055869,0.5581,0.821,1,5 donors (mean of 5 draws)
|
| 57 |
+
giroux2022,Proliferating T (label),zs_raw,-0.36094,0.49669,0.71356,1,5 donors (mean of 5 draws)
|
| 58 |
+
imperial_eskd,C1Q-high monocyte (reference),lora5,-2.5268,0.074885,0.54605,0.8,5 donors (mean of 5 draws)
|
| 59 |
+
imperial_eskd,C1Q-high monocyte (reference),scsemi5,-1.9428,0.17602,0.59084,1,5 donors (mean of 5 draws)
|
| 60 |
+
imperial_eskd,C1Q-high monocyte (reference),zs_cal,-2.5959,0.19024,0.61771,1,5 donors (mean of 5 draws)
|
| 61 |
+
imperial_eskd,C1Q-high monocyte (reference),zs_raw,-4.2642,0.16821,0.57267,0.4,5 donors (mean of 5 draws)
|
| 62 |
+
imperial_eskd,Cycling T/NK,lora5,-1.5941,0.23578,0.61006,1,5 donors (mean of 5 draws)
|
| 63 |
+
imperial_eskd,Cycling T/NK,scsemi5,-5.219,0.075909,0.51448,1,5 donors (mean of 5 draws)
|
| 64 |
+
imperial_eskd,Cycling T/NK,zs_cal,1.6569,0.33661,0.68745,1,5 donors (mean of 5 draws)
|
| 65 |
+
imperial_eskd,Cycling T/NK,zs_raw,1.6474,0.17797,0.57454,1,5 donors (mean of 5 draws)
|
| 66 |
+
imperial_eskd,Cycling activated T (CD38/HLA-DR),lora5,-3.065,0.079376,0.53833,1,5 donors (mean of 5 draws)
|
| 67 |
+
imperial_eskd,Cycling activated T (CD38/HLA-DR),scsemi5,-6.806,-0.065897,0.48248,1,5 donors (mean of 5 draws)
|
| 68 |
+
imperial_eskd,Cycling activated T (CD38/HLA-DR),zs_cal,-0.46332,0.12701,0.55668,1,5 donors (mean of 5 draws)
|
| 69 |
+
imperial_eskd,Cycling activated T (CD38/HLA-DR),zs_raw,-0.642,0.26082,0.62366,1,5 donors (mean of 5 draws)
|
| 70 |
+
imperial_eskd,Cycling monocyte (Ye 2026),lora5,-2.9764,0.12464,0.54596,1,5 donors (mean of 5 draws)
|
| 71 |
+
imperial_eskd,Cycling monocyte (Ye 2026),scsemi5,-6.5059,0.002497,0.50292,0.8,5 donors (mean of 5 draws)
|
| 72 |
+
imperial_eskd,Cycling monocyte (Ye 2026),zs_cal,-2.071,0.29831,0.60257,1,5 donors (mean of 5 draws)
|
| 73 |
+
imperial_eskd,Cycling monocyte (Ye 2026),zs_raw,-3.0721,-0.012999,0.45779,1,5 donors (mean of 5 draws)
|
| 74 |
+
imperial_eskd,Cytotoxic CD4 T,lora5,1.5757,0.19447,0.60248,0.6,5 donors (mean of 5 draws)
|
| 75 |
+
imperial_eskd,Cytotoxic CD4 T,scsemi5,2.0968,0.025512,0.51206,1,5 donors (mean of 5 draws)
|
| 76 |
+
imperial_eskd,Cytotoxic CD4 T,zs_cal,2.1449,0.18284,0.60292,0,5 donors (mean of 5 draws)
|
| 77 |
+
imperial_eskd,Cytotoxic CD4 T,zs_raw,-0.11863,0.11066,0.54365,0,5 donors (mean of 5 draws)
|
| 78 |
+
imperial_eskd,DN2 / ABC B,lora5,-1.242,0.045417,0.52668,0.6,5 donors (mean of 5 draws)
|
| 79 |
+
imperial_eskd,DN2 / ABC B,scsemi5,-5.5876,0.019939,0.4978,1,5 donors (mean of 5 draws)
|
| 80 |
+
imperial_eskd,DN2 / ABC B,zs_cal,-0.98847,0.036512,0.52235,0.2,5 donors (mean of 5 draws)
|
| 81 |
+
imperial_eskd,DN2 / ABC B,zs_raw,0.7528,0.26841,0.69335,1,5 donors (mean of 5 draws)
|
| 82 |
+
imperial_eskd,Granulocyte-like (LDG),lora5,-5.8088,0.12132,0.52185,0.2,5 donors (mean of 5 draws)
|
| 83 |
+
imperial_eskd,Granulocyte-like (LDG),scsemi5,-8.6877,0.076786,0.50712,0.2,5 donors (mean of 5 draws)
|
| 84 |
+
imperial_eskd,Granulocyte-like (LDG),zs_cal,-3.7011,0.16074,0.57652,0,5 donors (mean of 5 draws)
|
| 85 |
+
imperial_eskd,Granulocyte-like (LDG),zs_raw,-0.36266,0.23437,0.62665,0,5 donors (mean of 5 draws)
|
| 86 |
+
imperial_eskd,HSPC,lora5,0.35038,0.15173,0.58146,0.8,5 donors (mean of 5 draws)
|
| 87 |
+
imperial_eskd,HSPC,scsemi5,-5.4287,0.023071,0.5072,1,5 donors (mean of 5 draws)
|
| 88 |
+
imperial_eskd,HSPC,zs_cal,0.015592,0.16357,0.58055,1,5 donors (mean of 5 draws)
|
| 89 |
+
imperial_eskd,HSPC,zs_raw,-0.92453,0.039978,0.5544,1,5 donors (mean of 5 draws)
|
| 90 |
+
imperial_eskd,ISG-high T,lora5,-0.73614,0.78012,0.90403,1,5 donors (mean of 5 draws)
|
| 91 |
+
imperial_eskd,ISG-high T,scsemi5,-1.1842,0.72048,0.78139,1,5 donors (mean of 5 draws)
|
| 92 |
+
imperial_eskd,ISG-high T,zs_cal,-0.56073,0.83044,0.92781,1,5 donors (mean of 5 draws)
|
| 93 |
+
imperial_eskd,ISG-high T,zs_raw,-1.0601,0.7209,0.88099,1,5 donors (mean of 5 draws)
|
| 94 |
+
imperial_eskd,ISG-high monocyte (positive control),lora5,-0.024345,0.81582,0.94203,1,5 donors (mean of 5 draws)
|
| 95 |
+
imperial_eskd,ISG-high monocyte (positive control),scsemi5,-0.61931,0.76751,0.83652,1,5 donors (mean of 5 draws)
|
| 96 |
+
imperial_eskd,ISG-high monocyte (positive control),zs_cal,0.23791,0.84059,0.94953,1,5 donors (mean of 5 draws)
|
| 97 |
+
imperial_eskd,ISG-high monocyte (positive control),zs_raw,0.19971,0.8243,0.94582,1,5 donors (mean of 5 draws)
|
| 98 |
+
imperial_eskd,MS1 monocyte (IL1R2+),lora5,-1.4977,0.48356,0.6606,1,5 donors (mean of 5 draws)
|
| 99 |
+
imperial_eskd,MS1 monocyte (IL1R2+),scsemi5,-4.317,0.25148,0.51595,0.8,5 donors (mean of 5 draws)
|
| 100 |
+
imperial_eskd,MS1 monocyte (IL1R2+),zs_cal,1.3968,0.54708,0.75614,1,5 donors (mean of 5 draws)
|
| 101 |
+
imperial_eskd,MS1 monocyte (IL1R2+),zs_raw,-0.50803,0.48336,0.73743,1,5 donors (mean of 5 draws)
|
| 102 |
+
imperial_eskd,Plasmablast (label),lora5,-0.53716,0.30927,0.64917,1,5 donors (mean of 5 draws)
|
| 103 |
+
imperial_eskd,Plasmablast (label),scsemi5,-1.5114,0.29149,0.63487,1,5 donors (mean of 5 draws)
|
| 104 |
+
imperial_eskd,Plasmablast (label),zs_cal,-1.3827,0.40127,0.67384,1,5 donors (mean of 5 draws)
|
| 105 |
+
imperial_eskd,Plasmablast (label),zs_raw,-2.1512,0.17509,0.55031,1,5 donors (mean of 5 draws)
|
| 106 |
+
imperial_eskd,Plasmablast (markers),lora5,-0.93358,0.34253,0.64392,1,5 donors (mean of 5 draws)
|
| 107 |
+
imperial_eskd,Plasmablast (markers),scsemi5,-1.9505,0.22889,0.60406,1,5 donors (mean of 5 draws)
|
| 108 |
+
imperial_eskd,Plasmablast (markers),zs_cal,-2.0182,0.41191,0.66208,1,5 donors (mean of 5 draws)
|
| 109 |
+
imperial_eskd,Plasmablast (markers),zs_raw,-2.2436,0.32334,0.62821,1,5 donors (mean of 5 draws)
|
| 110 |
+
imperial_eskd,Proliferating T (label),lora5,0.44352,0.48631,0.74718,1,5 donors (mean of 5 draws)
|
| 111 |
+
imperial_eskd,Proliferating T (label),scsemi5,-1.2207,0.24198,0.6267,1,5 donors (mean of 5 draws)
|
| 112 |
+
imperial_eskd,Proliferating T (label),zs_cal,0.67016,0.44478,0.73313,1,5 donors (mean of 5 draws)
|
| 113 |
+
imperial_eskd,Proliferating T (label),zs_raw,1.4435,0.48753,0.73811,1,5 donors (mean of 5 draws)
|
| 114 |
+
ji2025_chili,C1Q-high monocyte (reference),lora5,-1.2799,-0.017944,0.45353,1,5 donors (mean of 5 draws)
|
| 115 |
+
ji2025_chili,C1Q-high monocyte (reference),scsemi5,-3.7782,0.17697,0.53225,0.4,5 donors (mean of 5 draws)
|
| 116 |
+
ji2025_chili,C1Q-high monocyte (reference),zs_cal,-4.1073,0.01102,0.54121,0.6,5 donors (mean of 5 draws)
|
| 117 |
+
ji2025_chili,C1Q-high monocyte (reference),zs_raw,-4.1752,0.2537,0.53495,0.4,5 donors (mean of 5 draws)
|
| 118 |
+
ji2025_chili,Cycling T/NK,lora5,-1.77,0.20095,0.57207,1,5 donors (mean of 5 draws)
|
| 119 |
+
ji2025_chili,Cycling T/NK,scsemi5,-6.0057,0.17264,0.53205,0.6,5 donors (mean of 5 draws)
|
| 120 |
+
ji2025_chili,Cycling T/NK,zs_cal,-1.3861,0.27854,0.61314,1,5 donors (mean of 5 draws)
|
| 121 |
+
ji2025_chili,Cycling T/NK,zs_raw,0.46595,0.36196,0.74526,1,5 donors (mean of 5 draws)
|
| 122 |
+
ji2025_chili,Cycling activated T (CD38/HLA-DR),lora5,-2.9091,0.21057,0.54731,0.8,5 donors (mean of 5 draws)
|
| 123 |
+
ji2025_chili,Cycling activated T (CD38/HLA-DR),scsemi5,-6.7997,0.2744,0.54872,0.8,5 donors (mean of 5 draws)
|
| 124 |
+
ji2025_chili,Cycling activated T (CD38/HLA-DR),zs_cal,-2.784,0.26617,0.61977,1,5 donors (mean of 5 draws)
|
| 125 |
+
ji2025_chili,Cycling activated T (CD38/HLA-DR),zs_raw,-1.101,0.57525,0.80784,1,5 donors (mean of 5 draws)
|
| 126 |
+
ji2025_chili,Cycling monocyte (Ye 2026),lora5,-4.5524,0.071524,0.52991,0.6,5 donors (mean of 5 draws)
|
| 127 |
+
ji2025_chili,Cycling monocyte (Ye 2026),scsemi5,,,0.5,0,5 donors (mean of 5 draws)
|
| 128 |
+
ji2025_chili,Cycling monocyte (Ye 2026),zs_cal,-3.8874,0.082357,0.49455,0.6,5 donors (mean of 5 draws)
|
| 129 |
+
ji2025_chili,Cycling monocyte (Ye 2026),zs_raw,-1.4595,0.19658,0.60197,1,5 donors (mean of 5 draws)
|
| 130 |
+
ji2025_chili,Cytotoxic CD4 T,lora5,0.34576,0.10596,0.53668,0.2,5 donors (mean of 5 draws)
|
| 131 |
+
ji2025_chili,Cytotoxic CD4 T,scsemi5,0.96177,0.15301,0.59526,1,5 donors (mean of 5 draws)
|
| 132 |
+
ji2025_chili,Cytotoxic CD4 T,zs_cal,0.94516,-0.033189,0.50219,0.6,5 donors (mean of 5 draws)
|
| 133 |
+
ji2025_chili,Cytotoxic CD4 T,zs_raw,0.81185,-0.081371,0.45298,0.2,5 donors (mean of 5 draws)
|
| 134 |
+
ji2025_chili,DN2 / ABC B,lora5,-1.5189,0.078677,0.59412,0.2,5 donors (mean of 5 draws)
|
| 135 |
+
ji2025_chili,DN2 / ABC B,scsemi5,,,0.5,0,5 donors (mean of 5 draws)
|
| 136 |
+
ji2025_chili,DN2 / ABC B,zs_cal,-1.4786,0.19776,0.56536,0.6,5 donors (mean of 5 draws)
|
| 137 |
+
ji2025_chili,DN2 / ABC B,zs_raw,0.67853,0.021323,0.49769,0.6,5 donors (mean of 5 draws)
|
| 138 |
+
ji2025_chili,Granulocyte-like (LDG),lora5,-6.4898,0.027918,0.50371,0.6,5 donors (mean of 5 draws)
|
| 139 |
+
ji2025_chili,Granulocyte-like (LDG),scsemi5,-7.3193,-0.067208,0.48526,0.4,5 donors (mean of 5 draws)
|
| 140 |
+
ji2025_chili,Granulocyte-like (LDG),zs_cal,-4.3718,0.13447,0.56684,0.8,5 donors (mean of 5 draws)
|
| 141 |
+
ji2025_chili,Granulocyte-like (LDG),zs_raw,-0.84518,0.0038266,0.47785,0.4,5 donors (mean of 5 draws)
|
| 142 |
+
ji2025_chili,HSPC,lora5,-1.1919,0.16958,0.57731,0.4,5 donors (mean of 5 draws)
|
| 143 |
+
ji2025_chili,HSPC,scsemi5,-6.7517,-0.010771,0.49936,0.2,5 donors (mean of 5 draws)
|
| 144 |
+
ji2025_chili,HSPC,zs_cal,-2.395,0.10895,0.56061,0.2,5 donors (mean of 5 draws)
|
| 145 |
+
ji2025_chili,HSPC,zs_raw,-1.6857,0.55505,0.78962,0.4,5 donors (mean of 5 draws)
|
| 146 |
+
ji2025_chili,ISG-high T,lora5,-1.7612,0.45854,0.6547,1,5 donors (mean of 5 draws)
|
| 147 |
+
ji2025_chili,ISG-high T,scsemi5,-6.5497,0.33994,0.50833,0.2,5 donors (mean of 5 draws)
|
| 148 |
+
ji2025_chili,ISG-high T,zs_cal,-0.56976,0.31567,0.61771,0.8,5 donors (mean of 5 draws)
|
| 149 |
+
ji2025_chili,ISG-high T,zs_raw,3.8752,0.39391,0.66193,1,5 donors (mean of 5 draws)
|
| 150 |
+
ji2025_chili,ISG-high monocyte (positive control),lora5,-1.6284,0.46939,0.77765,1,5 donors (mean of 5 draws)
|
| 151 |
+
ji2025_chili,ISG-high monocyte (positive control),scsemi5,,,0.5,0,5 donors (mean of 5 draws)
|
| 152 |
+
ji2025_chili,ISG-high monocyte (positive control),zs_cal,1.0452,0.35482,0.69081,1,5 donors (mean of 5 draws)
|
| 153 |
+
ji2025_chili,ISG-high monocyte (positive control),zs_raw,3.5183,0.4667,0.74015,1,5 donors (mean of 5 draws)
|
| 154 |
+
ji2025_chili,MS1 monocyte (IL1R2+),lora5,-2.8873,0.52392,0.76844,1,5 donors (mean of 5 draws)
|
| 155 |
+
ji2025_chili,MS1 monocyte (IL1R2+),scsemi5,-7.5061,0.28307,0.60705,0.6,5 donors (mean of 5 draws)
|
| 156 |
+
ji2025_chili,MS1 monocyte (IL1R2+),zs_cal,-6.7996,0.23522,0.58083,1,5 donors (mean of 5 draws)
|
| 157 |
+
ji2025_chili,MS1 monocyte (IL1R2+),zs_raw,-4.3666,0.39153,0.73948,1,5 donors (mean of 5 draws)
|
| 158 |
+
ji2025_chili,Plasmablast (label),lora5,-0.88561,-0.034929,0.46478,0.4,5 donors (mean of 5 draws)
|
| 159 |
+
ji2025_chili,Plasmablast (label),scsemi5,-2.5439,0.014897,0.48168,0.4,5 donors (mean of 5 draws)
|
| 160 |
+
ji2025_chili,Plasmablast (label),zs_cal,-0.58287,0.065111,0.47456,0.2,5 donors (mean of 5 draws)
|
| 161 |
+
ji2025_chili,Plasmablast (label),zs_raw,0.55194,-0.29478,0.31307,0,5 donors (mean of 5 draws)
|
| 162 |
+
ji2025_chili,Plasmablast (markers),lora5,-1.2353,0.023444,0.48088,0.6,5 donors (mean of 5 draws)
|
| 163 |
+
ji2025_chili,Plasmablast (markers),scsemi5,-2.7516,0.13267,0.54933,0.2,5 donors (mean of 5 draws)
|
| 164 |
+
ji2025_chili,Plasmablast (markers),zs_cal,-1.1607,0.1064,0.49114,0,5 donors (mean of 5 draws)
|
| 165 |
+
ji2025_chili,Plasmablast (markers),zs_raw,0.033521,-0.18774,0.41406,0,5 donors (mean of 5 draws)
|
| 166 |
+
ji2025_chili,Proliferating T (label),lora5,-0.65586,0.34095,0.67018,1,5 donors (mean of 5 draws)
|
| 167 |
+
ji2025_chili,Proliferating T (label),scsemi5,-2.6726,0.24416,0.58591,0.6,5 donors (mean of 5 draws)
|
| 168 |
+
ji2025_chili,Proliferating T (label),zs_cal,-0.26394,0.43167,0.71695,1,5 donors (mean of 5 draws)
|
| 169 |
+
ji2025_chili,Proliferating T (label),zs_raw,1.8519,0.33547,0.67553,1,5 donors (mean of 5 draws)
|
| 170 |
+
ye2026_sepsis,C1Q-high monocyte (reference),lora5,-2.8409,0.1882,0.58866,0.6,5 donors (mean of 5 draws)
|
| 171 |
+
ye2026_sepsis,C1Q-high monocyte (reference),scsemi5,-1.823,0.22469,0.61508,1,5 donors (mean of 5 draws)
|
| 172 |
+
ye2026_sepsis,C1Q-high monocyte (reference),zs_cal,-3.5349,0.22259,0.62756,0.8,5 donors (mean of 5 draws)
|
| 173 |
+
ye2026_sepsis,C1Q-high monocyte (reference),zs_raw,-5.4147,-0.0028043,0.46974,0,5 donors (mean of 5 draws)
|
| 174 |
+
ye2026_sepsis,Cycling T/NK,lora5,-1.2143,0.21513,0.64148,0,5 donors (mean of 5 draws)
|
| 175 |
+
ye2026_sepsis,Cycling T/NK,scsemi5,-4.7467,0.16851,0.54972,0.4,5 donors (mean of 5 draws)
|
| 176 |
+
ye2026_sepsis,Cycling T/NK,zs_cal,-0.31339,0.11086,0.5991,0,5 donors (mean of 5 draws)
|
| 177 |
+
ye2026_sepsis,Cycling T/NK,zs_raw,-0.30656,0.040769,0.55374,0,5 donors (mean of 5 draws)
|
| 178 |
+
ye2026_sepsis,Cycling activated T (CD38/HLA-DR),lora5,-1.9537,0.26887,0.65963,0,5 donors (mean of 5 draws)
|
| 179 |
+
ye2026_sepsis,Cycling activated T (CD38/HLA-DR),scsemi5,-5.3375,0.13218,0.54564,0.6,5 donors (mean of 5 draws)
|
| 180 |
+
ye2026_sepsis,Cycling activated T (CD38/HLA-DR),zs_cal,-1.1796,0.063948,0.54834,0,5 donors (mean of 5 draws)
|
| 181 |
+
ye2026_sepsis,Cycling activated T (CD38/HLA-DR),zs_raw,-1.4267,0.025108,0.53317,0,5 donors (mean of 5 draws)
|
| 182 |
+
ye2026_sepsis,Cycling monocyte (Ye 2026),lora5,-4.1296,0.24056,0.58596,1,5 donors (mean of 5 draws)
|
| 183 |
+
ye2026_sepsis,Cycling monocyte (Ye 2026),scsemi5,-6.5372,0.065502,0.5135,0.6,5 donors (mean of 5 draws)
|
| 184 |
+
ye2026_sepsis,Cycling monocyte (Ye 2026),zs_cal,-2.4648,0.37257,0.66884,1,5 donors (mean of 5 draws)
|
| 185 |
+
ye2026_sepsis,Cycling monocyte (Ye 2026),zs_raw,-3.6999,0.36827,0.63386,1,5 donors (mean of 5 draws)
|
| 186 |
+
ye2026_sepsis,Cytotoxic CD4 T,lora5,0.42101,0.57532,0.74861,0.4,5 donors (mean of 5 draws)
|
| 187 |
+
ye2026_sepsis,Cytotoxic CD4 T,scsemi5,0.4298,0.32199,0.67292,0.2,5 donors (mean of 5 draws)
|
| 188 |
+
ye2026_sepsis,Cytotoxic CD4 T,zs_cal,1.193,0.50154,0.72452,0,5 donors (mean of 5 draws)
|
| 189 |
+
ye2026_sepsis,Cytotoxic CD4 T,zs_raw,-1.3942,0.27159,0.58934,0,5 donors (mean of 5 draws)
|
| 190 |
+
ye2026_sepsis,DN2 / ABC B,lora5,-1.5065,0.16145,0.58303,0.6,5 donors (mean of 5 draws)
|
| 191 |
+
ye2026_sepsis,DN2 / ABC B,scsemi5,-5.6035,0.033892,0.50325,0.4,5 donors (mean of 5 draws)
|
| 192 |
+
ye2026_sepsis,DN2 / ABC B,zs_cal,-1.9167,0.042635,0.52375,0.2,5 donors (mean of 5 draws)
|
| 193 |
+
ye2026_sepsis,DN2 / ABC B,zs_raw,0.40284,0.27877,0.62327,0.6,5 donors (mean of 5 draws)
|
| 194 |
+
ye2026_sepsis,Granulocyte-like (LDG),lora5,-4.6078,0.33723,0.68449,0.6,5 donors (mean of 5 draws)
|
| 195 |
+
ye2026_sepsis,Granulocyte-like (LDG),scsemi5,-9.0099,0.17304,0.5241,0.8,5 donors (mean of 5 draws)
|
| 196 |
+
ye2026_sepsis,Granulocyte-like (LDG),zs_cal,-5.136,0.22926,0.59952,1,5 donors (mean of 5 draws)
|
| 197 |
+
ye2026_sepsis,Granulocyte-like (LDG),zs_raw,-2.2287,0.43872,0.72452,1,5 donors (mean of 5 draws)
|
| 198 |
+
ye2026_sepsis,HSPC,lora5,0.52995,0.030248,0.49245,1,5 donors (mean of 5 draws)
|
| 199 |
+
ye2026_sepsis,HSPC,scsemi5,-6.8556,0.08843,0.50789,0.6,5 donors (mean of 5 draws)
|
| 200 |
+
ye2026_sepsis,HSPC,zs_cal,2.4591,0.038305,0.47701,1,5 donors (mean of 5 draws)
|
| 201 |
+
ye2026_sepsis,HSPC,zs_raw,-0.8757,0.11692,0.50132,1,5 donors (mean of 5 draws)
|
| 202 |
+
ye2026_sepsis,ISG-high T,lora5,-0.72835,0.52286,0.72493,1,5 donors (mean of 5 draws)
|
| 203 |
+
ye2026_sepsis,ISG-high T,scsemi5,-5.421,0.31256,0.53947,0.8,5 donors (mean of 5 draws)
|
| 204 |
+
ye2026_sepsis,ISG-high T,zs_cal,-0.17526,0.26809,0.55429,0.8,5 donors (mean of 5 draws)
|
| 205 |
+
ye2026_sepsis,ISG-high T,zs_raw,0.84066,0.35084,0.62472,1,5 donors (mean of 5 draws)
|
| 206 |
+
ye2026_sepsis,ISG-high monocyte (positive control),lora5,-0.61369,0.55782,0.76178,0.8,5 donors (mean of 5 draws)
|
| 207 |
+
ye2026_sepsis,ISG-high monocyte (positive control),scsemi5,-4.8699,0.36059,0.55472,0,5 donors (mean of 5 draws)
|
| 208 |
+
ye2026_sepsis,ISG-high monocyte (positive control),zs_cal,-0.39815,0.42322,0.73089,1,5 donors (mean of 5 draws)
|
| 209 |
+
ye2026_sepsis,ISG-high monocyte (positive control),zs_raw,0.90375,0.44691,0.71468,1,5 donors (mean of 5 draws)
|
| 210 |
+
ye2026_sepsis,MS1 monocyte (IL1R2+),lora5,-3.3332,0.41391,0.69631,1,5 donors (mean of 5 draws)
|
| 211 |
+
ye2026_sepsis,MS1 monocyte (IL1R2+),scsemi5,-7.5412,0.21662,0.5309,1,5 donors (mean of 5 draws)
|
| 212 |
+
ye2026_sepsis,MS1 monocyte (IL1R2+),zs_cal,-1.2426,0.50396,0.73283,1,5 donors (mean of 5 draws)
|
| 213 |
+
ye2026_sepsis,MS1 monocyte (IL1R2+),zs_raw,-3.7862,0.5086,0.74584,1,5 donors (mean of 5 draws)
|
| 214 |
+
ye2026_sepsis,Plasmablast (label),lora5,-1.6494,0.28336,0.64384,1,5 donors (mean of 5 draws)
|
| 215 |
+
ye2026_sepsis,Plasmablast (label),scsemi5,-2.4978,0.31562,0.64702,1,5 donors (mean of 5 draws)
|
| 216 |
+
ye2026_sepsis,Plasmablast (label),zs_cal,-0.42046,0.35749,0.68248,1,5 donors (mean of 5 draws)
|
| 217 |
+
ye2026_sepsis,Plasmablast (label),zs_raw,-1.3406,0.36696,0.68857,1,5 donors (mean of 5 draws)
|
| 218 |
+
ye2026_sepsis,Plasmablast (markers),lora5,-2.6808,0.25829,0.62036,0.4,5 donors (mean of 5 draws)
|
| 219 |
+
ye2026_sepsis,Plasmablast (markers),scsemi5,-3.4603,0.1625,0.57645,0.4,5 donors (mean of 5 draws)
|
| 220 |
+
ye2026_sepsis,Plasmablast (markers),zs_cal,-1.6638,0.42223,0.69037,0.6,5 donors (mean of 5 draws)
|
| 221 |
+
ye2026_sepsis,Plasmablast (markers),zs_raw,-1.774,0.35632,0.63116,0.2,5 donors (mean of 5 draws)
|
| 222 |
+
ye2026_sepsis,Proliferating T (label),lora5,-0.30514,0.28563,0.6662,0,5 donors (mean of 5 draws)
|
| 223 |
+
ye2026_sepsis,Proliferating T (label),scsemi5,-2.2355,0.17617,0.55776,0,5 donors (mean of 5 draws)
|
| 224 |
+
ye2026_sepsis,Proliferating T (label),zs_cal,-0.12543,0.070704,0.54176,0,5 donors (mean of 5 draws)
|
| 225 |
+
ye2026_sepsis,Proliferating T (label),zs_raw,0.98045,0.02976,0.51032,0,5 donors (mean of 5 draws)
|
| 226 |
+
ye2026_sepsis,C1Q-high monocyte (reference),zs__raw,-5.2595,0.15638,0.5818,1,5-fold pooled
|
| 227 |
+
ye2026_sepsis,Cycling T/NK,zs__raw,-0.2839,0.16863,0.61035,0,5-fold pooled
|
| 228 |
+
ye2026_sepsis,Cycling activated T (CD38/HLA-DR),zs__raw,-1.4656,0.05262,0.5116,0,5-fold pooled
|
| 229 |
+
ye2026_sepsis,Proliferating T (label),zs__raw,0.97407,-0.018709,0.48215,0,5-fold pooled
|
| 230 |
+
ye2026_sepsis,Plasmablast (label),zs__raw,-1.3742,0.33208,0.67162,1,5-fold pooled
|
| 231 |
+
ye2026_sepsis,Plasmablast (markers),zs__raw,-1.8487,0.38111,0.64039,0,5-fold pooled
|
| 232 |
+
ye2026_sepsis,MS1 monocyte (IL1R2+),zs__raw,-3.6557,0.57012,0.80547,1,5-fold pooled
|
| 233 |
+
ye2026_sepsis,Cycling monocyte (Ye 2026),zs__raw,-3.379,0.18386,0.55651,1,5-fold pooled
|
| 234 |
+
ye2026_sepsis,ISG-high monocyte (positive control),zs__raw,0.84174,0.49779,0.71981,1,5-fold pooled
|
| 235 |
+
ye2026_sepsis,ISG-high T,zs__raw,0.799,0.3979,0.70553,1,5-fold pooled
|
| 236 |
+
ye2026_sepsis,DN2 / ABC B,zs__raw,0.55245,0.11146,0.5809,1,5-fold pooled
|
| 237 |
+
ye2026_sepsis,HSPC,zs__raw,-0.83139,-0.030124,0.47383,1,5-fold pooled
|
| 238 |
+
ye2026_sepsis,Cytotoxic CD4 T,zs__raw,-1.19,0.40328,0.6041,0,5-fold pooled
|
| 239 |
+
ye2026_sepsis,Granulocyte-like (LDG),zs__raw,-2.0936,0.4041,0.73766,1,5-fold pooled
|
| 240 |
+
ye2026_sepsis,C1Q-high monocyte (reference),zs__cal,-3.7934,0.43147,0.74777,1,5-fold pooled
|
| 241 |
+
ye2026_sepsis,Cycling T/NK,zs__cal,-0.67961,0.15863,0.5809,0,5-fold pooled
|
| 242 |
+
ye2026_sepsis,Cycling activated T (CD38/HLA-DR),zs__cal,-1.6134,0.05859,0.53123,0,5-fold pooled
|
| 243 |
+
ye2026_sepsis,Proliferating T (label),zs__cal,-0.48445,0.067533,0.53629,0,5-fold pooled
|
| 244 |
+
ye2026_sepsis,Plasmablast (label),zs__cal,-0.46986,0.38137,0.69631,1,5-fold pooled
|
| 245 |
+
ye2026_sepsis,Plasmablast (markers),zs__cal,-1.7517,0.53197,0.76205,1,5-fold pooled
|
| 246 |
+
ye2026_sepsis,MS1 monocyte (IL1R2+),zs__cal,-1.0857,0.60904,0.78911,1,5-fold pooled
|
| 247 |
+
ye2026_sepsis,Cycling monocyte (Ye 2026),zs__cal,-2.599,0.2345,0.61779,1,5-fold pooled
|
| 248 |
+
ye2026_sepsis,ISG-high monocyte (positive control),zs__cal,-0.5186,0.53959,0.7793,1,5-fold pooled
|
| 249 |
+
ye2026_sepsis,ISG-high T,zs__cal,-0.2819,0.45175,0.68055,1,5-fold pooled
|
| 250 |
+
ye2026_sepsis,DN2 / ABC B,zs__cal,-2.0198,-0.084526,0.4298,0,5-fold pooled
|
| 251 |
+
ye2026_sepsis,HSPC,zs__cal,2.0935,0.11366,0.5345,1,5-fold pooled
|
| 252 |
+
ye2026_sepsis,Cytotoxic CD4 T,zs__cal,1.2205,0.51551,0.70613,0,5-fold pooled
|
| 253 |
+
ye2026_sepsis,Granulocyte-like (LDG),zs__cal,-5.2013,0.28962,0.6514,1,5-fold pooled
|
| 254 |
+
ye2026_sepsis,C1Q-high monocyte (reference),scsemi__raw,-0.81433,0.37793,0.78186,1,5-fold pooled
|
| 255 |
+
ye2026_sepsis,Cycling T/NK,scsemi__raw,-2.7638,0.24412,0.57466,1,5-fold pooled
|
| 256 |
+
ye2026_sepsis,Cycling activated T (CD38/HLA-DR),scsemi__raw,-3.3321,0.17714,0.54194,1,5-fold pooled
|
| 257 |
+
ye2026_sepsis,Proliferating T (label),scsemi__raw,-1.3128,0.27257,0.61481,1,5-fold pooled
|
| 258 |
+
ye2026_sepsis,Plasmablast (label),scsemi__raw,0.13579,0.42628,0.70167,1,5-fold pooled
|
| 259 |
+
ye2026_sepsis,Plasmablast (markers),scsemi__raw,-0.79,0.36242,0.65675,1,5-fold pooled
|
| 260 |
+
ye2026_sepsis,MS1 monocyte (IL1R2+),scsemi__raw,-3.3289,0.31714,0.61704,1,5-fold pooled
|
| 261 |
+
ye2026_sepsis,Cycling monocyte (Ye 2026),scsemi__raw,-5.6498,0.15622,0.53082,1,5-fold pooled
|
| 262 |
+
ye2026_sepsis,ISG-high monocyte (positive control),scsemi__raw,-4.7455,0.41493,0.57895,0,5-fold pooled
|
| 263 |
+
ye2026_sepsis,ISG-high T,scsemi__raw,-4.7298,0.44141,0.57317,0,5-fold pooled
|
| 264 |
+
ye2026_sepsis,DN2 / ABC B,scsemi__raw,-7.7313,-0.055377,0.4884,1,5-fold pooled
|
| 265 |
+
ye2026_sepsis,HSPC,scsemi__raw,-5.6876,0.094708,0.5122,1,5-fold pooled
|
| 266 |
+
ye2026_sepsis,Cytotoxic CD4 T,scsemi__raw,0.68875,0.35213,0.67341,1,5-fold pooled
|
| 267 |
+
ye2026_sepsis,Granulocyte-like (LDG),scsemi__raw,-3.9998,0.011898,0.53242,1,5-fold pooled
|
| 268 |
+
ye2026_sepsis,C1Q-high monocyte (reference),real_lora__raw,-0.99664,0.22152,0.67728,1,5-fold pooled
|
| 269 |
+
ye2026_sepsis,Cycling T/NK,real_lora__raw,-0.90067,0.33213,0.66062,0,5-fold pooled
|
| 270 |
+
ye2026_sepsis,Cycling activated T (CD38/HLA-DR),real_lora__raw,-1.7519,0.16759,0.59191,0,5-fold pooled
|
| 271 |
+
ye2026_sepsis,Proliferating T (label),real_lora__raw,-0.36674,0.38631,0.72278,0,5-fold pooled
|
| 272 |
+
ye2026_sepsis,Plasmablast (label),real_lora__raw,-0.40104,0.19534,0.5925,1,5-fold pooled
|
| 273 |
+
ye2026_sepsis,Plasmablast (markers),real_lora__raw,-1.5773,0.43119,0.69007,1,5-fold pooled
|
| 274 |
+
ye2026_sepsis,MS1 monocyte (IL1R2+),real_lora__raw,-0.50546,0.58118,0.81559,1,5-fold pooled
|
| 275 |
+
ye2026_sepsis,Cycling monocyte (Ye 2026),real_lora__raw,-2.1303,0.16176,0.57139,1,5-fold pooled
|
| 276 |
+
ye2026_sepsis,ISG-high monocyte (positive control),real_lora__raw,-0.70608,0.65221,0.82927,1,5-fold pooled
|
| 277 |
+
ye2026_sepsis,ISG-high T,real_lora__raw,-0.8138,0.69575,0.7906,1,5-fold pooled
|
| 278 |
+
ye2026_sepsis,DN2 / ABC B,real_lora__raw,-1.7067,0.42306,0.74717,1,5-fold pooled
|
| 279 |
+
ye2026_sepsis,HSPC,real_lora__raw,-1.3301,0.051877,0.55919,0,5-fold pooled
|
| 280 |
+
ye2026_sepsis,Cytotoxic CD4 T,real_lora__raw,0.43312,0.69216,0.81202,1,5-fold pooled
|
| 281 |
+
ye2026_sepsis,Granulocyte-like (LDG),real_lora__raw,-3.865,0.38264,0.65497,1,5-fold pooled
|
| 282 |
+
imperial_eskd,C1Q-high monocyte (reference),zs__raw,-4.4053,0.1746,0.62114,0,5-fold pooled
|
| 283 |
+
imperial_eskd,Cycling T/NK,zs__raw,1.7453,0.26355,0.63486,1,5-fold pooled
|
| 284 |
+
imperial_eskd,Cycling activated T (CD38/HLA-DR),zs__raw,-0.56551,0.057545,0.52022,1,5-fold pooled
|
| 285 |
+
imperial_eskd,Proliferating T (label),zs__raw,1.5611,0.5439,0.77844,1,5-fold pooled
|
| 286 |
+
imperial_eskd,Plasmablast (label),zs__raw,-2.1527,0.30054,0.63133,1,5-fold pooled
|
| 287 |
+
imperial_eskd,Plasmablast (markers),zs__raw,-2.2835,0.27004,0.60076,1,5-fold pooled
|
| 288 |
+
imperial_eskd,MS1 monocyte (IL1R2+),zs__raw,-0.50379,0.46241,0.71926,1,5-fold pooled
|
| 289 |
+
imperial_eskd,Cycling monocyte (Ye 2026),zs__raw,-3.061,0.052516,0.51907,1,5-fold pooled
|
| 290 |
+
imperial_eskd,ISG-high monocyte (positive control),zs__raw,0.18981,0.81912,0.94839,1,5-fold pooled
|
| 291 |
+
imperial_eskd,ISG-high T,zs__raw,-1.0172,0.77354,0.9082,1,5-fold pooled
|
| 292 |
+
imperial_eskd,DN2 / ABC B,zs__raw,0.76768,0.19032,0.60897,1,5-fold pooled
|
| 293 |
+
imperial_eskd,HSPC,zs__raw,-0.94186,0.13845,0.54586,1,5-fold pooled
|
| 294 |
+
imperial_eskd,Cytotoxic CD4 T,zs__raw,0.0098678,0.15938,0.56291,0,5-fold pooled
|
| 295 |
+
imperial_eskd,Granulocyte-like (LDG),zs__raw,-0.40858,0.2923,0.62648,0,5-fold pooled
|
| 296 |
+
imperial_eskd,C1Q-high monocyte (reference),zs__cal,-2.6109,0.17248,0.65023,1,5-fold pooled
|
| 297 |
+
imperial_eskd,Cycling T/NK,zs__cal,1.827,0.34712,0.69707,1,5-fold pooled
|
| 298 |
+
imperial_eskd,Cycling activated T (CD38/HLA-DR),zs__cal,-0.33987,0.154,0.58194,1,5-fold pooled
|
| 299 |
+
imperial_eskd,Proliferating T (label),zs__cal,0.75873,0.44134,0.72017,1,5-fold pooled
|
| 300 |
+
imperial_eskd,Plasmablast (label),zs__cal,-1.3211,0.35945,0.65031,1,5-fold pooled
|
| 301 |
+
imperial_eskd,Plasmablast (markers),zs__cal,-1.974,0.42007,0.67562,1,5-fold pooled
|
| 302 |
+
imperial_eskd,MS1 monocyte (IL1R2+),zs__cal,1.3417,0.52802,0.74162,1,5-fold pooled
|
| 303 |
+
imperial_eskd,Cycling monocyte (Ye 2026),zs__cal,-2.0301,0.32298,0.62582,1,5-fold pooled
|
| 304 |
+
imperial_eskd,ISG-high monocyte (positive control),zs__cal,0.24206,0.86697,0.95891,1,5-fold pooled
|
| 305 |
+
imperial_eskd,ISG-high T,zs__cal,-0.4629,0.79913,0.91075,1,5-fold pooled
|
| 306 |
+
imperial_eskd,DN2 / ABC B,zs__cal,-1.0075,0.1315,0.58383,0,5-fold pooled
|
| 307 |
+
imperial_eskd,HSPC,zs__cal,-0.0051408,0.16817,0.58859,1,5-fold pooled
|
| 308 |
+
imperial_eskd,Cytotoxic CD4 T,zs__cal,1.9586,0.22763,0.62076,0,5-fold pooled
|
| 309 |
+
imperial_eskd,Granulocyte-like (LDG),zs__cal,-3.4479,0.055175,0.5332,0,5-fold pooled
|
| 310 |
+
imperial_eskd,C1Q-high monocyte (reference),scsemi__raw,-1.1436,0.16529,0.5538,1,5-fold pooled
|
| 311 |
+
imperial_eskd,Cycling T/NK,scsemi__raw,-4.8187,0.053882,0.51274,1,5-fold pooled
|
| 312 |
+
imperial_eskd,Cycling activated T (CD38/HLA-DR),scsemi__raw,-6.7839,0.10832,0.50616,0,5-fold pooled
|
| 313 |
+
imperial_eskd,Proliferating T (label),scsemi__raw,-1.9643,0.29303,0.61637,1,5-fold pooled
|
| 314 |
+
imperial_eskd,Plasmablast (label),scsemi__raw,-0.52439,0.13076,0.55539,1,5-fold pooled
|
| 315 |
+
imperial_eskd,Plasmablast (markers),scsemi__raw,-1.2278,0.066058,0.52737,1,5-fold pooled
|
| 316 |
+
imperial_eskd,MS1 monocyte (IL1R2+),scsemi__raw,-4.697,0.23486,0.51948,1,5-fold pooled
|
| 317 |
+
imperial_eskd,Cycling monocyte (Ye 2026),scsemi__raw,,,0.5,0,5-fold pooled
|
| 318 |
+
imperial_eskd,ISG-high monocyte (positive control),scsemi__raw,-0.25885,0.71148,0.80486,1,5-fold pooled
|
| 319 |
+
imperial_eskd,ISG-high T,scsemi__raw,-0.8893,0.64154,0.75608,1,5-fold pooled
|
| 320 |
+
imperial_eskd,DN2 / ABC B,scsemi__raw,-5.5176,0.086456,0.51257,1,5-fold pooled
|
| 321 |
+
imperial_eskd,HSPC,scsemi__raw,-7.5597,-0.066676,0.5,0,5-fold pooled
|
| 322 |
+
imperial_eskd,Cytotoxic CD4 T,scsemi__raw,1.8284,0.093167,0.57592,0,5-fold pooled
|
| 323 |
+
imperial_eskd,Granulocyte-like (LDG),scsemi__raw,-9.6476,-0.027571,0.5,0,5-fold pooled
|
| 324 |
+
imperial_eskd,C1Q-high monocyte (reference),real_lora__raw,-2.0746,0.070101,0.5563,1,5-fold pooled
|
| 325 |
+
imperial_eskd,Cycling T/NK,real_lora__raw,-1.4198,0.23453,0.58909,1,5-fold pooled
|
| 326 |
+
imperial_eskd,Cycling activated T (CD38/HLA-DR),real_lora__raw,-2.8306,0.13319,0.54915,1,5-fold pooled
|
| 327 |
+
imperial_eskd,Proliferating T (label),real_lora__raw,0.5385,0.53938,0.77334,1,5-fold pooled
|
| 328 |
+
imperial_eskd,Plasmablast (label),real_lora__raw,-0.037175,0.37215,0.66823,1,5-fold pooled
|
| 329 |
+
imperial_eskd,Plasmablast (markers),real_lora__raw,-0.59279,0.41692,0.67102,1,5-fold pooled
|
| 330 |
+
imperial_eskd,MS1 monocyte (IL1R2+),real_lora__raw,-0.91175,0.48684,0.67612,1,5-fold pooled
|
| 331 |
+
imperial_eskd,Cycling monocyte (Ye 2026),real_lora__raw,-3.7049,0.11606,0.51709,1,5-fold pooled
|
| 332 |
+
imperial_eskd,ISG-high monocyte (positive control),real_lora__raw,0.0162,0.79803,0.93664,1,5-fold pooled
|
| 333 |
+
imperial_eskd,ISG-high T,real_lora__raw,-0.45676,0.74868,0.89785,1,5-fold pooled
|
| 334 |
+
imperial_eskd,DN2 / ABC B,real_lora__raw,-2.1387,0.29104,0.64563,1,5-fold pooled
|
| 335 |
+
imperial_eskd,HSPC,real_lora__raw,-0.49542,0.095651,0.55893,1,5-fold pooled
|
| 336 |
+
imperial_eskd,Cytotoxic CD4 T,real_lora__raw,1.1634,0.35302,0.72508,0,5-fold pooled
|
| 337 |
+
imperial_eskd,Granulocyte-like (LDG),real_lora__raw,-5.4426,0.031395,0.50197,0,5-fold pooled
|
| 338 |
+
giroux2022,C1Q-high monocyte (reference),zs__raw,-3.7922,-0.62684,0.25694,0,5-fold pooled
|
| 339 |
+
giroux2022,Cycling T/NK,zs__raw,-1.1571,0.18435,0.54167,1,5-fold pooled
|
| 340 |
+
giroux2022,Cycling activated T (CD38/HLA-DR),zs__raw,-2.3242,0.24282,0.65972,1,5-fold pooled
|
| 341 |
+
giroux2022,Proliferating T (label),zs__raw,-0.35243,0.46435,0.65972,1,5-fold pooled
|
| 342 |
+
giroux2022,Plasmablast (label),zs__raw,-0.83162,0.22891,0.64931,0,5-fold pooled
|
| 343 |
+
giroux2022,Plasmablast (markers),zs__raw,-1.7087,0.099106,0.56597,0,5-fold pooled
|
| 344 |
+
giroux2022,MS1 monocyte (IL1R2+),zs__raw,0.11022,-0.078638,0.625,0,5-fold pooled
|
| 345 |
+
giroux2022,Cycling monocyte (Ye 2026),zs__raw,-3.8804,0.24994,0.66667,1,5-fold pooled
|
| 346 |
+
giroux2022,ISG-high monocyte (positive control),zs__raw,0.34126,0.78522,0.90278,1,5-fold pooled
|
| 347 |
+
giroux2022,ISG-high T,zs__raw,-0.70336,0.58609,0.74306,1,5-fold pooled
|
| 348 |
+
giroux2022,DN2 / ABC B,zs__raw,-0.57963,0.15355,0.61806,0,5-fold pooled
|
| 349 |
+
giroux2022,HSPC,zs__raw,-0.65703,-0.31386,0.48611,1,5-fold pooled
|
| 350 |
+
giroux2022,Cytotoxic CD4 T,zs__raw,-1.5039,0.46551,0.76389,1,5-fold pooled
|
| 351 |
+
giroux2022,Granulocyte-like (LDG),zs__raw,-2.4718,0.46108,0.63542,1,5-fold pooled
|
| 352 |
+
giroux2022,C1Q-high monocyte (reference),zs__cal,-2.6256,0.046928,0.66319,0,5-fold pooled
|
| 353 |
+
giroux2022,Cycling T/NK,zs__cal,-3.0733,0.43788,0.60417,1,5-fold pooled
|
| 354 |
+
giroux2022,Cycling activated T (CD38/HLA-DR),zs__cal,-4.1315,0.32333,0.625,0,5-fold pooled
|
| 355 |
+
giroux2022,Proliferating T (label),zs__cal,-0.1136,0.27739,0.55556,1,5-fold pooled
|
| 356 |
+
giroux2022,Plasmablast (label),zs__cal,-1.1046,0.46344,0.68403,0,5-fold pooled
|
| 357 |
+
giroux2022,Plasmablast (markers),zs__cal,-2.9074,0.16126,0.62153,0,5-fold pooled
|
| 358 |
+
giroux2022,MS1 monocyte (IL1R2+),zs__cal,2.0763,0.23105,0.63194,0,5-fold pooled
|
| 359 |
+
giroux2022,Cycling monocyte (Ye 2026),zs__cal,-5.1532,0.10688,0.46875,1,5-fold pooled
|
| 360 |
+
giroux2022,ISG-high monocyte (positive control),zs__cal,0.77333,0.7713,0.90278,1,5-fold pooled
|
| 361 |
+
giroux2022,ISG-high T,zs__cal,-0.016223,0.81043,0.91667,1,5-fold pooled
|
| 362 |
+
giroux2022,DN2 / ABC B,zs__cal,-2.1269,-0.028346,0.52083,0,5-fold pooled
|
| 363 |
+
giroux2022,HSPC,zs__cal,-2.2367,-0.15229,0.54167,1,5-fold pooled
|
| 364 |
+
giroux2022,Cytotoxic CD4 T,zs__cal,0.62402,0.38729,0.64583,1,5-fold pooled
|
| 365 |
+
giroux2022,Granulocyte-like (LDG),zs__cal,-3.9365,0.35467,0.71528,1,5-fold pooled
|
| 366 |
+
giroux2022,C1Q-high monocyte (reference),scsemi__raw,-3.5655,0.015918,0.45833,1,5-fold pooled
|
| 367 |
+
giroux2022,Cycling T/NK,scsemi__raw,-2.6618,0.61554,0.71181,1,5-fold pooled
|
| 368 |
+
giroux2022,Cycling activated T (CD38/HLA-DR),scsemi__raw,-1.7879,0.39802,0.56944,1,5-fold pooled
|
| 369 |
+
giroux2022,Proliferating T (label),scsemi__raw,2.105,0.52261,0.625,1,5-fold pooled
|
| 370 |
+
giroux2022,Plasmablast (label),scsemi__raw,-1.7354,-0.084437,0.54861,0,5-fold pooled
|
| 371 |
+
giroux2022,Plasmablast (markers),scsemi__raw,0.42163,0.32824,0.62847,1,5-fold pooled
|
| 372 |
+
giroux2022,MS1 monocyte (IL1R2+),scsemi__raw,,,,0,5-fold pooled
|
| 373 |
+
giroux2022,Cycling monocyte (Ye 2026),scsemi__raw,-2.5057,-0.069628,0.51389,0,5-fold pooled
|
| 374 |
+
giroux2022,ISG-high monocyte (positive control),scsemi__raw,1.0164,0.66854,0.70833,1,5-fold pooled
|
| 375 |
+
giroux2022,ISG-high T,scsemi__raw,2.5134,0.71017,0.70833,1,5-fold pooled
|
| 376 |
+
giroux2022,DN2 / ABC B,scsemi__raw,-3.6383,0.015094,0.54167,0,5-fold pooled
|
| 377 |
+
giroux2022,HSPC,scsemi__raw,-2.814,-0.10244,0.49653,1,5-fold pooled
|
| 378 |
+
giroux2022,Cytotoxic CD4 T,scsemi__raw,3.8103,0.62805,0.81944,1,5-fold pooled
|
| 379 |
+
giroux2022,Granulocyte-like (LDG),scsemi__raw,,,0.5,0,5-fold pooled
|
| 380 |
+
giroux2022,C1Q-high monocyte (reference),real_lora__raw,-2.887,0.16068,0.5625,1,5-fold pooled
|
| 381 |
+
giroux2022,Cycling T/NK,real_lora__raw,-1.8241,0.36957,0.65972,1,5-fold pooled
|
| 382 |
+
giroux2022,Cycling activated T (CD38/HLA-DR),real_lora__raw,-2.8981,0.58696,0.76389,1,5-fold pooled
|
| 383 |
+
giroux2022,Proliferating T (label),real_lora__raw,-0.60792,0.5913,0.64583,1,5-fold pooled
|
| 384 |
+
giroux2022,Plasmablast (label),real_lora__raw,-0.98916,0.24767,0.5,0,5-fold pooled
|
| 385 |
+
giroux2022,Plasmablast (markers),real_lora__raw,-3.0116,0.25387,0.55556,0,5-fold pooled
|
| 386 |
+
giroux2022,MS1 monocyte (IL1R2+),real_lora__raw,-3.3482,-0.1922,0.41667,1,5-fold pooled
|
| 387 |
+
giroux2022,Cycling monocyte (Ye 2026),real_lora__raw,-4.6811,0.23019,0.53472,0,5-fold pooled
|
| 388 |
+
giroux2022,ISG-high monocyte (positive control),real_lora__raw,-0.24172,0.6113,0.81944,1,5-fold pooled
|
| 389 |
+
giroux2022,ISG-high T,real_lora__raw,-0.93987,0.54656,0.72222,1,5-fold pooled
|
| 390 |
+
giroux2022,DN2 / ABC B,real_lora__raw,-2.4522,-0.15737,0.41667,0,5-fold pooled
|
| 391 |
+
giroux2022,HSPC,real_lora__raw,-4.1106,0.43557,0.58333,1,5-fold pooled
|
| 392 |
+
giroux2022,Cytotoxic CD4 T,real_lora__raw,-0.68263,0.3018,0.60069,1,5-fold pooled
|
| 393 |
+
giroux2022,Granulocyte-like (LDG),real_lora__raw,-5.7442,-0.029032,0.47222,1,5-fold pooled
|
| 394 |
+
ji2025_chili,C1Q-high monocyte (reference),zs__raw,-4.7209,0.1654,0.53516,0,5-fold pooled
|
| 395 |
+
ji2025_chili,Cycling T/NK,zs__raw,0.33136,0.22405,0.59766,1,5-fold pooled
|
| 396 |
+
ji2025_chili,Cycling activated T (CD38/HLA-DR),zs__raw,-1.3286,0.3493,0.63672,1,5-fold pooled
|
| 397 |
+
ji2025_chili,Proliferating T (label),zs__raw,1.8171,0.35896,0.63672,1,5-fold pooled
|
| 398 |
+
ji2025_chili,Plasmablast (label),zs__raw,0.49615,-0.17516,0.33789,0,5-fold pooled
|
| 399 |
+
ji2025_chili,Plasmablast (markers),zs__raw,-0.041195,0.028713,0.50586,0,5-fold pooled
|
| 400 |
+
ji2025_chili,MS1 monocyte (IL1R2+),zs__raw,-4.7609,0.17394,0.67383,1,5-fold pooled
|
| 401 |
+
ji2025_chili,Cycling monocyte (Ye 2026),zs__raw,-1.3797,0.18593,0.56836,1,5-fold pooled
|
| 402 |
+
ji2025_chili,ISG-high monocyte (positive control),zs__raw,3.2445,0.64357,0.83203,1,5-fold pooled
|
| 403 |
+
ji2025_chili,ISG-high T,zs__raw,3.8984,0.25385,0.54688,1,5-fold pooled
|
| 404 |
+
ji2025_chili,DN2 / ABC B,zs__raw,0.51852,0.075401,0.56836,0,5-fold pooled
|
| 405 |
+
ji2025_chili,HSPC,zs__raw,-2.2118,0.048309,0.5332,0,5-fold pooled
|
| 406 |
+
ji2025_chili,Cytotoxic CD4 T,zs__raw,0.26965,-0.10192,0.43359,0,5-fold pooled
|
| 407 |
+
ji2025_chili,Granulocyte-like (LDG),zs__raw,-0.92142,0.049946,0.5957,1,5-fold pooled
|
| 408 |
+
ji2025_chili,C1Q-high monocyte (reference),zs__cal,-4.5223,0.1435,0.52344,0,5-fold pooled
|
| 409 |
+
ji2025_chili,Cycling T/NK,zs__cal,-1.5863,0.34648,0.75586,1,5-fold pooled
|
| 410 |
+
ji2025_chili,Cycling activated T (CD38/HLA-DR),zs__cal,-3.8155,0.34027,0.67188,1,5-fold pooled
|
| 411 |
+
ji2025_chili,Proliferating T (label),zs__cal,-0.12541,0.18082,0.5625,1,5-fold pooled
|
| 412 |
+
ji2025_chili,Plasmablast (label),zs__cal,-0.41074,-0.013252,0.42188,0,5-fold pooled
|
| 413 |
+
ji2025_chili,Plasmablast (markers),zs__cal,-1.0379,0.036514,0.48242,0,5-fold pooled
|
| 414 |
+
ji2025_chili,MS1 monocyte (IL1R2+),zs__cal,-6.5634,0.27743,0.62695,1,5-fold pooled
|
| 415 |
+
ji2025_chili,Cycling monocyte (Ye 2026),zs__cal,-4.287,-0.16756,0.46484,0,5-fold pooled
|
| 416 |
+
ji2025_chili,ISG-high monocyte (positive control),zs__cal,0.9915,0.26436,0.70703,1,5-fold pooled
|
| 417 |
+
ji2025_chili,ISG-high T,zs__cal,-0.70728,0.15487,0.53906,1,5-fold pooled
|
| 418 |
+
ji2025_chili,DN2 / ABC B,zs__cal,-1.1633,0.24959,0.57812,1,5-fold pooled
|
| 419 |
+
ji2025_chili,HSPC,zs__cal,-2.7089,-0.045708,0.5,0,5-fold pooled
|
| 420 |
+
ji2025_chili,Cytotoxic CD4 T,zs__cal,0.98941,0.37311,0.67969,0,5-fold pooled
|
| 421 |
+
ji2025_chili,Granulocyte-like (LDG),zs__cal,-4.127,0.0089641,0.50781,1,5-fold pooled
|
| 422 |
+
ji2025_chili,C1Q-high monocyte (reference),scsemi__raw,-2.0675,0.30905,0.76172,1,5-fold pooled
|
| 423 |
+
ji2025_chili,Cycling T/NK,scsemi__raw,-4.5317,0.24319,0.5625,1,5-fold pooled
|
| 424 |
+
ji2025_chili,Cycling activated T (CD38/HLA-DR),scsemi__raw,-6.4818,0.25991,0.53125,1,5-fold pooled
|
| 425 |
+
ji2025_chili,Proliferating T (label),scsemi__raw,-1.8188,0.40455,0.73828,1,5-fold pooled
|
| 426 |
+
ji2025_chili,Plasmablast (label),scsemi__raw,-2.0482,-0.07634,0.51562,0,5-fold pooled
|
| 427 |
+
ji2025_chili,Plasmablast (markers),scsemi__raw,-2.5344,0.10028,0.50586,0,5-fold pooled
|
| 428 |
+
ji2025_chili,MS1 monocyte (IL1R2+),scsemi__raw,-5.0055,0.38139,0.625,1,5-fold pooled
|
| 429 |
+
ji2025_chili,Cycling monocyte (Ye 2026),scsemi__raw,,,0.5,0,5-fold pooled
|
| 430 |
+
ji2025_chili,ISG-high monocyte (positive control),scsemi__raw,-7.5899,0.29704,0.53125,1,5-fold pooled
|
| 431 |
+
ji2025_chili,ISG-high T,scsemi__raw,-6.8431,0.29729,0.53125,1,5-fold pooled
|
| 432 |
+
ji2025_chili,DN2 / ABC B,scsemi__raw,,,0.5,0,5-fold pooled
|
| 433 |
+
ji2025_chili,HSPC,scsemi__raw,-6.7979,-0.1671,0.46875,0,5-fold pooled
|
| 434 |
+
ji2025_chili,Cytotoxic CD4 T,scsemi__raw,-0.20529,0.13457,0.63281,1,5-fold pooled
|
| 435 |
+
ji2025_chili,Granulocyte-like (LDG),scsemi__raw,-8.0265,0.14671,0.5,0,5-fold pooled
|
| 436 |
+
ji2025_chili,C1Q-high monocyte (reference),real_lora__raw,-0.77546,0.029604,0.58398,1,5-fold pooled
|
| 437 |
+
ji2025_chili,Cycling T/NK,real_lora__raw,-1.1641,0.48638,0.76953,1,5-fold pooled
|
| 438 |
+
ji2025_chili,Cycling activated T (CD38/HLA-DR),real_lora__raw,-2.2529,0.53694,0.79492,1,5-fold pooled
|
| 439 |
+
ji2025_chili,Proliferating T (label),real_lora__raw,-0.2173,0.33542,0.74414,1,5-fold pooled
|
| 440 |
+
ji2025_chili,Plasmablast (label),real_lora__raw,-0.61818,-0.14907,0.38867,1,5-fold pooled
|
| 441 |
+
ji2025_chili,Plasmablast (markers),real_lora__raw,-1.3148,-0.12291,0.42773,1,5-fold pooled
|
| 442 |
+
ji2025_chili,MS1 monocyte (IL1R2+),real_lora__raw,-0.95584,0.77039,0.93359,1,5-fold pooled
|
| 443 |
+
ji2025_chili,Cycling monocyte (Ye 2026),real_lora__raw,-4.9673,0.38258,0.59375,1,5-fold pooled
|
| 444 |
+
ji2025_chili,ISG-high monocyte (positive control),real_lora__raw,-2.2278,0.3548,0.71289,1,5-fold pooled
|
| 445 |
+
ji2025_chili,ISG-high T,real_lora__raw,-2.2632,0.29438,0.60547,1,5-fold pooled
|
| 446 |
+
ji2025_chili,DN2 / ABC B,real_lora__raw,-1.5208,-0.0037906,0.41016,0,5-fold pooled
|
| 447 |
+
ji2025_chili,HSPC,real_lora__raw,-1.9153,-0.1087,0.41797,1,5-fold pooled
|
| 448 |
+
ji2025_chili,Cytotoxic CD4 T,real_lora__raw,0.40659,0.076345,0.53125,1,5-fold pooled
|
| 449 |
+
ji2025_chili,Granulocyte-like (LDG),real_lora__raw,-5.8577,-0.030476,0.50781,1,5-fold pooled
|
paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/legacy_rare/fig5_rare_states_slide_text.json
ADDED
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| 1 |
+
{
|
| 2 |
+
"section": "fig5-rare",
|
| 3 |
+
"scripts": [
|
| 4 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/fig5_rare_states.py"
|
| 5 |
+
],
|
| 6 |
+
"generated_from": "tools/fig5_rare_states.py (rerun to refresh; do not edit by hand)",
|
| 7 |
+
"slides": [
|
| 8 |
+
{
|
| 9 |
+
"title": "Rare states with 5 pairs: how many cells",
|
| 10 |
+
"layout": "full",
|
| 11 |
+
"figures": [
|
| 12 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/legacy_rare/fig5_rare_fraction.png"
|
| 13 |
+
],
|
| 14 |
+
"keywords": [
|
| 15 |
+
"Within 2-fold: LoRA-5 19/56, scSemiProfiler-5 5/56",
|
| 16 |
+
"Closer to the observed fraction than scSemiProfiler-5: 51/56",
|
| 17 |
+
"Rare states kept, not averaged away"
|
| 18 |
+
],
|
| 19 |
+
"footnote_short": "4 paired disease cohorts; 5 donors, mean of 5 draws. 0 = observed fraction; band = within 2-fold.",
|
| 20 |
+
"footnote": "Main comparison: 5 donors per draw (LoRA-5 vs scSemiProfiler with the same 5 donors as representatives, and zero-shot), every other usable sample tested, mean over 5 draws of log2(generated % / observed %) of the state within its parent type. Left: one point per state x cohort; below the diagonal = LoRA-5 closer; states a method never generates are drawn as 'not generated' (scSemiProfiler-5: 6 of 56; LoRA-5: 0). Zero-shot (no pairs) is closer than LoRA-5 on 28 of 56 fractions, LoRA-5 ranks donors better on 35 of 56. State × cohort pairs with ≥ 30 observed state cells in ≥ 3 donors (native depth); negative control left out. Marker rules from the literature (plans/rare_states_screen_20261004/tools/states.json); observed parent cells thinned to the generated depth; labels = the benchmark's frozen scANVI calls; the benchmark's Poisson read-out reproduced cell by cell. Source: data/fig5_rare_states.csv (plans/rare_states_paired_20261008/out/summary.csv).",
|
| 21 |
+
"numbers": [
|
| 22 |
+
{
|
| 23 |
+
"value": "{\"5 donors\": {\"n\": 56, \"frac_closer\": 51, \"within2_lora\": 19, \"within2_sc\": 5, \"not_generated_lora\": 0, \"not_generated_sc\": 6, \"rho_better\": 43, \"rho_median_lora\": 0.2381686657463106, \"rho_median_sc\": 0.17609850402537303, \"dir_lora\": 0.7321428571428571, \"dir_sc\": 0.6071428571428571}, \"5-fold\": {\"n\": 56, \"frac_closer\": 47, \"within2_lora\": 25, \"within2_sc\": 9, \"not_generated_lora\": 0, \"not_generated_sc\": 5, \"rho_better\": 38, \"rho_median_lora\": 0.31696815102004133, \"rho_median_sc\": 0.2431928042007824, \"dir_lora\": 0.8035714285714286, \"dir_sc\": 0.6785714285714286}}",
|
| 24 |
+
"source": "data/fig5_rare_states.csv"
|
| 25 |
+
}
|
| 26 |
+
]
|
| 27 |
+
},
|
| 28 |
+
{
|
| 29 |
+
"title": "Rare states with 5 pairs: in the right donors",
|
| 30 |
+
"layout": "full",
|
| 31 |
+
"figures": [
|
| 32 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/legacy_rare/fig5_rare_donors.png"
|
| 33 |
+
],
|
| 34 |
+
"keywords": [
|
| 35 |
+
"Donor ranking: median ρ 0.24 vs 0.18 (scSemiProfiler-5)",
|
| 36 |
+
"Better donor ranking than scSemiProfiler-5: 43/56",
|
| 37 |
+
"Disease direction kept: 73% vs 61% of draws"
|
| 38 |
+
],
|
| 39 |
+
"footnote_short": "Spearman over donors of generated vs observed state %; direction = case-vs-control sign.",
|
| 40 |
+
"footnote": "Main comparison (5 donors, 5 draws). Left: Spearman over the tested donors of the generated vs observed (thinned) state percentage, mean over draws. Right: share of draws where the case-vs-control difference of donor means has the observed sign (sepsis vs controls, COVID+ vs COVID-, severe vs mild, ChILI vs controls). State × cohort pairs with ≥ 30 observed state cells in ≥ 3 donors (native depth); negative control left out. Marker rules from the literature (plans/rare_states_screen_20261004/tools/states.json); observed parent cells thinned to the generated depth; labels = the benchmark's frozen scANVI calls; the benchmark's Poisson read-out reproduced cell by cell. Source: data/fig5_rare_states.csv (out/summary.csv, out/contrasts.csv).",
|
| 41 |
+
"numbers": [
|
| 42 |
+
{
|
| 43 |
+
"value": "{\"5 donors\": {\"n\": 56, \"frac_closer\": 51, \"within2_lora\": 19, \"within2_sc\": 5, \"not_generated_lora\": 0, \"not_generated_sc\": 6, \"rho_better\": 43, \"rho_median_lora\": 0.2381686657463106, \"rho_median_sc\": 0.17609850402537303, \"dir_lora\": 0.7321428571428571, \"dir_sc\": 0.6071428571428571}, \"5-fold\": {\"n\": 56, \"frac_closer\": 47, \"within2_lora\": 25, \"within2_sc\": 9, \"not_generated_lora\": 0, \"not_generated_sc\": 5, \"rho_better\": 38, \"rho_median_lora\": 0.31696815102004133, \"rho_median_sc\": 0.2431928042007824, \"dir_lora\": 0.8035714285714286, \"dir_sc\": 0.6785714285714286}}",
|
| 44 |
+
"source": "data/fig5_rare_states.csv"
|
| 45 |
+
}
|
| 46 |
+
]
|
| 47 |
+
},
|
| 48 |
+
{
|
| 49 |
+
"title": "5-fold CV: rare states",
|
| 50 |
+
"layout": "full",
|
| 51 |
+
"figures": [
|
| 52 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/legacy_rare/fig5_rare_fivefold.png"
|
| 53 |
+
],
|
| 54 |
+
"keywords": [
|
| 55 |
+
"Within 2-fold: LoRA 25/56, scSemiProfiler 9/56",
|
| 56 |
+
"Donor ranking: median ρ 0.32 vs 0.24",
|
| 57 |
+
"Better donor ranking: 38/56"
|
| 58 |
+
],
|
| 59 |
+
"footnote_short": "Donor-level 5-fold CV, pooled; reported separately from the 5-pair comparison.",
|
| 60 |
+
"footnote": "Reported separately: 5-fold CV, every sample generated by the fold model that never trained on it; scSemiProfiler with exactly LoRA's training pairs as representatives. State × cohort pairs with ≥ 30 observed state cells in ≥ 3 donors (native depth); negative control left out. Marker rules from the literature (plans/rare_states_screen_20261004/tools/states.json); observed parent cells thinned to the generated depth; labels = the benchmark's frozen scANVI calls; the benchmark's Poisson read-out reproduced cell by cell. Source: data/fig5_rare_states.csv.",
|
| 61 |
+
"numbers": [
|
| 62 |
+
{
|
| 63 |
+
"value": "{\"5 donors\": {\"n\": 56, \"frac_closer\": 51, \"within2_lora\": 19, \"within2_sc\": 5, \"not_generated_lora\": 0, \"not_generated_sc\": 6, \"rho_better\": 43, \"rho_median_lora\": 0.2381686657463106, \"rho_median_sc\": 0.17609850402537303, \"dir_lora\": 0.7321428571428571, \"dir_sc\": 0.6071428571428571}, \"5-fold\": {\"n\": 56, \"frac_closer\": 47, \"within2_lora\": 25, \"within2_sc\": 9, \"not_generated_lora\": 0, \"not_generated_sc\": 5, \"rho_better\": 38, \"rho_median_lora\": 0.31696815102004133, \"rho_median_sc\": 0.2431928042007824, \"dir_lora\": 0.8035714285714286, \"dir_sc\": 0.6785714285714286}}",
|
| 64 |
+
"source": "data/fig5_rare_states.csv"
|
| 65 |
+
}
|
| 66 |
+
]
|
| 67 |
+
}
|
| 68 |
+
]
|
| 69 |
+
}
|