diff --git a/paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/page_map.csv b/paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/page_map.csv new file mode 100644 index 0000000000000000000000000000000000000000..d720f1236796528b7a9e0bbd74f9a9afb4726f7b --- /dev/null +++ b/paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/page_map.csv @@ -0,0 +1,141 @@ +current_page,parent_reordered_page,original_expanded_page,original_76_page,group,panel,title,addition_key +1,1,1,1,Introduction,Introduction,PBISC-Diffusion: manuscript evidence, +2,2,2,2,Introduction,Introduction,Figures 1-6: the expanded evidence map, +3,3,3,,Introduction,Introduction,How this expanded deck is organized,guide:scope +4,4,4,3,Introduction,Current scope,Manuscript map: the six figures, +5,5,6,4,Figure 1,Figure 1,Figure 1. Overview and corpus, +6,6,7,5,Figure 1,Figure 1 plan,"Figure 1: overview, corpus and denoising", +7,7,9,7,Figure 1,Fig. 1a,Experimental overview, +8,8,11,9,Figure 1,Fig. 1b,Pretraining corpus, +9,9,16,13,Figure 1,Fig. 1c,Corpus scale and generation workflow, +10,,,,Figure 1,Fig. 1d,From Gaussian noise to generated cell states,enrichment:trajectory_four_pca_frames +11,10,19,15,Figure 2,Figure 2,Figure 2. SLE model ablations, +12,11,20,16,Figure 2,Figure 2 plan,Figure 2: architecture and gene context, +13,,,,Figure 2,Fig. 2a,Where context width and trunk width change,enrichment:arch_context_vs_trunk +14,,,,Figure 2,Fig. 2b,Predicted and oracle hints: one trained denoiser,enrichment:arch_hint_injection +15,43,12,10,Figure 2,Fig. 2c,Architecture: full and late validation progression, +16,12,13,11,Figure 2,Fig. 2d,Width & context ablation: benchmark, +17,,,,Figure 2,Fig. 2 details,Architecture arms: dimensions and endpoints,enrichment:arch_width_arm_register +18,13,14,12,Figure 2,Fig. 2e,Gene context: 2k / 3k / 6k / 15k, +19,,,,Figure 2,Fig. 2f,Gene panels: progression relative to each endpoint,enrichment:arch_panel_loss_progression +20,,,,Figure 2,Fig. 2 details,Gene-panel arms: exact sizes and training provenance,enrichment:arch_panel_arm_register +21,,,,Figure 2,Fig. 2g,All ablation arms: parameters and training time,enrichment:arch_all_arm_compute +22,,,,Figure 2,Fig. 2h,Real-cell repeat: a sampling reference,enrichment:real_cell_repeat +23,14,15,,Figure 2,Fig. 2i,Native-pseudobulk model comparisons,review:6 +24,15,52,28,Figure 3,Figure 3,Figure 3. Real-bulk adaptation, +25,16,53,29,Figure 3,Figure 3 plan,Figure 3: the paired-adaptation story, +26,17,21,17,Figure 3,Fig. 3a,Bulk and pooled cells: different expression values, +27,,,,Figure 3,Fig. 3a detail,Paired calibration reduces same-donor expression error,enrichment:mismatch_same_donor_errors +28,18,23,19,Figure 3,Fig. 3b detail,Consequence: cells off-manifold, +29,19,5,,Figure 3,Fig. 3b,Healthy paired data: full FT and LoRA,guide:availability +30,20,51,,Figure 3,Fig. 3c,Full FT and LoRA ranks: quality and parameters,review:8 +31,21,49,26,Figure 3,Fig. 3d,Healthy paired-data budget: n training + 7 validation, +32,22,54,30,Figure 3,Fig. 3e,"Five pairs, no extra validation: LoRA vs scSemi", +33,23,55,,Figure 3,Fig. 3f,Composition: error and donor-level wins,review:13 +34,24,60,35,Figure 4,Figure 4,Figure 4. Disease signal preservation, +35,25,61,36,Figure 4,Figure 4 plan,Figure 4: disease signal preservation, +36,26,63,38,Figure 4,Fig. 4a,Disease signals with five training donors, +37,27,67,39,Figure 4,Fig. 4b,5-fold CV: disease signal, +38,28,68,40,Figure 4,Fig. 4c,Disease genes at every list length (CAT), +39,29,71,41,Figure 4,Fig. 4d,"Cell-type deconvolution, same pairs: disease signal", +40,30,86,47,Figure 5,Figure 5,Figure 5. Rare-population identity, +41,31,87,48,Figure 5,Figure 5 plan,Figure 5: paired rare-population identity, +42,32,102,53,Figure 6,Figure 6,Figure 6. Published-finding reproduction, +43,33,103,54,Figure 6,Figure 6 plan,Figure 6: published-finding reproduction, +44,34,107,,Figure 6,Figure 6,Figure 6: what the reproduction must establish,guide:figure6 +45,35,108,56,Supplementary,Supplementary,Supplementary evidence, +46,36,109,57,Supplementary,Supplementary,Supplementary evidence map, +47,37,8,6,Supp S01,Supp. S01,Backbone: SDD → PBISC-Diffusion, +48,38,10,8,Supp S01,Supp. S01,Bulk conditioning, +49,39,17,14,Supp S01,Supp. S01,Denoiser: joint value + support diffusion, +50,40,38,20,Supp S01,Supp. S01,Fine-tuning with paired bulk + sc, +51,41,39,21,Supp S01,Supp. S01,Evaluation design, +52,42,41,22,Supp S01,Supp. S01,How we score generated cells, +53,44,18,,Supp S02,Supp. S02,Does the model follow its bulk conditioning?,healthy_sle_conditioning_interventions +54,45,72,42,Supp S02,Supp. S02,SLE benchmark: PBISC vs scSemiProfiler, +55,46,73,43,Supp S02,Supp. S02,SLE benchmark: per cell type, +56,47,74,,Supp S02,Supp. S02,Disjoint-cell controls test the bulk-broadcast baseline,healthy_sle_disjoint_truth_control +57,48,75,,Supp S02,Supp. S02,SLE: what is added beyond the bulk broadcast?,disease_sle_broadcast +58,49,22,18,Supp S03,Supp. S03,Same shift in three paired cohorts, +59,50,24,,Supp S03,Supp. S03,Input corrections on one real-reference UMAP,healthy_stored_real_reference_umap +60,51,25,,Supp S03,Supp. S03,Where generated-cell density differs from real cells,healthy_saved_density_difference +61,52,26,,Supp S03,Supp. S03,Input calibration changes cell-type composition,healthy_input_control_composition +62,53,27,,Supp S03,Supp. S03,"Same noise, different input: matched-cell shifts",healthy_stored_matched_trajectories +63,54,28,,Supp S03,Supp. S03,Matched noise separates cell state from cell identity,healthy_matched_similarity +64,55,29,,Supp S03,Supp. S03,Input changes can switch the generated cell label,healthy_label_transitions +65,56,30,,Supp S03,Supp. S03,Nearest real cells: distance and label agreement,healthy_nearest_real_by_type +66,57,31,,Supp S03,Supp. S03,Composition agreement does not ensure state agreement,healthy_within_type_centroids +67,58,32,,Supp S03,Supp. S03,Gene-length effects in the bulk input,healthy_gene_length_input +68,59,33,,Supp S03,Supp. S03,Gene-length effects within label-stable cells,healthy_gene_length_stable +69,60,34,,Supp S03,Supp. S03,Raw and TPM shifts persist within cell labels,healthy_raw_tpm_top_genes +70,61,35,,Supp S03,Supp. S03,Reference calibration leaves specific gene-state shifts,healthy_refcal_top_genes +71,62,36,,Supp S03,Supp. S03,Donor trait axes and donor identification differ,healthy_donor_axes +72,63,37,,Supp S03,Supp. S03,Reference choice changes different quality endpoints,healthy_reference_choice +73,64,40,,Supp S04,Supp. S04,Why the historical and strict protocols differ,guide:protocol +74,65,42,,Supp S04,Supp. S04,Technical repeats and follow-up are different controls,healthy_immicro_replicate_controls +75,66,43,,Supp S04,Supp. S04,Annotation agreement and difficult categories,healthy_annotation_agreement +76,67,46,,Supp S04,Supp. S04,Depth matching changes precision and coverage,healthy_depth_matched_quality +77,68,47,,Supp S04,Supp. S04,Detection and library size are separate diagnostics,healthy_detection_and_library +78,69,44,23,Supp S05,Supp. S05,Healthy cohort: LoRA cells cover the real ones, +79,70,45,24,Supp S05,Supp. S05,Healthy cohort: realism beyond precision/coverage, +80,71,48,25,Supp S05,Supp. S05,Healthy cohort: full vs LoRA vs condition encoder, +81,72,57,32,Supp S05,Supp. S05,Representative-dependent composition, +82,73,116,64,Supp S05,Supp. S05,Full vs LoRA vs cond.-encoder-only, +83,74,50,27,Supp S06,Supp. S06,Healthy cohort: LoRA rank and K, +84,75,56,31,Supp S06,Supp. S06,Healthy paired-data learning curves, +85,76,58,33,Supp S06,Supp. S06,"Time: days for scSemiProfiler, minutes for LoRA", +86,77,59,34,Supp S06,Supp. S06,5 donors: time to apply, +87,78,117,65,Supp S06,Supp. S06,"Pairs needed: composition, coverage, training steps", +88,79,118,66,Supp S06,Supp. S06,"LoRA rank: r = 4, 16, 64", +89,80,119,67,Supp S06,Supp. S06,K diversification: no gain, +90,81,62,37,Supp S07,Supp. S07,Five paired cohorts, +91,82,64,,Supp S07,Supp. S07,Sepsis: exact-five reconstruction across five draws,disease_strict_sepsis_quality +92,83,65,,Supp S07,Supp. S07,Sepsis: realism beyond precision and coverage,disease_strict_sepsis_realism +93,84,66,,Supp S07,Supp. S07,Imperial: first completed exact-five comparison,disease_strict_imperial_quality +94,85,110,58,Supp S07,Supp. S07,5 donors: LoRA vs scSemiProfiler — cells, +95,86,111,59,Supp S07,Supp. S07,5 donors: realism beyond precision/coverage, +96,87,112,60,Supp S07,Supp. S07,"5 donors: precision/coverage at k = 3, 5, 10", +97,88,113,61,Supp S07,Supp. S07,5-fold: realism beyond precision/coverage, +98,89,114,62,Supp S07,Supp. S07,Same training pairs: LoRA vs scSemiProfiler, +99,90,115,63,Supp S07,Supp. S07,scSemiProfiler and the representative-copy baseline, +100,91,69,,Supp S08,Supp. S08,Sepsis: patient-aware disease-gene agreement,disease_strict_ye2026_sepsis_deg +101,92,70,,Supp S08,Supp. S08,Imperial: patient-aware disease-gene agreement,disease_strict_imperial_eskd_deg +102,93,82,44,Supp S08,Supp. S08,Sepsis: fine-tuning variants, +103,94,83,45,Supp S08,Supp. S08,Pairs needed: donor and disease signal, +104,95,84,46,Supp S08,Supp. S08,"Cell-type deconvolution, same pairs: composition", +105,96,85,,Supp S08,Supp. S08,Deconvolution: expression coverage limits the comparison,disease_deconv_expression_coverage +106,97,120,,Supp S08,Supp. S08,"K=4,000 recipe: paired reconstruction quality",disease_k4000_quality +107,98,121,,Supp S08,Supp. S08,"K=4,000 recipe: disease signal does not improve uniformly",disease_k4000_disease +108,99,122,,Supp S08,Supp. S08,"K=4,000 recipe: calibration gains are selective",disease_k4000_calibration +109,100,76,,Supp S09,Supp. S09,Influenza: response order versus response genes,disease_influenza_response +110,101,77,,Supp S09,Supp. S09,COVID: calibration on a shared real-cell map,disease_covid_map +111,102,78,,Supp S09,Supp. S09,COVID monocytes: direction after depth matching,disease_covid_direction +112,103,79,,Supp S09,Supp. S09,"COVID monocytes: direction, magnitude and null",disease_covid_monocyte_direction_detail +113,104,80,,Supp S09,Supp. S09,"COVID CD14 monocytes: direction, magnitude and null",disease_covid_cd14_direction_detail +114,105,81,,Supp S09,Supp. S09,COVID: biological endpoints give a mixed verdict,disease_covid_endpoints +115,106,89,,Supp S10,Supp. S10,Rare-state frequencies in observed cells,review:22 +116,107,91,,Supp S10,Supp. S10,Rare-state misses: rules 1–8,disease_rare_misses_1 +117,108,92,,Supp S10,Supp. S10,Rare-state misses: rules 9–15,disease_rare_misses_2 +118,109,93,,Supp S10,Supp. S10,Rare-state fidelity: zero-aware reanalysis,review:23 +119,110,95,,Supp S10,Supp. S10,Sepsis rare states across paired-data budgets,disease_sepsis_rare_support +120,111,96,,Supp S10,Supp. S10,Sepsis rare-state direction across support budgets,disease_sepsis_rare_direction +121,112,97,,Supp S11,Supp. S11,"Rare-state screen in DRESS, Kawasaki and SLE",disease_external_rare_screen +122,113,98,52,Supp S11,Supp. S11,Consequence: disease direction flips, +123,114,99,,Supp S11,Supp. S11,C1Q: single-gene detection versus co-detection,disease_c1q_cross_disease +124,115,100,,Supp S11,Supp. S11,"Behçet: K=4,000 changes direction more than identity",disease_behcet_k4000 +125,116,101,,Supp S11,Supp. S11,Behcet: one-gene and multi-gene C1Q rules,review:24 +126,117,123,68,Supp S12,Supp. S12,Pairs from other cohorts do not transfer, +127,118,124,69,Supp S12,Supp. S12,Longer training on other cohorts: gap stays, +128,119,125,70,Supp S12,Supp. S12,"No pretraining: same cohort, from scratch", +129,120,126,71,Supp S12,Supp. S12,"No pretraining: other cohorts, from scratch", +130,121,127,72,Supp S12,Supp. S12,Rare states: from scratch vs pretrained, +131,122,129,74,Supp S13,Supp. S13,Appendix: scSemiProfiler without output threshold, +132,123,106,,Supp S14,Supp. S14,Bulk-only exploration: calibration populations differ,disease_bulkonly_imperial_wave_shift +133,124,128,73,Historical archive,Historical archive,Historical scoring and plans, +134,125,88,49,Historical archive,Historical only,Rare-state fractions: original analysis, +135,126,90,50,Historical archive,Historical only,Rare-state ranking: original analysis, +136,127,94,51,Historical archive,Historical only,Rare states: original five-fold analysis, +137,128,104,55,Historical archive,Historical archive,Bulk-only cohort plan: original snapshot, +138,129,105,,Historical archive,Historical archive,Historical bulk-only search: no confirmed new finding,disease_bulkonly_verification_history +139,130,130,75,Discussion,Discussion,Discussion and outlook, +140,131,131,76,Discussion,Discussion,Next: other tissues from a few dozen pairs, diff --git 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