Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/result.json

@@ -0,0 +1,537 @@
+{
+  "schema": "pbisc.strengthening.rare-literature.v1",
+  "slides": [
+    {
+      "kind": "content",
+      "key": "rare_literature_published_population_targets",
+      "role": "f5_original_paper_observed_gate",
+      "title": "Figure 5 targets begin with the source paper",
+      "section_label": "Fig. 5 \u00b7 Source-defined populations",
+      "layout": "full",
+      "keywords": [],
+      "figures": [
+        "figures/strengthening_20261013/rare_literature/published_population_targets.png"
+      ],
+      "palette": "biological",
+      "footnote": "Ye: Fig. 5 proliferating pediatric monocytes. Imperial: Fig. 5 wave-2 steroid-associated monocytes; fine labels/timing still needed.",
+      "footnote_full": "Original-cohort retrospective analysis. No new generation, label inference or embedding fit. Literature targets are not automatically rare; rarity and identity require observed evidence. Ye: Fig. 5 proliferating pediatric monocytes. Imperial: Fig. 5 wave-2 steroid-associated monocytes; fine labels/timing still needed. [{\"cohort\": \"ye2026_sepsis\", \"citation\": \"Ye et al., Nature Immunology 2026\", \"doi\": \"10.1038/s41590-025-02345-x\", \"url\": \"https://www.nature.com/articles/s41590-025-02345-x\", \"figure\": \"Fig. 5a\\u2013f; validation Fig. 7f / Extended Data Fig. 9e\", \"population\": \"Mono_c06-CD14-MKI67\", \"kind\": \"Reported discrete proliferating monocyte subset; rarity must be measured locally\", \"setting\": \"Pediatric pulmonary sepsis (paper: within 48 h of onset); pediatric HC/ICU, abdominal sepsis and adults remain controls.\", \"markers\": [\"CD14\", \"MKI67\", \"STMN1\", \"MPO\", \"ELANE\"], \"negative_markers\": [], \"interpretation\": \"MKI67/STMN1/MPO/ELANE jointly support the published proliferative program in a CD14 monocyte context. PCLAF is not required by this original Fig. 5 definition.\", \"gate\": \"No fine-cluster labels found in 133 audited canonical obs schemas or the paired table. Marker co-detection is not a Mono_c06 cluster assignment.\", \"pdf\": \"/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Single-cell multi-omic landscape reveals anatomical-specific immune features in adult and pediatric sepsis.pdf\", \"all_paired_samples\": 85, \"identity_passed_samples\": 82, \"identity_passed_donors\": 82, \"legacy_cache_genes\": 73, \"legacy_cache_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/ye2026_sepsis/draw0/lora5.npz\", \"observed_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_obs.parquet\", \"observed_author_labels\": {\"\": 610713}, \"observed_full_panel_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_panel6k.npz\", \"wave_counts\": {}, \"sex_by_group\": {}, \"available_cache_markers\": [\"MKI67\", \"MPO\", \"ELANE\"], \"missing_cache_markers\": [\"CD14\", \"STMN1\"]}, {\"cohort\": \"imperial_eskd\", \"citation\": \"Stephenson et al., Cell Genomics 2025\", \"doi\": \"10.1016/j.xgen.2025.100918\", \"url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC12366655/\", \"figure\": \"Fig. 5A\\u2013G (especially 5C\\u2013E)\", \"population\": \"Dexamethasone-related monocytes\", \"kind\": \"Reported treatment-associated discrete subset; not automatically rare\", \"setting\": \"Wave 2 COVID-positive patients receiving glucocorticoids; align each blood visit to treatment start.\", \"markers\": [\"CD163\", \"ADAMTS2\", \"SLC1A3\", \"SESN1\", \"FPR1\", \"MTSS1\", \"MFGE8\", \"MRC1\"], \"negative_markers\": [\"JUN\", \"CXCL8\", \"HLA-DRA\", \"HLA-DRB5\"], \"interpretation\": \"The paper contrasts an anti-inflammatory/phagocytic program with lower inflammatory and antigen-presentation expression. Fig. 3 HLA-II suppression is a program, not a rare-cell identity.\", \"gate\": \"Paired metadata include wave 2, but the available author labels collapse these cells into broad monocytes. Treatment dates and fine labels must be joined before frequency recovery.\", \"pdf\": \"/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Stephenson2025_CellGenom_temporal_multiomics_COVID19_ESKD.pdf\", \"all_paired_samples\": 172, \"identity_passed_samples\": 158, \"identity_passed_donors\": 58, \"legacy_cache_genes\": 73, \"legacy_cache_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/imperial_eskd/draw0/lora5.npz\", \"observed_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/cells_obs.parquet\", \"observed_author_labels\": {\"T CD4 Helper\": 85235, \"NK\": 77242, \"T CD8 CTL\": 70657, \"CD14mono\": 53967, \"T CD4 Naive\": 49943, \"B_naive\": 33633, \"CD16mono\": 29056, \"T CD8 CM\": 19962, \"T CD8 Naive\": 18113, \"T CD4 CTL\": 17209, \"B_switched_mem\": 9223, \"T reg\": 9176, \"NK CD56 bright\": 8610, \"Int.mono\": 7136, \"DC2\": 5972, \"NKT\": 4647, \"DC3\": 4318, \"T g/d\": 3911, \"pDC\": 3034, \"B_non-switched_mem\": 2815, \"RBC\": 2604, \"Platelet\": 2576, \"B_ASC_IgA\": 2538, \"B_CD11c\": 2108, \"MAIT\": 1984, \"T CD8 EM\": 1860, \"B_ASC_dividing\": 1785, \"B_ASC_IgG\": 1182, \"HSPC\": 1004, \"DC1\": 754, \"B_ASC_IgM\": 499, \"T CD4 cycling\": 447, \"T CD8 EMRA\": 400, \"ASDC\": 231, \"ILC\": 147, \"B_ASC_other\": 36}, \"observed_full_panel_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/cells_panel6k.npz\", \"wave_counts\": {\"w2\": 83, \"w1\": 75, \"w1|w2\": 14}, \"sex_by_group\": {}, \"available_cache_markers\": [\"CD163\", \"HLA-DRA\"], \"missing_cache_markers\": [\"ADAMTS2\", \"SLC1A3\", \"SESN1\", \"FPR1\", \"MTSS1\", \"MFGE8\", \"MRC1\", \"JUN\", \"CXCL8\", \"HLA-DRB5\"]}]",
+      "notes": "Original-cohort retrospective analysis. No new generation, label inference or embedding fit. Literature targets are not automatically rare; rarity and identity require observed evidence. Ye: Fig. 5 proliferating pediatric monocytes. Imperial: Fig. 5 wave-2 steroid-associated monocytes; fine labels/timing still needed. [{\"cohort\": \"ye2026_sepsis\", \"citation\": \"Ye et al., Nature Immunology 2026\", \"doi\": \"10.1038/s41590-025-02345-x\", \"url\": \"https://www.nature.com/articles/s41590-025-02345-x\", \"figure\": \"Fig. 5a\\u2013f; validation Fig. 7f / Extended Data Fig. 9e\", \"population\": \"Mono_c06-CD14-MKI67\", \"kind\": \"Reported discrete proliferating monocyte subset; rarity must be measured locally\", \"setting\": \"Pediatric pulmonary sepsis (paper: within 48 h of onset); pediatric HC/ICU, abdominal sepsis and adults remain controls.\", \"markers\": [\"CD14\", \"MKI67\", \"STMN1\", \"MPO\", \"ELANE\"], \"negative_markers\": [], \"interpretation\": \"MKI67/STMN1/MPO/ELANE jointly support the published proliferative program in a CD14 monocyte context. PCLAF is not required by this original Fig. 5 definition.\", \"gate\": \"No fine-cluster labels found in 133 audited canonical obs schemas or the paired table. Marker co-detection is not a Mono_c06 cluster assignment.\", \"pdf\": \"/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Single-cell multi-omic landscape reveals anatomical-specific immune features in adult and pediatric sepsis.pdf\", \"all_paired_samples\": 85, \"identity_passed_samples\": 82, \"identity_passed_donors\": 82, \"legacy_cache_genes\": 73, \"legacy_cache_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/ye2026_sepsis/draw0/lora5.npz\", \"observed_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_obs.parquet\", \"observed_author_labels\": {\"\": 610713}, \"observed_full_panel_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_panel6k.npz\", \"wave_counts\": {}, \"sex_by_group\": {}, \"available_cache_markers\": [\"MKI67\", \"MPO\", \"ELANE\"], \"missing_cache_markers\": [\"CD14\", \"STMN1\"]}, {\"cohort\": \"imperial_eskd\", \"citation\": \"Stephenson et al., Cell Genomics 2025\", \"doi\": \"10.1016/j.xgen.2025.100918\", \"url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC12366655/\", \"figure\": \"Fig. 5A\\u2013G (especially 5C\\u2013E)\", \"population\": \"Dexamethasone-related monocytes\", \"kind\": \"Reported treatment-associated discrete subset; not automatically rare\", \"setting\": \"Wave 2 COVID-positive patients receiving glucocorticoids; align each blood visit to treatment start.\", \"markers\": [\"CD163\", \"ADAMTS2\", \"SLC1A3\", \"SESN1\", \"FPR1\", \"MTSS1\", \"MFGE8\", \"MRC1\"], \"negative_markers\": [\"JUN\", \"CXCL8\", \"HLA-DRA\", \"HLA-DRB5\"], \"interpretation\": \"The paper contrasts an anti-inflammatory/phagocytic program with lower inflammatory and antigen-presentation expression. Fig. 3 HLA-II suppression is a program, not a rare-cell identity.\", \"gate\": \"Paired metadata include wave 2, but the available author labels collapse these cells into broad monocytes. Treatment dates and fine labels must be joined before frequency recovery.\", \"pdf\": \"/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Stephenson2025_CellGenom_temporal_multiomics_COVID19_ESKD.pdf\", \"all_paired_samples\": 172, \"identity_passed_samples\": 158, \"identity_passed_donors\": 58, \"legacy_cache_genes\": 73, \"legacy_cache_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/imperial_eskd/draw0/lora5.npz\", \"observed_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/cells_obs.parquet\", \"observed_author_labels\": {\"T CD4 Helper\": 85235, \"NK\": 77242, \"T CD8 CTL\": 70657, \"CD14mono\": 53967, \"T CD4 Naive\": 49943, \"B_naive\": 33633, \"CD16mono\": 29056, \"T CD8 CM\": 19962, \"T CD8 Naive\": 18113, \"T CD4 CTL\": 17209, \"B_switched_mem\": 9223, \"T reg\": 9176, \"NK CD56 bright\": 8610, \"Int.mono\": 7136, \"DC2\": 5972, \"NKT\": 4647, \"DC3\": 4318, \"T g/d\": 3911, \"pDC\": 3034, \"B_non-switched_mem\": 2815, \"RBC\": 2604, \"Platelet\": 2576, \"B_ASC_IgA\": 2538, \"B_CD11c\": 2108, \"MAIT\": 1984, \"T CD8 EM\": 1860, \"B_ASC_dividing\": 1785, \"B_ASC_IgG\": 1182, \"HSPC\": 1004, \"DC1\": 754, \"B_ASC_IgM\": 499, \"T CD4 cycling\": 447, \"T CD8 EMRA\": 400, \"ASDC\": 231, \"ILC\": 147, \"B_ASC_other\": 36}, \"observed_full_panel_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/cells_panel6k.npz\", \"wave_counts\": {\"w2\": 83, \"w1\": 75, \"w1|w2\": 14}, \"sex_by_group\": {}, \"available_cache_markers\": [\"CD163\", \"HLA-DRA\"], \"missing_cache_markers\": [\"ADAMTS2\", \"SLC1A3\", \"SESN1\", \"FPR1\", \"MTSS1\", \"MFGE8\", \"MRC1\", \"JUN\", \"CXCL8\", \"HLA-DRB5\"]}]",
+      "sources": "https://www.nature.com/articles/s41590-025-02345-x; https://pmc.ncbi.nlm.nih.gov/articles/PMC12366655/; https://pmc.ncbi.nlm.nih.gov/articles/PMC9271053/; https://pmc.ncbi.nlm.nih.gov/articles/PMC12049347/"
+    },
+    {
+      "kind": "content",
+      "key": "rare_literature_ye_observed_paper_markers",
+      "role": "f5_original_paper_observed_gate",
+      "title": "Ye sepsis: the published markers in observed paired cells",
+      "section_label": "Fig. 5 \u00b7 Source-defined populations",
+      "layout": "full",
+      "keywords": [],
+      "figures": [
+        "figures/strengthening_20261013/rare_literature/ye_observed_paper_markers.png"
+      ],
+      "palette": "biological",
+      "footnote": "Native-depth diagnostic, not Mono_c06 identity. MKI67/STMN1 mean: pulmonary 2.33%, abdominal 4.10%; pulmonary specificity is not reproduced.",
+      "footnote_full": "Original-cohort retrospective analysis. No new generation, label inference or embedding fit. Literature targets are not automatically rare; rarity and identity require observed evidence. Native-depth diagnostic, not Mono_c06 identity. MKI67/STMN1 mean: pulmonary 2.33%, abdominal 4.10%; pulmonary specificity is not reproduced. {\"n_cells\": 610713, \"input_genes\": 6000, \"retained_genes\": 5, \"csr_entries_streamed\": 255556515, \"max_entries_per_block\": 1000000, \"no_full_sparse_or_dense_matrix_loaded\": true, \"identity_passed_samples\": 82, \"analyzed_samples\": 82, \"analyzed_monocytes\": 111269, \"all_five_genes_measured_in_all_source_samples\": true, \"labels_npz_rows_exact\": true, \"author_fine_labels_present\": false, \"source_sha256\": \"c814b53d04ffdbe8e257f1fb35df80e7945479db95a924774522b9a967745280\", \"limitations\": [\"Native depth; marker dropout and depth differ between donors.\", \"Parent uses the frozen AIFI label; published Mono_c06 fine labels are absent.\", \"Co-detection patterns are diagnostics, not author-cluster calls.\", \"This is reuse of the original cohort, not independent replication.\"], \"no_new_inference\": true, \"no_embedding_fit\": true, \"observed_pattern_comparison\": {\"pattern\": \"MKI67+STMN1\", \"pediatric_pulmonary_mean_percent\": 2.331039105701644, \"pediatric_abdominal_mean_percent\": 4.103247268955951, \"pulmonary_specificity_reproduced\": false}, \"author_label_inventory\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/ye_author_label_inventory.json\"}",
+      "notes": "Original-cohort retrospective analysis. No new generation, label inference or embedding fit. Literature targets are not automatically rare; rarity and identity require observed evidence. Native-depth diagnostic, not Mono_c06 identity. MKI67/STMN1 mean: pulmonary 2.33%, abdominal 4.10%; pulmonary specificity is not reproduced. {\"n_cells\": 610713, \"input_genes\": 6000, \"retained_genes\": 5, \"csr_entries_streamed\": 255556515, \"max_entries_per_block\": 1000000, \"no_full_sparse_or_dense_matrix_loaded\": true, \"identity_passed_samples\": 82, \"analyzed_samples\": 82, \"analyzed_monocytes\": 111269, \"all_five_genes_measured_in_all_source_samples\": true, \"labels_npz_rows_exact\": true, \"author_fine_labels_present\": false, \"source_sha256\": \"c814b53d04ffdbe8e257f1fb35df80e7945479db95a924774522b9a967745280\", \"limitations\": [\"Native depth; marker dropout and depth differ between donors.\", \"Parent uses the frozen AIFI label; published Mono_c06 fine labels are absent.\", \"Co-detection patterns are diagnostics, not author-cluster calls.\", \"This is reuse of the original cohort, not independent replication.\"], \"no_new_inference\": true, \"no_embedding_fit\": true, \"observed_pattern_comparison\": {\"pattern\": \"MKI67+STMN1\", \"pediatric_pulmonary_mean_percent\": 2.331039105701644, \"pediatric_abdominal_mean_percent\": 4.103247268955951, \"pulmonary_specificity_reproduced\": false}, \"author_label_inventory\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/ye_author_label_inventory.json\"}",
+      "sources": "https://www.nature.com/articles/s41590-025-02345-x; https://pmc.ncbi.nlm.nih.gov/articles/PMC12366655/; https://pmc.ncbi.nlm.nih.gov/articles/PMC9271053/; https://pmc.ncbi.nlm.nih.gov/articles/PMC12049347/"
+    },
+    {
+      "kind": "content",
+      "key": "rare_literature_published_program_boundaries",
+      "role": "f5_original_paper_observed_gate",
+      "title": "A transcriptional program is not automatically a rare population",
+      "section_label": "Fig. 5 \u00b7 Source-defined populations",
+      "layout": "full",
+      "keywords": [],
+      "figures": [
+        "figures/strengthening_20261013/rare_literature/published_program_boundaries.png"
+      ],
+      "palette": "biological",
+      "footnote": "Giroux: pre-seroconversion RNA/regulon states and sex imbalance. Ji: common-cell-type DE/TCR changes; no paper-defined rare identity established.",
+      "footnote_full": "Original-cohort retrospective analysis. No new generation, label inference or embedding fit. Literature targets are not automatically rare; rarity and identity require observed evidence. Giroux: pre-seroconversion RNA/regulon states and sex imbalance. Ji: common-cell-type DE/TCR changes; no paper-defined rare identity established. [{\"cohort\": \"giroux2022\", \"citation\": \"Giroux et al., Scientific Reports 2022\", \"doi\": \"10.1038/s41598-022-15668-8\", \"url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC9271053/\", \"figure\": \"Fig. 5A\\u2013F; Supplementary Tables S8/S9\", \"population\": \"IgG-negative CD14 monocyte clusters 2/4 (mild) and 7 (moderate)\", \"kind\": \"Transcriptomic/regulon states with epigenetic corroboration; rarity not established\", \"setting\": \"Before IgG seroconversion, mild versus moderate outpatients; local severe label must be checked against the paper\\u2019s moderate definition.\", \"markers\": [\"CD14\", \"IRF7\", \"IRF1\", \"STAT1\", \"CEBPB\", \"KLF3\", \"CCR2\"], \"negative_markers\": [], \"interpretation\": \"IRF7/IRF1/STAT1 versus CEBPB/KLF3 are regulatory-program findings, not an exact RNA-only positivity gate. scRNA clusters connect to scATAC states.\", \"gate\": \"No author fine labels locally; IRF1/KLF3 are outside the saved 6k panel. Align serostatus, longitudinal donors and marked sex imbalance; no exact rare-cluster claim.\", \"xml\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/Giroux2022_PMC9271053.xml\", \"all_paired_samples\": 26, \"identity_passed_samples\": 24, \"identity_passed_donors\": 9, \"legacy_cache_genes\": 73, \"legacy_cache_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/giroux2022/draw0/lora5.npz\", \"observed_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_obs.parquet\", \"observed_author_labels\": {\"\": 276615}, \"observed_full_panel_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_panel6k.npz\", \"wave_counts\": {}, \"sex_by_group\": {\"FEMALE\": {\"mild\": 0, \"severe\": 11}, \"MALE\": {\"mild\": 13, \"severe\": 2}}, \"available_cache_markers\": [], \"missing_cache_markers\": [\"CD14\", \"IRF7\", \"IRF1\", \"STAT1\", \"CEBPB\", \"KLF3\", \"CCR2\"]}, {\"cohort\": \"ji2025_chili\", \"citation\": \"Ji et al., Cancer Immunology, Immunotherapy 2025\", \"doi\": \"10.1007/s00262-025-04033-z\", \"url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC12049347/\", \"figure\": \"Fig. 2 (TCR clonality); Fig. 4A/B and Table 2 (cell-type DE/programs)\", \"population\": \"CD8 TEM, CD8 naive, CD4 TCM and CD16 monocyte programs\", \"kind\": \"Common cell-type expression changes; no specific rare subset established in the original paper\", \"setting\": \"Liver-injury timepoint TOL versus pretreatment BC / control AC; FU1 is follow-up and must not be silently pooled with TOL.\", \"markers\": [], \"negative_markers\": [], \"interpretation\": \"Original HuBMAP-type labels survive locally. DEG counts and pathways can be reproduced as Figure 4 evidence; TCR clonality cannot be recovered from generated 6k expression alone.\", \"gate\": \"Do not substitute a generic cycling/plasmablast rule for the paper\\u2019s main finding. Select a genuinely paper-defined rare target only if supplementary evidence supports one.\", \"pdf\": \"/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Ji2025_CancerImmunolImmunother_checkpoint_inhibitor_liver_injury.pdf\", \"all_paired_samples\": 40, \"identity_passed_samples\": 33, \"identity_passed_donors\": 20, \"legacy_cache_genes\": 72, \"legacy_cache_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/ji2025_chili/draw0/lora5.npz\", \"observed_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/cells_obs.parquet\", \"observed_author_labels\": {\"CD4 TCM\": 48811, \"CD14 Mono\": 38304, \"NK\": 19796, \"CD8 TEM\": 15575, \"CD16 Mono\": 6512, \"B naive\": 4822, \"CD8 Naive\": 2736, \"CD4 Naive\": 2559, \"B intermediate\": 2372, \"Platelet\": 2165, \"Treg\": 2001, \"cDC2\": 1259, \"CD8 TCM\": 1134, \"NK_CD56bright\": 1010, \"B memory\": 878, \"Plasmablast\": 852, \"MAIT\": 801, \"HSPC\": 724, \"CD4 TEM\": 600, \"pDC\": 582, \"NK Proliferating\": 358, \"dnT\": 314, \"Eryth\": 230, \"CD4 CTL\": 80, \"ILC\": 68, \"cDC1\": 55, \"ASDC\": 50, \"CD8 Proliferating\": 28, \"gdT\": 14, \"CD4 Proliferating\": 8}, \"observed_full_panel_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/cells_panel6k.npz\", \"wave_counts\": {}, \"sex_by_group\": {}, \"available_cache_markers\": [], \"missing_cache_markers\": []}]",
+      "notes": "Original-cohort retrospective analysis. No new generation, label inference or embedding fit. Literature targets are not automatically rare; rarity and identity require observed evidence. Giroux: pre-seroconversion RNA/regulon states and sex imbalance. Ji: common-cell-type DE/TCR changes; no paper-defined rare identity established. [{\"cohort\": \"giroux2022\", \"citation\": \"Giroux et al., Scientific Reports 2022\", \"doi\": \"10.1038/s41598-022-15668-8\", \"url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC9271053/\", \"figure\": \"Fig. 5A\\u2013F; Supplementary Tables S8/S9\", \"population\": \"IgG-negative CD14 monocyte clusters 2/4 (mild) and 7 (moderate)\", \"kind\": \"Transcriptomic/regulon states with epigenetic corroboration; rarity not established\", \"setting\": \"Before IgG seroconversion, mild versus moderate outpatients; local severe label must be checked against the paper\\u2019s moderate definition.\", \"markers\": [\"CD14\", \"IRF7\", \"IRF1\", \"STAT1\", \"CEBPB\", \"KLF3\", \"CCR2\"], \"negative_markers\": [], \"interpretation\": \"IRF7/IRF1/STAT1 versus CEBPB/KLF3 are regulatory-program findings, not an exact RNA-only positivity gate. scRNA clusters connect to scATAC states.\", \"gate\": \"No author fine labels locally; IRF1/KLF3 are outside the saved 6k panel. 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+      "url": "https://www.nature.com/articles/s41590-025-02345-x",
+      "figure": "Fig. 5a\u2013f; validation Fig. 7f / Extended Data Fig. 9e",
+      "population": "Mono_c06-CD14-MKI67",
+      "kind": "Reported discrete proliferating monocyte subset; rarity must be measured locally",
+      "setting": "Pediatric pulmonary sepsis (paper: within 48 h of onset); pediatric HC/ICU, abdominal sepsis and adults remain controls.",
+      "markers": [
+        "CD14",
+        "MKI67",
+        "STMN1",
+        "MPO",
+        "ELANE"
+      ],
+      "negative_markers": [],
+      "interpretation": "MKI67/STMN1/MPO/ELANE jointly support the published proliferative program in a CD14 monocyte context. PCLAF is not required by this original Fig. 5 definition.",
+      "gate": "No fine-cluster labels found in 133 audited canonical obs schemas or the paired table. Marker co-detection is not a Mono_c06 cluster assignment.",
+      "pdf": "/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Single-cell multi-omic landscape reveals anatomical-specific immune features in adult and pediatric sepsis.pdf",
+      "all_paired_samples": 85,
+      "identity_passed_samples": 82,
+      "identity_passed_donors": 82,
+      "legacy_cache_genes": 73,
+      "legacy_cache_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/ye2026_sepsis/draw0/lora5.npz",
+      "observed_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_obs.parquet",
+      "observed_author_labels": {
+        "": 610713
+      },
+      "observed_full_panel_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_panel6k.npz",
+      "wave_counts": {},
+      "sex_by_group": {},
+      "available_cache_markers": [
+        "MKI67",
+        "MPO",
+        "ELANE"
+      ],
+      "missing_cache_markers": [
+        "CD14",
+        "STMN1"
+      ]
+    },
+    {
+      "cohort": "imperial_eskd",
+      "citation": "Stephenson et al., Cell Genomics 2025",
+      "doi": "10.1016/j.xgen.2025.100918",
+      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12366655/",
+      "figure": "Fig. 5A\u2013G (especially 5C\u2013E)",
+      "population": "Dexamethasone-related monocytes",
+      "kind": "Reported treatment-associated discrete subset; not automatically rare",
+      "setting": "Wave 2 COVID-positive patients receiving glucocorticoids; align each blood visit to treatment start.",
+      "markers": [
+        "CD163",
+        "ADAMTS2",
+        "SLC1A3",
+        "SESN1",
+        "FPR1",
+        "MTSS1",
+        "MFGE8",
+        "MRC1"
+      ],
+      "negative_markers": [
+        "JUN",
+        "CXCL8",
+        "HLA-DRA",
+        "HLA-DRB5"
+      ],
+      "interpretation": "The paper contrasts an anti-inflammatory/phagocytic program with lower inflammatory and antigen-presentation expression. Fig. 3 HLA-II suppression is a program, not a rare-cell identity.",
+      "gate": "Paired metadata include wave 2, but the available author labels collapse these cells into broad monocytes. Treatment dates and fine labels must be joined before frequency recovery.",
+      "pdf": "/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Stephenson2025_CellGenom_temporal_multiomics_COVID19_ESKD.pdf",
+      "all_paired_samples": 172,
+      "identity_passed_samples": 158,
+      "identity_passed_donors": 58,
+      "legacy_cache_genes": 73,
+      "legacy_cache_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/imperial_eskd/draw0/lora5.npz",
+      "observed_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/cells_obs.parquet",
+      "observed_author_labels": {
+        "T CD4 Helper": 85235,
+        "NK": 77242,
+        "T CD8 CTL": 70657,
+        "CD14mono": 53967,
+        "T CD4 Naive": 49943,
+        "B_naive": 33633,
+        "CD16mono": 29056,
+        "T CD8 CM": 19962,
+        "T CD8 Naive": 18113,
+        "T CD4 CTL": 17209,
+        "B_switched_mem": 9223,
+        "T reg": 9176,
+        "NK CD56 bright": 8610,
+        "Int.mono": 7136,
+        "DC2": 5972,
+        "NKT": 4647,
+        "DC3": 4318,
+        "T g/d": 3911,
+        "pDC": 3034,
+        "B_non-switched_mem": 2815,
+        "RBC": 2604,
+        "Platelet": 2576,
+        "B_ASC_IgA": 2538,
+        "B_CD11c": 2108,
+        "MAIT": 1984,
+        "T CD8 EM": 1860,
+        "B_ASC_dividing": 1785,
+        "B_ASC_IgG": 1182,
+        "HSPC": 1004,
+        "DC1": 754,
+        "B_ASC_IgM": 499,
+        "T CD4 cycling": 447,
+        "T CD8 EMRA": 400,
+        "ASDC": 231,
+        "ILC": 147,
+        "B_ASC_other": 36
+      },
+      "observed_full_panel_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/cells_panel6k.npz",
+      "wave_counts": {
+        "w2": 83,
+        "w1": 75,
+        "w1|w2": 14
+      },
+      "sex_by_group": {},
+      "available_cache_markers": [
+        "CD163",
+        "HLA-DRA"
+      ],
+      "missing_cache_markers": [
+        "ADAMTS2",
+        "SLC1A3",
+        "SESN1",
+        "FPR1",
+        "MTSS1",
+        "MFGE8",
+        "MRC1",
+        "JUN",
+        "CXCL8",
+        "HLA-DRB5"
+      ]
+    },
+    {
+      "cohort": "giroux2022",
+      "citation": "Giroux et al., Scientific Reports 2022",
+      "doi": "10.1038/s41598-022-15668-8",
+      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9271053/",
+      "figure": "Fig. 5A\u2013F; Supplementary Tables S8/S9",
+      "population": "IgG-negative CD14 monocyte clusters 2/4 (mild) and 7 (moderate)",
+      "kind": "Transcriptomic/regulon states with epigenetic corroboration; rarity not established",
+      "setting": "Before IgG seroconversion, mild versus moderate outpatients; local severe label must be checked against the paper\u2019s moderate definition.",
+      "markers": [
+        "CD14",
+        "IRF7",
+        "IRF1",
+        "STAT1",
+        "CEBPB",
+        "KLF3",
+        "CCR2"
+      ],
+      "negative_markers": [],
+      "interpretation": "IRF7/IRF1/STAT1 versus CEBPB/KLF3 are regulatory-program findings, not an exact RNA-only positivity gate. scRNA clusters connect to scATAC states.",
+      "gate": "No author fine labels locally; IRF1/KLF3 are outside the saved 6k panel. Align serostatus, longitudinal donors and marked sex imbalance; no exact rare-cluster claim.",
+      "xml": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/Giroux2022_PMC9271053.xml",
+      "all_paired_samples": 26,
+      "identity_passed_samples": 24,
+      "identity_passed_donors": 9,
+      "legacy_cache_genes": 73,
+      "legacy_cache_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/giroux2022/draw0/lora5.npz",
+      "observed_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_obs.parquet",
+      "observed_author_labels": {
+        "": 276615
+      },
+      "observed_full_panel_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_panel6k.npz",
+      "wave_counts": {},
+      "sex_by_group": {
+        "FEMALE": {
+          "mild": 0,
+          "severe": 11
+        },
+        "MALE": {
+          "mild": 13,
+          "severe": 2
+        }
+      },
+      "available_cache_markers": [],
+      "missing_cache_markers": [
+        "CD14",
+        "IRF7",
+        "IRF1",
+        "STAT1",
+        "CEBPB",
+        "KLF3",
+        "CCR2"
+      ]
+    },
+    {
+      "cohort": "ji2025_chili",
+      "citation": "Ji et al., Cancer Immunology, Immunotherapy 2025",
+      "doi": "10.1007/s00262-025-04033-z",
+      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12049347/",
+      "figure": "Fig. 2 (TCR clonality); Fig. 4A/B and Table 2 (cell-type DE/programs)",
+      "population": "CD8 TEM, CD8 naive, CD4 TCM and CD16 monocyte programs",
+      "kind": "Common cell-type expression changes; no specific rare subset established in the original paper",
+      "setting": "Liver-injury timepoint TOL versus pretreatment BC / control AC; FU1 is follow-up and must not be silently pooled with TOL.",
+      "markers": [],
+      "negative_markers": [],
+      "interpretation": "Original HuBMAP-type labels survive locally. DEG counts and pathways can be reproduced as Figure 4 evidence; TCR clonality cannot be recovered from generated 6k expression alone.",
+      "gate": "Do not substitute a generic cycling/plasmablast rule for the paper\u2019s main finding. Select a genuinely paper-defined rare target only if supplementary evidence supports one.",
+      "pdf": "/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Ji2025_CancerImmunolImmunother_checkpoint_inhibitor_liver_injury.pdf",
+      "all_paired_samples": 40,
+      "identity_passed_samples": 33,
+      "identity_passed_donors": 20,
+      "legacy_cache_genes": 72,
+      "legacy_cache_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/ji2025_chili/draw0/lora5.npz",
+      "observed_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/cells_obs.parquet",
+      "observed_author_labels": {
+        "CD4 TCM": 48811,
+        "CD14 Mono": 38304,
+        "NK": 19796,
+        "CD8 TEM": 15575,
+        "CD16 Mono": 6512,
+        "B naive": 4822,
+        "CD8 Naive": 2736,
+        "CD4 Naive": 2559,
+        "B intermediate": 2372,
+        "Platelet": 2165,
+        "Treg": 2001,
+        "cDC2": 1259,
+        "CD8 TCM": 1134,
+        "NK_CD56bright": 1010,
+        "B memory": 878,
+        "Plasmablast": 852,
+        "MAIT": 801,
+        "HSPC": 724,
+        "CD4 TEM": 600,
+        "pDC": 582,
+        "NK Proliferating": 358,
+        "dnT": 314,
+        "Eryth": 230,
+        "CD4 CTL": 80,
+        "ILC": 68,
+        "cDC1": 55,
+        "ASDC": 50,
+        "CD8 Proliferating": 28,
+        "gdT": 14,
+        "CD4 Proliferating": 8
+      },
+      "observed_full_panel_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/cells_panel6k.npz",
+      "wave_counts": {},
+      "sex_by_group": {},
+      "available_cache_markers": [],
+      "missing_cache_markers": []
+    }
+  ],
+  "observed_ye": {
+    "n_cells": 610713,
+    "input_genes": 6000,
+    "retained_genes": 5,
+    "csr_entries_streamed": 255556515,
+    "max_entries_per_block": 1000000,
+    "no_full_sparse_or_dense_matrix_loaded": true,
+    "identity_passed_samples": 82,
+    "analyzed_samples": 82,
+    "analyzed_monocytes": 111269,
+    "all_five_genes_measured_in_all_source_samples": true,
+    "labels_npz_rows_exact": true,
+    "author_fine_labels_present": false,
+    "source_sha256": "c814b53d04ffdbe8e257f1fb35df80e7945479db95a924774522b9a967745280",
+    "limitations": [
+      "Native depth; marker dropout and depth differ between donors.",
+      "Parent uses the frozen AIFI label; published Mono_c06 fine labels are absent.",
+      "Co-detection patterns are diagnostics, not author-cluster calls.",
+      "This is reuse of the original cohort, not independent replication."
+    ],
+    "no_new_inference": true,
+    "no_embedding_fit": true,
+    "observed_pattern_comparison": {
+      "pattern": "MKI67+STMN1",
+      "pediatric_pulmonary_mean_percent": 2.331039105701644,
+      "pediatric_abdominal_mean_percent": 4.103247268955951,
+      "pulmonary_specificity_reproduced": false
+    },
+    "author_label_inventory": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/ye_author_label_inventory.json"
+  },
+  "no_new_inference": true,
+  "generated_population_recovery_claim": false,
+  "completion_scope": "Four primary-paper target definitions plus observed Ye five-marker diagnostics; exact paper-cluster/PBISC/scSemi identity comparison remains gated."
+}

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/target_matrix.csv

@@ -0,0 +1,5 @@
+cohort,citation,doi,url,figure,population,kind,setting,markers,negative_markers,interpretation,gate,pdf,all_paired_samples,identity_passed_samples,identity_passed_donors,legacy_cache_genes,legacy_cache_path,observed_path,observed_full_panel_path,available_cache_markers,missing_cache_markers,xml
+ye2026_sepsis,"Ye et al., Nature Immunology 2026",10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,Fig. 5a–f; validation Fig. 7f / Extended Data Fig. 9e,Mono_c06-CD14-MKI67,Reported discrete proliferating monocyte subset; rarity must be measured locally,"Pediatric pulmonary sepsis (paper: within 48 h of onset); pediatric HC/ICU, abdominal sepsis and adults remain controls.",CD14; MKI67; STMN1; MPO; ELANE,,MKI67/STMN1/MPO/ELANE jointly support the published proliferative program in a CD14 monocyte context. PCLAF is not required by this original Fig. 5 definition.,No fine-cluster labels found in 133 audited canonical obs schemas or the paired table. Marker co-detection is not a Mono_c06 cluster assignment.,/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Single-cell multi-omic landscape reveals anatomical-specific immune features in adult and pediatric sepsis.pdf,85,82,82,73,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/ye2026_sepsis/draw0/lora5.npz,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_obs.parquet,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_panel6k.npz,MKI67; MPO; ELANE,CD14; STMN1,
+imperial_eskd,"Stephenson et al., Cell Genomics 2025",10.1016/j.xgen.2025.100918,https://pmc.ncbi.nlm.nih.gov/articles/PMC12366655/,Fig. 5A–G (especially 5C–E),Dexamethasone-related monocytes,Reported treatment-associated discrete subset; not automatically rare,Wave 2 COVID-positive patients receiving glucocorticoids; align each blood visit to treatment start.,CD163; ADAMTS2; SLC1A3; SESN1; FPR1; MTSS1; MFGE8; MRC1,JUN; CXCL8; HLA-DRA; HLA-DRB5,"The paper contrasts an anti-inflammatory/phagocytic program with lower inflammatory and antigen-presentation expression. Fig. 3 HLA-II suppression is a program, not a rare-cell identity.","Paired metadata include wave 2, but the available author labels collapse these cells into broad monocytes. Treatment dates and fine labels must be joined before frequency recovery.",/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Stephenson2025_CellGenom_temporal_multiomics_COVID19_ESKD.pdf,172,158,58,73,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/imperial_eskd/draw0/lora5.npz,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/cells_obs.parquet,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/cells_panel6k.npz,CD163; HLA-DRA,ADAMTS2; SLC1A3; SESN1; FPR1; MTSS1; MFGE8; MRC1; JUN; CXCL8; HLA-DRB5,
+giroux2022,"Giroux et al., Scientific Reports 2022",10.1038/s41598-022-15668-8,https://pmc.ncbi.nlm.nih.gov/articles/PMC9271053/,Fig. 5A–F; Supplementary Tables S8/S9,IgG-negative CD14 monocyte clusters 2/4 (mild) and 7 (moderate),Transcriptomic/regulon states with epigenetic corroboration; rarity not established,"Before IgG seroconversion, mild versus moderate outpatients; local severe label must be checked against the paper’s moderate definition.",CD14; IRF7; IRF1; STAT1; CEBPB; KLF3; CCR2,,"IRF7/IRF1/STAT1 versus CEBPB/KLF3 are regulatory-program findings, not an exact RNA-only positivity gate. scRNA clusters connect to scATAC states.","No author fine labels locally; IRF1/KLF3 are outside the saved 6k panel. Align serostatus, longitudinal donors and marked sex imbalance; no exact rare-cluster claim.",,26,24,9,73,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/giroux2022/draw0/lora5.npz,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_obs.parquet,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_panel6k.npz,,CD14; IRF7; IRF1; STAT1; CEBPB; KLF3; CCR2,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/Giroux2022_PMC9271053.xml
+ji2025_chili,"Ji et al., Cancer Immunology, Immunotherapy 2025",10.1007/s00262-025-04033-z,https://pmc.ncbi.nlm.nih.gov/articles/PMC12049347/,Fig. 2 (TCR clonality); Fig. 4A/B and Table 2 (cell-type DE/programs),"CD8 TEM, CD8 naive, CD4 TCM and CD16 monocyte programs",Common cell-type expression changes; no specific rare subset established in the original paper,Liver-injury timepoint TOL versus pretreatment BC / control AC; FU1 is follow-up and must not be silently pooled with TOL.,,,Original HuBMAP-type labels survive locally. DEG counts and pathways can be reproduced as Figure 4 evidence; TCR clonality cannot be recovered from generated 6k expression alone.,Do not substitute a generic cycling/plasmablast rule for the paper’s main finding. Select a genuinely paper-defined rare target only if supplementary evidence supports one.,/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Ji2025_CancerImmunolImmunother_checkpoint_inhibitor_liver_injury.pdf,40,33,20,72,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/ji2025_chili/draw0/lora5.npz,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/cells_obs.parquet,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/cells_panel6k.npz,,,

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/target_matrix.json

@@ -0,0 +1,252 @@
+[
+  {
+    "cohort": "ye2026_sepsis",
+    "citation": "Ye et al., Nature Immunology 2026",
+    "doi": "10.1038/s41590-025-02345-x",
+    "url": "https://www.nature.com/articles/s41590-025-02345-x",
+    "figure": "Fig. 5a\u2013f; validation Fig. 7f / Extended Data Fig. 9e",
+    "population": "Mono_c06-CD14-MKI67",
+    "kind": "Reported discrete proliferating monocyte subset; rarity must be measured locally",
+    "setting": "Pediatric pulmonary sepsis (paper: within 48 h of onset); pediatric HC/ICU, abdominal sepsis and adults remain controls.",
+    "markers": [
+      "CD14",
+      "MKI67",
+      "STMN1",
+      "MPO",
+      "ELANE"
+    ],
+    "negative_markers": [],
+    "interpretation": "MKI67/STMN1/MPO/ELANE jointly support the published proliferative program in a CD14 monocyte context. PCLAF is not required by this original Fig. 5 definition.",
+    "gate": "No fine-cluster labels found in 133 audited canonical obs schemas or the paired table. Marker co-detection is not a Mono_c06 cluster assignment.",
+    "pdf": "/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Single-cell multi-omic landscape reveals anatomical-specific immune features in adult and pediatric sepsis.pdf",
+    "all_paired_samples": 85,
+    "identity_passed_samples": 82,
+    "identity_passed_donors": 82,
+    "legacy_cache_genes": 73,
+    "legacy_cache_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/ye2026_sepsis/draw0/lora5.npz",
+    "observed_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_obs.parquet",
+    "observed_author_labels": {
+      "": 610713
+    },
+    "observed_full_panel_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_panel6k.npz",
+    "wave_counts": {},
+    "sex_by_group": {},
+    "available_cache_markers": [
+      "MKI67",
+      "MPO",
+      "ELANE"
+    ],
+    "missing_cache_markers": [
+      "CD14",
+      "STMN1"
+    ]
+  },
+  {
+    "cohort": "imperial_eskd",
+    "citation": "Stephenson et al., Cell Genomics 2025",
+    "doi": "10.1016/j.xgen.2025.100918",
+    "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12366655/",
+    "figure": "Fig. 5A\u2013G (especially 5C\u2013E)",
+    "population": "Dexamethasone-related monocytes",
+    "kind": "Reported treatment-associated discrete subset; not automatically rare",
+    "setting": "Wave 2 COVID-positive patients receiving glucocorticoids; align each blood visit to treatment start.",
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+      "SLC1A3",
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+      "CXCL8",
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+    "gate": "Paired metadata include wave 2, but the available author labels collapse these cells into broad monocytes. Treatment dates and fine labels must be joined before frequency recovery.",
+    "pdf": "/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Stephenson2025_CellGenom_temporal_multiomics_COVID19_ESKD.pdf",
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+      "B_naive": 33633,
+      "CD16mono": 29056,
+      "T CD8 CM": 19962,
+      "T CD8 Naive": 18113,
+      "T CD4 CTL": 17209,
+      "B_switched_mem": 9223,
+      "T reg": 9176,
+      "NK CD56 bright": 8610,
+      "Int.mono": 7136,
+      "DC2": 5972,
+      "NKT": 4647,
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+      "T g/d": 3911,
+      "pDC": 3034,
+      "B_non-switched_mem": 2815,
+      "RBC": 2604,
+      "Platelet": 2576,
+      "B_ASC_IgA": 2538,
+      "B_CD11c": 2108,
+      "MAIT": 1984,
+      "T CD8 EM": 1860,
+      "B_ASC_dividing": 1785,
+      "B_ASC_IgG": 1182,
+      "HSPC": 1004,
+      "DC1": 754,
+      "B_ASC_IgM": 499,
+      "T CD4 cycling": 447,
+      "T CD8 EMRA": 400,
+      "ASDC": 231,
+      "ILC": 147,
+      "B_ASC_other": 36
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+    "observed_full_panel_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/cells_panel6k.npz",
+    "wave_counts": {
+      "w2": 83,
+      "w1": 75,
+      "w1|w2": 14
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+    "sex_by_group": {},
+    "available_cache_markers": [
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+      "HLA-DRA"
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+    "missing_cache_markers": [
+      "ADAMTS2",
+      "SLC1A3",
+      "SESN1",
+      "FPR1",
+      "MTSS1",
+      "MFGE8",
+      "MRC1",
+      "JUN",
+      "CXCL8",
+      "HLA-DRB5"
+    ]
+  },
+  {
+    "cohort": "giroux2022",
+    "citation": "Giroux et al., Scientific Reports 2022",
+    "doi": "10.1038/s41598-022-15668-8",
+    "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9271053/",
+    "figure": "Fig. 5A\u2013F; Supplementary Tables S8/S9",
+    "population": "IgG-negative CD14 monocyte clusters 2/4 (mild) and 7 (moderate)",
+    "kind": "Transcriptomic/regulon states with epigenetic corroboration; rarity not established",
+    "setting": "Before IgG seroconversion, mild versus moderate outpatients; local severe label must be checked against the paper\u2019s moderate definition.",
+    "markers": [
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+      "IRF7",
+      "IRF1",
+      "STAT1",
+      "CEBPB",
+      "KLF3",
+      "CCR2"
+    ],
+    "negative_markers": [],
+    "interpretation": "IRF7/IRF1/STAT1 versus CEBPB/KLF3 are regulatory-program findings, not an exact RNA-only positivity gate. scRNA clusters connect to scATAC states.",
+    "gate": "No author fine labels locally; IRF1/KLF3 are outside the saved 6k panel. Align serostatus, longitudinal donors and marked sex imbalance; no exact rare-cluster claim.",
+    "xml": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/Giroux2022_PMC9271053.xml",
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+    "observed_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_obs.parquet",
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+    "observed_full_panel_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_panel6k.npz",
+    "wave_counts": {},
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+      "MALE": {
+        "mild": 13,
+        "severe": 2
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+      "IRF1",
+      "STAT1",
+      "CEBPB",
+      "KLF3",
+      "CCR2"
+    ]
+  },
+  {
+    "cohort": "ji2025_chili",
+    "citation": "Ji et al., Cancer Immunology, Immunotherapy 2025",
+    "doi": "10.1007/s00262-025-04033-z",
+    "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12049347/",
+    "figure": "Fig. 2 (TCR clonality); Fig. 4A/B and Table 2 (cell-type DE/programs)",
+    "population": "CD8 TEM, CD8 naive, CD4 TCM and CD16 monocyte programs",
+    "kind": "Common cell-type expression changes; no specific rare subset established in the original paper",
+    "setting": "Liver-injury timepoint TOL versus pretreatment BC / control AC; FU1 is follow-up and must not be silently pooled with TOL.",
+    "markers": [],
+    "negative_markers": [],
+    "interpretation": "Original HuBMAP-type labels survive locally. DEG counts and pathways can be reproduced as Figure 4 evidence; TCR clonality cannot be recovered from generated 6k expression alone.",
+    "gate": "Do not substitute a generic cycling/plasmablast rule for the paper\u2019s main finding. Select a genuinely paper-defined rare target only if supplementary evidence supports one.",
+    "pdf": "/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Ji2025_CancerImmunolImmunother_checkpoint_inhibitor_liver_injury.pdf",
+    "all_paired_samples": 40,
+    "identity_passed_samples": 33,
+    "identity_passed_donors": 20,
+    "legacy_cache_genes": 72,
+    "legacy_cache_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/ji2025_chili/draw0/lora5.npz",
+    "observed_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/cells_obs.parquet",
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+      "CD16 Mono": 6512,
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+      "B intermediate": 2372,
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+      "dnT": 314,
+      "Eryth": 230,
+      "CD4 CTL": 80,
+      "ILC": 68,
+      "cDC1": 55,
+      "ASDC": 50,
+      "CD8 Proliferating": 28,
+      "gdT": 14,
+      "CD4 Proliferating": 8
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+    "available_cache_markers": [],
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