diff --git a/paper-releases/pbisc-diffusion/updates/20261003T105229Z-deck-cross-cohort-loco-k1000/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/zs_K2000/per_donor.csv b/paper-releases/pbisc-diffusion/updates/20261003T105229Z-deck-cross-cohort-loco-k1000/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/zs_K2000/per_donor.csv new file mode 100644 index 0000000000000000000000000000000000000000..6bfe84665d151c5a6240c7a04f63588582649b71 --- /dev/null +++ b/paper-releases/pbisc-diffusion/updates/20261003T105229Z-deck-cross-cohort-loco-k1000/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/ye2026_sepsis/zs_K2000/per_donor.csv @@ -0,0 +1,83 @@ +arm,donor,group,n_generated_cells,n_observed_cells,n_reference_cells,gen_T cell,obs_T cell,gen_B cell,obs_B cell,gen_Monocyte,obs_Monocyte,gen_NK cell,obs_NK 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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ye2026_sepsis/zs_K2000.npz", + "receipt": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ye2026_sepsis/zs_K2000.log", + "seed": 20260927, + "sha256": "641f4362f0e52d48e6a9369f67e66552a6caf8e25222c2c585ad1f0ebaea4281", + "state": "completed", + "steps": 50 + }, + { + "artifact_role": "inference_output", + "cohort": "imperial_eskd", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim zs_imperial_eskd_K2000)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/imperial_eskd/zs_K2000.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "giroux2022", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim xcal_hoL_giroux2022_K2000)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/giroux2022/hoL_giroux2022/xcal_K2000.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "ji2025_chili", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim xcal_hoL_ji2025_chili_K2000)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ji2025_chili/hoL_ji2025_chili/xcal_K2000.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "ye2026_sepsis", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim xcal_hoL_ye2026_sepsis_K2000)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ye2026_sepsis/hoL_ye2026_sepsis/xcal_K2000.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "immicro", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim xcal_hoL_immicro_K2000)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/immicro/hoL_immicro/xcal_K2000.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "imperial_eskd", + 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"ji2025_chili", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_ji2025_chili_K2000_lora16sat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ji2025_chili/hoL_ji2025_chili/K2000_lora16sat.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "ye2026_sepsis", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_ye2026_sepsis_K2000_lora16sat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ye2026_sepsis/hoL_ye2026_sepsis/K2000_lora16sat.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "immicro", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_immicro_K2000_lora16sat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/immicro/hoL_immicro/K2000_lora16sat.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "imperial_eskd", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_imperial_eskd_K2000_lora16sat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/imperial_eskd/hoL_imperial_eskd/K2000_lora16sat.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "giroux2022", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_giroux2022_K2000_lora64sat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/giroux2022/hoL_giroux2022/K2000_lora64sat.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "ji2025_chili", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_ji2025_chili_K2000_lora64sat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ji2025_chili/hoL_ji2025_chili/K2000_lora64sat.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "ye2026_sepsis", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_ye2026_sepsis_K2000_lora64sat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ye2026_sepsis/hoL_ye2026_sepsis/K2000_lora64sat.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "immicro", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_immicro_K2000_lora64sat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/immicro/hoL_immicro/K2000_lora64sat.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "imperial_eskd", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_imperial_eskd_K2000_lora64sat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/imperial_eskd/hoL_imperial_eskd/K2000_lora64sat.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "giroux2022", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_giroux2022_K2000_fullsat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/giroux2022/hoL_giroux2022/K2000_fullsat.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "ji2025_chili", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_ji2025_chili_K2000_fullsat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ji2025_chili/hoL_ji2025_chili/K2000_fullsat.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "ye2026_sepsis", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_ye2026_sepsis_K2000_fullsat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/ye2026_sepsis/hoL_ye2026_sepsis/K2000_fullsat.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "immicro", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_immicro_K2000_fullsat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/immicro/hoL_immicro/K2000_fullsat.npz", + "state": "stopped" + }, + { + "artifact_role": "inference_output", + "cohort": "imperial_eskd", + "experiment": "paired_crosscohort_loco_20261002", + "host": "server_1", + "note": "not run: user decision 2026-10-03 19:45, the cross-cohort benchmark is reported at K = 1000 only; queue stopped (claim loco_hoL_imperial_eskd_K2000_fullsat)", + "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/imperial_eskd/hoL_imperial_eskd/K2000_fullsat.npz", + "state": "stopped" + } + ], + "project_id": "pbisc-diffusion", + "summary": "Paper summary deck 2026-10-03 (presentations/2026-09-30--paper-summary--r00, 37 slides): new section 8 slides 25-26 from the cross-cohort leave-one-cohort-out benchmark at K = 1000 ('Pairs from other cohorts do not transfer', 'Longer training on other cohorts: no gain'; tools/sec08_cross_cohort.py, figures, data), agenda item 8 updated. || Cross-cohort (LOCO) benchmark closed at K = 1000 (user decision 2026-10-03 19:45: K = 2000 not needed; the experiment explains why PBISC fits LoRA on a few pairs of each cohort). Final score tables and aggregates, run receipts, K = 2000 zero-shot outputs that finished, and the stopped K = 2000 units registered as stopped (one partial Imperial zero-shot NPZ kept as .partial_stopped)." +}