Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/logs/imperial_eskd-features.log

@@ -0,0 +1 @@
+{"dataset": "imperial_eskd", "meta_rows": 321, "composition_rows": 59220, "state_rows": 35585, "calibration_rows": 250, "bulkonly_draws": [0, 1, 2, 3, 4]}

paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/logs/imperial_eskd-observed.log

@@ -0,0 +1 @@
+{"dataset": "imperial_eskd", "set": "observed", "cells": 514260, "samples": 157, "seconds": 15.8}

paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/logs/manifest.log

@@ -0,0 +1 @@
+{"files": 13, "bytes": 3491646479}

paper-releases/pbisc-diffusion/updates/20261006T033847Z-bulkonly-lora5-k4000/diffusion/dataset/server_1/model8/plans/bulkonly_lora5_k4000_20261006/logs/run_cpu_20261006T075220.log

@@ -0,0 +1,111 @@
+2026-10-06T07:52:20 ye2026_sepsis-observed: done already
+2026-10-06T08:02:20 ye2026_sepsis-d0-merge: done already
+2026-10-06T08:02:20 ye2026_sepsis-d0-score: done already
+2026-10-06T08:02:20 ye2026_sepsis-d0-pgen: done already
+2026-10-06T08:02:20 ye2026_sepsis-d0-annot: start (cap 40G)
+2026-10-06T08:03:55 ye2026_sepsis-d0-annot: {"dataset": "ye2026_sepsis", "draw": 0, "cells": 488000, "samples": 122, "seconds": 93.7, "labels_l1": {"T cell": 270960, "Monocyte": 75452, "B cell": 70604, "NK cell": 49692, "Other": 18788, "DC": 2504}}
+2026-10-06T08:03:55 ye2026_sepsis-d0-pack: start (cap 40G)
+2026-10-06T08:05:07 ye2026_sepsis-d0-pack: {"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/share/ye2026_sepsis/lora5k4_bulkonly_ye2026_sepsis_draw0.h5ad", "cells": 488000, "samples": 122, "nnz": 139243257, "bytes": 31
+2026-10-06T08:33:07 ye2026_sepsis-d1-merge: start (cap 16G)
+2026-10-06T08:33:36 ye2026_sepsis-d1-merge: {"output_sha256": "a066cc774fe1b70344cf889e213d134dbe85921f8bdfb267f78b487e134e29a5", "cells": 115500, "bulks": 77, "seed": 21260930, "seconds": 28.0}
+2026-10-06T08:33:36 ye2026_sepsis-d1-score: start (cap 32G)
+2026-10-06T08:34:35 ye2026_sepsis-d1-score: {"lora5": {"comp_l1": 0.4726, "coverage": 0.6619, "pb_r_median": 0.8837, "contrast_mean_cp10k_r_gen": 0.0812, "deg_top50_sum": 16}, "lora5_k4000": {"comp_l1": 0.4676, "coverage": 0.681, "pb_r_median": 0.8809, "contrast_mean_cp10k_r_gen": 0.
+2026-10-06T08:34:35 ye2026_sepsis-d1-pgen: start (cap 24G)
+2026-10-06T08:34:53 ye2026_sepsis-d1-pgen: {"dataset": "ye2026_sepsis", "draw": 1, "cells": 115500, "samples": 77, "seconds": 17.9}
+2026-10-06T08:34:53 ye2026_sepsis-d1-annot: start (cap 40G)
+2026-10-06T08:36:02 ye2026_sepsis-d1-annot: {"dataset": "ye2026_sepsis", "draw": 1, "cells": 488000, "samples": 122, "seconds": 68.0, "labels_l1": {"T cell": 212885, "Monocyte": 188708, "Other": 29377, "B cell": 28287, "NK cell": 25125, "DC": 3618}}
+2026-10-06T08:36:02 ye2026_sepsis-d1-pack: start (cap 40G)
+2026-10-06T08:37:17 ye2026_sepsis-d1-pack: {"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/share/ye2026_sepsis/lora5k4_bulkonly_ye2026_sepsis_draw1.h5ad", "cells": 488000, "samples": 122, "nnz": 153973296, "bytes": 34
+2026-10-06T09:01:17 ye2026_sepsis-d2-merge: start (cap 16G)
+2026-10-06T09:01:45 ye2026_sepsis-d2-merge: {"output_sha256": "2544d78f4c79b58f8ac43af31560b62460933336c0797b2551411fda81f2cd7a", "cells": 115500, "bulks": 77, "seed": 22260933, "seconds": 28.2}
+2026-10-06T09:01:45 ye2026_sepsis-d2-score: start (cap 32G)
+2026-10-06T09:02:41 ye2026_sepsis-d2-score: {"lora5": {"comp_l1": 0.4987, "coverage": 0.7606, "pb_r_median": 0.8865, "contrast_mean_cp10k_r_gen": 0.3272, "deg_top50_sum": 26}, "lora5_k4000": {"comp_l1": 0.4953, "coverage": 0.7569, "pb_r_median": 0.8853, "contrast_mean_cp10k_r_gen": 0
+2026-10-06T09:02:41 ye2026_sepsis-d2-pgen: start (cap 24G)
+2026-10-06T09:02:58 ye2026_sepsis-d2-pgen: {"dataset": "ye2026_sepsis", "draw": 2, "cells": 115500, "samples": 77, "seconds": 16.2}
+2026-10-06T09:02:58 ye2026_sepsis-d2-annot: start (cap 40G)
+2026-10-06T09:04:12 ye2026_sepsis-d2-annot: {"dataset": "ye2026_sepsis", "draw": 2, "cells": 488000, "samples": 122, "seconds": 73.5, "labels_l1": {"T cell": 337898, "B cell": 69909, "Monocyte": 46051, "NK cell": 17979, "Other": 15335, "DC": 828}}
+2026-10-06T09:04:12 ye2026_sepsis-d2-pack: start (cap 40G)
+2026-10-06T09:05:19 ye2026_sepsis-d2-pack: {"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/share/ye2026_sepsis/lora5k4_bulkonly_ye2026_sepsis_draw2.h5ad", "cells": 488000, "samples": 122, "nnz": 142128320, "bytes": 32
+2026-10-06T09:29:19 ye2026_sepsis-d3-merge: start (cap 16G)
+2026-10-06T09:29:47 ye2026_sepsis-d3-merge: {"output_sha256": "f6bafba98412167223c2f59a6ab12c00e09cea68cac7375c2e6c861c3a24c35c", "cells": 115500, "bulks": 77, "seed": 23260936, "seconds": 27.3}
+2026-10-06T09:29:47 ye2026_sepsis-d3-score: start (cap 32G)
+2026-10-06T09:30:43 ye2026_sepsis-d3-score: {"lora5": {"comp_l1": 0.4969, "coverage": 0.6553, "pb_r_median": 0.8822, "contrast_mean_cp10k_r_gen": 0.4109, "deg_top50_sum": 17}, "lora5_k4000": {"comp_l1": 0.4018, "coverage": 0.663, "pb_r_median": 0.8867, "contrast_mean_cp10k_r_gen": 0.
+2026-10-06T09:30:43 ye2026_sepsis-d3-pgen: start (cap 24G)
+2026-10-06T09:31:00 ye2026_sepsis-d3-pgen: {"dataset": "ye2026_sepsis", "draw": 3, "cells": 115500, "samples": 77, "seconds": 16.3}
+2026-10-06T09:31:00 ye2026_sepsis-d3-annot: start (cap 40G)
+2026-10-06T09:32:08 ye2026_sepsis-d3-annot: {"dataset": "ye2026_sepsis", "draw": 3, "cells": 488000, "samples": 122, "seconds": 67.2, "labels_l1": {"T cell": 296763, "Monocyte": 98818, "B cell": 38407, "NK cell": 31026, "Other": 20264, "DC": 2722}}
+2026-10-06T09:32:08 ye2026_sepsis-d3-pack: start (cap 40G)
+2026-10-06T09:33:13 ye2026_sepsis-d3-pack: {"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/share/ye2026_sepsis/lora5k4_bulkonly_ye2026_sepsis_draw3.h5ad", "cells": 488000, "samples": 122, "nnz": 130670034, "bytes": 29
+2026-10-06T09:57:13 ye2026_sepsis-d4-merge: start (cap 16G)
+2026-10-06T09:57:41 ye2026_sepsis-d4-merge: {"output_sha256": "aae53a450b3fef8321081bcef6fc0946b4ad3f4841eeb83258b79822fb559c43", "cells": 115500, "bulks": 77, "seed": 24260939, "seconds": 27.1}
+2026-10-06T09:57:41 ye2026_sepsis-d4-score: start (cap 32G)
+2026-10-06T09:58:37 ye2026_sepsis-d4-score: {"lora5": {"comp_l1": 0.3905, "coverage": 0.687, "pb_r_median": 0.885, "contrast_mean_cp10k_r_gen": 0.4953, "deg_top50_sum": 16}, "lora5_k4000": {"comp_l1": 0.3801, "coverage": 0.6954, "pb_r_median": 0.8863, "contrast_mean_cp10k_r_gen": 0.4
+2026-10-06T09:58:37 ye2026_sepsis-d4-pgen: start (cap 24G)
+2026-10-06T09:58:55 ye2026_sepsis-d4-pgen: {"dataset": "ye2026_sepsis", "draw": 4, "cells": 115500, "samples": 77, "seconds": 16.5}
+2026-10-06T09:58:55 ye2026_sepsis-d4-annot: start (cap 40G)
+2026-10-06T10:00:15 ye2026_sepsis-d4-annot: {"dataset": "ye2026_sepsis", "draw": 4, "cells": 488000, "samples": 122, "seconds": 79.6, "labels_l1": {"T cell": 274922, "Monocyte": 106075, "B cell": 56016, "NK cell": 24601, "Other": 24159, "DC": 2227}}
+2026-10-06T10:00:15 ye2026_sepsis-d4-pack: start (cap 40G)
+2026-10-06T10:01:19 ye2026_sepsis-d4-pack: {"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/share/ye2026_sepsis/lora5k4_bulkonly_ye2026_sepsis_draw4.h5ad", "cells": 488000, "samples": 122, "nnz": 135515762, "bytes": 31
+2026-10-06T10:01:19 ye2026_sepsis-features: start (cap 28G)
+2026-10-06T10:01:59 ye2026_sepsis-features: {"dataset": "ye2026_sepsis", "meta_rows": 204, "composition_rows": 37695, "state_rows": 21485, "calibration_rows": 250, "bulkonly_draws": [0, 1, 2, 3, 4]}
+2026-10-06T10:01:59 ye2026_sepsis-aggregate: start (cap 4G)
+2026-10-06T10:02:00 ye2026_sepsis-aggregate: Scorer check: this plan's K = 1,000 arm vs the benchmark's stored draw scores, max |difference| per draw: draw0 0 (25 metrics), draw1 0 (25 metrics), draw2 0 (25 metrics), draw3 0 (25 metrics), draw4 0 (25 metrics).
+2026-10-06T10:02:00 imperial_eskd-observed: start (cap 32G)
+2026-10-06T10:02:16 imperial_eskd-observed: {"dataset": "imperial_eskd", "set": "observed", "cells": 514260, "samples": 157, "seconds": 15.8}
+2026-10-06T10:36:16 imperial_eskd-d0-merge: start (cap 16G)
+2026-10-06T10:37:07 imperial_eskd-d0-merge: {"output_sha256": "0758f1d6c54c41d7109a89fc0927612c162a4c48fe4462bfeaaf43afc0e4d738", "cells": 213000, "bulks": 142, "seed": 20260927, "seconds": 50.0}
+2026-10-06T10:37:07 imperial_eskd-d0-score: start (cap 32G)
+2026-10-06T10:38:57 imperial_eskd-d0-score: {"lora5": {"comp_l1": 0.4781, "coverage": 0.757, "pb_r_median": 0.8742, "contrast_mean_cp10k_r_gen": 0.7799, "deg_top50_sum": 116}, "lora5_k4000": {"comp_l1": 0.4542, "coverage": 0.7516, "pb_r_median": 0.8744, "contrast_mean_cp10k_r_gen": 0
+2026-10-06T10:38:57 imperial_eskd-d0-pgen: start (cap 24G)
+2026-10-06T10:39:22 imperial_eskd-d0-pgen: {"dataset": "imperial_eskd", "draw": 0, "cells": 213000, "samples": 142, "seconds": 24.6}
+2026-10-06T10:39:22 imperial_eskd-d0-annot: start (cap 40G)
+2026-10-06T10:41:12 imperial_eskd-d0-annot: {"dataset": "imperial_eskd", "draw": 0, "cells": 656000, "samples": 164, "seconds": 108.9, "labels_l1": {"T cell": 357021, "Monocyte": 123601, "NK cell": 91114, "B cell": 45000, "Other": 21096, "DC": 18168}}
+2026-10-06T10:41:12 imperial_eskd-d0-pack: start (cap 40G)
+2026-10-06T10:42:38 imperial_eskd-d0-pack: {"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/share/imperial_eskd/lora5k4_bulkonly_imperial_eskd_draw0.h5ad", "cells": 656000, "samples": 164, "nnz": 170048565, "bytes": 38
+2026-10-06T11:14:39 imperial_eskd-d1-merge: start (cap 16G)
+2026-10-06T11:15:23 imperial_eskd-d1-merge: {"output_sha256": "05991e2292443dbb1e81354c9fae4fd19d13165021af2e43494cbd7d5baf0f44", "cells": 214500, "bulks": 143, "seed": 21260930, "seconds": 44.0}
+2026-10-06T11:15:23 imperial_eskd-d1-score: start (cap 32G)
+2026-10-06T11:17:04 imperial_eskd-d1-score: {"lora5": {"comp_l1": 0.516, "coverage": 0.7829, "pb_r_median": 0.8694, "contrast_mean_cp10k_r_gen": 0.7571, "deg_top50_sum": 119}, "lora5_k4000": {"comp_l1": 0.5142, "coverage": 0.7696, "pb_r_median": 0.8694, "contrast_mean_cp10k_r_gen": 0
+2026-10-06T11:17:04 imperial_eskd-d1-pgen: start (cap 24G)
+2026-10-06T11:17:31 imperial_eskd-d1-pgen: {"dataset": "imperial_eskd", "draw": 1, "cells": 214500, "samples": 143, "seconds": 26.1}
+2026-10-06T11:17:31 imperial_eskd-d1-annot: start (cap 40G)
+2026-10-06T11:19:08 imperial_eskd-d1-annot: {"dataset": "imperial_eskd", "draw": 1, "cells": 656000, "samples": 164, "seconds": 96.7, "labels_l1": {"T cell": 399305, "Monocyte": 108412, "B cell": 75537, "NK cell": 42234, "DC": 21733, "Other": 8779}}
+2026-10-06T11:19:08 imperial_eskd-d1-pack: start (cap 40G)
+2026-10-06T11:20:32 imperial_eskd-d1-pack: {"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/share/imperial_eskd/lora5k4_bulkonly_imperial_eskd_draw1.h5ad", "cells": 656000, "samples": 164, "nnz": 163401652, "bytes": 37
+2026-10-06T11:20:32 imperial_eskd-d2-merge: start (cap 16G)
+2026-10-06T11:21:20 imperial_eskd-d2-merge: {"output_sha256": "9123da6e1eb062049c9028bf317c5f4e86be34600584c0e49645a0f92577fd21", "cells": 213000, "bulks": 142, "seed": 22260933, "seconds": 47.5}
+2026-10-06T11:21:20 imperial_eskd-d2-score: start (cap 32G)
+2026-10-06T11:23:01 imperial_eskd-d2-score: {"lora5": {"comp_l1": 0.5118, "coverage": 0.665, "pb_r_median": 0.8619, "contrast_mean_cp10k_r_gen": 0.714, "deg_top50_sum": 103}, "lora5_k4000": {"comp_l1": 0.5091, "coverage": 0.6098, "pb_r_median": 0.8614, "contrast_mean_cp10k_r_gen": 0.
+2026-10-06T11:23:01 imperial_eskd-d2-pgen: start (cap 24G)
+2026-10-06T11:23:27 imperial_eskd-d2-pgen: {"dataset": "imperial_eskd", "draw": 2, "cells": 213000, "samples": 142, "seconds": 25.1}
+2026-10-06T11:23:27 imperial_eskd-d2-annot: start (cap 40G)
+2026-10-06T11:25:24 imperial_eskd-d2-annot: {"dataset": "imperial_eskd", "draw": 2, "cells": 656000, "samples": 164, "seconds": 116.3, "labels_l1": {"T cell": 325909, "Monocyte": 160965, "B cell": 78123, "NK cell": 51207, "DC": 27009, "Other": 12787}}
+2026-10-06T11:25:24 imperial_eskd-d2-pack: start (cap 40G)
+2026-10-06T11:26:47 imperial_eskd-d2-pack: {"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/share/imperial_eskd/lora5k4_bulkonly_imperial_eskd_draw2.h5ad", "cells": 656000, "samples": 164, "nnz": 148164333, "bytes": 33
+2026-10-06T11:26:47 imperial_eskd-d3-merge: start (cap 16G)
+2026-10-06T11:27:39 imperial_eskd-d3-merge: {"output_sha256": "1591cc471523687baec49a1f29318b245b822ae7e0a5e744ec20e01ad4794e29", "cells": 217500, "bulks": 145, "seed": 23260936, "seconds": 51.9}
+2026-10-06T11:27:39 imperial_eskd-d3-score: start (cap 32G)
+2026-10-06T11:29:23 imperial_eskd-d3-score: {"lora5": {"comp_l1": 0.5275, "coverage": 0.8427, "pb_r_median": 0.8725, "contrast_mean_cp10k_r_gen": 0.7456, "deg_top50_sum": 117}, "lora5_k4000": {"comp_l1": 0.5088, "coverage": 0.8355, "pb_r_median": 0.8747, "contrast_mean_cp10k_r_gen": 
+2026-10-06T11:29:23 imperial_eskd-d3-pgen: start (cap 24G)
+2026-10-06T11:29:50 imperial_eskd-d3-pgen: {"dataset": "imperial_eskd", "draw": 3, "cells": 217500, "samples": 145, "seconds": 26.5}
+2026-10-06T11:29:50 imperial_eskd-d3-annot: start (cap 40G)
+2026-10-06T11:31:50 imperial_eskd-d3-annot: {"dataset": "imperial_eskd", "draw": 3, "cells": 656000, "samples": 164, "seconds": 119.3, "labels_l1": {"T cell": 317277, "Monocyte": 181585, "NK cell": 98658, "B cell": 39612, "DC": 12792, "Other": 6076}}
+2026-10-06T11:31:50 imperial_eskd-d3-pack: start (cap 40G)
+2026-10-06T11:33:17 imperial_eskd-d3-pack: {"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/share/imperial_eskd/lora5k4_bulkonly_imperial_eskd_draw3.h5ad", "cells": 656000, "samples": 164, "nnz": 184990314, "bytes": 42
+2026-10-06T11:33:17 imperial_eskd-d4-merge: start (cap 16G)
+2026-10-06T11:33:59 imperial_eskd-d4-merge: {"output_sha256": "b286609b60048aef6987258f8e767efae1fa0e80761375662dc33afd9723637d", "cells": 214500, "bulks": 143, "seed": 24260939, "seconds": 41.8}
+2026-10-06T11:33:59 imperial_eskd-d4-score: start (cap 32G)
+2026-10-06T11:35:41 imperial_eskd-d4-score: {"lora5": {"comp_l1": 0.4814, "coverage": 0.6369, "pb_r_median": 0.8718, "contrast_mean_cp10k_r_gen": 0.7492, "deg_top50_sum": 113}, "lora5_k4000": {"comp_l1": 0.4498, "coverage": 0.639, "pb_r_median": 0.8727, "contrast_mean_cp10k_r_gen": 0
+2026-10-06T11:35:41 imperial_eskd-d4-pgen: start (cap 24G)
+2026-10-06T11:36:08 imperial_eskd-d4-pgen: {"dataset": "imperial_eskd", "draw": 4, "cells": 214500, "samples": 143, "seconds": 25.9}
+2026-10-06T11:36:08 imperial_eskd-d4-annot: start (cap 40G)
+2026-10-06T11:37:46 imperial_eskd-d4-annot: {"dataset": "imperial_eskd", "draw": 4, "cells": 656000, "samples": 164, "seconds": 97.4, "labels_l1": {"T cell": 325592, "Monocyte": 115033, "B cell": 102250, "NK cell": 82190, "DC": 15894, "Other": 15041}}
+2026-10-06T11:37:46 imperial_eskd-d4-pack: start (cap 40G)
+2026-10-06T11:39:09 imperial_eskd-d4-pack: {"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bulkonly_lora5_k4000_20261006/share/imperial_eskd/lora5k4_bulkonly_imperial_eskd_draw4.h5ad", "cells": 656000, "samples": 164, "nnz": 158864609, "bytes": 36
+2026-10-06T11:39:09 imperial_eskd-features: start (cap 28G)
+2026-10-06T11:39:44 imperial_eskd-features: {"dataset": "imperial_eskd", "meta_rows": 321, "composition_rows": 59220, "state_rows": 35585, "calibration_rows": 250, "bulkonly_draws": [0, 1, 2, 3, 4]}
+2026-10-06T11:39:44 imperial_eskd-aggregate: start (cap 4G)
+2026-10-06T11:39:45 imperial_eskd-aggregate: Scorer check: this plan's K = 1,000 arm vs the benchmark's stored draw scores, max |difference| per draw: draw0 0 (25 metrics), draw1 0 (25 metrics), draw2 0 (25 metrics), draw3 0 (25 metrics), draw4 0 (25 metrics).
+2026-10-06T11:39:45 manifest: start (cap 8G)
+2026-10-06T11:39:50 manifest: {"files": 13, "bytes": 3491646479}
+2026-10-06T11:39:50 all jobs attempted; failed=0