Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec03_width_bench_summary.csv

@@ -0,0 +1,13 @@
+arm,readout,logfc_r,top50,comp_l1,panel_genes,n_donors,source,run_to_run_resolution_r,run_to_run_resolution_deg
+1x,bernoulli,0.28634830577858145,67.66666666666667,0.1965802312187439,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+1x,cut_p>0.5,0.2454306757496367,59.666666666666664,0.19869969115206496,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+4x,bernoulli,0.2587798754002981,59.333333333333336,0.26355193673169414,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+4x,cut_p>0.5,0.2531444292242156,58.666666666666664,0.2638292168410435,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+ctx4x,bernoulli,0.2783976735416536,68.0,0.16122444256041193,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+ctx4x,cut_p>0.5,0.24548355965577903,61.0,0.16135845886185732,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+prop_oracle,cut_p>0.5,0.2658679517393759,61.666666666666664,0.24375773441517443,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+prop_pred,cut_p>0.5,0.26302786049672094,61.333333333333336,0.24473855778352002,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+trunk4x,bernoulli,0.2681776909360299,61.666666666666664,0.18140091685493046,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+trunk4x,cut_p>0.5,0.265002442274151,60.666666666666664,0.18134384231801878,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+scSemiProfiler,reference,0.2431693343193305,52.0,0.2489601293057801,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+PBISC-VAE,reference,0.3024433815889974,75.0,0.1659300038958973,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec03_width_loss.csv

@@ -0,0 +1,83 @@
+variant,label,run,source,n_genes,hidden_dims,context_dim,condition_dim,params,params_source,status,error,epoch,train_loss,val_loss,val_batches,val_support_elements,train_hours,corpus_fingerprint
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+1x,1x,s0_6k_allK_topup16_seed20260627_bundle_v2,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2,6000,1024/1024/512/256,512,18006.0,54185184,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2/RUN_STATUS.json,COMPLETED,,2.0,0.23202139921451892,0.20473863179174323,48.0,71664704.0,7.909456141178056,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
+1x,1x,s0_6k_allK_topup16_seed20260627_bundle_v2,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2,6000,1024/1024/512/256,512,18006.0,54185184,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2/RUN_STATUS.json,COMPLETED,,3.0,0.2255722844470039,0.2024312690198269,48.0,71664704.0,7.869713902826964,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
+1x,1x,s0_6k_allK_topup16_seed20260627_bundle_v2,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2,6000,1024/1024/512/256,512,18006.0,54185184,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2/RUN_STATUS.json,COMPLETED,,4.0,0.22538006052831375,0.20112108404024034,48.0,71664704.0,7.886052343224162,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
+1x,1x,s0_6k_allK_topup16_seed20260627_bundle_v2,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2,6000,1024/1024/512/256,512,18006.0,54185184,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2/RUN_STATUS.json,COMPLETED,,5.0,0.22297009279248356,0.20023802761499732,48.0,71664704.0,7.865286767811114,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
+1x,1x,s0_6k_allK_topup16_seed20260627_bundle_v2,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2,6000,1024/1024/512/256,512,18006.0,54185184,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2/RUN_STATUS.json,COMPLETED,,6.0,0.22204926203445355,0.199543590804856,48.0,71664704.0,0.8412666869652458,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
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+1x,1x,s0_6k_allK_topup16_seed20260627_bundle_v2,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2,6000,1024/1024/512/256,512,18006.0,54185184,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2/RUN_STATUS.json,COMPLETED,,8.0,0.22053580699843003,0.1986065118093504,48.0,71664704.0,0.8592313445991345,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
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+1x,1x,s0_6k_allK_topup16_seed20260627_bundle_v2,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2,6000,1024/1024/512/256,512,18006.0,54185184,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2/RUN_STATUS.json,COMPLETED,,10.0,0.21930339920364067,0.1980309911671051,48.0,71664704.0,0.8693530401169038,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
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+ctx4x,context x4,s0_6k_allK_topup16_seed20260627_archctx2048_v1,server_2:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_archctx2048_v1,6000,1024/1024/512/256,2048,18006.0,102106848,server_2:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_archctx2048_v1/RUN_STATUS.json,COMPLETED,,1.0,0.25296481637083607,0.2124463326087258,48.0,71664704.0,10.03651941557473,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
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+trunk4x,trunk x4,s0_6k_allK_topup16_seed20260627_arch4x_ctx512_v1,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_arch4x_ctx512_v1,6000,4096/4096/2048/1024,512,18006.0,239955168,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_arch4x_ctx512_v1/RUN_STATUS.json,COMPLETED,,9.0,0.15629562724292115,0.13909846215567084,48.0,71664704.0,2.3306868970252497,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
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+trunk4x,trunk x4,s0_6k_allK_topup16_seed20260627_arch4x_ctx512_v1,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_arch4x_ctx512_v1,6000,4096/4096/2048/1024,512,18006.0,239955168,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_arch4x_ctx512_v1/RUN_STATUS.json,COMPLETED,,14.0,0.15141480748258182,0.13616134970845795,48.0,71664704.0,2.3429699872644334,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
+trunk4x,trunk x4,s0_6k_allK_topup16_seed20260627_arch4x_ctx512_v1,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_arch4x_ctx512_v1,6000,4096/4096/2048/1024,512,18006.0,239955168,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_arch4x_ctx512_v1/RUN_STATUS.json,COMPLETED,,15.0,0.15122120808951672,0.13571725870278167,48.0,71664704.0,2.3052973599661426,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
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+prop,1x + proportion hint,s0_6k_allK_topup16_seed20260627_prop_v1,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1,6000,1024/1024/512/256,512,18015.0,54189792,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1/RUN_STATUS.json,COMPLETED,,9.0,0.2209783890977518,0.19825012307186557,48.0,71664704.0,1.133232349011685,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
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+prop,1x + proportion hint,s0_6k_allK_topup16_seed20260627_prop_v1,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1,6000,1024/1024/512/256,512,18015.0,54189792,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1/RUN_STATUS.json,COMPLETED,,11.0,0.21931412004360093,0.19762870210785763,48.0,71664704.0,0.8707197979052499,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
+prop,1x + proportion hint,s0_6k_allK_topup16_seed20260627_prop_v1,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1,6000,1024/1024/512/256,512,18015.0,54189792,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1/RUN_STATUS.json,COMPLETED,,12.0,0.22120801692314904,0.1973445714886434,48.0,71664704.0,0.8775037639839057,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
+prop,1x + proportion hint,s0_6k_allK_topup16_seed20260627_prop_v1,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1,6000,1024/1024/512/256,512,18015.0,54189792,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1/RUN_STATUS.json,COMPLETED,,13.0,0.2182121478773677,0.1971458503818902,48.0,71664704.0,0.8799358152294816,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
+prop,1x + proportion hint,s0_6k_allK_topup16_seed20260627_prop_v1,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1,6000,1024/1024/512/256,512,18015.0,54189792,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1/RUN_STATUS.json,COMPLETED,,14.0,0.21842328271899053,0.19697703334478006,48.0,71664704.0,0.8788443905289104,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
+prop,1x + proportion hint,s0_6k_allK_topup16_seed20260627_prop_v1,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1,6000,1024/1024/512/256,512,18015.0,54189792,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1/RUN_STATUS.json,COMPLETED,,15.0,0.2186864161183099,0.19674517015745907,48.0,71664704.0,0.8523645868230637,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007
+prop,1x + proportion hint,s0_6k_allK_topup16_seed20260627_prop_v1,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1,6000,1024/1024/512/256,512,18015.0,54189792,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1/RUN_STATUS.json,COMPLETED,,16.0,0.2177424053599396,0.1966288537508436,48.0,71664704.0,0.8700038866955503,eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec03_width_loss_headline.csv

@@ -0,0 +1,15 @@
+quantity,value,source
+val_loss_e16_1x,0.19683827167344528,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"
+val_loss_e16_trunk4x,0.13552372691340842,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"
+val_loss_e16_4x,0.13555952362068185,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"
+val_loss_e16_ctx4x,0.19690110062305166,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"
+val_loss_e16_prop,0.1966288537508436,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"
+val_loss_change_pct_trunk4x_vs_1x,-31.149706933902422,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"
+sat_epoch_1x,8,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"
+sat_epoch_trunk4x,13,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"
+val_drop_pct_per_part_e12_16_1x,0.08342930928496829,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"
+val_drop_pct_per_part_e12_16_trunk4x,0.264364764549507,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"
+parts_done_16x,2,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"
+status_16x,FAILED_PRESERVED: system memory safety floor crossed: 19.59 GiB < 24.00 GiB (472 s into part 3); not resumed,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"
+hours_per_part_16x_old_loader,25.912562533498324,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"
+hours_per_part_1x_parts1-5_old_loader,7.928003585887836,"data/sec03_width_loss.csv, data/sec03_width_saturation.csv (history.json / RUN_STATUS.json of each run)"

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec03_width_saturation.csv

@@ -0,0 +1,6 @@
+variant,sat_epoch,val_at_sat,val_e16,val_e1,train_e16,sat_epoch_tol0.5pct,sat_epoch_tol2pct,val_drop_pct_per_part_e12_16,rule,source
+1x,8,0.1986065118093504,0.19683827167344528,0.214239367541846,0.21796313272947557,11,5,0.08342930928496829,first part after which val stays within 1% of its part-16 value,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2/history.json
+ctx4x,9,0.19858956610811687,0.19690110062305166,0.2124463326087258,0.2180165075346353,12,5,0.09443923588673364,first part after which val stays within 1% of its part-16 value,server_2:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_archctx2048_v1/history.json
+trunk4x,13,0.1364451094644726,0.13552372691340842,0.19049126496803853,0.1503220506663736,14,11,0.264364764549507,first part after which val stays within 1% of its part-16 value,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_arch4x_ctx512_v1/history.json
+4x,13,0.13654129606199597,0.13555952362068185,0.19074054537299634,0.15030342727578544,15,11,0.2781372801479504,first part after which val stays within 1% of its part-16 value,server_2:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_arch4x_v1/history.json
+prop,8,0.19857406709983574,0.1966288537508436,0.2143726271726606,0.2177424053599396,12,5,0.09099856457317208,first part after which val stays within 1% of its part-16 value,server_1:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1/history.json