Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/arch_training_arms.csv

@@ -0,0 +1,11 @@
+key,label,family,run,original_host,original_path,local_metadata,status,n_genes,detection_floor,hidden_dims,context_dim,condition_dim,hint_dim,parameters,completed_parts,optimizer_steps,train_seconds_completed_parts,validation_seconds_completed_parts,train_seconds_per_step_weighted,last_part_seconds_per_step,final_val_loss,saturation_part_0_5pct,saturation_part_1pct,saturation_part_2pct,late_loss_drop_pct_per_part,training_seed,batch_size,error,runtime_note
+base,1× baseline,architecture,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,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_bundle_v2,COMPLETED,6000,1%,1024 / 1024 / 512 / 256,512,18006,0,54185184,16,764249,176822.3321379937,1167.0891583766206,0.2313674367097552,0.06473128057010676,0.19683827167344528,11,8,5,0.08342930928496829,20260627,256,,"Observed train-loop elapsed time including loading; excludes validation, checkpoint writes, restart gaps and failed partial parts. Loader/host changes prevent controlled speed claims."
+context,Context ×4,architecture,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,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec03_server2_snapshots/s0_6k_allK_topup16_seed20260627_archctx2048_v1,COMPLETED,6000,1%,1024 / 1024 / 512 / 256,2048,18006,0,102106848,16,764249,106707.89305611711,786.8413274749182,0.13962451119480315,0.08819584193376406,0.19690110062305166,12,9,5,0.09443923588673364,20260627,256,,"Observed train-loop elapsed time including loading; excludes validation, checkpoint writes, restart gaps and failed partial parts. Loader/host changes prevent controlled speed claims."
+trunk,Trunk ×4,architecture,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,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_arch4x_ctx512_v1,COMPLETED,6000,1%,4096 / 4096 / 2048 / 1024,512,18006,0,239955168,16,764249,151235.99787977268,398.05442768963985,0.1978883817705652,0.17504237867490582,0.13552372691340842,14,13,11,0.264364764549507,20260627,256,,"Observed train-loop elapsed time including loading; excludes validation, checkpoint writes, restart gaps and failed partial parts. Loader/host changes prevent controlled speed claims."
+both,Trunk + context ×4,architecture,s0_6k_allK_topup16_seed20260627_arch4x_v1,server_2,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_arch4x_v1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec03_server2_snapshots/s0_6k_allK_topup16_seed20260627_arch4x_v1,COMPLETED,6000,1%,4096 / 4096 / 2048 / 1024,2048,18006,0,312649440,16,764249,322438.22501901106,1684.0632234032964,0.4219020568152671,0.20469666056602828,0.13555952362068185,15,13,11,0.2781372801479504,20260627,256,,"Observed train-loop elapsed time including loading; excludes validation, checkpoint writes, restart gaps and failed partial parts. Loader/host changes prevent controlled speed claims."
+sixteen,Trunk + context ×16,architecture,s0_6k_allK_topup16_seed20260627_arch16x_v1,server_2,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_arch16x_v1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec03_server2_snapshots/s0_6k_allK_topup16_seed20260627_arch16x_v1,FAILED_PRESERVED,6000,1%,16384 / 16384 / 8192 / 4096,8192,18006,0,2785677024,2,95530,186570.45024118794,463.53801696607843,1.9530037709744368,1.9496703651200036,0.16072304531534484,,,,,20260627,256,system memory safety floor crossed: 19.59 GiB < 24.00 GiB,"Observed train-loop elapsed time including loading; excludes validation, checkpoint writes, restart gaps and failed partial parts. Loader/host changes prevent controlled speed claims."
+hint,1× + 9-fraction hint,architecture,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,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_prop_v1,COMPLETED,6000,1%,1024 / 1024 / 512 / 256,512,18015,9,54189792,16,764249,60731.40985992015,425.9925848096609,0.07946547507411872,0.0655671996337293,0.1966288537508436,12,8,5,0.09099856457317208,20260627,256,,"Observed train-loop elapsed time including loading; excludes validation, checkpoint writes, restart gaps and failed partial parts. Loader/host changes prevent controlled speed claims."
+2k,2k genes,gene_panel,f01_2k_1x_seed20260627,server_1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_2k_1x_seed20260627,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_2k_1x_seed20260627,COMPLETED,2000,0.1%,1024 / 1024 / 512 / 256,512,6006,0,23457184,16,764249,34066.42545101768,377.5519448919222,0.04457503438148782,0.04497687796116856,0.09676088026571901,13,11,7,0.13684003756071167,20260627,256,,"Observed train-loop elapsed time including loading; excludes validation, checkpoint writes, restart gaps and failed partial parts. Loader/host changes prevent controlled speed claims."
+3k,3k genes,gene_panel,f01_3k_1x_seed20260627,server_2,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_3k_1x_seed20260627,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec03_server2_snapshots/f01_3k_1x_seed20260627,COMPLETED,3000,0.1%,1024 / 1024 / 512 / 256,512,9006,0,31139184,16,764249,37654.961138040526,396.823458771687,0.04927054027946458,0.04966004506119121,0.10918324212700364,13,11,8,0.14476964796401198,20260627,256,,"Observed train-loop elapsed time including loading; excludes validation, checkpoint writes, restart gaps and failed partial parts. Loader/host changes prevent controlled speed claims."
+6k,6k genes,gene_panel,f01_6k_1x_seed20260627,server_1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627,COMPLETED,6000,0.1%,1024 / 1024 / 512 / 256,512,18006,0,54185184,16,764249,56837.97292509512,384.55782031221315,0.07437101379929201,0.06658664176649529,0.1369124204543195,12,9,6,0.10963983536681889,20260627,256,,"Observed train-loop elapsed time including loading; excludes validation, checkpoint writes, restart gaps and failed partial parts. Loader/host changes prevent controlled speed claims."
+15k,"15,114 genes",gene_panel,f01_p15k_1x_seed20260627,server_2,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_p15k_1x_seed20260627,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec03_server2_snapshots/f01_p15k_1x_seed20260627,COMPLETED,15114,0.1%,1024 / 1024 / 512 / 256,512,45348,0,124198932,16,764249,93508.17207414983,411.9685714279767,0.12235301855043294,0.12277845161719136,0.18702995903269065,10,7,4,0.06047990947770272,20260627,256,,"Observed train-loop elapsed time including loading; excludes validation, checkpoint writes, restart gaps and failed partial parts. Loader/host changes prevent controlled speed claims."

paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/labels_ablation.json

@@ -0,0 +1,184 @@
+{
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+  "composition_means": [
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+  "recipe": {
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+    "pca_fit": "real R1 only; randomized SVD; all common measured genes",
+    "normalization": "panel CP10k and log1p, independent per cell",
+    "readout": "generated_counts as Poisson rate; one draw after common-gene subset; real counts untouched",
+    "poisson_seed": 20260916,
+    "local_k": 10,
+    "real_split_seed": 20261012,
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+    "per_donor_per_set": 100,
+    "distance": "Euclidean in fixed real-R1 PCA50; exact brute kNN in bounded batches",
+    "cells_as_replicates": false
+  }
+}

paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/labels_detection_and_library.csv

@@ -0,0 +1,8 @@
+input_arm,set,readout,n_cells,detected_median,detected_p10,detected_p90,library_median,zero_fraction
+R1,real_R1,counts>0,16050,361.0,265.0,535.0,1980.0,0.9303590133411158
+R2,real_R2,counts>0,16050,364.0,267.0,534.0,2004.0,0.9300460276414708
+raw,raw,Poisson counts>0 (as embedded and labelled),160500,331.0,162.0,499.0,1342.0,0.9396550370234628
+tpm,tpm,Poisson counts>0 (as embedded and labelled),160500,317.0,206.0,458.0,2184.0,0.9413131700816936
+refcal,refcal,Poisson counts>0 (as embedded and labelled),160500,248.0,191.0,349.0,2490.0,0.9527645961580664
+cal,cal,Poisson counts>0 (as embedded and labelled),160500,266.0,203.0,335.0,2302.0,0.9512745109350996
+pseudo,pseudo,Poisson counts>0 (as embedded and labelled),160500,269.0,209.0,337.0,2486.0,0.9506440035111772

paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/labels_detection_and_library.provenance.json

@@ -0,0 +1,26 @@
+{
+  "key": "labels_detection_and_library",
+  "source_records": [
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+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json",
+      "sha256": "45e6836942e894e51cfba5e4f9925a0d8affa9bbe95f1adebaf87af2830adf1b",
+      "role": "historical input/control provenance"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md",
+      "sha256": "83ec5eec39f15ccb7615da81c4b8f6345563b3a224934f3f942d29bf87b9054c",
+      "role": "historical scope and limitations"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/e_detected_genes.csv",
+      "sha256": "350744d2458ce406e3c58e2c98322e33a545f626888db66c64a8328080769da0",
+      "role": "saved analysis input"
+    }
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "new_embedding": false,
+  "new_statistical_scoring": false,
+  "display_transform_notes": "Observed counts and the previously computed Poisson readout of generated cells. Whiskers are saved 10th\u201390th cell percentiles, not donor confidence intervals. Scoring-gene libraries are not full-transcriptome UMI totals.",
+  "palette": "native"
+}