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/sec02_bulk_conditioning.csv

@@ -0,0 +1,23 @@
+quantity,value,source_path,source_key,source_sha256_16
+canonical_gene_axis,20097,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/manifest.json,n_full_genes,acbc8bc2cca5ecf3
+canonical_gene_axis_conditioner,20097,/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/runs/E2_full_no_annotation_4epoch_seed20260627/conditioner_cache.pt,conditioner_state.n_genes,81ba53ed96fab03c
+panel_genes_G,6000,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/RUN_STATUS.json,n_genes,d70a2c283d712342
+condition_dim,18006,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/RUN_STATUS.json,condition_dim,d70a2c283d712342
+n_scalars,6,/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/runs/E2_full_no_annotation_4epoch_seed20260627/conditioner_cache.pt,conditioner_state.feature_names[n_genes:],81ba53ed96fab03c
+scalar_names,bulk_total_log1p;bulk_per_cell_log1p;bulk_detected_fraction;bulk_log_mean;bulk_log_std;bulk_top1pct_mass_fraction,/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/runs/E2_full_no_annotation_4epoch_seed20260627/conditioner_cache.pt,conditioner_state.feature_names[n_genes:],81ba53ed96fab03c
+clip_z,8.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/runs/E2_full_no_annotation_4epoch_seed20260627/conditioner_cache.pt,conditioner_state.clip_z,81ba53ed96fab03c
+recipe_k_real_bulk,1000,/home/sj_server_1/PBISC/paper-release-20260928/manuscript/sections/methods.tex,'$K=1000$ cells and a fixed per-cell depth' (regex),3cbd1664a02ec715
+context_dim,512,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/effective_config.json,model.context_dim,0a8e9a0ce0b82d13
+time_embedding_dim,128,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/effective_config.json,model.time_embedding_dim,0a8e9a0ce0b82d13
+hidden_dims,1024;1024;512;256,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/effective_config.json,model.hidden_dims,0a8e9a0ce0b82d13
+conditioned_blocks,7,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/src/pbisc_sdd/model.py,len(down_blocks)+len(up_blocks),c3d725b97d003b9b
+block_widths,1024;1024;512;256;512;1024;1024,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/src/pbisc_sdd/model.py,down then up widths,c3d725b97d003b9b
+parameters,54185184,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/RUN_STATUS.json,parameters (recomputed from structure: equal),d70a2c283d712342
+state_dim_2G,12000,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/src/pbisc_sdd/model.py,state_dim = 2 * n_genes,c3d725b97d003b9b
+denoiser_input_dim,24000,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/src/pbisc_sdd/model.py,"first block input 2 * state_dim = [x_t, self-cond]",c3d725b97d003b9b
+value_head_out,6000,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/src/pbisc_sdd/model.py,"value_head = Linear(widths[0], n_genes)",c3d725b97d003b9b
+logit_head_out,6000,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/src/pbisc_sdd/model.py,"active_head = Linear(widths[0], n_genes)",c3d725b97d003b9b
+ddim_steps,50,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/effective_config.json,sampling.steps,0a8e9a0ce0b82d13
+ddim_eta,0.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/effective_config.json,sampling.eta,0a8e9a0ce0b82d13
+scdiffusion_latent_dim,128,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/refs/sec02_ref_scdiffusion_arxiv2401.03968v2.txt,Sec 2.1 text,eb40bc8ed7738a33
+sdd_condition_hits_all_self,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/refs/sec02_ref_sdd_arxiv2502.02448v3.txt,regex 'condition' before References,9750ab583c90f85e

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec02_slide_text.csv

@@ -0,0 +1,6 @@
+slide,keyword_line,n_words,source_paths,evidence_quotes
+backbone,"Kept from SDD: value + bit, skip-MLP",7,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/refs/sec02_ref_sdd_arxiv2502.02448v3.txt ; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/refs/sec02_ref_sdd_upstream_1d5423c_sparsity_bit_diffusion.py ; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/src/pbisc_sdd/model.py,[sdd_paper] our forward–backward process diffuses continuous and discrete variables jointly || [sdd_upstream] h = self.fc(x) h = h + self.emb_layer(emb) h = self.norm(h) h = self.act(h) || [model_py] hidden = self.input_projection(inputs) + self.context_projection(context) hidden = self.normalization(hidden) hidden = self.activation(hidden)
+backbone,"Changed: bulk condition, masked loss, Bernoulli read-out",7,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/THIRD_PARTY_NOTICES.md ; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/scripts/sample_sdd_standalone.py,"[notices] adds conditional bulk/depth inputs, a three-state measurement contract, measured-only BCE/L2 losses || [sampler_py] ``bernoulli`` instead draws each gene from its own probability"
+conditioning,Same bulk condition for every generated cell,7,/home/sj_server_1/PBISC/paper-release-20260928/manuscript/sections/methods.tex,[methods] Cells generated from the same bulk shared its features and output-assay mask.
+conditioning,"Final: no cell types, proportions, sum constraint",7,/home/sj_server_1/PBISC/paper-release-20260928/manuscript/sections/introduction.tex,"[intro] it receives no cell-type labels, no target proportions and no term that forces generated counts to sum to the bulk"
+conditioning,"18,006 → 512 context into every block",7,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/src/pbisc_sdd/model.py,"[model_py] context = self.context_mixer(time_context + condition_context) || [model_py] for block in self.down_blocks: hidden = block(hidden, context)"

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec03_panel_bench.csv

@@ -0,0 +1,7 @@
+arm,method,n_genes,params,val_loss_e16,n_seeds,logfc_r,top50,comp_l1,logfc_r_sd,top50_sd,comp_l1_sd,logfc_r_base_seed,top50_base_seed,comp_l1_base_seed,eval_genes,n_donors,part,readout,source
+2k,diffusion_f012k_e16,2000.0,23457184.0,0.09676088026571901,1.0,0.3482764431678152,53.0,0.1312519655714672,,,,,,,1006,42,16,Bernoulli (drawn),/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+3k,diffusion_f013k_e16,3000.0,31139184.0,0.10918324212700364,1.0,0.3584411943962801,72.0,0.163812117118193,,,,,,,1006,42,16,Bernoulli (drawn),/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+6k,diffusion_f016k_e16,6000.0,54185184.0,0.1369124204543195,5.0,0.37128127582159925,76.2,0.18076362220515757,0.017657234388334934,3.7013511046643495,0.003104479026911492,0.3991172272882592,81.0,0.1811408199822934,1006,42,16,Bernoulli (drawn),/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+15k,diffusion_f01p15k_e16,15114.0,124198932.0,0.18702995903269065,1.0,0.3437945151700011,62.0,0.2971466704417127,,,,,,,1006,42,16,Bernoulli (drawn),/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+scSemiProfiler,scSemiProfiler,,,,,0.3179103699610459,56.0,0.2643486790566219,,,,,,,1006,42,16,Bernoulli (drawn),/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+PBISC-VAE,PBISC-VAE,,,,,0.3741551919281764,78.0,0.1769999357126608,,,,,,,1006,42,16,Bernoulli (drawn),/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec03_panel_headline.csv

@@ -0,0 +1,13 @@
+quantity,value,source
+6k_seed_mean_r_top50_l1,0.371/76.200/0.181,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+6k_seed_sd_r_top50_l1,0.018/3.701/0.003,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+6k_seed_min_max_r,0.358-0.399,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+6k_seed_min_max_top50,72-81,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+6k_base_seed_rank_of_5_r_top50_l1,1/1/3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+3k_inside_6k_seed_range_r_top50_l1,True/True/False,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+6k_mean_minus_3k_r,0.012840081425319172,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+6k_mean_minus_3k_top50,4.200000000000003,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+best_comp_l1_panel,2k,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+worst_comp_l1_panel,15k,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+CLEC9A_population_rank_smallest_panel,"cDC1/3,793/6k",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/floor01_campaign_20260923/RESULTS.md
+final_checkpoint_sha256,8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/MANIFEST.json