Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261010T153319Z-manuscript-rewrite-from-deck/diffusion/dataset/server_1/manuscript/archive/pre_rewrite_20261010/tables/results_behcet.tex

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+\begin{table}[t]
+\centering
+\footnotesize
+\setlength{\tabcolsep}{4pt}
+\caption{A subset-level question inside monocytes. Within each sample, C1Q-high-like monocytes are compared with the other monocytes of that sample. Each entry is the module difference as a background-corrected pseudobulk $\log_2$ fold change, followed by the number of samples with a positive difference. Observed cells are GSE198616 (4 Behçet, 4 control); generated cells come from one model conditioned on GSE198533 bulk (9 Behçet, 10 control), at the inherited read-out ($\tau=0$) and at the swept threshold $\tau=-2.0$ (Supplementary Note~S5). [TODO: columns under the drawn read-out.] All three sets use the same frozen annotator, the same 5,762-gene space and the same frozen module definitions. Group sizes differ, so only means, direction consistency and the intervals quoted in the text are compared.}
+\label{tab:behcet}
+\begin{tabular}{llrrrrrr}
+\toprule
+ & & \multicolumn{2}{c}{Observed} & \multicolumn{2}{c}{Generated, $\tau=0$} & \multicolumn{2}{c}{Generated, $\tau=-2.0$} \\
+\cmidrule(lr){3-4}\cmidrule(lr){5-6}\cmidrule(lr){7-8}
+Module & Group & mean & $+$ & mean & $+$ & mean & $+$ \\
+\midrule
+Interferon-$\gamma$ response & Behçet  & $+0.113$ & 3/4 & $+0.317$ & 7/9  & $+0.157$ & 9/9 \\
+                             & Control & $+0.156$ & 3/4 & $+0.234$ & 8/10 & $+0.136$ & 9/10 \\
+\addlinespace
+Pro-inflammatory             & Behçet  & $-0.124$ & 0/4 & $-0.369$ & 0/9  & $-0.343$ & 0/9 \\
+                             & Control & $-0.156$ & 1/4 & $-0.198$ & 1/10 & $-0.371$ & 0/10 \\
+\addlinespace
+Phagocytosis and             & Behçet  & $+0.157$ & 4/4 & $+0.093$ & 6/9  & $+0.011$ & 7/9 \\
+antigen presentation         & Control & $+0.097$ & 4/4 & $+0.121$ & 10/10 & $-0.036$ & 4/10 \\
+\midrule
+\multicolumn{2}{l}{C1Q-high-like share of control monocytes} & \multicolumn{2}{c}{5.00\%} & \multicolumn{2}{c}{0.85\%} & \multicolumn{2}{c}{4.68\%} \\
+\multicolumn{2}{l}{Samples with fewer than 20 such cells} & \multicolumn{2}{c}{1 of 8} & \multicolumn{2}{c}{19 of 19} & \multicolumn{2}{c}{0 of 19} \\
+\bottomrule
+\end{tabular}
+\end{table}

paper-releases/pbisc-diffusion/updates/20261010T153319Z-manuscript-rewrite-from-deck/diffusion/dataset/server_1/manuscript/archive/pre_rewrite_20261010/tables/results_benchmark.tex

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+\begin{table}[t]
+\centering
+\footnotesize
+\setlength{\tabcolsep}{4pt}
+\caption{The bulk condition sets the generated disease effect. Held-out lupus split (42 donors, 2,980 shared genes, scANVI six-type gate). Top block: one model (base arm, part 16), one sampler seed and 50 deterministic steps at the inherited read-out; only the bulk that conditions each donor is replaced, so cell $i$ starts from the same noise in every row. Cell $r$ is the median Pearson correlation between matched cells of that row and the true-condition row; ``closest donor'' counts, of 42, whether the generated pseudobulk is nearest to the donor itself or to the donor whose bulk it was given. Two context rows give the scale of a change. Bottom block: absolute scores at the recommended read-out, the semi-profiling baseline on the same donors, genes and annotator, and the resolution of a score. $r$ and DEG are higher-better, composition $L_1$ lower-better.}
+\label{tab:benchmark}
+\begin{tabular}{lrrrrrr}
+\toprule
+ & & & & & \multicolumn{2}{c}{Closest donor} \\
+\cmidrule(lr){6-7}
+Condition given to every donor & $r$ & DEG & comp.\ $L_1$ & cell $r$ & self & source \\
+\midrule
+Donor's own bulk                       & $+0.241$ & 57 & 0.227 & --- & --- & --- \\
+Bulk of the opposite disease group     & $-0.272$ & 16 & 0.430 & 0.972 & 0 & 40 \\
+Bulk of another donor (derangement)    & $+0.140$ & 0  & 0.502 & 0.969 & 0 & 42 \\
+Cohort-mean bulk (null)                & $-0.041$ & 10 & 0.350 & 0.981 & 1 & --- \\
+\textit{Context}: independent noise    & --- & --- & --- & 0.778 & --- & --- \\
+\textit{Context}: 50 vs 200 steps      & --- & --- & --- & 0.996 & --- & --- \\
+\midrule
+\method{}, drawn read-out, part 16     & 0.287 & 73 & 0.225 & --- & --- & --- \\
+\method{}, drawn read-out, parts 14--16 & 0.286 & 67.7 & 0.197 & --- & --- & --- \\
+scSemiProfiler\cite{wang2024scsemiprofiler} & 0.243 & 52 & 0.249 & --- & --- & --- \\
+\midrule
+Resolution: five sampling seeds (s.d.) & 0.005 & 4.7 & 0.002 & --- & --- & --- \\
+Resolution: two training runs (s.d.\ of paired parts) & 0.018 & 7.2 & 0.023 & --- & --- & --- \\
+\bottomrule
+\end{tabular}
+\end{table}

paper-releases/pbisc-diffusion/updates/20261010T153319Z-manuscript-rewrite-from-deck/diffusion/dataset/server_1/manuscript/archive/pre_rewrite_20261010/tables/results_conditioning.tex

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+\begin{table}[t]
+\centering
+\footnotesize
+\caption{The bulk condition sets the generated disease effect. One model (base arm, part 16), one sampler seed and 50 deterministic steps; only the bulk that conditions each donor is replaced, so cell $i$ starts from the same noise in every row. Cell $r$ is the median Pearson correlation between matched cells of that row and the true-condition row. ``Closest donor'' counts, of 42 donors, whether the generated pseudobulk is nearest to the donor itself or to the donor whose bulk it was given. Two context rows give the scale of a change: independent noise and a fourfold change in sampler steps.}
+\label{tab:conditioning}
+\begin{tabular}{lrrrrrr}
+\toprule
+ & & & & & \multicolumn{2}{c}{Closest donor} \\
+\cmidrule(lr){6-7}
+Condition & $r$ & DEG & comp.\ $L_1$ & cell $r$ & self & source \\
+\midrule
+Donor's own bulk                       & $+0.241$ & 57 & 0.227 & --- & --- & --- \\
+Bulk of the opposite disease group     & $-0.272$ & 16 & 0.430 & 0.972 & 0 & 40 \\
+Bulk of another donor (derangement)    & $+0.140$ & 0  & 0.502 & 0.969 & 0 & 42 \\
+Cohort-mean bulk                       & $-0.041$ & 10 & 0.350 & 0.981 & 1 & --- \\
+\midrule
+\textit{Context}: independent noise    & --- & --- & --- & 0.778 & --- & --- \\
+\textit{Context}: 50 vs 200 steps      & --- & --- & --- & 0.996 & --- & --- \\
+\bottomrule
+\end{tabular}
+\end{table}

paper-releases/pbisc-diffusion/updates/20261010T153319Z-manuscript-rewrite-from-deck/diffusion/dataset/server_1/manuscript/archive/pre_rewrite_20261010/tables/results_deg_by_type.tex

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+\begin{longtable}{llrrrrrr}
+\caption{Disease-effect agreement for each cell type in the Welch test. All models use the same donors and measured genes within each cell type. J counts shared genes and divides by all distinct genes in the two sets. Full J uses all genes called significant. The last column uses up to 50 significant genes ranked by absolute effect.}\label{tab:deg_by_type}\\
+\toprule
+Type & Checkpoint & $r$ & RMSE & Real DEGs & Gen. DEGs & Full $J$ & Top-50 $J$ \\
+\midrule
+\endfirsthead
+\toprule
+Type & Checkpoint & $r$ & RMSE & Real DEGs & Gen. DEGs & Full $J$ & Top-50 $J$ \\
+\midrule
+\endhead
+T cell & 2K E1 & 0.568 & 0.1095 & 835 & 770 & 0.396 & 0.299 \\
+T cell & 6K E1 & 0.528 & 0.1139 & 835 & 276 & 0.181 & 0.250 \\
+T cell & 11.6K E1 & 0.438 & 0.1195 & 835 & 273 & 0.159 & 0.235 \\
+T cell & 2K E2 & 0.648 & 0.1030 & 835 & 624 & 0.366 & 0.351 \\
+T cell & 2K E3 & 0.733 & 0.0969 & 835 & 427 & 0.304 & 0.389 \\
+\midrule
+B cell & 2K E1 & 0.373 & 0.1058 & 266 & 238 & 0.140 & 0.220 \\
+B cell & 6K E1 & 0.267 & 0.1116 & 266 & 30 & 0.042 & 0.067 \\
+B cell & 11.6K E1 & 0.145 & 0.1155 & 266 & 22 & 0.029 & 0.043 \\
+B cell & 2K E2 & 0.563 & 0.0952 & 266 & 215 & 0.206 & 0.316 \\
+B cell & 2K E3 & 0.660 & 0.0881 & 266 & 167 & 0.209 & 0.351 \\
+\midrule
+Monocyte & 2K E1 & 0.444 & 0.1340 & 289 & 261 & 0.211 & 0.149 \\
+Monocyte & 6K E1 & 0.244 & 0.1441 & 289 & 69 & 0.088 & 0.042 \\
+Monocyte & 11.6K E1 & 0.155 & 0.1500 & 289 & 95 & 0.082 & 0.042 \\
+Monocyte & 2K E2 & 0.649 & 0.1179 & 289 & 219 & 0.283 & 0.389 \\
+Monocyte & 2K E3 & 0.767 & 0.1010 & 289 & 279 & 0.318 & 0.562 \\
+\midrule
+NK cell & 2K E1 & 0.358 & 0.1370 & 231 & 131 & 0.168 & 0.205 \\
+NK cell & 6K E1 & 0.347 & 0.1385 & 231 & 58 & 0.095 & 0.176 \\
+NK cell & 11.6K E1 & 0.160 & 0.1509 & 231 & 85 & 0.097 & 0.099 \\
+NK cell & 2K E2 & 0.432 & 0.1344 & 231 & 95 & 0.164 & 0.282 \\
+NK cell & 2K E3 & 0.594 & 0.1207 & 231 & 110 & 0.209 & 0.333 \\
+\midrule
+\bottomrule
+\end{longtable}