Archive 4 checkpoints (1-4)

.gitattributes

@@ -117,3 +117,4 @@ paper-releases/pbisc-diffusion/updates/20261010T153319Z-manuscript-rewrite-from-
 paper-releases/pbisc-diffusion/updates/20261010T153319Z-manuscript-rewrite-from-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pptx filter=lfs diff=lfs merge=lfs -text
 paper-releases/pbisc-diffusion/updates/20261010T153319Z-manuscript-rewrite-from-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pdf filter=lfs diff=lfs merge=lfs -text
 paper-releases/pbisc-diffusion/updates/20261011T120708Z-manuscript-introduction-docx/diffusion/dataset/server_1/manuscript/main.pdf filter=lfs diff=lfs merge=lfs -text
+paper-releases/pbisc-diffusion/updates/20261011T120708Z-manuscript-introduction-docx/diffusion/dataset/server_1/manuscript/supplementary.pdf filter=lfs diff=lfs merge=lfs -text

paper-releases/pbisc-diffusion/updates/20261011T120708Z-manuscript-introduction-docx/diffusion/dataset/server_1/manuscript/editorial/main_introduction_20261011_build.log

@@ -0,0 +1,160 @@
+note: Running TeX ...
+warning: sections/introduction:8: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig1:7: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig2:16: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig2:27: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig3:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig4:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig4:15: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig5:12: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig6:4: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/discussion:20: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:22: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:35: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:54: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:66: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:74: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_paired:22: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_paired:36: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_paired:47: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_paired:59: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_eval:21: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_eval:35: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_eval:46: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_eval:54: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/declarations:9: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/declarations:15: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig1:1: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: Trying to include PDF file with version (1.7), which is newer than current output PDF setting (1.5).
+warning: sections/fig1:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig1:9: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig2:2: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig2:7: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig2:10: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig2:23: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig3:1: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig3:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig3:7: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig4:1: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig4:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig4:8: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig5:3: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig5:7: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig5:9: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig6:1: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.tex:45: Underfull \vbox (badness 10000) has occurred while \output is active
+note: Running BibTeX on main.aux ...
+note: Rerunning TeX because bibtex was run ...
+warning: sections/introduction:8: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig1:7: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig2:16: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig2:27: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig3:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig4:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig4:15: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig5:12: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig6:4: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/discussion:20: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:22: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:35: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:54: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:66: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:74: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_paired:22: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_paired:36: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_paired:47: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_paired:59: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_eval:21: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_eval:35: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_eval:46: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_eval:54: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/declarations:9: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/declarations:15: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.bbl:44: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.bbl:140: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.bbl:236: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.bbl:247: Underfull \hbox (badness 6725) in paragraph at lines 237--247
+warning: main.bbl:317: Underfull \hbox (badness 1783) in paragraph at lines 311--317
+warning: main.bbl:335: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.bbl:437: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.bbl:531: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig1:1: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: Trying to include PDF file with version (1.7), which is newer than current output PDF setting (1.5).
+warning: sections/fig1:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig1:9: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig2:2: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig2:7: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig2:10: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig2:23: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig3:1: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig3:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig3:7: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig4:1: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig4:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig4:8: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig5:3: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig5:7: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig5:9: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig6:1: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.tex:45: Underfull \vbox (badness 10000) has occurred while \output is active
+note: Rerunning TeX because "main.aux" changed ...
+warning: sections/introduction:8: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig1:7: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig2:16: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig2:27: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig3:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig4:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig4:15: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig5:12: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/results_fig6:4: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/discussion:20: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:22: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:35: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:54: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:66: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_model:74: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_paired:22: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_paired:36: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_paired:47: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_paired:59: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_eval:21: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_eval:35: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_eval:46: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/methods_eval:54: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/declarations:9: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/declarations:15: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.bbl:44: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.bbl:140: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.bbl:236: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.bbl:247: Underfull \hbox (badness 6725) in paragraph at lines 237--247
+warning: main.bbl:317: Underfull \hbox (badness 1783) in paragraph at lines 311--317
+warning: main.bbl:335: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.bbl:437: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.bbl:531: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig1:1: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: Trying to include PDF file with version (1.7), which is newer than current output PDF setting (1.5).
+warning: sections/fig1:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig1:9: Underfull \hbox (badness 3029) in paragraph at lines 9--9
+warning: sections/fig1:9: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig2:2: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig2:7: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig2:10: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig2:23: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig3:1: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig3:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig3:7: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig4:1: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig4:6: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig4:8: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig5:3: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig5:7: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig5:9: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: sections/fig6:1: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: main.tex:45: Underfull \vbox (badness 10000) has occurred while \output is active
+warning: warnings were issued by the TeX engine; use --print and/or --keep-logs for details.
+note: Running xdvipdfmx ...
+warning: Trying to include PDF file with version (1.7), which is newer than current output PDF setting (1.5).
+note: Writing `main.log` (28.326171875 KiB)
+note: Writing `main.blg` (246 B)
+note: Writing `main.pdf` (1.3968381881713867 MiB)
+note: Skipped writing 3 intermediate files (use --keep-intermediates to keep them)

paper-releases/pbisc-diffusion/updates/20261011T120708Z-manuscript-introduction-docx/diffusion/dataset/server_1/manuscript/editorial/main_introduction_20261011_tex.log

@@ -0,0 +1,877 @@
+**
+(main.tex
+LaTeX2e <2021-11-15> patch level 1
+L3 programming layer <2022-02-24> (sn-jnl.cls
+Document Class: sn-jnl 2019/11/18 v0.1: An authoring template for Springer Jour
+nal articles
+(article.cls
+Document Class: article 2021/10/04 v1.4n Standard LaTeX document class
+(fleqn.clo
+File: fleqn.clo 2016/12/29 v1.2b Standard LaTeX option (flush left equations)
+\mathindent=\skip47
+Applying: [2015/01/01] Make \[ robust on input line 50.
+LaTeX Info: Redefining \[ on input line 51.
+Already applied: [0000/00/00] Make \[ robust on input line 62.
+Applying: [2015/01/01] Make \] robust on input line 74.
+LaTeX Info: Redefining \] on input line 75.
+Already applied: [0000/00/00] Make \] robust on input line 83.
+) (size10.clo
+File: size10.clo 2021/10/04 v1.4n Standard LaTeX file (size option)
+)
+\c@part=\count181
+\c@section=\count182
+\c@subsection=\count183
+\c@subsubsection=\count184
+\c@paragraph=\count185
+\c@subparagraph=\count186
+\c@figure=\count187
+\c@table=\count188
+\abovecaptionskip=\skip48
+\belowcaptionskip=\skip49
+\bibindent=\dimen138
+)
+LaTeX Info: Redefining \rm on input line 146.
+LaTeX Info: Redefining \sf on input line 147.
+LaTeX Info: Redefining \tt on input line 148.
+LaTeX Info: Redefining \bf on input line 149.
+LaTeX Info: Redefining \it on input line 150.
+LaTeX Info: Redefining \sl on input line 151.
+LaTeX Info: Redefining \sc on input line 152.
+LaTeX Info: Redefining \cal on input line 153.
+LaTeX Info: Redefining \mit on input line 154.
+LaTeX Info: Redefining \textsubscript on input line 212.
+\columnhsize=\skip50
+ (geometry.sty
+Package: geometry 2020/01/02 v5.9 Page Geometry
+ (keyval.sty
+Package: keyval 2014/10/28 v1.15 key=value parser (DPC)
+\KV@toks@=\toks16
+) (ifvtex.sty
+Package: ifvtex 2019/10/25 v1.7 ifvtex legacy package. Use iftex instead.
+ (iftex.sty
+Package: iftex 2022/02/03 v1.0f TeX engine tests
+))
+\Gm@cnth=\count189
+\Gm@cntv=\count190
+\c@Gm@tempcnt=\count191
+\Gm@bindingoffset=\dimen139
+\Gm@wd@mp=\dimen140
+\Gm@odd@mp=\dimen141
+\Gm@even@mp=\dimen142
+\Gm@layoutwidth=\dimen143
+\Gm@layoutheight=\dimen144
+\Gm@layouthoffset=\dimen145
+\Gm@layoutvoffset=\dimen146
+\Gm@dimlist=\toks17
+)
+\artcatbox=\box50
+\aucount=\count192
+\corraucount=\count193
+\punctcount=\count194
+\emailcnt=\count195
+\c@affn=\count196
+\addcount=\count197
+\PacsCount=\count198
+\PacsTmpCnt=\count199
+\FMremarkdim=\dimen147
+\fmremarkbox=\box51
+
+(cuted.sty
+Package: cuted 2021/10/04 v2.0 Mixing onecolumn and twocolumn modes
+\At@ViperColsBreak=\toks18
+\preCutedStrip=\toks19
+\postCutedStrip=\toks20
+\cuted@@tempbox@a=\box52
+\cuted@@tempbox@c=\box53
+\cuted@@tempbox@var=\box54
+\hold@viper=\box55
+\@viper=\box56
+\cuted@@varbox@a=\box57
+\cuted@@varbox@c=\box58
+\cuted@@tempdim@spread=\dimen148
+\cuted@@tempdim@a=\dimen149
+\cuted@@tempdim@b=\dimen150
+\ht@hold@viper=\dimen151
+\ht@viper=\dimen152
+\var@@pagediscards@ht=\dimen153
+\stripsep=\skip51
+\viper@penalty=\count266
+)
+\firstpagehtcheck=\dimen154
+\labelwidthi=\dimen155
+\labelwidthii=\dimen156
+\labelwidthiii=\dimen157
+\labelwidthiv=\dimen158
+\figwidth=\dimen159
+\figheight=\dimen160
+\sidecapwidth=\dimen161
+\wrapcapline=\dimen162
+\totalwrapline=\dimen163
+\wraptotline=\dimen164
+\figurebox=\box59
+\wrapfigcapbox=\box60
+\figcapbox=\box61
+\capbox=\box62
+\headwidthskip=\skip52
+\tabcapbox=\box63
+\temptbox=\box64
+\tempdime=\dimen165
+\tabhtdime=\dimen166
+ (rotating.sty
+Package: rotating 2016/08/11 v2.16d rotated objects in LaTeX
+ (graphicx.sty
+Package: graphicx 2021/09/16 v1.2d Enhanced LaTeX Graphics (DPC,SPQR)
+ (graphics.sty
+Package: graphics 2021/03/04 v1.4d Standard LaTeX Graphics (DPC,SPQR)
+ (trig.sty
+Package: trig 2021/08/11 v1.11 sin cos tan (DPC)
+) (graphics.cfg
+File: graphics.cfg 2016/06/04 v1.11 sample graphics configuration
+)
+Package graphics Info: Driver file: xetex.def on input line 107.
+(xetex.def
+File: xetex.def 2021/03/18 v5.0k Graphics/color driver for xetex
+))
+\Gin@req@height=\dimen167
+\Gin@req@width=\dimen168
+) (ifthen.sty
+Package: ifthen 2020/11/24 v1.1c Standard LaTeX ifthen package (DPC)
+)
+\c@r@tfl@t=\count267
+\rotFPtop=\skip53
+\rotFPbot=\skip54
+\rot@float@box=\box65
+\rot@mess@toks=\toks21
+) (threeparttable.sty
+Package: threeparttable 2003/06/13  v 3.0
+\@tempboxb=\box66
+) (appendix.sty
+Package: appendix 2020/02/08 v1.2c extra appendix facilities
+\c@@pps=\count268
+\c@@ppsavesec=\count269
+\c@@ppsaveapp=\count270
+) (hyperref.sty
+Package: hyperref 2022-02-21 v7.00n Hypertext links for LaTeX
+
+(ltxcmds.sty
+Package: ltxcmds 2020-05-10 v1.25 LaTeX kernel commands for general use (HO)
+) (pdftexcmds.sty
+Package: pdftexcmds 2020-06-27 v0.33 Utility functions of pdfTeX for LuaTeX (HO
+)
+ (infwarerr.sty
+Package: infwarerr 2019/12/03 v1.5 Providing info/warning/error messages (HO)
+)
+Package pdftexcmds Info: \pdf@primitive is available.
+Package pdftexcmds Info: \pdf@ifprimitive is available.
+Package pdftexcmds Info: \pdfdraftmode not found.
+) (kvsetkeys.sty
+Package: kvsetkeys 2019/12/15 v1.18 Key value parser (HO)
+)
+(kvdefinekeys.sty
+Package: kvdefinekeys 2019-12-19 v1.6 Define keys (HO)
+) (pdfescape.sty
+Package: pdfescape 2019/12/09 v1.15 Implements pdfTeX's escape features (HO)
+) (hycolor.sty
+Package: hycolor 2020-01-27 v1.10 Color options for hyperref/bookmark (HO)
+) (letltxmacro.sty
+Package: letltxmacro 2019/12/03 v1.6 Let assignment for LaTeX macros (HO)
+) (auxhook.sty
+Package: auxhook 2019-12-17 v1.6 Hooks for auxiliary files (HO)
+) (kvoptions.sty
+Package: kvoptions 2020-10-07 v3.14 Key value format for package options (HO)
+)
+\@linkdim=\dimen169
+\Hy@linkcounter=\count271
+\Hy@pagecounter=\count272
+ (pd1enc.def
+File: pd1enc.def 2022-02-21 v7.00n Hyperref: PDFDocEncoding definition (HO)
+) (intcalc.sty
+Package: intcalc 2019/12/15 v1.3 Expandable calculations with integers (HO)
+) (etexcmds.sty
+Package: etexcmds 2019/12/15 v1.7 Avoid name clashes with e-TeX commands (HO)
+)
+\Hy@SavedSpaceFactor=\count273
+ (puenc.def
+File: puenc.def 2022-02-21 v7.00n Hyperref: PDF Unicode definition (HO)
+)
+Package hyperref Info: Hyper figures OFF on input line 4137.
+Package hyperref Info: Link nesting OFF on input line 4142.
+Package hyperref Info: Hyper index ON on input line 4145.
+Package hyperref Info: Plain pages OFF on input line 4152.
+Package hyperref Info: Backreferencing OFF on input line 4157.
+Package hyperref Info: Implicit mode ON; LaTeX internals redefined.
+Package hyperref Info: Bookmarks ON on input line 4390.
+\c@Hy@tempcnt=\count274
+
+(url.sty
+\Urlmuskip=\muskip16
+Package: url 2013/09/16  ver 3.4  Verb mode for urls, etc.
+)
+LaTeX Info: Redefining \url on input line 4749.
+\XeTeXLinkMargin=\dimen170
+ (bitset.sty
+Package: bitset 2019/12/09 v1.3 Handle bit-vector datatype (HO)
+ (bigintcalc.sty
+Package: bigintcalc 2019/12/15 v1.5 Expandable calculations on big integers (HO
+)
+))
+\Fld@menulength=\count275
+\Field@Width=\dimen171
+\Fld@charsize=\dimen172
+Package hyperref Info: Hyper figures OFF on input line 6027.
+Package hyperref Info: Link nesting OFF on input line 6032.
+Package hyperref Info: Hyper index ON on input line 6035.
+Package hyperref Info: backreferencing OFF on input line 6042.
+Package hyperref Info: Link coloring OFF on input line 6047.
+Package hyperref Info: Link coloring with OCG OFF on input line 6052.
+Package hyperref Info: PDF/A mode OFF on input line 6057.
+LaTeX Info: Redefining \ref on input line 6097.
+LaTeX Info: Redefining \pageref on input line 6101.
+ (atbegshi-ltx.sty
+Package: atbegshi-ltx 2021/01/10 v1.0c Emulation of the original atbegshi
+package with kernel methods
+)
+\Hy@abspage=\count276
+\c@Item=\count277
+\c@Hfootnote=\count278
+)
+Package hyperref Info: Driver (autodetected): hxetex.
+ (hxetex.def
+File: hxetex.def 2022-02-21 v7.00n Hyperref driver for XeTeX
+
+(stringenc.sty
+Package: stringenc 2019/11/29 v1.12 Convert strings between diff. encodings (HO
+)
+)
+\pdfm@box=\box67
+\c@Hy@AnnotLevel=\count279
+\HyField@AnnotCount=\count280
+\Fld@listcount=\count281
+\c@bookmark@seq@number=\count282
+ (rerunfilecheck.sty
+Package: rerunfilecheck 2019/12/05 v1.9 Rerun checks for auxiliary files (HO)
+ (atveryend-ltx.sty
+Package: atveryend-ltx 2020/08/19 v1.0a Emulation of the original atveryend pac
+kage
+with kernel methods
+) (uniquecounter.sty
+Package: uniquecounter 2019/12/15 v1.4 Provide unlimited unique counter (HO)
+)
+Package uniquecounter Info: New unique counter `rerunfilecheck' on input line 2
+86.
+)
+\Hy@SectionHShift=\skip55
+)
+Package hyperref Info: Option `colorlinks' set `true' on input line 1471.
+Package hyperref Info: Option `breaklinks' set `true' on input line 1471.
+Package hyperref Info: Option `plainpages' set `false' on input line 1471.
+Package hyperref Info: Option `bookmarksopen' set `true' on input line 1471.
+Package hyperref Info: Option `bookmarksnumbered' set `false' on input line 147
+1.
+
+(wrapfig.sty
+\wrapoverhang=\dimen173
+\WF@size=\dimen174
+\c@WF@wrappedlines=\count283
+\WF@box=\box68
+\WF@everypar=\toks22
+Package: wrapfig 2003/01/31  v 3.6
+)
+\wraplines=\count284
+\@authorfigbox=\box69
+\@authorfigboxdim=\skip56
+\biofigadjskip=\skip57
+ (amsthm.sty
+Package: amsthm 2020/05/29 v2.20.6
+\thm@style=\toks23
+\thm@bodyfont=\toks24
+\thm@headfont=\toks25
+\thm@notefont=\toks26
+\thm@headpunct=\toks27
+\thm@preskip=\skip58
+\thm@postskip=\skip59
+\thm@headsep=\skip60
+\dth@everypar=\toks28
+) (fix-cm.sty
+Package: fix-cm 2020/11/24 v1.1t fixes to LaTeX
+ (ts1enc.def
+File: ts1enc.def 2001/06/05 v3.0e (jk/car/fm) Standard LaTeX file
+LaTeX Font Info:    Redeclaring font encoding TS1 on input line 47.
+)) (natbib.sty
+Package: natbib 2010/09/13 8.31b (PWD, AO)
+\bibhang=\skip61
+\bibsep=\skip62
+LaTeX Info: Redefining \cite on input line 694.
+\c@NAT@ctr=\count285
+)) (amsmath.sty
+Package: amsmath 2021/10/15 v2.17l AMS math features
+\@mathmargin=\skip63
+For additional information on amsmath, use the `?' option.
+(amstext.sty
+Package: amstext 2021/08/26 v2.01 AMS text
+ (amsgen.sty
+File: amsgen.sty 1999/11/30 v2.0 generic functions
+\@emptytoks=\toks29
+\ex@=\dimen175
+)) (amsbsy.sty
+Package: amsbsy 1999/11/29 v1.2d Bold Symbols
+\pmbraise@=\dimen176
+) (amsopn.sty
+Package: amsopn 2021/08/26 v2.02 operator names
+)
+\inf@bad=\count286
+LaTeX Info: Redefining \frac on input line 234.
+\uproot@=\count287
+\leftroot@=\count288
+LaTeX Info: Redefining \overline on input line 399.
+\classnum@=\count289
+\DOTSCASE@=\count290
+LaTeX Info: Redefining \ldots on input line 496.
+LaTeX Info: Redefining \dots on input line 499.
+LaTeX Info: Redefining \cdots on input line 620.
+\Mathstrutbox@=\box70
+\strutbox@=\box71
+\big@size=\dimen177
+LaTeX Font Info:    Redeclaring font encoding OML on input line 743.
+LaTeX Font Info:    Redeclaring font encoding OMS on input line 744.
+\macc@depth=\count291
+\c@MaxMatrixCols=\count292
+\dotsspace@=\muskip17
+\c@parentequation=\count293
+\dspbrk@lvl=\count294
+\tag@help=\toks30
+\row@=\count295
+\column@=\count296
+\maxfields@=\count297
+\andhelp@=\toks31
+\eqnshift@=\dimen178
+\alignsep@=\dimen179
+\tagshift@=\dimen180
+\tagwidth@=\dimen181
+\totwidth@=\dimen182
+\lineht@=\dimen183
+\@envbody=\toks32
+\multlinegap=\skip64
+\multlinetaggap=\skip65
+\mathdisplay@stack=\toks33
+LaTeX Info: Redefining \[ on input line 2938.
+LaTeX Info: Redefining \] on input line 2939.
+) (amssymb.sty
+Package: amssymb 2013/01/14 v3.01 AMS font symbols
+
+(amsfonts.sty
+Package: amsfonts 2013/01/14 v3.01 Basic AMSFonts support
+\symAMSa=\mathgroup4
+\symAMSb=\mathgroup5
+LaTeX Font Info:    Redeclaring math symbol \hbar on input line 98.
+LaTeX Font Info:    Overwriting math alphabet `\mathfrak' in version `bold'
+(Font)                  U/euf/m/n --> U/euf/b/n on input line 106.
+)) (booktabs.sty
+Package: booktabs 2020/01/12 v1.61803398 Publication quality tables
+\heavyrulewidth=\dimen184
+\lightrulewidth=\dimen185
+\cmidrulewidth=\dimen186
+\belowrulesep=\dimen187
+\belowbottomsep=\dimen188
+\aboverulesep=\dimen189
+\abovetopsep=\dimen190
+\cmidrulesep=\dimen191
+\cmidrulekern=\dimen192
+\defaultaddspace=\dimen193
+\@cmidla=\count298
+\@cmidlb=\count299
+\@aboverulesep=\dimen194
+\@belowrulesep=\dimen195
+\@thisruleclass=\count300
+\@lastruleclass=\count301
+\@thisrulewidth=\dimen196
+) (array.sty
+Package: array 2021/10/04 v2.5f Tabular extension package (FMi)
+\col@sep=\dimen197
+\ar@mcellbox=\box72
+\extrarowheight=\dimen198
+\NC@list=\toks34
+\extratabsurround=\skip66
+\backup@length=\skip67
+\ar@cellbox=\box73
+) (multirow.sty
+Package: multirow 2021/03/15 v2.8 Span multiple rows of a table
+\multirow@colwidth=\skip68
+\multirow@cntb=\count302
+\multirow@dima=\skip69
+\bigstrutjot=\dimen199
+) (longtable.sty
+Package: longtable 2021-09-01 v4.17 Multi-page Table package (DPC)
+\LTleft=\skip70
+\LTright=\skip71
+\LTpre=\skip72
+\LTpost=\skip73
+\LTchunksize=\count303
+\LTcapwidth=\dimen256
+\LT@head=\box74
+\LT@firsthead=\box75
+\LT@foot=\box76
+\LT@lastfoot=\box77
+\LT@gbox=\box78
+\LT@cols=\count304
+\LT@rows=\count305
+\c@LT@tables=\count306
+\c@LT@chunks=\count307
+\LT@p@ftn=\toks35
+)
+(microtype.sty
+Package: microtype 2022/03/14 v3.0d Micro-typographical refinements (RS)
+ (etoolbox.sty
+Package: etoolbox 2020/10/05 v2.5k e-TeX tools for LaTeX (JAW)
+\etb@tempcnta=\count308
+)
+\MT@toks=\toks36
+\MT@tempbox=\box79
+\MT@count=\count309
+LaTeX Info: Redefining \noprotrusionifhmode on input line 1027.
+LaTeX Info: Redefining \leftprotrusion on input line 1028.
+LaTeX Info: Redefining \rightprotrusion on input line 1036.
+LaTeX Info: Redefining \textls on input line 1195.
+\MT@outer@kern=\dimen257
+LaTeX Info: Redefining \textmicrotypecontext on input line 1781.
+\MT@listname@count=\count310
+ (microtype-xetex.def
+File: microtype-xetex.def 2022/03/14 v3.0d Definitions specific to xetex (RS)
+LaTeX Info: Redefining \lsstyle on input line 236.
+)
+Package microtype Info: Loading configuration file microtype.cfg.
+ (microtype.cfg
+File: microtype.cfg 2022/03/14 v3.0d microtype main configuration file (RS)
+))
+(xcolor.sty
+Package: xcolor 2021/10/31 v2.13 LaTeX color extensions (UK)
+ (color.cfg
+File: color.cfg 2016/01/02 v1.6 sample color configuration
+)
+Package xcolor Info: Driver file: xetex.def on input line 227.
+Package xcolor Info: Model `cmy' substituted by `cmy0' on input line 1352.
+Package xcolor Info: Model `RGB' extended on input line 1368.
+Package xcolor Info: Model `HTML' substituted by `rgb' on input line 1370.
+Package xcolor Info: Model `Hsb' substituted by `hsb' on input line 1371.
+Package xcolor Info: Model `tHsb' substituted by `hsb' on input line 1372.
+Package xcolor Info: Model `HSB' substituted by `hsb' on input line 1373.
+Package xcolor Info: Model `Gray' substituted by `gray' on input line 1374.
+Package xcolor Info: Model `wave' substituted by `hsb' on input line 1375.
+) (macros) (l3backend-xetex.def
+File: l3backend-xetex.def 2022-02-07 L3 backend support: XeTeX
+\c__kernel_sys_dvipdfmx_version_int=\count311
+\l__color_backend_stack_int=\count312
+\g__color_backend_stack_int=\count313
+\g__graphics_track_int=\count314
+\l__pdf_internal_box=\box80
+\g__pdf_backend_object_int=\count315
+\g__pdf_backend_annotation_int=\count316
+\g__pdf_backend_link_int=\count317
+) (main.aux)
+\openout1 = `main.aux'.
+
+LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 15.
+LaTeX Font Info:    ... okay on input line 15.
+LaTeX Font Info:    Checking defaults for OMS/cmsy/m/n on input line 15.
+LaTeX Font Info:    ... okay on input line 15.
+LaTeX Font Info:    Checking defaults for OT1/cmr/m/n on input line 15.
+LaTeX Font Info:    ... okay on input line 15.
+LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 15.
+LaTeX Font Info:    ... okay on input line 15.
+LaTeX Font Info:    Checking defaults for TS1/cmr/m/n on input line 15.
+LaTeX Font Info:    ... okay on input line 15.
+LaTeX Font Info:    Checking defaults for TU/lmr/m/n on input line 15.
+LaTeX Font Info:    ... okay on input line 15.
+LaTeX Font Info:    Checking defaults for OMX/cmex/m/n on input line 15.
+LaTeX Font Info:    ... okay on input line 15.
+LaTeX Font Info:    Checking defaults for U/cmr/m/n on input line 15.
+LaTeX Font Info:    ... okay on input line 15.
+LaTeX Font Info:    Checking defaults for PD1/pdf/m/n on input line 15.
+LaTeX Font Info:    ... okay on input line 15.
+LaTeX Font Info:    Checking defaults for PU/pdf/m/n on input line 15.
+LaTeX Font Info:    ... okay on input line 15.
+
+*geometry* driver: auto-detecting
+*geometry* detected driver: xetex
+*geometry* verbose mode - [ preamble ] result:
+* driver: xetex
+* paper: custom
+* layout: <same size as paper>
+* layoutoffset:(h,v)=(0.0pt,0.0pt)
+* bindingoffset: 17.07164pt
+* modes: twoside 
+* h-part:(L,W,R)=(83.37448pt, 372.0pt, 125.06175pt)
+* v-part:(T,H,B)=(73.97716pt, 552.69478pt, 218.37491pt)
+* \paperwidth=597.50787pt
+* \paperheight=845.04684pt
+* \textwidth=372.0pt
+* \textheight=552.69478pt
+* \oddsidemargin=28.17613pt
+* \evensidemargin=52.79176pt
+* \topmargin=-19.72638pt
+* \headheight=5.5pt
+* \headsep=15.93355pt
+* \topskip=10.0pt
+* \footskip=28.45274pt
+* \marginparwidth=34.1433pt
+* \marginparsep=14.22636pt
+* \columnsep=14.22636pt
+* \skip\footins=8.0pt plus 4.0pt
+* \hoffset=0.0pt
+* \voffset=0.0pt
+* \mag=1000
+* \@twocolumnfalse
+* \@twosidetrue
+* \@mparswitchtrue
+* \@reversemargintrue
+* (1in=72.27pt=25.4mm, 1cm=28.453pt)
+
+LaTeX Info: Redefining \S on input line 15.
+LaTeX Font Info:    Redeclaring symbol font `AMSa' on input line 15.
+LaTeX Font Info:    Overwriting symbol font `AMSa' in version `normal'
+(Font)                  U/msa/m/n --> U/msa/m/n on input line 15.
+LaTeX Font Info:    Overwriting symbol font `AMSa' in version `bold'
+(Font)                  U/msa/m/n --> U/msa/m/n on input line 15.
+Package hyperref Info: Link coloring ON on input line 15.
+(nameref.sty
+Package: nameref 2021-04-02 v2.47 Cross-referencing by name of section
+ (refcount.sty
+Package: refcount 2019/12/15 v3.6 Data extraction from label references (HO)
+) (gettitlestring.sty
+Package: gettitlestring 2019/12/15 v1.6 Cleanup title references (HO)
+)
+\c@section@level=\count318
+)
+LaTeX Info: Redefining \ref on input line 15.
+LaTeX Info: Redefining \pageref on input line 15.
+LaTeX Info: Redefining \nameref on input line 15.
+ (main.out) (main.out)
+\@outlinefile=\write3
+\openout3 = `main.out'.
+
+LaTeX Info: Redefining \microtypecontext on input line 15.
+Package microtype Info: Applying patch `item' on input line 15.
+Package microtype Info: Applying patch `toc' on input line 15.
+Package microtype Info: Applying patch `eqnum' on input line 15.
+Package microtype Info: Applying patch `footnote' on input line 15.
+Package microtype Info: Character protrusion enabled (level 2).
+Package microtype Info: Using default protrusion set `alltext'.
+Package microtype Info: No adjustment of tracking.
+Package microtype Info: No adjustment of spacing.
+Package microtype Info: No adjustment of kerning.
+
+(mt-LatinModernRoman.cfg
+File: mt-LatinModernRoman.cfg 2021/02/21 v1.1 microtype config. file: Latin Mod
+ern Roman (RS)
+) (authors) (sections/abstract)
+LaTeX Font Info:    Calculating math sizes for size <10.03749> on input line 22
+.
+ (mt-cmr.cfg
+File: mt-cmr.cfg 2013/05/19 v2.2 microtype config. file: Computer Modern Roman 
+(RS)
+)
+LaTeX Font Info:    Trying to load font information for U+msa on input line 22.
+
+ (umsa.fd
+File: umsa.fd 2013/01/14 v3.01 AMS symbols A
+)
+(mt-msa.cfg
+File: mt-msa.cfg 2006/02/04 v1.1 microtype config. file: AMS symbols (a) (RS)
+)
+LaTeX Font Info:    Trying to load font information for U+msb on input line 22.
+
+ (umsb.fd
+File: umsb.fd 2013/01/14 v3.01 AMS symbols B
+) (mt-msb.cfg
+File: mt-msb.cfg 2005/06/01 v1.0 microtype config. file: AMS symbols (b) (RS)
+) (sections/introduction
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [1
+
+])
+(sections/results_fig1
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [2])
+(sections/results_fig2
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [3]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [4])
+(sections/results_fig3
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [5])
+(sections/results_fig4
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [6]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [7])
+(sections/results_fig5
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [8])
+(sections/results_fig6
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [9])
+(sections/discussion
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [10])
+(sections/methods_model
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [11]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [12]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [13]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [14]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [15])
+(sections/methods_paired
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [16]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [17]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [18]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [19])
+(sections/methods_eval
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [20]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [21]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [22]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [23])
+(sections/declarations
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [24]
+Package microtype Info: Loading generic protrusion settings for font family
+(microtype)             `lmtt' (encoding: TU).
+(microtype)             For optimal results, create family-specific settings.
+(microtype)             See the microtype manual for details.
+
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [25])
+(main.bbl
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [26]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [27]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [28]
+Underfull \hbox (badness 6725) in paragraph at lines 237--247
+\TU/lmr/m/n/10.03749 Precision and Recall Metric for Assessing Generative Model
+s.  In
+ []
+
+
+Underfull \hbox (badness 1783) in paragraph at lines 311--317
+\TU/lmr/m/n/10.03749 protein biomarkers of checkpoint inhibitor-induced liver i
+njury.  \TU/lmr/m/it/10.03749 Cancer
+ []
+
+
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [29]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [30]
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [31])
+(sections/fig1
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [32]
+File: figures/deck_20261010/sec02_backbone_compare.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec02_backbone_compare.pdf>
+File: figures/deck_20261010/fig01_architecture_nature.pdf Graphic file (type pd
+f)
+<use figures/deck_20261010/fig01_architecture_nature.pdf>
+File: figures/deck_20261010/sec02_bulk_conditioning.pdf Graphic file (type pdf)
+
+<use figures/deck_20261010/sec02_bulk_conditioning.pdf>
+File: figures/deck_20261010/fig01_corpus_nature.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig01_corpus_nature.pdf>
+
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [33
+
+]
+File: figures/deck_20261010/sec03_width_loss.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec03_width_loss.pdf>
+File: figures/deck_20261010/sec03_width_bench.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec03_width_bench.pdf>
+File: figures/deck_20261010/sec03_panel.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec03_panel.pdf>
+
+Underfull \hbox (badness 3029) in paragraph at lines 9--9
+\TU/lmr/bx/n/9 Design and performance of PBISC-Diffusion. a\TU/lmr/m/n/9 , Thre
+e diffusion backbones:
+ []
+
+
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [34])
+(sections/fig2
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [35]
+File: figures/deck_20261010/sec05_condition_space.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec05_condition_space.pdf>
+File: figures/deck_20261010/sec05_shift_cohorts.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec05_shift_cohorts.pdf>
+File: figures/deck_20261010/sec05_cells_umap.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec05_cells_umap.pdf>
+File: figures/deck_20261010/sec05_cells_metrics.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec05_cells_metrics.pdf>
+File: figures/deck_20261010/sec06_ft_method.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec06_ft_method.pdf>
+File: figures/deck_20261010/sec06_eval_design.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec06_eval_design.pdf>
+
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [36
+
+]
+File: figures/deck_20261010/sec04_metrics_overview.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec04_metrics_overview.pdf>
+File: figures/deck_20261010/fig2_healthy_cells.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig2_healthy_cells.pdf>
+File: figures/deck_20261010/fig2_healthy_realism.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig2_healthy_realism.pdf>
+
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [37]
+File: figures/deck_20261010/fig2_healthy_modes.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig2_healthy_modes.pdf>
+File: figures/deck_20261010/fig2_healthy_pairs.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig2_healthy_pairs.pdf>
+File: figures/deck_20261010/fig2_healthy_rank.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig2_healthy_rank.pdf>
+
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [38])
+(sections/fig3
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [39]
+File: figures/deck_20261010/fig3_healthy_fewpair.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig3_healthy_fewpair.pdf>
+File: figures/deck_20261010/fig3_healthy_pairs.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig3_healthy_pairs.pdf>
+File: figures/deck_20261010/fig3_healthy_copy.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig3_healthy_copy.pdf>
+File: figures/deck_20261010/fig3_time_days.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig3_time_days.pdf>
+
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [40
+
+]
+File: figures/deck_20261010/sec09_time_to_apply.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec09_time_to_apply.pdf>
+
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [41])
+(sections/fig4
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [42]
+File: figures/deck_20261010/sec09_cohorts.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec09_cohorts.pdf>
+File: figures/deck_20261010/fig4_disease_fewpair.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig4_disease_fewpair.pdf>
+File: figures/deck_20261010/fig4_disease_fivefold.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig4_disease_fivefold.pdf>
+File: figures/deck_20261010/sec09_cat_curves.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec09_cat_curves.pdf>
+
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [43
+
+]
+File: figures/deck_20261010/secS_deconv_disease.pdf Graphic file (type pdf)
+<use figures/deck_20261010/secS_deconv_disease.pdf>
+File: figures/deck_20261010/sec04_sle_benchmark.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec04_sle_benchmark.pdf>
+File: figures/deck_20261010/sec04_sle_per_celltype.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec04_sle_per_celltype.pdf>
+
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [44])
+(sections/fig5
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [45]
+File: figures/deck_20261010/fig5_rare_fraction.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig5_rare_fraction.pdf>
+File: figures/deck_20261010/fig5_rare_donors.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig5_rare_donors.pdf>
+File: figures/deck_20261010/fig5_rare_fivefold.pdf Graphic file (type pdf)
+<use figures/deck_20261010/fig5_rare_fivefold.pdf>
+
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [46
+
+]
+File: figures/deck_20261010/sec05_behcet_direction.pdf Graphic file (type pdf)
+<use figures/deck_20261010/sec05_behcet_direction.pdf>
+
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [47])
+(sections/fig6
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [48])
+Underfull \vbox (badness 10000) has occurred while \output is active []
+
+ [49
+
+]
+(main.aux)
+Package rerunfilecheck Info: File `main.out' has not changed.
+(rerunfilecheck)             Checksum: D41D8CD98F00B204E9800998ECF8427E;0.
+ )
+Output written on main.xdv (49 pages, 1155840 bytes).

paper-releases/pbisc-diffusion/updates/20261011T120708Z-manuscript-introduction-docx/diffusion/dataset/server_1/manuscript/sections/introduction.tex

@@ -0,0 +1,13 @@
+% Introduction imported from PBISC-Diffusion_Abstract_Introduction.docx on 2026-10-11.
+% Wording and paragraph boundaries preserved; numeric citations mapped to BibTeX keys.
+\section*{Introduction}
+
+Bulk RNA sequencing of blood and tissue remains the most widely used transcriptomic assay in clinical research, including large clinical trials, biobanks and disease cohorts. Each bulk profile, however, is a mixture: changes in cell-type abundance are confounded with changes in cell-state-specific expression, and disease signals carried by minority populations are diluted. Single-cell RNA sequencing resolves these components, but cost and sample logistics still limit it to tens or hundreds of donors per study.
+
+Computational deconvolution has been the principal bridge between the two. Digital cytometry methods such as CIBERSORTx\cite{newman2019cibersortx}, MuSiC\cite{wang2019music}, Bisque\cite{jew2020bisque}, DWLS\cite{tsoucas2019dwls}, Scaden\cite{menden2020scaden} and TAPE\cite{chen2022tape} estimate cell-type proportions from bulk using single-cell-derived signatures, and BayesPrism\cite{chu2022bayesprism}, BLADE\cite{barbosa2021blade} and bMIND\cite{wang2021bmind} additionally infer cell-type-specific expression. Despite of the highly advanced calculation algorithms, the accuracy of each model's output highly depends on data transformation, reference choice and annotation granularity, degrades for closely related and rare cell types, and changes rank when the reference differs from the bulk cohort\cite{avilacobos2020benchmarking,sturm2019evaluation,dietrich2026omnideconv,community2024assessment}. These methods also return proportions or cell-type averages, which cannot represent heterogeneity within a cell type, thus masking many disease-associated states that could be inferred by transcriptomics.
+
+Due to the advance in machine learning and neural networking, generative models now offer a route to single-cell resolution. Bulk2Space\cite{liao2022bulk2space} and BulkTrajBlend\cite{zeng2024omicverse} estimate proportions and then draw cells from a matched reference, and scSemiProfiler\cite{wang2024scsemiprofiler} adapts real single cells from actively selected cohort representatives toward each target's bulk profile. These designs either constrain generated populations to a proportion-weighted sum or anchor every generated sample to a representative donor profiled within the same cohort, and their evaluation has relied largely on pseudobulk aggregated from single-cell data\cite{wang2024scsemiprofiler}. In parallel, diffusion models now generate realistic single-cell transcriptomes\cite{luo2024scdiffusion,scdiffusionx2026}, and sparsity-aware formulations that diffuse expression values and their zero pattern jointly preserve the exact zeros that dominate single-cell data\cite{ostheimer2025sparse}. These models are conditioned on labels, not on a donor's bulk transcriptome.
+
+A largely untested assumption shared by these approaches is that measured bulk RNA-seq and single-cell pseudobulk are interchangeable. The two assays differ in library chemistry, transcript coverage, capture efficiency and gene-length sensitivity, and distribution shifts between pseudobulk used for training and real bulk encountered at inference are currently unaccounted for\cite{delafuente2025sweetwater}. If this gap is large and systematic, a model trained on pseudobulk is evaluated in one domain and deployed in another, and the consequences for biological conclusions drawn from generated or deconvolved cells have not been quantified.
+
+Here we present PBISC-Diffusion, a bulk-conditioned generative model that combines joint value--support diffusion in gene space, adapted from Sparse Data Diffusion\cite{ostheimer2025sparse}, with deterministic sampling\cite{song2021ddim} and pretraining on peripheral blood mononuclear cells from 22 independent bulk to single cell paired datasets.

paper-releases/pbisc-diffusion/updates/20261011T120708Z-manuscript-introduction-docx/diffusion/dataset/server_1/manuscript/supplementary.pdf

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a02ed4b4ce1f452edae524bfd2e899bc9cc600bf32935fc53ee00fdec893f787
+size 1524546