Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261010T153319Z-manuscript-rewrite-from-deck/diffusion/dataset/server_1/manuscript/macros.tex

@@ -0,0 +1,19 @@
+% Shared macros for main.tex and supplementary.tex.
+\newcommand{\method}{PBISC-Diffusion}
+\newcommand{\todo}[1]{\textcolor{red}{[TODO: #1]}}
+% Figures are typeset in place after the references (not as floats), so a figure can run over more than one page.
+\newcommand{\figureprefix}{Figure}
+\newcommand{\mainfigure}[2]{\clearpage\refstepcounter{figure}\label{#1}%
+  \noindent{\large\textbf{\figureprefix~\thefigure\ $|$ #2}}\par\medskip}
+\newcommand{\suppfigure}[2]{\clearpage\refstepcounter{figure}\label{#1}%
+  \noindent{\large\textbf{Supplementary Fig.~\thefigure\ $|$ #2}}\par\medskip}
+\newcommand{\figpanel}[2]{\par\noindent\textbf{#1}\par\nopagebreak
+  {\centering\includegraphics[width=\textwidth,height=0.31\textheight,keepaspectratio]{#2}\par}\medskip}
+\newcommand{\figpanelh}[3]{\par\noindent\textbf{#1}\par\nopagebreak
+  {\centering\includegraphics[width=\textwidth,height=#3\textheight,keepaspectratio]{#2}\par}\medskip}
+\newcommand{\figpanelpair}[5]{\par\noindent\textbf{#1}\par\nopagebreak
+  {\centering\includegraphics[width=#4\textwidth,height=0.31\textheight,keepaspectratio]{#2}\hfill
+  \includegraphics[width=#5\textwidth,height=0.31\textheight,keepaspectratio]{#3}\par}\medskip}
+\newcommand{\tbcpanel}[1]{\par\noindent\fbox{\parbox{\dimexpr\textwidth-2\fboxsep-2\fboxrule\relax}{\centering
+  \vspace*{1.5cm}{\Large\textbf{To be continued}}\par\medskip #1\par\vspace*{1.5cm}}}\par\medskip}
+\newcommand{\figlegend}[1]{\par\medskip\noindent{\small #1}\par}

paper-releases/pbisc-diffusion/updates/20261010T153319Z-manuscript-rewrite-from-deck/diffusion/dataset/server_1/manuscript/main.tex

@@ -0,0 +1,45 @@
+% Overleaf main document. Uses the official Springer Nature authoring class.
+% Select pdfLaTeX on Overleaf; all figures and citations are local files.
+% Rewritten from scratch on 2026-10-10 from the paper-summary deck (76 slides, 2026-10-08).
+% The previous version is kept in archive/pre_rewrite_20261010/.
+\documentclass[pdflatex,sn-nature]{sn-jnl}
+\usepackage{graphicx}
+\usepackage{amsmath,amssymb}
+\usepackage{booktabs}
+\usepackage{array}
+\usepackage{multirow}
+\usepackage{longtable}
+\usepackage{microtype}
+\usepackage{xcolor}
+\input{macros}
+\begin{document}
+\raggedbottom
+\title{Five paired donors and minutes of fine-tuning turn blood bulk RNA-seq into single cells}
+\input{authors}
+\abstract{\input{sections/abstract}}
+\keywords{bulk RNA sequencing, single-cell generation, diffusion model, low-rank adaptation, paired bulk and single-cell data, immune cells}
+\maketitle
+\raggedbottom
+\input{sections/introduction}
+\section*{Results}
+\input{sections/results_fig1}
+\input{sections/results_fig2}
+\input{sections/results_fig3}
+\input{sections/results_fig4}
+\input{sections/results_fig5}
+\input{sections/results_fig6}
+\input{sections/discussion}
+\input{sections/methods_model}
+\input{sections/methods_paired}
+\input{sections/methods_eval}
+\input{sections/declarations}
+\bibliography{references}
+% Figures with their legends, each on its own page(s). Panels are the deck's vector graphics, placed as-is;
+% the 180 mm journal layout is still to be drawn.
+\input{sections/fig1}
+\input{sections/fig2}
+\input{sections/fig3}
+\input{sections/fig4}
+\input{sections/fig5}
+\input{sections/fig6}
+\end{document}

paper-releases/pbisc-diffusion/updates/20261010T153319Z-manuscript-rewrite-from-deck/diffusion/dataset/server_1/manuscript/references.bib

@@ -0,0 +1,741 @@
+% references.bib for the PBISC-Diffusion manuscript (rewrite of 2026-10-10).
+% Holds exactly the 51 keys cited in sections/*.tex. Entries kept from the previous verified file are marked "Kept"
+% and were re-checked against Crossref; all other entries are new and were checked against Crossref, Europe PMC, the
+% PDFs in reference-papers/, or the official proceedings pages (PMLR, JMLR, NeurIPS, OpenReview via mlanthology.org).
+% Conventions (sn-nature.bst):
+%  - Conference papers (NeurIPS, ICML, ICLR) are misc entries with the venue in howpublished, as in the previous
+%    verified file. The inproceedings type of sn-nature.bst never prints the booktitle and makes BibTeX report
+%    "You can't pop an empty literal stack" (tested with BibTeX 0.99d on 2026-10-10). booktitle, volume, pages and
+%    year are kept as fields, so these entries can become inproceedings if the style file is fixed.
+%  - arXiv-only works are misc entries with eprint and archivePrefix.
+%  - Journal articles print their url (sn-nature.bst does not print the doi field); every url is https://doi.org/.
+%  - Non-ASCII letters are written as LaTeX accents; the file is plain ASCII.
+
+% New. Verified: Crossref; Europe PMC (PMID 32788292, also the PubMed ID of GEO GSE152418 and GSE155673); PDF
+%  paired-cohorts/Arunachalam2020_Science_systems_immunity_mild_vs_severe_COVID19.pdf. Author 10 is written as in the
+%  article byline (Owen Tak-Yin Tsang); Crossref and PubMed split it as Tak-Yin Tsang, O.
+@article{arunachalam2020systems,
+  author = {Arunachalam, Prabhu S. and Wimmers, Florian and Mok, Chris Ka Pun and Perera, Ranawaka A. P. M. and Scott, Madeleine and Hagan, Thomas and Sigal, Natalia and Feng, Yupeng and Bristow, Laurel and Tsang, Owen Tak-Yin and Wagh, Dhananjay and Coller, John and Pellegrini, Kathryn L. and Kazmin, Dmitri and Alaaeddine, Ghina and Leung, Wai Shing and Chan, Jacky Man Chun and Chik, Thomas Shiu Hong and Choi, Chris Yau Chung and Huerta, Christopher and Paine McCullough, Michele and Lv, Huibin and Anderson, Evan and Edupuganti, Srilatha and Upadhyay, Amit A. and Bosinger, Steve E. and Maecker, Holden Terry and Khatri, Purvesh and Rouphael, Nadine and Peiris, Malik and Pulendran, Bali},
+  title = {{Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans}},
+  journal = {Science},
+  volume = {369},
+  number = {6508},
+  pages = {1210--1220},
+  year = {2020},
+  doi = {10.1126/science.abc6261},
+  url = {https://doi.org/10.1126/science.abc6261}
+}
+
+% Kept from the previous verified references.bib; re-checked against Crossref on 2026-10-10.
+@article{avilacobos2020benchmarking,
+  author = {Avila Cobos, Francisco and Alquicira-Hernandez, Jos{\'e} and Powell, Joseph E. and Mestdagh, Pieter and De Preter, Katleen},
+  title = {{Benchmarking of cell type deconvolution pipelines for transcriptomics data}},
+  journal = {Nature Communications},
+  volume = {11},
+  number = {1},
+  pages = {5650},
+  year = {2020},
+  doi = {10.1038/s41467-020-19015-1},
+  url = {https://doi.org/10.1038/s41467-020-19015-1}
+}
+
+% Kept from the previous verified references.bib; re-checked against Crossref on 2026-10-10.
+@article{babdor2026immicro,
+  author = {Babdor, Joel and Patel, Ravi K. and Davidson, Brittany and Koser, Kelvin and Noecker, Cecilia and Rahim, Maha K. and Bisanz, Jordan E. and Tenvooren, Iliana and Marquez, Diana and Calvo, Maria and Johri, Vrinda and McCarthy, Elizabeth E. and Shaheed, Avneet and Ekstrand, Christina and Weakley, Allison M. and Yu, Feiqiao B. and Krip, Kristen and Shaikh, Kashif A. and Amatullah, Hajera and Fiehn, Oliver and Turnbaugh, Peter J. and Combes, Alexis J. and Fragiadakis, Gabriela K. and Spitzer, Matthew H.},
+  title = {{Immune-microbiome coordination defines interferon setpoints in healthy humans}},
+  journal = {Cell},
+  volume = {189},
+  number = {10},
+  pages = {3144--3163.e20},
+  year = {2026},
+  doi = {10.1016/j.cell.2026.02.003},
+  url = {https://doi.org/10.1016/j.cell.2026.02.003}
+}
+
+% Kept from the previous verified references.bib; re-checked against Crossref on 2026-10-10.
+@article{benjamini1995fdr,
+  author = {Benjamini, Yoav and Hochberg, Yosef},
+  title = {{Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing}},
+  journal = {Journal of the Royal Statistical Society Series B: Statistical Methodology},
+  volume = {57},
+  number = {1},
+  pages = {289--300},
+  year = {1995},
+  doi = {10.1111/j.2517-6161.1995.tb02031.x},
+  url = {https://doi.org/10.1111/j.2517-6161.1995.tb02031.x}
+}
+
+% New. Verified: Crossref; Europe PMC (PMID 12642603); PDF
+%  rare-disease-states/Bennett2003_Interferon_granulopoiesis_signatures_SLE_PBMC.pdf.
+@article{bennett2003interferon,
+  author = {Bennett, Lynda and Palucka, A. Karolina and Arce, Edsel and Cantrell, Victoria and Borvak, Josef and Banchereau, Jacques and Pascual, Virginia},
+  title = {{Interferon and Granulopoiesis Signatures in Systemic Lupus Erythematosus Blood}},
+  journal = {The Journal of Experimental Medicine},
+  volume = {197},
+  number = {6},
+  pages = {711--723},
+  year = {2003},
+  doi = {10.1084/jem.20021553},
+  url = {https://doi.org/10.1084/jem.20021553}
+}
+
+% New. Verified: arXiv 2208.04202 (comment "ICLR'23") and mlanthology.org/iclr/2023 (OpenReview forum 3itjR9QxFw).
+@misc{chen2023analog,
+  howpublished = {In \emph{International Conference on Learning Representations}},
+  author = {Chen, Ting and Zhang, Ruixiang and Hinton, Geoffrey},
+  title = {{Analog Bits: Generating Discrete Data using Diffusion Models with Self-Conditioning}},
+  booktitle = {International Conference on Learning Representations},
+  year = {2023},
+  url = {https://openreview.net/forum?id=3itjR9QxFw}
+}
+
+% Kept from the previous verified references.bib; re-checked against Crossref on 2026-10-10.
+@article{chu2022bayesprism,
+  author = {Chu, Tinyi and Wang, Zhong and Pe'er, Dana and Danko, Charles G.},
+  title = {{Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology}},
+  journal = {Nature Cancer},
+  volume = {3},
+  number = {4},
+  pages = {505--517},
+  year = {2022},
+  doi = {10.1038/s43018-022-00356-3},
+  url = {https://doi.org/10.1038/s43018-022-00356-3}
+}
+
+% Kept from the previous verified references.bib; re-checked against Crossref on 2026-10-10.
+@article{cui2024scgpt,
+  author = {Cui, Haotian and Wang, Chloe and Maan, Hassaan and Pang, Kuan and Luo, Fengning and Duan, Nan and Wang, Bo},
+  title = {{scGPT: toward building a foundation model for single-cell multi-omics using generative AI}},
+  journal = {Nature Methods},
+  volume = {21},
+  number = {8},
+  pages = {1470--1480},
+  year = {2024},
+  doi = {10.1038/s41592-024-02201-0},
+  url = {https://doi.org/10.1038/s41592-024-02201-0}
+}
+
+% New. Verified: Crossref; Europe PMC (PMID 35810186, the PubMed ID of GEO GSE206263, GSE206283 and SuperSeries
+%  GSE206284). No PDF in reference-papers.
+@article{giroux2022differential,
+  author = {Giroux, Nicholas S. and Ding, Shengli and McClain, Micah T. and Burke, Thomas W. and Petzold, Elizabeth and Chung, Hong A. and Rivera, Grecia O. and Wang, Ergang and Xi, Rui and Bose, Shree and Rotstein, Tomer and Nicholson, Bradly P. and Chen, Tianyi and Henao, Ricardo and Sempowski, Gregory D. and Denny, Thomas N. and De Ussel, Maria Iglesias and Satterwhite, Lisa L. and Ko, Emily R. and Ginsburg, Geoffrey S. and Kraft, Bryan D. and Tsalik, Ephraim L. and Shen, Xiling and Woods, Christopher W.},
+  title = {{Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion}},
+  journal = {Scientific Reports},
+  volume = {12},
+  number = {1},
+  pages = {11714},
+  year = {2022},
+  doi = {10.1038/s41598-022-15668-8},
+  url = {https://doi.org/10.1038/s41598-022-15668-8}
+}
+
+% New. Verified: Crossref; Europe PMC (PMID 36522333); PDF
+%  paired-cohorts/Gisby2022_NatCommun_multiomics_LRRC15_COVID19_haemodialysis.pdf.
+@article{gisby2022multiomics,
+  author = {Gisby, Jack S. and Buang, Norzawani B. and Papadaki, Artemis and Clarke, Candice L. and Malik, Talat H. and Medjeral-Thomas, Nicholas and Pinheiro, Damiola and Mortimer, Paige M. and Lewis, Shanice and Sandhu, Eleanor and McAdoo, Stephen P. and Prendecki, Maria F. and Willicombe, Michelle and Pickering, Matthew C. and Botto, Marina and Thomas, David C. and Peters, James E.},
+  title = {{Multi-omics identify falling LRRC15 as a COVID-19 severity marker and persistent pro-thrombotic signals in convalescence}},
+  journal = {Nature Communications},
+  volume = {13},
+  number = {1},
+  pages = {7775},
+  year = {2022},
+  doi = {10.1038/s41467-022-35454-4},
+  url = {https://doi.org/10.1038/s41467-022-35454-4}
+}
+
+% New. Verified: Crossref; Europe PMC (PMID 41162704); PDF
+%  rare-disease-states/Gong2025_Multiomic_profiling_age_related_immune_dynamics_healthy_adults.pdf.
+@article{gong2025multiomic,
+  author = {Gong, Qiuyu and Sharma, Mehul and Glass, Marla C. and Kuan, Emma L. and Chander, Aishwarya and Singh, Mansi and Graybuck, Lucas T. and Thomson, Zachary J. and LaFrance, Christian M. and Rachid Zaim, Samir and Peng, Tao and Okada, Lauren Y. and Genge, Palak C. and Henderson, Katherine E. and Dornisch, Elisabeth M. and Layton, Erik D. and Wittig, Peter J. and Heubeck, Alexander T. and Mukuka, Nelson M. and Reading, Julian and Strawn, Garrett and Titus-Adewunmi, Teminijesu and Abadie, Kathleen and Roll, Charles R. and Hernandez, Veronica and Parthasarathy, Vaishnavi and Stuckey, Tyanna J. and Musgrove, Blessing and Swanson, Elliott and Lord, Cara and Weiss, Morgan D. A. and Phalen, Cole G. and Mettey, Regina R. and Lee, Kevin J. and Johanneson, John B. and Kawelo, Erin K. and Garber, Jessica and Krishnan, Upaasana and Smithmyer, Megan and Wherry, E. John and Vella, Laura A. and Henrickson, Sarah E. and Kopp, Mackenzie S. and Savage, Adam K. and Becker, Lynne A. and Meijer, Paul and Coffey, Ernest M. and Goronzy, Jorg J. and Sigvardsson, Mikael and Speake, Cate and Bumol, Thomas F. and Goldrath, Ananda W. and Torgerson, Troy R. and Li, Xiao-jun and Skene, Peter J. and Buckner, Jane H. and Gustafson, Claire E.},
+  title = {{Multi-omic profiling reveals age-related immune dynamics in healthy adults}},
+  journal = {Nature},
+  volume = {648},
+  number = {8094},
+  pages = {696--706},
+  year = {2025},
+  doi = {10.1038/s41586-025-09686-5},
+  url = {https://doi.org/10.1038/s41586-025-09686-5}
+}
+
+% New. Verified: PDF (JMLR 13 (2012) 723-773) and jmlr.org/papers/v13/gretton12a.html (issue 25). JMLR assigns no DOI.
+@article{gretton2012kernel,
+  author = {Gretton, Arthur and Borgwardt, Karsten M. and Rasch, Malte J. and Sch{\"o}lkopf, Bernhard and Smola, Alexander},
+  title = {{A Kernel Two-Sample Test}},
+  journal = {Journal of Machine Learning Research},
+  volume = {13},
+  number = {25},
+  pages = {723--773},
+  year = {2012},
+  url = {https://jmlr.org/papers/v13/gretton12a.html}
+}
+
+% New. Verified: Crossref; Europe PMC (PMID 31719197); PDF
+%  rare-disease-states/Hashimoto2019_CD4_CTL_supercentenarians.pdf.
+@article{hashimoto2019single,
+  author = {Hashimoto, Kosuke and Kouno, Tsukasa and Ikawa, Tomokatsu and Hayatsu, Norihito and Miyajima, Yurina and Yabukami, Haruka and Terooatea, Tommy and Sasaki, Takashi and Suzuki, Takahiro and Valentine, Matthew and Pascarella, Giovanni and Okazaki, Yasushi and Suzuki, Harukazu and Shin, Jay W. and Minoda, Aki and Taniuchi, Ichiro and Okano, Hideyuki and Arai, Yasumichi and Hirose, Nobuyoshi and Carninci, Piero},
+  title = {{Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians}},
+  journal = {Proceedings of the National Academy of Sciences},
+  volume = {116},
+  number = {48},
+  pages = {24242--24251},
+  year = {2019},
+  doi = {10.1073/pnas.1907883116},
+  url = {https://doi.org/10.1073/pnas.1907883116}
+}
+
+% Kept from the previous verified references.bib (official NeurIPS 2020 BibTeX; NeurIPS 33, 6840-6851).
+@misc{ho2020ddpm,
+  howpublished = {In \emph{Advances in Neural Information Processing Systems} \textbf{33}, 6840--6851 (Curran Associates, Inc.)},
+  author = {Ho, Jonathan and Jain, Ajay and Abbeel, Pieter},
+  title = {{Denoising Diffusion Probabilistic Models}},
+  booktitle = {Advances in Neural Information Processing Systems},
+  volume = {33},
+  pages = {6840--6851},
+  year = {2020},
+  url = {https://proceedings.neurips.cc/paper_files/paper/2020/file/4c5bcfec8584af0d967f1ab10179ca4b-Paper.pdf}
+}
+
+% New. Verified: arXiv 2106.09685 (title, authors) and mlanthology.org/iclr/2022 (ICLR 2022, OpenReview forum
+%  nZeVKeeFYf9).
+@misc{hu2022lora,
+  howpublished = {In \emph{International Conference on Learning Representations}},
+  author = {Hu, Edward J. and Shen, Yelong and Wallis, Phillip and Allen-Zhu, Zeyuan and Li, Yuanzhi and Wang, Shean and Wang, Lu and Chen, Weizhu},
+  title = {{LoRA: Low-Rank Adaptation of Large Language Models}},
+  booktitle = {International Conference on Learning Representations},
+  year = {2022},
+  url = {https://openreview.net/forum?id=nZeVKeeFYf9}
+}
+
+% New. Verified: Crossref; Europe PMC (PMID 15846361); PDF
+%  evaluation-metrics/Irizarry2005_Multiple_laboratory_comparison_microarray_platforms.pdf.
+@article{irizarry2005multiple,
+  author = {Irizarry, Rafael A. and Warren, Daniel and Spencer, Forrest and Kim, Irene F. and Biswal, Shyam and Frank, Bryan C. and Gabrielson, Edward and Garcia, Joe G. N. and Geoghegan, Joel and Germino, Gregory and Griffin, Constance and Hilmer, Sara C. and Hoffman, Eric and Jedlicka, Anne E. and Kawasaki, Ernest and Mart{\'\i}nez-Murillo, Francisco and Morsberger, Laura and Lee, Hannah and Petersen, David and Quackenbush, John and Scott, Alan and Wilson, Michael and Yang, Yanqin and Ye, Shui Qing and Yu, Wayne},
+  title = {{Multiple-laboratory comparison of microarray platforms}},
+  journal = {Nature Methods},
+  volume = {2},
+  number = {5},
+  pages = {345--350},
+  year = {2005},
+  doi = {10.1038/nmeth756},
+  url = {https://doi.org/10.1038/nmeth756}
+}
+
+% New. Verified: Crossref; Europe PMC (PMID 30314758). No PDF in reference-papers (INDEX lists it as not downloaded).
+@article{jenks2018distinct,
+  author = {Jenks, Scott A. and Cashman, Kevin S. and Zumaquero, Esther and Marigorta, Urko M. and Patel, Aakash V. and Wang, Xiaoqian and Tomar, Deepak and Woodruff, Matthew C. and Simon, Zoe and Bugrovsky, Regina and Blalock, Emily L. and Scharer, Christopher D. and Tipton, Christopher M. and Wei, Chungwen and Lim, S. Sam and Petri, Michelle and Niewold, Timothy B. and Anolik, Jennifer H. and Gibson, Greg and Lee, F. Eun-Hyung and Boss, Jeremy M. and Lund, Frances E. and Sanz, Ignacio},
+  title = {{Distinct Effector B Cells Induced by Unregulated Toll-like Receptor 7 Contribute to Pathogenic Responses in Systemic Lupus Erythematosus}},
+  journal = {Immunity},
+  volume = {49},
+  number = {4},
+  pages = {725--739.e6},
+  year = {2018},
+  doi = {10.1016/j.immuni.2018.08.015},
+  url = {https://doi.org/10.1016/j.immuni.2018.08.015}
+}
+
+% New. Verified: Crossref; Europe PMC (PMID 40317333); PDF
+%  paired-cohorts/Ji2025_CancerImmunolImmunother_checkpoint_inhibitor_liver_injury.pdf (same title as GEO GSE287540
+%  and GSE287541).
+@article{ji2025chili,
+  author = {Ji, Changhua and Kumpf, Steven and Qian, Jessie and Federspiel, Joel D. and Sheehan, Mark and Capunitan, Darien and Atallah, Edmond and Astbury, Stuart and Arat, Seda and Oziolor, Elias and Ocana, Mireia Fernandez and Ramaiah, Shashi K. and Grove, Jane and Aithal, Guruprasad P. and Lanz, Thomas A.},
+  title = {{Transcriptomic and proteomic characterization of cell and protein biomarkers of checkpoint inhibitor-induced liver injury}},
+  journal = {Cancer Immunology, Immunotherapy},
+  volume = {74},
+  number = {6},
+  pages = {190},
+  year = {2025},
+  doi = {10.1007/s00262-025-04033-z},
+  url = {https://doi.org/10.1007/s00262-025-04033-z}
+}
+
+% New. Verified: PDF (PMLR 202, 2023) and proceedings.mlr.press/v202/khayatkhoei23a.html (pages 16326-16343).
+% Second author spelled as in the paper byline (AbdAlmageed); the PMLR BibTeX writes Abdalmageed.
+@misc{khayatkhoei2023emergent,
+  howpublished = {In \emph{Proceedings of the 40th International Conference on Machine Learning}, Proceedings of Machine Learning Research \textbf{202}, 16326--16343 (PMLR)},
+  author = {Khayatkhoei, Mahyar and AbdAlmageed, Wael},
+  title = {{Emergent Asymmetry of Precision and Recall for Measuring Fidelity and Diversity of Generative Models in High Dimensions}},
+  booktitle = {Proceedings of the 40th International Conference on Machine Learning},
+  series = {Proceedings of Machine Learning Research},
+  volume = {202},
+  pages = {16326--16343},
+  publisher = {PMLR},
+  year = {2023},
+  url = {https://proceedings.mlr.press/v202/khayatkhoei23a.html}
+}
+
+% New. Verified: PDF (arXiv 1904.06991v3, "NeurIPS 2019") and the official proceedings.neurips.cc BibTeX (volume 32).
+% UNVERIFIED: kynkaanniemi2019improved page range (the official NeurIPS 2019 BibTeX has an empty pages field; none
+%  given)
+@misc{kynkaanniemi2019improved,
+  howpublished = {In \emph{Advances in Neural Information Processing Systems} \textbf{32} (Curran Associates, Inc.)},
+  author = {Kynk{\"a}{\"a}nniemi, Tuomas and Karras, Tero and Laine, Samuli and Lehtinen, Jaakko and Aila, Timo},
+  title = {{Improved Precision and Recall Metric for Assessing Generative Models}},
+  booktitle = {Advances in Neural Information Processing Systems},
+  volume = {32},
+  publisher = {Curran Associates, Inc.},
+  year = {2019},
+  url = {https://proceedings.neurips.cc/paper_files/paper/2019/file/0234c510bc6d908b28c70ff313743079-Paper.pdf}
+}
+
+% New. Verified: Crossref; Europe PMC (PMID 24485249). No PDF in reference-papers.
+@article{law2014voom,
+  author = {Law, Charity W. and Chen, Yunshun and Shi, Wei and Smyth, Gordon K.},
+  title = {{voom: precision weights unlock linear model analysis tools for RNA-seq read counts}},
+  journal = {Genome Biology},
+  volume = {15},
+  number = {2},
+  pages = {R29},
+  year = {2014},
+  doi = {10.1186/gb-2014-15-2-r29},
+  url = {https://doi.org/10.1186/gb-2014-15-2-r29}
+}
+
+% New. Verified: Crossref; Europe PMC (PMID 42715312); PDF
+%  evaluation-metrics/Li2026_Systematic_comparison_sc_perturbation_response_prediction_models.pdf.
+@article{li2026systematic,
+  author = {Li, Lanxiang and You, Yue and Fu, Yunlin and Liao, Wenyu and Fan, Xueying and Lu, Shihong and Cao, Ye and Li, Bo and Ren, Wenle and Kong, Jiaming and Zheng, Shuangjia and Chen, Jizheng and Liu, Xiaodong and Tian, Luyi},
+  title = {{A systematic comparison of single-cell perturbation response prediction models}},
+  journal = {Science Advances},
+  volume = {12},
+  number = {37},
+  pages = {eaed3414},
+  year = {2026},
+  doi = {10.1126/sciadv.aed3414},
+  url = {https://doi.org/10.1126/sciadv.aed3414}
+}
+
+% New. Verified: Crossref; Europe PMC (PMID 33713619, the PubMed ID of GEO GSE161918). Byline as in Europe PMC, with
+%  the two collective authors; Crossref also lists ten consortium members. No PDF in reference-papers.
+@article{liu2021timeresolved,
+  author = {Liu, Can and Martins, Andrew J. and Lau, William W. and Rachmaninoff, Nicholas and Chen, Jinguo and Imberti, Luisa and Mostaghimi, Darius and Fink, Danielle L. and Burbelo, Peter D. and Dobbs, Kerry and Delmonte, Ottavia M. and Bansal, Neha and Failla, Laura and Sottini, Alessandra and Quiros-Roldan, Eugenia and Han, Kyu Lee and Sellers, Brian A. and Cheung, Foo and Sparks, Rachel and Chun, Tae-Wook and Moir, Susan and Lionakis, Michail S. and {NIAID COVID Consortium} and {COVID Clinicians} and Rossi, Camillo and Su, Helen C. and Kuhns, Douglas B. and Cohen, Jeffrey I. and Notarangelo, Luigi D. and Tsang, John S.},
+  title = {{Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19}},
+  journal = {Cell},
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+  pages = {1836--1857.e22},
+  year = {2021},
+  doi = {10.1016/j.cell.2021.02.018},
+  url = {https://doi.org/10.1016/j.cell.2021.02.018}
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+@article{lopez2018scvi,
+  author = {Lopez, Romain and Regier, Jeffrey and Cole, Michael B. and Jordan, Michael I. and Yosef, Nir},
+  title = {{Deep generative modeling for single-cell transcriptomics}},
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+  url = {https://doi.org/10.1038/s41592-018-0229-2}
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+
+% New. Verified: PDF ("Published as a conference paper at ICLR 2017") and mlanthology.org/iclr/2017 (OpenReview forum
+%  SJkXfE5xx).
+@misc{lopezpaz2017revisiting,
+  howpublished = {In \emph{International Conference on Learning Representations}},
+  author = {Lopez-Paz, David and Oquab, Maxime},
+  title = {{Revisiting Classifier Two-Sample Tests}},
+  booktitle = {International Conference on Learning Representations},
+  year = {2017},
+  url = {https://openreview.net/forum?id=SJkXfE5xx}
+}
+
+% New. Verified: arXiv 1711.05101 (comment "Published as a conference paper at ICLR 2019") and
+%  mlanthology.org/iclr/2019 (OpenReview forum Bkg6RiCqY7).
+@misc{loshchilov2019decoupled,
+  howpublished = {In \emph{International Conference on Learning Representations}},
+  author = {Loshchilov, Ilya and Hutter, Frank},
+  title = {{Decoupled Weight Decay Regularization}},
+  booktitle = {International Conference on Learning Representations},
+  year = {2019},
+  url = {https://openreview.net/forum?id=Bkg6RiCqY7}
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+@article{luo2024scdiffusion,
+  author = {Luo, Erpai and Hao, Minsheng and Wei, Lei and Zhang, Xuegong},
+  title = {{scDiffusion: conditional generation of high-quality single-cell data using diffusion model}},
+  journal = {Bioinformatics},
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+  pages = {btae518},
+  year = {2024},
+  doi = {10.1093/bioinformatics/btae518},
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+
+% New. Verified: Crossref; Europe PMC (PMID 32669297); PDF
+%  rare-disease-states/Mathew2020_COVID_immunotypes_CD38_HLADR_T_cells.pdf. Byline as printed (the UPenn COVID
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+  title = {{Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications}},
+  journal = {Science},
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+  pages = {eabc8511},
+  year = {2020},
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+  url = {https://doi.org/10.1126/science.abc8511}
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+@misc{mcinnes2018umap,
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+  title = {{UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction}},
+  howpublished = {Preprint},
+  year = {2018},
+  doi = {10.48550/ARXIV.1802.03426},
+  eprint = {1802.03426},
+  archivePrefix = {arXiv}
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+
+% New. Verified: PDF (arXiv 2002.09797v2, "PMLR 119, 2020") and proceedings.mlr.press/v119/naeem20a.html (pages
+%  7176-7185).
+@misc{naeem2020reliable,
+  howpublished = {In \emph{Proceedings of the 37th International Conference on Machine Learning}, Proceedings of Machine Learning Research \textbf{119}, 7176--7185 (PMLR)},
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+  booktitle = {Proceedings of the 37th International Conference on Machine Learning},
+  series = {Proceedings of Machine Learning Research},
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+  publisher = {PMLR},
+  year = {2020},
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+  doi = {10.1038/s41590-020-0743-0},
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+@misc{nichol2021improved,
+  howpublished = {In \emph{Proceedings of the 38th International Conference on Machine Learning}, Proceedings of Machine Learning Research \textbf{139}, 8162--8171 (PMLR)},
+  author = {Nichol, Alexander Quinn and Dhariwal, Prafulla},
+  title = {{Improved Denoising Diffusion Probabilistic Models}},
+  booktitle = {Proceedings of the 38th International Conference on Machine Learning},
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+  publisher = {PMLR},
+  year = {2021},
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+  howpublished = {Preprint},
+  year = {2025},
+  doi = {10.48550/ARXIV.2502.02448},
+  eprint = {2502.02448},
+  archivePrefix = {arXiv},
+  note = {Version 3, 22 January 2026}
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+  title = {{Genetic ancestry effects on the response to viral infection are pervasive but cell type specific}},
+  journal = {Science},
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+  year = {2021},
+  doi = {10.1126/science.abg0928},
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+% New. Verified: Crossref; Europe PMC (PMID 32066974); PDF
+%  rare-disease-states/Reyes2020_Immune_cell_signature_bacterial_sepsis.pdf (author manuscript).
+@article{reyes2020immune,
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+@article{roohani2024gears,
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+  booktitle = {International Conference on Learning Representations},
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+  url = {https://openreview.net/forum?id=St1giarCHLP}
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+% New. Verified: Crossref; Europe PMC (PMID 34584091); PDF
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+%  rare-disease-states/Stephenson2021_Single_cell_multiomics_COVID19.pdf. The CITIID-NIHR collaboration is placed as
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+%  paired-cohorts/Stephenson2025_CellGenom_temporal_multiomics_COVID19_ESKD.pdf.
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+  doi = {10.1016/j.xgen.2025.100918},
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+@article{wang2021kawasaki,
+  author = {Wang, Zhen and Xie, Lijian and Ding, Guohui and Song, Sirui and Chen, Liqin and Li, Guang and Xia, Min and Han, Dingding and Zheng, Yue and Liu, Jia and Xiao, Tingting and Zhang, Hong and Huang, Yujuan and Li, Yixue and Huang, Min},
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+  year = {2026},
+  doi = {10.1038/s41590-025-02345-x},
+  url = {https://doi.org/10.1038/s41590-025-02345-x}
+}
+
+% New. Verified: Crossref; Europe PMC (PMID 35727985, the PubMed ID of GEO GSE198533 and GSE198616); PDF
+%  paired-cohorts/bechet_c1q.pdf. Replaces the earlier incomplete entry ("and others").
+@article{zheng2022c1qbehcet,
+  author = {Zheng, Wenjie and Wang, Xiaoman and Liu, Jinjing and Yu, Xin and Li, Lu and Wang, Heping and Yu, Jijun and Pei, Xiaoya and Li, Chaoran and Wang, Zhimian and Zhang, Menghao and Zeng, Xiaofeng and Zhang, Fengchun and Wang, Chenfei and Chen, Hua and Chen, Hou-Zao},
+  title = {{Single-cell analyses highlight the proinflammatory contribution of C1q-high monocytes to Beh{\c{c}}et's disease}},
+  journal = {Proceedings of the National Academy of Sciences},
+  volume = {119},
+  number = {26},
+  pages = {e2204289119},
+  year = {2022},
+  doi = {10.1073/pnas.2204289119},
+  url = {https://doi.org/10.1073/pnas.2204289119}
+}
+
+% Added by the coordinator on 2026-10-10 (introduction, bulk-to-cell models). Titles, authors, journal, volume and
+% article number checked against the PDFs in reference-papers/bulk-to-sc/ (first page and footer).
+@article{liao2022bulk2space,
+  author = {Liao, Jie and Qian, Jingyang and Fang, Yin and Chen, Zhuo and Zhuang, Xiang and Zhang, Ningyu and Shao, Xin and Hu, Yining and Yang, Penghui and Cheng, Junyun and Hu, Yang and Yu, Lingqi and Yang, Haihong and Zhang, Jinlu and Lu, Xiaoyan and Shao, Li and Wu, Dan and Gao, Yue and Chen, Huajun and Fan, Xiaohui},
+  title = {{De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution}},
+  journal = {Nature Communications},
+  volume = {13},
+  pages = {6498},
+  year = {2022},
+  doi = {10.1038/s41467-022-34271-z},
+  url = {https://doi.org/10.1038/s41467-022-34271-z}
+}
+
+@article{zeng2024omicverse,
+  author = {Zeng, Zehua and Ma, Yuqing and Hu, Lei and Tan, Bowen and Liu, Peng and Wang, Yixuan and Xing, Cencan and Xiong, Yuanyan and Du, Hongwu},
+  title = {{OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing}},
+  journal = {Nature Communications},
+  volume = {15},
+  pages = {5983},
+  year = {2024},
+  doi = {10.1038/s41467-024-50194-3},
+  url = {https://doi.org/10.1038/s41467-024-50194-3}
+}
+
+@misc{cho2024bulk2sc,
+  author = {Cho, Hyun Jae and Xie, Eric and Zhang, Aidong and Bekiranov, Stefan},
+  title = {{Generating synthetic single cell data from bulk RNA-seq using a pretrained variational autoencoder}},
+  howpublished = {Preprint at bioRxiv},
+  year = {2024},
+  doi = {10.1101/2024.05.18.594837},
+  url = {https://doi.org/10.1101/2024.05.18.594837}
+}
+
+% Added by the coordinator on 2026-10-10 (limma lmFit/eBayes; metadata as confirmed on Crossref by the references agent).
+@article{ritchie2015limma,
+  author = {Ritchie, Matthew E. and Phipson, Belinda and Wu, Di and Hu, Yifang and Law, Charity W. and Shi, Wei and Smyth, Gordon K.},
+  title = {{limma powers differential expression analyses for RNA-sequencing and microarray studies}},
+  journal = {Nucleic Acids Research},
+  volume = {43},
+  number = {7},
+  pages = {e47},
+  year = {2015},
+  doi = {10.1093/nar/gkv007},
+  url = {https://doi.org/10.1093/nar/gkv007}
+}

paper-releases/pbisc-diffusion/updates/20261010T153319Z-manuscript-rewrite-from-deck/diffusion/dataset/server_1/manuscript/supplementary.tex

@@ -0,0 +1,37 @@
+% Supplementary Information. Compile independently with pdfLaTeX; all dependencies are local.
+% Rewritten from scratch on 2026-10-10 from the paper-summary deck; previous version in archive/pre_rewrite_20261010/.
+\documentclass[pdflatex,sn-nature]{sn-jnl}
+\usepackage{graphicx}
+\usepackage{amsmath,amssymb}
+\usepackage{booktabs,array,longtable,multirow}
+\usepackage{microtype}
+\usepackage{xcolor}
+\usepackage{adjustbox}
+\input{macros}
+\renewcommand{\theequation}{S\arabic{equation}}
+\begin{document}
+\raggedbottom
+\renewcommand\tablename{Supplementary Table}
+\title{Supplementary Information for: Five paired donors and minutes of fine-tuning turn blood bulk RNA-seq into single cells}
+\input{authors}
+\maketitle
+\raggedbottom
+
+\section*{Supplementary Notes}
+\renewcommand{\thesection}{Supplementary Note \arabic{section}:}
+\input{sections/supp_notes}
+
+\section*{Supplementary Methods}
+\input{sections/supp_methods_model}
+\input{sections/supp_methods_eval}
+
+\section*{Supplementary Tables}
+\input{sections/supp_table_cohorts}
+\input{sections/supp_tables}
+
+\section*{Supplementary Figures}
+\input{sections/supp_figures}
+
+\clearpage
+\bibliography{references}
+\end{document}