thesis.tex

%% thesis.tex 2014/04/11
%
% Based on sample files of unknown authorship.
%
% The Current Maintainer of this work is Paul Vojta.

\documentclass{ucbthesis}

\input{packages}


% To compile this file, run "latex thesis", then "biber thesis"
% (or "bibtex thesis", if the output from latex asks for that instead),
% and then "latex thesis" (without the quotes in each case).

% Double spacing, if you want it.  Do not use for the final copy.
% \def\dsp{\def\baselinestretch{2.0}\large\normalsize}
% \dsp

% If the Grad. Division insists that the first paragraph of a section
% be indented (like the others), then include this line:
% \usepackage{indentfirst}

\addtolength{\abovecaptionskip}{\baselineskip}
\input{math_preamble}

\bibliography{references}

\listfiles
\begin{document}

% Declarations for Front Matter

\title{\textbf{Charting Cellular States, One Cell at a Time:\\ Computational, Inferential and Modeling Perspectives}}
\author{Romain Lopez}
\degreesemester{Spring}
\degreeyear{2021}
\degree{Doctor of Philosophy}
\othermembers{Professor Sandrine Dudoit}
\cochairs{Professor Michael I. Jordan}{Associate Professor Nir Yosef}
\numberofmembers{3}
\field{Engineering --- Electrical Engineering and Computer Sciences}

% This affects the title and approval pages, which by default calls this
% document a "dissertation", not a "thesis".

\maketitle
% Delete (or comment out) the \approvalpage line for the final version.
% \approvalpage
\copyrightpage

\include{abstract}

\begin{frontmatter}

\begin{dedication}
\null\vfil
\begin{center}
\begin{itshape}
To my parents, Marie \& Fran\c{c}ois, \\
To my brother, Mathieu.
\end{itshape}
\end{center}
\vfil\null
\end{dedication}

% You can delete the \clearpage lines if you don't want these to start on
% separate pages.
\setcounter{tocdepth}{2}
\setcounter{secnumdepth}{2}
\tableofcontents
\clearpage
\listoffigures
\clearpage
\listoftables

\input{acknowledgement}
\end{frontmatter}

\pagestyle{headings}

\include{introduction/introduction}

\chapter{Background on Deep Generative Models}
\label{background}
\input{review/1_introduction}
\input{review/2_review}

\part{Bayesian Models for Single-cell Transcriptomics}
\label{part1}

\chapter{Large-scale Analysis of Single-cell Transcriptomics}
\chaptermark{Single-cell Variational Inference}
\label{scvi}
\input{scvi/1_introduction.tex}
\input{scvi/2_results.tex}
\input{scvi/3_discussion.tex}
\input{scvi/5_supplementary_material.tex}

\chapter{Harmonization and Annotation of Multiple Single-cell Experiments}
\chaptermark{Single-cell Annotation using Variational Inference}
\label{scanvi}
\input{scanvi/1_introduction.tex}
\input{scanvi/2_results.tex}
\input{scanvi/3_discussion.tex}
\input{scanvi/6_supplementary_material.tex}

\part{Machine Learning for Science}
\label{part2}
\chapter{Information Constraints on Auto-Encoding Variational Bayes}
\chaptermark{HSIC-Constrained VAES}
\label{hcv}
% \input{hsic/0_opening}
\input{hsic/1_introduction}
\input{hsic/2_background}
\input{hsic/3_HCV}
\input{hsic/4_independence}
\input{hsic/5_invariant}
\input{hsic/6_structured}
\input{hsic/7_discussion}

\chapter{Decision-making with Auto-Encoding Variational Bayes}
\chaptermark{Decision-making with AEVB}
\label{decision}
% \input{decision/0_opening.tex}
\input{decision/1_introduction}
\input{decision/2_relatedwork}
\input{decision/3_theory_and_algs}
\input{decision/5_posterior_query_diagnosis}
\input{decision/4_experiments}
\input{decision/6_label_decision}
\input{decision/7_FDR}
\input{decision/8_discussion}
\input{decision/9_appendix}

\part{~~Conclusion}
\chapter{Discussion}
\label{perspectives}
\input{review/3_applications}
\section{Perspectives}
\input{review/4_perspectives}

\printbibliography
\end{document}