main.tex

%for a more compact document, add the option openany to avoid
%starting all chapters on odd numbered pages
\documentclass[11pt]{cmuthesis}

% This is a template for a CMU thesis.  It is 18 pages without any content :-)
% The source for this is pulled from a variety of sources and people.
% Here's a partial list of people who may or may have not contributed:
%
%        bnoble   = Brian Noble
%        caruana  = Rich Caruana
%        colohan  = Chris Colohan
%        jab      = Justin Boyan
%        josullvn = Joseph O'Sullivan
%        jrs      = Jonathan Shewchuk
%        kosak    = Corey Kosak
%        mjz      = Matt Zekauskas (mattz@cs)
%        pdinda   = Peter Dinda
%        pfr      = Patrick Riley
%        dkoes = David Koes (me)

% My main contribution is putting everything into a single class files and small
% template since I prefer this to some complicated sprawling directory tree with
% makefiles.

% some useful packages
\usepackage{times}
\usepackage{fullpage}
\usepackage{graphicx}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage[numbers,sort]{natbib}
\usepackage[backref,pageanchor=true,plainpages=false, pdfpagelabels, bookmarks,bookmarksnumbered,
%pdfborder=0 0 0,  %removes outlines around hyper links in online display
]{hyperref}
\usepackage{subfigure}
\newtheorem{theorem}{Theorem}[section]
\newtheorem{corollary}{Corollary}[theorem]
\newtheorem{lemma}{Lemma}[theorem]
\newtheorem{definition}{Definition}
\newtheorem{proposition}{Proposition}
\newenvironment{proof}{\paragraph{Proof:}}{\hfill$\square$}
\newcommand{\theHalgorithm}{\arabic{algorithm}}

% Approximately 1" margins, more space on binding side
%\usepackage[letterpaper,twoside,vscale=.8,hscale=.75,nomarginpar]{geometry}
%for general printing (not binding)
\usepackage[letterpaper,twoside,vscale=.8,hscale=.75,nomarginpar,hmarginratio=1:1]{geometry}

% Provides a draft mark at the top of the document. 
% \draftstamp{\today}{DRAFT}

\usepackage{tikz}
\usetikzlibrary{
  arrows.meta, % for Straight Barb arrow tip
  fit, % to fit the group box around the central neurons
  positioning, % for relative positioning of the neurons
  bayesnet
}

\DeclareMathOperator{\argmax}{\arg\max}
\DeclareMathOperator{\argmin}{\arg\min}

\DeclareMathOperator*{\minimize}{\text{minimize}}
\DeclareMathOperator*{\maximize}{\text{maximize}}
\DeclareMathOperator*{\st}{\text{subject to}}
\usepackage{tabularx,booktabs}
\def\usevspace{1}

\usepackage{algorithm}
\usepackage[noend]{algorithmic}
\usepackage[algo2e,linesnumbered,vlined,ruled]{algorithm2e}
\usepackage{multirow}
\usepackage{centernot}
\tikzset{
  neuron/.style={ % style for each neuron
    circle,draw,thick, % drawn as a thick circle
    inner sep=0pt, % no built-in padding between the text and the circle shape
    minimum size=3em, % make each neuron the same size regardless of the text inside
    node distance=1ex and 2em, % spacing between neurons (y and x)
  },
  group/.style={ % style for the groups of neurons
    rectangle,draw,thick, % drawn as a thick rectangle
    inner sep=7pt, % no padding between the node contents and the rectangle shape
  },
  group2/.style={ % style for the groups of neurons
    rectangle,draw,thick, % drawn as a thick rectangle
    inner sep=7pt, % no padding between the node contents and the rectangle shape
  },
  io/.style={ % style for the inputs/outputs
    neuron, % inherit the neuron style
    fill=gray!15, % add a fill color
  },
  conn/.style={ % style for the connections
    -{Straight Barb[angle=60:2pt 3]}, % simple barbed arrow tip
    thick, % draw in a thick weight to match other drawing elements
  },
}

\begin {document} 
\frontmatter

%initialize page style, so contents come out right (see bot) -mjz
\pagestyle{empty}

\title{ {\it \huge Thesis Proposal}\\
{\bf Practical Methods for Automated Algorithm Design \\ in Machine Learning and Computational Biology}}
\author{Minh Hoang}
\date{May 2022}
\Year{2022}
\trnumber{}

\committee{
Prof. Carl Kingsford, Chair \\
Prof. David P. Woodruff \\
Prof. Maria-Florina Balcan \\
Prof. Risto Miikkulainen
}

% \support{}
% \disclaimer{}

% copyright notice generated automatically from Year and author.
% permission added if \permission{} given.

\maketitle

% \begin{dedication}
% For my dog
% \end{dedication}

\pagestyle{plain} % for toc, was empty

%% Obviously, it's probably a good idea to break the various sections of your thesis
%% into different files and input them into this file...
\begin{abstract}
\input{abstract.tex}
\end{abstract}
\keywords{Automated Machine Learning, Optimization}
% \begin{acknowledgments}
% \input{acknowledgement.tex}
% \end{acknowledgments}



\tableofcontents
\listoffigures
\listoftables

\mainmatter

%% Double space document for easy review:
\renewcommand{\baselinestretch}{1.66}\normalsize

% The other requirements Catherine has:
%
%  - avoid large margins.  She wants the thesis to use fewer pages, 
%    especially if it requires colour printing.
%
%  - The thesis should be formatted for double-sided printing.  This
%    means that all chapters, acknowledgements, table of contents, etc.
%    should start on odd numbered (right facing) pages.
%
%  - You need to use the department standard tech report title page.  I
%    have tried to ensure that the title page here conforms to this
%    standard.
%
%  - Use a nice serif font, such as Times Roman.  Sans serif looks bad.
%
% Other than that, just make it look good...


\chapter{Introduction}
\input{intro.tex}
\label{sec:intro}

\chapter{Kernel Selection}
\input{kernel.tex}
\label{sec:kernel}

\chapter{Minimizer Sketch Design}
\input{minimizer.tex}
\label{sec:minimizer}

\chapter{Neural Architecture Search}
\input{nas.tex}
\label{sec:nas}

\chapter{Other work and future directions}
\label{sec:future}
\input{future.tex}

% \chapter{Conclusion}
% \label{sec:conclusion}
% \input{conclusion.tex}

\appendix
\include{appendix}
\chapter{Kernel Selection Appendix}
\input{kernel_appendix}
\chapter{Minimizer Sketch Design Appendix}
\input{msd_appendix}
\chapter{Masked Minimizer Appendix}
\input{maskmnz_appendix.tex}
\chapter{Neural Architecture Search Appendix}
\input{nas_appendix}
\backmatter

%\renewcommand{\baselinestretch}{1.0}\normalsize

% By default \bibsection is \chapter*, but we really want this to show
% up in the table of contents and pdf bookmarks.
\renewcommand{\bibsection}{\chapter{\bibname}}
%\newcommand{\bibpreamble}{This text goes between the ``Bibliography''
%  header and the actual list of references}
\bibliographystyle{plainnat}
\bibliography{thesis} %your bib file

\end{document}