thesis.Rnw

% Layout ideas:

\documentclass[twoside]{memoir}



% Set paper size
\setstocksize{24cm}{17cm}
\settrimmedsize{\stockheight}{\stockwidth}{*}
\setulmarginsandblock{2.5cm}{2.25cm}{*} %\setulmarginsandblock{3.5cm}{2cm}{*}
\setlrmarginsandblock{2.25cm}{2cm}{*} %\setlrmarginsandblock{2cm}{3cm}{*}
\checkandfixthelayout

\usepackage{xcolor}
\definecolor{ThesisGreen}{HTML}{336E7C}
\definecolor{ThesisLight}{HTML}{4DA5BA}
\definecolor{ThesisDark}{HTML}{244D57}
\usepackage[nopagecolor={none},pagecolor={none}]{pagecolor}
\usepackage{afterpage}
\usepackage{csquotes}
\usepackage[dutch,british]{babel}

\usepackage[pdfstartpage=3]{hyperref}
\newsubfloat{figure}
%\usepackage{subfig}
\usepackage{longtable}
%\usepackage[b5paper,top=25mm,bottom=25mm]{geometry}
\usepackage{graphicx}
\usepackage{booktabs}
\usepackage{pdfpages}
\usepackage{tikz}
\usetikzlibrary{fit,positioning}
%\newsubfloat[caption=false,position=bottom]{figure}
% \RequirePackage[caption=false,position=bottom]{subfig}
\let\subfloat\subbottom

\newcommand{\inlinecode}{\texttt}





\renewcommand*{\memUChead}[1]{\textsc{\MakeTextLowercase{#1}}}

\usepackage[natbib=true, backend=biber, defernums=true, style=authoryear,citestyle=authoryear,giveninits=true,dashed=true,maxbibnames=99,sorting=nyt,maxcitenames=2,minnames=1,uniquename=false,url=false,isbn=false]{biblatex}
\addbibresource{library.bib}
\addbibresource{chapter6.bib}
\renewcommand{\cite}{\citep}
\renewcommand*{\bibfont}{\footnotesize}  
  
\title{Robust Semi-supervised Learning}
\author{Jesse Hendrik Krijthe}

\renewcommand*\contentsname{Table of Contents}

\tightlists

\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{amsfonts}
\newcommand{\Xe}{\mathbf{X}_\mathrm{e}  }
\newcommand{\XeT}{\mathbf{X}_\mathrm{e}^T}

\newcommand{\ye}{\begin{bmatrix} \mathbf{y}  \\ \mathbf{y}_\textrm{u} \end{bmatrix}}

\let\MyG\G
\let\G\relax
\newcommand{\G}{\left(\Xe^T \Xe \right)^{-1}}
\newcommand{\missidentity}{\begin{bmatrix} 0 & 0 \\ 0 & \textbf{I }\end{bmatrix}}
\newcommand{\Greg}{\left(\Xe^T \Xe + \lambda \missidentity \right)^{-1}}
\newcommand{\Cb}{\mathcal{C}_{\beta}}

\DeclareMathOperator*{\argmin}{arg\,min}
\DeclareMathOperator*{\argmax}{arg\,max}
\newcommand{\featdim}{d}
\newcommand{\Nunl}{U}
\newcommand{\Nlab}{L}
\newcommand{\X}{\mathbf{X}}
\renewcommand{\vec}{\mathbf}

\newtheorem{theorem}{Theorem}
\newtheorem{lemma}{Lemma}
\newtheorem{definition}{Definition}
\newtheorem{remark}{Remark}

\hyphenation{moment-con-straint}
\hyphenation{express-ion-based}

% Footnotes
\let\oldfootnoterule\footnoterule
\renewcommand*{\footnoterule}{}

\setfootins{\bigskipamount}{\bigskipamount}

\newcommand\blfootnote[1]{%
  \begingroup
  \renewcommand\thefootnote{}\footnote{\itshape#1}%
  \addtocounter{footnote}{-1}%
  \endgroup
}

% \usepackage{fancyhdr}
% \pagestyle{fancy}
% \fancyhead{}
% \fancyhead[RO,LE]{\thepage}
% \fancyfoot{}

% \setlength{\unitlength}{18mm}
% \newcommand{\blob}{\rule[-.2\unitlength]{2\unitlength}{.5\unitlength}}
% \newcommand\rblob{\thepage
% \begin{picture}(0,0)
% \put(1,-\value{section}){\blob}
% \end{picture}}
% \newcommand\lblob{%
% \begin{picture}(0,0)
% \put(-3,-\value{section}){\blob}
% \end{picture}
% 
% \fancyhead[RE]{\rightmark}
% \fancyhead[RO]{\rblob}
% \fancyhead[LE]{\lblob}
% \fancyhead[LO]{{\leftmark}
\makeatletter
\def\mysequence#1{\expandafter\@mysequence\csname c@#1\endcsname}
\def\@mysequence#1{%
  \ifcase#1\or One\or Two\or Three\or Four\or Five\or Six\or Seven\or Eight\or Nine\or Ten\or Eleven\or Twelve\or Thirteen\or Fourteen\or Fifteen\or Sixteen\or Seventeen\or Eighteen\else\@ctrerr\fi}
\makeatother

\renewcommand*\rmdefault{ppl}
%\renewcommand*\sfdefault{phv}
\linespread{1.15}

\usepackage{mathpazo}
\usepackage{microtype}


\RequirePackage[]{fontspec}
% \RequirePackage[math-style=TeX,vargreek-shape=unicode]{unicode-math}
% \defaultfontfeatures{Mapping=tex-text}
\setmainfont
     [ BoldFont       = texgyrepagella-bold.otf ,
       ItalicFont     = texgyrepagella-italic.otf ,
       BoldItalicFont = texgyrepagella-bolditalic.otf,
       Numbers=OldStyle]
     {texgyrepagella-regular.otf}
\setsansfont[BoldFont={* SemiBold}]{Gill Sans}

% Figures
\captionnamefont{\bfseries \sffamily}
\captiontitlefont{\sffamily}
\captiondelim{ | }
\hangcaption

% Titles
\renewcommand{\thepart}{\mysequence{part}}



\usepackage{titlesec}
\titleformat{\chapter}[display]
  {\rmfamily\LARGE}
  {\textsf{\MakeUppercase{Chapter \mysequence{chapter}}}}{10pt}{\Huge\itshape}
\titleformat{name=\chapter,numberless}[display]
  {\rmfamily\Large\itshape}
  {}{20pt}{\Huge}
\titleformat{\section}
  {\rmfamily\Large\itshape}
  {\thesection}{1em}{\Large}
\titleformat{\subsection}
  {\rmfamily\itshape\bfseries\large}
  {\thesubsection}{1em}{\large}
% \titleformat{\part}[display]
%   {\sffamily\HUGE}
%   {\LARGE\itshape{\textrm{Part \mysequence{part}}}}{0.5em}{}
  
%\usepackage{tocloft}
% Table of Contents formatting
\renewcommand{\tocheadstart}{}
\maxtocdepth{chapter}
\renewcommand{\printtoctitle}[1]{\hfill\rmfamily\HUGE\itshape #1}
\renewcommand{\cftchapterfont}{\rmfamily\itshape}
\renewcommand{\cftsectionfont}{\rmfamily}
\renewcommand{\cftpartfont}{\sffamily Part\space}
\cftpagenumbersoff{part}
\renewcommand*{\cftchapterpagefont}{\itshape}
\setlength{\cftbeforechapterskip}{0.3em}
\setlength{\cftbeforepartskip}{1.5em}


\usepackage[capitalise,nameinlink]{cleveref}
\crefname{section}{Sect.}{Sect.}
\Crefname{section}{Section}{Sections}
\crefname{figure}{Fig.}{Fig.}
\Crefname{figure}{Figure}{Figures}


% Abstract
\renewcommand{\abstracttextfont}{\normalfont\small\sffamily}
\addto{\captionsbritish}{\renewcommand{\abstractname}{}}
\addto{\captionsenglish}{\renewcommand{\abstractname}{}}

\newcommand{\mypartpic}{cover/part2.pdf}
\newcommand\PartPic{
\checkoddpage
\ifoddpage
\put(\LenToUnit{-1mm},\LenToUnit{0mm}){
\includegraphics{\mypartpic}
}
\fi
}

\aliaspagestyle{part}{empty}

\begin{document}
<<settings, echo=FALSE>>=
knit_hooks$set(document = function(x) {
  sub('\\usepackage[]{color}','\\usepackage{xcolor}', x, fixed = TRUE)
})
options(tikzDefaultEngine='xetex')
opts_chunk$set(dev='cairo_pdf')
knit_theme$set("print")
@

<<theme-thesis,echo=FALSE,warning=FALSE,message=FALSE>>=
library(ggthemes)
library(extrafont)
loadfonts()
theme_thesis <- function(base_size=12) {
  theme_classic() +
  theme(legend.position="bottom",
    text=element_text(family="Palatino",face = "italic",colour="black"),
    title=element_text(family="Gill Sans",face = "plain"),
    plot.title=element_text(hjust = 0.5),
    strip.background=element_rect(size = 0,color=NA,fill=NA),
    axis.title.y=element_text(size=rel(1)),
    axis.title.x=element_text(size=rel(1)),
    axis.text=element_text(size=rel(0.8),face="plain"),
    axis.line.x=element_line(size=0.5 ,color="black",linetype=1),
    axis.line.y=element_line(size=0.5 ,color="black",linetype=1),
    legend.text=element_text(size=rel(1)),
    panel.grid.major=element_line(colour = "darkgrey",size = 0.2,linetype = "dashed"),
    panel.grid.major.x=element_line(colour = "darkgrey",size = 0.2,linetype = "dashed"),
    panel.grid.minor.x=element_blank(),
    panel.grid.major.y=element_line(colour = "darkgrey",size = 0.2,linetype = "dashed"),
    panel.grid.minor.y=element_blank(),
    strip.text=element_text(size=rel(1))
  )
}
scale_color_thesis <- scale_color_tableau
scale_fill_thesis <- scale_fill_tableau

opts_chunk$set(dev='cairo_pdf')
@

% Include cover
%\includepdf[pages={1}]{cover/projection2.pdf}
\cleartorecto
\setcounter{page}{1}

\frontmatter*
% Starting pages
\include{rest/official-matter}
% \newpage\null\thispagestyle{empty}\newpage
\thispagestyle{empty}
\vspace*{5cm}
\epigraphposition{center}
\epigraphfontsize{\Large}
\setlength{\epigraphwidth}{0.8\textwidth}
\setlength{\epigraphrule}{0pt}
\epigraph{\textit{The only way of discovering the limits of the possible is to venture a little way past them into the impossible.}}{\textsc{\\Arthur C. Clarke}\vspace{0.2cm}\\\footnotesize{``Hazards of Prophecy'' in \\Profiles of the Future (1962)}} \nocite{Clarke1962}
\cleardoublepage

\tableofcontents*


% Contents
<<introduction, child='introduction/introduction.Rnw', cache=TRUE>>=
@
\afterpage{\newpagecolor{ThesisLight}}
\mainmatter*
\nopagebreak
% standard part pages should be suppressed, custom part page used instead
\renewcommand{\printpartname}{}
\renewcommand{\printpartnum}{}
\renewcommand{\printparttitle}{\phantom}

% Custom part page for Part I
% \cleartoverso
% \null
% \thispagestyle{empty}
\afterpage{\restorepagecolor}
% \newpage
\renewcommand{\mypartpic}{cover/part1.pdf}
\AddToShipoutPicture{\PartPic}
\part{CONSTRAINTS \& PROJECTIONS}
\afterpage{\restorepagecolor}
\ClearShipoutPicture


\chapter[Implicitly Constrained Semi-supervised Least Squares Classification]{Implicitly Constrained Semi-supervised\\Least Squares Classification}
\chaptermark{Implicitly Constrained Least Squares}
\label{chapter:icls}
\blfootnote{This chapter appeared as: Krijthe, J.H. \& Loog, M., 2017. Robust Semi-supervised Least Squares Classification by Implicit Constraints. Pattern Recognition, 63, pp.115–126. An earlier, shorter, version of this work appeared as: Krijthe, J. H., \& Loog, M. (2015). Implicitly Constrained Semi-Supervised Least Squares Classification. In E. Fromont, T. De Bie, \& M. van Leeuwen (Eds.), Advances in Intelligent Data Analysis XIV. Lecture Notes in Computer Science, vol 9385. (pp. 158–169).}
<<chapter1, child='chapter1/chapter1.Rnw', cache=TRUE>>=
@

\chapter[Implicitly Constrained Semi-supervised Linear Discriminant Analysis]{Implicitly Constrained Semi-supervised\\Linear Discriminant Analysis}
\chaptermark{Implicitly Constrained LDA}
\label{chapter:iclda}
\blfootnote{This chapter appeared as: Krijthe, J.H. \& Loog, M., 2014. Implicitly Constrained Semi-Supervised Linear Discriminant Analysis. In Proceedings of the 22nd International Conference on Pattern Recognition (pp. 3762–3767).}
<<chapter2, child='chapter2/chapter2.Rnw', cache=TRUE>>=
  @
  
  \chapter[Projected Estimators for Robust Semi-supervised Classification]{Projected Estimators for\\Robust Semi-supervised Classification}
\chaptermark{Projected Estimators}
\label{chapter:projection}
\blfootnote{This is chapter appeared as: Krijthe, J. H., \& Loog, M., 2017. Projected estimators for robust semi-supervised classification. Machine Learning, 106(7), pp. 993–1008. Springer}
<<chapter3, child='chapter3/chapter3.Rnw', cache=TRUE>>=
@
\cleartoverso
\null
\thispagestyle{empty}
\newpagecolor{ThesisDark}\afterpage{\restorepagecolor}
\newpage
\renewcommand{\mypartpic}{cover/part2.pdf}
\AddToShipoutPicture{\PartPic}
\part{SURROGATE LOSSES}
\ClearShipoutPicture

\chapter[On Measuring and Quantifying Performance]{On Measuring and Quantifying Performance: Error Rates, Surrogate Loss,\\and an Example in SSL}
\chaptermark{Measuring and Quantifying Performance}
\label{chapter:quantifying}
\blfootnote{This chapter appeared as: Loog, M., Krijthe, J.H. \& Jensen, A.C., (2016). On Measuring and Quantifying Performance: Error Rates, Surrogate Loss, and an Example in SSL. In C. H. Chen, ed. Handbook of Pattern Recognition and Computer Vision. World Scientific.}
<<chapter5, child='chapter5/chapter5.Rnw', cache=TRUE>>=
@

\chapter[The Pessimistic Limits of Margin-based Losses in Semi-supervised Learning]{The Pessimistic Limits of\\Margin-based Losses\\in Semi-supervised Learning}
\chaptermark{Margin-based Losses in SSL}
\label{chapter:marginbased}
\blfootnote{The work in this chapter has been submitted and was under review at the time of printing.}
<<chapter6, child='chapter6/chapter6.Rnw', cache=TRUE>>=
@

\chapter[Optimistic Semi-supervised Least Squares Classification]{Optimistic Semi-supervised\\Least Squares Classification}
\chaptermark{Optimistic Least Squares}
\label{chapter:optimistic}
\blfootnote{This chapter appeared as: Krijthe, J. H., \& Loog, M. 2016. Optimistic Semi-supervised Least Squares Classification. In Proceedings of the 23rd International Conference on Pattern Recognition (pp. 1677–1682).}
<<chapter7, child='chapter7/chapter7.Rnw', cache=TRUE>>=
@

\chapter[The Peaking Phenomenon in Semi-supervised Learning]{The Peaking Phenomenon\\in Semi-supervised Learning}
\chaptermark{Peaking in SSL}
\label{chapter:peaking}
\blfootnote{This chapter appeared as: Krijthe, J. H., \& Loog, M. 2016. The Peaking Phenomenon in Semi-supervised Learning. In A. Robles-Kelly, M. Loog, B. Biggio, F. Escolano, \& R. Wilson (Eds.), Structural, Syntactic, and Statistical Pattern Recognition. S+SSPR 2016. Lecture Notes in Computer Science, vol 10029. (pp. 299–309). Springer}
<<chapter8, child='chapter8/chapter8.Rnw', cache=TRUE>>=
@
\cleartoverso
\null
\thispagestyle{empty}
\newpagecolor{ThesisGreen}\afterpage{\restorepagecolor}
\newpage
\renewcommand{\mypartpic}{cover/part3.pdf}
\AddToShipoutPicture{\PartPic}
\part{REPRODUCIBILITY}
\ClearShipoutPicture

\chapter[Reproducible Pattern Recognition Research]{Reproducible Pattern Recognition Research:\\The Case of Optimistic SSL}
\chaptermark{Reproducible Pattern Recognition Research}
\label{chapter:reproducing}
\blfootnote{This chapter appeared as: Krijthe, J. H., \& Loog, M. 2016. Reproducible Pattern Recognition Research: The Case of Optimistic SSL. In B. Kerautret, M. Colom, \& P. Monasse (Eds.), Reproducible Research in Pattern Recognition. RRPR 2016. Lecture Notes in Computer Science, vol 10214. (pp. 48–59). Springer}

<<chapter9, child='chapter7/chapter9.Rnw', cache=TRUE>>=
@

\chapter{Semi-supervised Learning in R}
\chaptermark{Semi-supervised Learning in R}
\label{chapter:rssl}
\blfootnote{This chapter appeared as: Krijthe, J. H. 2016. RSSL: R package for Semi-supervised Learning. In B. Kerautret, M. Colom, \& P. Monasse (Eds.), Reproducible Research in Pattern Recognition. RRPR 2016. Lecture Notes in Computer Science, vol 10214. (pp. 104–115). Springer}
<<chapter10, child='chapter10/chapter10.Rnw', cache=TRUE>>=
@

\backmatter

\addtocontents{toc}{\vspace{\normalbaselineskip}}
<<discussion, child='introduction/discussion.Rnw', cache=TRUE>>=
@

\scriptsize{\printbibliography[heading=bibintoc,title={References}]}

\normalsize
\include{rest/summary}
\include{rest/acknowledgements}
\include{rest/about-the-author}
\end{document}