presentation.tex

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\title{Extensible Software for Research}
%\subtitle{principles and an example in julia}
\author{Aaron Peikert}
\date{Maximilian Ernst}

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\begin{document}

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	\frame{\titlepage}

	\setcounter{framenumber}{0}
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    \begin{frame}
        \frametitle{Contents}
        \vspace{1cm}
        \begin{wideitemize}
            \item Principles of Extensible Research Software
        \end{wideitemize}
        \vspace{1cm}
        \begin{wideitemize}
            \item Application: StructuralEquationModels.jl
        \end{wideitemize}
    \end{frame}

	%\begin{frame}
    %    \frametitle{Who writes research software?}
    %    \begin{wideitemize}
    %        \item research software engineers
    %        \item research software developer
    %        \item applied user
    %    \end{wideitemize}
    %\end{frame}

    \begin{frame}
        \frametitle{A day in the life of \ldots}
        a statistical methods researcher\\
        \vspace{0.8cm}
        \begin{wideitemize}
            \item<2-> work with a specific type of model
            \begin{itemize}
            \item<2-> regression, structural equation models, deep learning, \ldots
            \end{itemize}
            \item<3-> have an idea
            \item<4-> test it
            \item<5-> make it available to applied researchers
        \end{wideitemize}
    \end{frame}

    \begin{frame}
        \frametitle{We need to write Software}
        \begin{wideitemize}
            \item to test $\to$ prototype
            \item to make it available $\to$ distribute
        \end{wideitemize}

    \vspace{0.5cm}

    \pause

    What's the fastest way to get there?

    \vspace{0.5cm}

    \pause

    We are already working with existing software.

    \vspace{0.5cm}

    \pause

    \textbf{It would be nice if we could extend existing software!}
    \end{frame}

    \begin{frame}
        \frametitle{But \ldots}
        \begin{wideitemize}
            \item<2-> \textbf{understand} 1000s of lines of code
            \item<3-> make \textbf{changes}, possibly breaking stuff
            \item<4-> get maintainers to \textbf{adopt} our changes
        \end{wideitemize}

        \vspace{1cm}

        \only<5>{\textbf{These hurdles are often too high!}}
    \end{frame}

    \begin{frame}
        \frametitle{A \only<1-2>{day}\only<3>{year} in the life of \ldots}
        \vspace{0.8cm}
        \begin{wideitemize}
            \item<2-> to test: minimal reimplementation
            \begin{itemize}
                \item waste of time
                \item not well tested
                \item hard to reproduce
                \item slow
            \end{itemize}
            \item<3-> to deploy: put code on github
            \begin{itemize}
                \item bad user interface, no documentation
                \item missing features
                \item incompatible to existing software
            \end{itemize}
        \end{wideitemize}
    \end{frame}

    \begin{frame}
        \frametitle{My Experience}
        \vspace{1cm}
        \begin{wideitemize}
            \item from R $\to$ \raisebox{-.07\height}{\includegraphics[width=0.08\textwidth, valign=m]{figures/julia_logo.pdf}}
        \end{wideitemize}
    \end{frame}

    \begin{frame}
        \frametitle{Culture}
        \vspace{0.8cm}
        \begin{wideitemize}
            \item care about extensibility
            \item developer documentation
            \item assume their code is read
        \end{wideitemize}
    \end{frame}

    \begin{frame}
        \frametitle{An Example}
        Let's make a thought experiment...
        \vspace{0.8cm}
        \begin{wideitemize}
            \item encyclopedia
            \begin{itemize}
                \item add an entry
                \item some syntactical requirements\\
                {\small 300-400 words, alphabetical, \ldots}
            \end{itemize}
            \item book
            \begin{itemize}
                \item a draft already exists
                \item add something everywhere it is applicable
            \end{itemize}
        \end{wideitemize}
    \end{frame}

    \begin{frame}
        \frametitle{An Example}\vspace{0.5cm}
        \includegraphics[width=0.5\textwidth]{figures/lorem_ipsum_red.pdf}%
        \includegraphics[width=0.5\textwidth]{figures/lorem_ipsum_green.pdf}
    \end{frame}

    \begin{frame}
        \frametitle{Software Design}
        \only<1>{Not all research articles can be encyclopedias, but maybe all research software can be...}
        \pause
        You need to be able to add new features...
        \vspace{0.8cm}
        \begin{wideitemize}
            \item without \textbf{understanding} existing code
            \item without \textbf{changing} existing code
            \item syntactical requirements need to be \textbf{clear} and \textbf{easy communicable}!
        \end{wideitemize}
    \end{frame}

    \begin{frame}
        \frametitle{The Benefits}
        \vspace{0.5cm}
        \begin{wideitemize}
            \item Applied Researchers
            \begin{itemize}
                \item user interface
                \item better documentation
                \item faster availability of new features
                \item less bugs
                \item higher performance
            \end{itemize}
            \item Statistical Researchers
            \begin{itemize}
                \item no re-implementation $\to$ less time-consuming
                \item more users
                \item no software engineering skills needed
            \end{itemize}
            \item Maintainers
            \begin{itemize}
                \item changes are easier to integrate
            \end{itemize}
        \end{wideitemize}
    \end{frame}
    
    %%%%%%%%%%%%%%%%%%%%%%%%%% Aaron %%%%%%%%%%%%%%%%%%%%%%%%%%%%

    \begin{frame}[c]
    \centering \Huge Less Abstract
    \end{frame}

    \begin{frame}{A few days in a methods researchers life}
        \begin{wideitemize}
        \item Do you have any ideas why this does not converge?
        \item Staring puzzled at the theory (should work?!).
        \item Staring very puzzled at the implementation in C++.
        \item Rinse and repeat for a couple of days and researchers.
        \end{wideitemize}
    \end{frame}

    \begin{frame}{An hour in our life}
      \begin{wideitemize}
        \item Look at the formula: $ridge(x, \lambda{}) = \lambda{}\sum^p_{j=1}x^2$
        \item Implement in Julia: \monob{ridge(x, λ) = λ ∗ sum(x.\^{}2)}
        \item add 30 lines of API (formal requirements)
        \item Enjoy.
      \end{wideitemize}
    \end{frame}

    \begin{frame}{Two hours in our life}
        \begin{wideitemize}
        \item Simulation in Juila works (converges as it should)
        \item<2> Original simulation takes weeks on a dedicated workstation.
        \item<2> Original simulation freezes our cluster due to poor parallelization.
        \item<2> Simulation in Julia takes 2 hours on my laptop.
        \end{wideitemize}
    \end{frame}

    \begin{frame}{Why?}
        \begin{wideitemize}
        \item Some investments in extensibility
        \item division of labor: \begin{itemize}
            \item optimizing linear algebra is done by Intel
            \item numerical optimization is done by dedicated experts
            \item differentiation is automated
        \end{itemize}
        \item modern infrastructure
        \end{wideitemize}
    \end{frame}

    \begin{frame}{But why?}
    \centering \huge convenience
    \end{frame}

    \begin{frame}{How to improve convenience?}
      \begin{enumerate}
        \item Extensible Software
        \item Documentation
        \item User Interface
      \end{enumerate}
    \end{frame}
    
    \begin{frame}[c]{The leverage of extensible software}
      \centering
      \includegraphics[width=.8\textwidth]{figures/users.pdf}
    \end{frame}
    
    \begin{frame}[c]{Time is limited}
      \centering
      \includegraphics[width=.8\textwidth]{figures/difficulty.pdf}
    \end{frame}

    \begin{frame}{Documentation}
      \begin{wideitemize}
        \item Documentation for users
        \item Documentation for contributors/developers
        \item<2-> Documentation is not always called documentation (e.g. papers/talks/blog posts)
                \item<3> Code itself is the best developer documentation
      \end{wideitemize}
    \end{frame}

    \begin{frame}{User Interface}
      \begin{wideitemize}
        \item Frictionless
        \item Connected to prior knowledge
      \end{wideitemize}
    \end{frame}
    
    \begin{frame}[c]
      \centering{
      \huge
        \only<1>{More Concrete}
        \only<2>{
          \href{https://structuralequationmodels.github.io/StructuralEquationModels.jl/dev/}{
          \textcolor[rgb]{0.796,0.235,0.2}{Structural}\textcolor[rgb]{0.22,0.596,0.149}{Equation}\textcolor[rgb]{0.584,0.345,0.698}{Models}\textcolor[rgb]{0.251,0.388,0.847}{.jl}
          }
        }
      }
    \end{frame}

\end{document}