plos_latex_template.tex

% Template for PLoS
% Version 3.5 March 2018
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% amsmath and amssymb packages, useful for mathematical formulas and symbols
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% Use Unicode characters when possible
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%% END MACROS SECTION

\usepackage{latexsym, mathrsfs}
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%%%%%%% adjust spacing
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%%%%%%%%%%% Theorem templates
\newtheorem{theorem}{Theorem}
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\newtheorem{example}{Example}
\newtheorem{formulation}{Problem}
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\newtheorem{observation}[theorem]{\textbf{Observation}}
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%\theoremstyle{slplain}


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%%%%%%%%%%%%%%% special words
\newcommand{\topk}{top-k\xspace}
\newcommand{\topthree}{top-3 }
\newcommand{\toptwenty}{top-20 }
\newcommand{\tophundred}{top-100 }
\newcommand{\topthousand}{top-1000 }
%\newcommand{\topthree}{{\sc T{\small OP-3}}\xspace}
\newcommand{\trans}{{\sc T{\small RANS\-FORMATION}}\xspace}
\newcommand{\genviz}{{\sc G{\small ENVISAGE}}\xspace}
\newcommand{\earlyT}{{\sc E{\small ARLY}S{\small TOP}}\xspace}
\newcommand{\sampling}{{\sc S{\small AMPLING}}\xspace} %\hspace{.2mm}
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\newcommand{\msig}{{\sc MSigDB}\xspace}
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\newcommand{\sinha}[1]{\noindent{\textcolor{blue}{[Saurabh: #1]}}}
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\newcommand{\cut}[1]{}
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\newcommand{\tr}[1]{}
\newcommand{\tleftout}[1]{}
\newcommand{\new}[1]{\noindent{\textcolor{red}{#1}}}


\begin{document}
\vspace*{0.2in}

% Title must be 250 characters or less.
\begin{flushleft}
{\Large
\textbf\newline{G{\large ENVISAGE}: Rapid Identification of Discriminative and Explainable Feature Pairs for Genomic Analysis} % Please use "sentence case" for title and headings (capitalize only the first word in a title (or heading), the first word in a subtitle (or subheading), and any proper nouns).
}
\newline
% Insert author names, affiliations and corresponding author email (do not include titles, positions, or degrees).
\\
Silu Huang\textsuperscript{1\ddag},
Charles Blatti\textsuperscript{2\ddag},
Saurabh Sinha\textsuperscript{1,2\dag},
Aditya Parameswaran\textsuperscript{1,2,3\dag},
%with the Lorem Ipsum Consortium\textsuperscript{\textpilcrow}
\\
\bigskip
\textbf{1} Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
\\
\textbf{2} Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
\\
\textbf{3} School of Information and Department of Electrical Engineering and Computer Sciences, UC Berkeley, Berkeley CA, 94704, USA
\bigskip

% Insert additional author notes using the symbols described below. Insert symbol callouts after author names as necessary.
%
% Remove or comment out the author notes below if they aren't used.
%
% Primary Equal Contribution Note

\ddag These authors contributed equally to this work.
\\
\dag To whom correspondence should be addressed.
\\
* sinhas@illinois.edu, adityagp@berkeley.edu
% \Yinyang These authors contributed equally to this work.

% % Additional Equal Contribution Note
% % Also use this double-dagger symbol for special authorship notes, such as senior authorship.
% \ddag These authors also contributed equally to this work.

% % Current address notes
% \textcurrency Current Address: Dept/Program/Center, Institution Name, City, State, Country % change symbol to "\textcurrency a" if more than one current address note
% % \textcurrency b Insert second current address
% % \textcurrency c Insert third current address

% % Deceased author note
% \dag Deceased

% % Group/Consortium Author Note
% \textpilcrow Membership list can be found in the Acknowledgments section.

% Use the asterisk to denote corresponding authorship and provide email address in note below.


\end{flushleft}
% Please keep the abstract below 300 words
\section*{Abstract}
\textbf{Motivation.} \new{A common but critical task in genomic data analysis is 
finding features that {\em separate} and thereby help explain  
differences between two classes of biological objects (e.g., genes that help 
explain the difference between healthy versus 
diseased patients).  As lower-cost, high-throughput experimental methods greatly 
increase the number of samples that are assayed as objects for analysis, 
computational methods are needed to quickly provide insights into 
high-dimensional datasets with tens of thousands of objects and features.}\\
\noindent
\textbf{Results.} We develop an \new{interactive exploration} tool called 
\genviz that \new{rapidly discovers the most discriminative 
feature pairs in a dataset} and \new{displays} the corresponding 
visualizations. Since quickly finding top feature pairs is computationally 
challenging, especially when the numbers of objects and features are large, we 
propose a suite of optimizations to make \genviz more responsive and demonstrate 
that our optimizations lead to a \new{{\em 400X}} speedup over competitive 
baselines for multiple biological data sets. With this speedup, \genviz enables 
the exploration of more \new{large-scale} datasets \new{and alternate} 
hypotheses in an interactive fashion. We apply \genviz to uncover pairs of genes 
whose transcriptomic responses significantly discriminate 
treatments of \new{several} chemotherapy drugs.\\

\noindent \textbf{Availability.} Free webserver at 
\url{http://genvisage.knoweng.org:443/} with source code at 
\url{https://github.com/KnowEnG/Genvisage} \\

\linenumbers

\input{body_short.tex}

% Please keep the Author Summary between 150 and 200 words
% Use first person. PLOS ONE authors please skip this step.
% Author Summary not valid for PLOS ONE submissions.
% \section*{Author summary}
% Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur eget porta erat. Morbi consectetur est vel gravida pretium. Suspendisse ut dui eu ante cursus gravida non sed sem. Nullam sapien tellus, commodo id velit id, eleifend volutpat quam. Phasellus mauris velit, dapibus finibus elementum vel, pulvinar non tellus. Nunc pellentesque pretium diam, quis maximus dolor faucibus id. Nunc convallis sodales ante, ut ullamcorper est egestas vitae. Nam sit amet enim ultrices, ultrices elit pulvinar, volutpat risus.



% % Use "Eq" instead of "Equation" for equation citations.
% \section*{Introduction}
% Lorem ipsum dolor sit~\cite{bib1} amet, consectetur adipiscing elit. Curabitur eget porta erat. Morbi consectetur est vel gravida pretium. Suspendisse ut dui eu ante cursus gravida non sed sem. Nullam Eq~(\ref{eq:schemeP}) sapien tellus, commodo id velit id, eleifend volutpat quam. Phasellus mauris velit, dapibus finibus elementum vel, pulvinar non tellus. Nunc pellentesque pretium diam, quis maximus dolor faucibus id.~\cite{bib2} Nunc convallis sodales ante, ut ullamcorper est egestas vitae. Nam sit amet enim ultrices, ultrices elit pulvinar, volutpat risus.

% \begin{eqnarray}
% \label{eq:schemeP}
% 	\mathrm{P_Y} = \underbrace{H(Y_n) - H(Y_n|\mathbf{V}^{Y}_{n})}_{S_Y} + \underbrace{H(Y_n|\mathbf{V}^{Y}_{n})- H(Y_n|\mathbf{V}^{X,Y}_{n})}_{T_{X\rightarrow Y}},
% \end{eqnarray}

% \section*{Materials and methods}
% \subsection*{Etiam eget sapien nibh}

% % For figure citations, please use "Fig" instead of "Figure".
% Nulla mi mi, Fig~\ref{fig1} venenatis sed ipsum varius, volutpat euismod diam. Proin rutrum vel massa non gravida. Quisque tempor sem et dignissim rutrum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Morbi at justo vitae nulla elementum commodo eu id massa. In vitae diam ac augue semper tincidunt eu ut eros. Fusce fringilla erat porttitor lectus cursus, \nameref{S1_Video} vel sagittis arcu lobortis. Aliquam in enim semper, aliquam massa id, cursus neque. Praesent faucibus semper libero.

% % Place figure captions after the first paragraph in which they are cited.
% \begin{figure}[!h]
% \caption{{\bf Bold the figure title.}
% Figure caption text here, please use this space for the figure panel descriptions instead of using subfigure commands. A: Lorem ipsum dolor sit amet. B: Consectetur adipiscing elit.}
% \label{fig1}
% \end{figure}

% % Results and Discussion can be combined.
% \section*{Results}
% Nulla mi mi, venenatis sed ipsum varius, Table~\ref{table1} volutpat euismod diam. Proin rutrum vel massa non gravida. Quisque tempor sem et dignissim rutrum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Morbi at justo vitae nulla elementum commodo eu id massa. In vitae diam ac augue semper tincidunt eu ut eros. Fusce fringilla erat porttitor lectus cursus, vel sagittis arcu lobortis. Aliquam in enim semper, aliquam massa id, cursus neque. Praesent faucibus semper libero.

% % Place tables after the first paragraph in which they are cited.
% \begin{table}[!ht]
% \begin{adjustwidth}{-2.25in}{0in} % Comment out/remove adjustwidth environment if table fits in text column.
% \centering
% \caption{
% {\bf Table caption Nulla mi mi, venenatis sed ipsum varius, volutpat euismod diam.}}
% \begin{tabular}{|l+l|l|l|l|l|l|l|}
% \hline
% \multicolumn{4}{|l|}{\bf Heading1} & \multicolumn{4}{|l|}{\bf Heading2}\\ \thickhline
% $cell1 row1$ & cell2 row 1 & cell3 row 1 & cell4 row 1 & cell5 row 1 & cell6 row 1 & cell7 row 1 & cell8 row 1\\ \hline
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% $cell1 row3$ & cell2 row 3 & cell3 row 3 & cell4 row 3 & cell5 row 3 & cell6 row 3 & cell7 row 3 & cell8 row 3\\ \hline
% \end{tabular}
% \begin{flushleft} Table notes Phasellus venenatis, tortor nec vestibulum mattis, massa tortor interdum felis, nec pellentesque metus tortor nec nisl. Ut ornare mauris tellus, vel dapibus arcu suscipit sed.
% \end{flushleft}
% \label{table1}
% \end{adjustwidth}
% \end{table}


% %PLOS does not support heading levels beyond the 3rd (no 4th level headings).
% \subsection*{\lorem\ and \ipsum\ nunc blandit a tortor}
% \subsubsection*{3rd level heading}
% Maecenas convallis mauris sit amet sem ultrices gravida. Etiam eget sapien nibh. Sed ac ipsum eget enim egestas ullamcorper nec euismod ligula. Curabitur fringilla pulvinar lectus consectetur pellentesque. Quisque augue sem, tincidunt sit amet feugiat eget, ullamcorper sed velit. Sed non aliquet felis. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris commodo justo ac dui pretium imperdiet. Sed suscipit iaculis mi at feugiat.

% \begin{enumerate}
% 	\item{react}
% 	\item{diffuse free particles}
% 	\item{increment time by dt and go to 1}
% \end{enumerate}


% \subsection*{Sed ac quam id nisi malesuada congue}

% Nulla mi mi, venenatis sed ipsum varius, volutpat euismod diam. Proin rutrum vel massa non gravida. Quisque tempor sem et dignissim rutrum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Morbi at justo vitae nulla elementum commodo eu id massa. In vitae diam ac augue semper tincidunt eu ut eros. Fusce fringilla erat porttitor lectus cursus, vel sagittis arcu lobortis. Aliquam in enim semper, aliquam massa id, cursus neque. Praesent faucibus semper libero.

% \begin{itemize}
% 	\item First bulleted item.
% 	\item Second bulleted item.
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% \section*{Discussion}
% Nulla mi mi, venenatis sed ipsum varius, Table~\ref{table1} volutpat euismod diam. Proin rutrum vel massa non gravida. Quisque tempor sem et dignissim rutrum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Morbi at justo vitae nulla elementum commodo eu id massa. In vitae diam ac augue semper tincidunt eu ut eros. Fusce fringilla erat porttitor lectus cursus, vel sagittis arcu lobortis. Aliquam in enim semper, aliquam massa id, cursus neque. Praesent faucibus semper libero~\cite{bib3}.

% \section*{Conclusion}

% CO\textsubscript{2} Maecenas convallis mauris sit amet sem ultrices gravida. Etiam eget sapien nibh. Sed ac ipsum eget enim egestas ullamcorper nec euismod ligula. Curabitur fringilla pulvinar lectus consectetur pellentesque. Quisque augue sem, tincidunt sit amet feugiat eget, ullamcorper sed velit.

% Sed non aliquet felis. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris commodo justo ac dui pretium imperdiet. Sed suscipit iaculis mi at feugiat. Ut neque ipsum, luctus id lacus ut, laoreet scelerisque urna. Phasellus venenatis, tortor nec vestibulum mattis, massa tortor interdum felis, nec pellentesque metus tortor nec nisl. Ut ornare mauris tellus, vel dapibus arcu suscipit sed. Nam condimentum sem eget mollis euismod. Nullam dui urna, gravida venenatis dui et, tincidunt sodales ex. Nunc est dui, sodales sed mauris nec, auctor sagittis leo. Aliquam tincidunt, ex in facilisis elementum, libero lectus luctus est, non vulputate nisl augue at dolor. For more information, see \nameref{S1_Appendix}.

% \section*{Supporting information}

% % Include only the SI item label in the paragraph heading. Use the \nameref{label} command to cite SI items in the text.
% \paragraph*{S1 Fig.}
% \label{S1_Fig}
% {\bf Bold the title sentence.} Add descriptive text after the title of the item (optional).

% \paragraph*{S2 Fig.}
% \label{S2_Fig}
% {\bf Lorem ipsum.} Maecenas convallis mauris sit amet sem ultrices gravida. Etiam eget sapien nibh. Sed ac ipsum eget enim egestas ullamcorper nec euismod ligula. Curabitur fringilla pulvinar lectus consectetur pellentesque.

% \paragraph*{S1 File.}
% \label{S1_File}
% {\bf Lorem ipsum.}  Maecenas convallis mauris sit amet sem ultrices gravida. Etiam eget sapien nibh. Sed ac ipsum eget enim egestas ullamcorper nec euismod ligula. Curabitur fringilla pulvinar lectus consectetur pellentesque.

% \paragraph*{S1 Video.}
% \label{S1_Video}
% {\bf Lorem ipsum.}  Maecenas convallis mauris sit amet sem ultrices gravida. Etiam eget sapien nibh. Sed ac ipsum eget enim egestas ullamcorper nec euismod ligula. Curabitur fringilla pulvinar lectus consectetur pellentesque.

% \paragraph*{S1 Appendix.}
% \label{S1_Appendix}
% {\bf Lorem ipsum.} Maecenas convallis mauris sit amet sem ultrices gravida. Etiam eget sapien nibh. Sed ac ipsum eget enim egestas ullamcorper nec euismod ligula. Curabitur fringilla pulvinar lectus consectetur pellentesque.

% \paragraph*{S1 Table.}
% \label{S1_Table}
% {\bf Lorem ipsum.} Maecenas convallis mauris sit amet sem ultrices gravida. Etiam eget sapien nibh. Sed ac ipsum eget enim egestas ullamcorper nec euismod ligula. Curabitur fringilla pulvinar lectus consectetur pellentesque.

% \section*{Acknowledgments}
% Cras egestas velit mauris, eu mollis turpis pellentesque sit amet. Interdum et malesuada fames ac ante ipsum primis in faucibus. Nam id pretium nisi. Sed ac quam id nisi malesuada congue. Sed interdum aliquet augue, at pellentesque quam rhoncus vitae.
%\input{appendix.tex}

\nolinenumbers

% Either type in your references using
% \begin{thebibliography}{}
% \bibitem{}
% Text
% \end{thebibliography}
%
% or
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% Compile your BiBTeX database using our plos2015.bst
% style file and paste the contents of your .bbl file
% here. See http://journals.plos.org/plosone/s/latex for
% step-by-step instructions.
%


% \bibliographystyle{plain}
% \bibliography{ref}

\begin{thebibliography}{10}

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\begin{appendices}
\input{appendix.tex}
\end{appendices}

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