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\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
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% % 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 
explain the differences between healthy and 
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 that best separate two classes 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 \new{and interpretable} 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}

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% \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}
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% % For figure citations, please use "Fig" instead of "Figure".
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% \section*{Discussion}
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% \section*{Conclusion}

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% 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}

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% \paragraph*{S1 Appendix.}
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% \section*{Acknowledgments}
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%\input{appendix.tex}

\nolinenumbers

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

\end{document}