Commit cb06c6dc authored by Carlos GO's avatar Carlos GO
Browse files

todo refs

parent 0ddcab7e
......@@ -96,7 +96,7 @@
\begin{figure}[h!]
\centering
\includegraphics[width=0.6\textwidth]{struc.jpeg}
\caption{This is RNA.}
\caption{This is RNA. ~\cite{reinharz2016algorithmic}}
\label{fig:rna}
\end{figure}
......@@ -117,7 +117,7 @@
\end{centering}
\end{column}
\begin{column}{0.7\textwidth}
\includegraphics[width=\textwidth]{lws.png}
\includegraphics[width=\textwidth]{lws.png} \cite{leontis2001geometric}
\end{column}
\end{columns}
......@@ -180,7 +180,7 @@
\begin{itemize}
\item Thermodynamic ensembles could have shaped the discovery of complex structures.
\item More complex evolutionary explorations needed to explain full distribution.
\item Manuscript accepted at RNA journal. \footnote{Oliver, Carlos G., Vladimir Reinharz, and Jerome Waldispuhl. ``The necessary emergence of structural complexity in self-replicating RNA populations." bioRxiv (2019): 218990.}
\item Manuscript accepted at RNA journal. \cite{oliver2019necessary}
\end{itemize}
\item Next Steps
\begin{itemize}
......@@ -352,10 +352,10 @@
\hline
& flexible motifs & all ss & graph-based & inductive \\ \hline
rna3dmotif & \xmark & \xmark & \cmark & \xmark \\ \hline
3d motif atlas & \xmark\cmark & \xmark & \xmark\cmark & \xmark \\ \hline
3d motif atlas & $\sim$ & \xmark & $\sim$ & \xmark \\ \hline
carnaval & \xmark & \xmark & \cmark & \xmark \\ \hline
RNAMSC & \cmark & \xmark & \xmark & \xmark \\ \hline
{\bf VERNAL} & \cmark & \cmark & \cmark & \cmark
RNAMSC \cite{ge2018novo} & \cmark & \xmark & \xmark & \xmark \\ \hline
{\bf \vernal} & \cmark & \cmark & \cmark & \cmark
\end{tabular}%
}
\end{table}
......@@ -519,8 +519,25 @@
\frametitle{Related Work}
\begin{itemize}
\item Hajun Dai
\item Existing methods focus on strict edge conservation.
\item Mostly applied to aligning protein-protein interaction networks.
\end{itemize}
\begin{table}[]
\resizebox{\textwidth}{!}{%
\begin{tabular}{lllll}
\hline
& Node cost & Edge Cost & Custom Cost & Inductive \\ \hline
IsoRank & \cmark & $\sim$ & \cmark & \xmark \\ \hline
GRALL & \cmark & \xmark & $\sim$ & \xmark \\ \hline
WAVE & \xmark & $\sim$ & \xmark & \xmark \\ \hline
Gromov-Wasserstein \cite{ge2018novo} & \cmark & \xmark & \xmark & \xmark \\ \hline
{\bf \garl} & \cmark & \cmark & \cmark & \cmark
\end{tabular}%
}
\end{table}
\end{frame}
\begin{frame}
......@@ -646,6 +663,13 @@
}
\begin{frame}[allowframebreaks]
\frametitle{References}
\bibliographystyle{plain}
\bibliography{biblio}
\end{frame}
\begin{frame}{Picking $d$: Graphlet Distance}
Idea: Compare structure of nodes in each ring with alignments.
\begin{equation}
......
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