removed thesis

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 \tikzstyle{block} = [rectangle, draw, fill=blue!20, text width=5em, text centered, rounded corners, minimum height=4em] \tikzstyle{line} = [draw, -latex'] \begin{figure}[h] \begin{tikzpicture}[node distance = 1cm] \node [block] (datamodel) {Data Modeling}; \node [block, left= of datamodel] (input) {Input}; \node [block, below= of datamodel] (reduce) {Reduction Rules}; \node [block, below right = of reduce] (solveILP) {ILP Solver}; \node [block, below left = of reduce] (solveHeuristic) {Heuristic Solver}; \node [block, below right= of solveHeuristic] (output) {Generate Output}; \path [line] (input) -- (datamodel); \path [line] (datamodel) -- (reduce); \path [line] (reduce) -- (solveILP); \path [line] (reduce) -- (solveHeuristic); \path [line] (solveILP) -- (output); \path [line] (solveHeuristic) -- (output); \end{tikzpicture} \caption{Overview of the Yoshiko Algorithm} \label{algOverview} \end{figure} ROUGH IDEA: COMPLETE GRAPH, CHOOSE EDGES SO THAT sum of C(E) is MAX while satisfying Triangle inequalities > Fully Disjunct Clique-Graph \ No newline at end of file
 The Yoshiko Wrapper provides a clean and simple interface to generate the model. \subparagraph{Mapping edge costs} The user has the possibility to use a numeric Cytoscape column of the node table as a source for the edge-cost function $C$. \subparagraph{Insertion and deletion cost} The default values $C_I$ and $C_D$ can be set by the user with the default values being $C_I=-1$ and $C_D=1$. It should be noted, that the insertion cost value is not normalized or in any way adjusted when a mapping is used. This means that the user needs to adjust this value wisely to fit the data. As an example the user might have mapped the edge costs to a column containing values in the range of $10^6-10^7$. The default insertion cost of $-1$ will be irrelevant in comparison and the algorithm will most likely insert all missing edges and generate one big cluster as a solution. Overall the ratio $R = \frac{|C_I|}{C_D}$ should give you a rough idea how the algorithm will operate.\\ $R > 1$ means, that the algorithm is more likely to delete edges to generate cliques, a value of $R<1$ means insertions are more likely. \subparagraph{Mapping permanent or forbidden edges} The Yoshiko app has additional convenience functions: The user can map edges to a boolean Cytoscape column to mark them as either \textbf{forbidden} (meaning that those edges will never be part of the solution) or \textbf{permanent} (meaning that those edges will always be part of the solution). Marking an edge e as forbidden is equivalent to $C(e)=-\infty$, marking an edge e as permanent is equivalent to $C(e)=\infty$. This way the user is able to apply expert knowledge about the input instance to increase the quality of the solution.
 The Yoshiko algorithm models the data as a complete graph $G=(V,E)$ with an associated edge-cost function $C: E \rightarrow \mathbb{R} \cup \lbrace -\infty \rbrace \cup \lbrace \infty \rbrace$. As many input instances do not describe a full graph, missing edges and costs need to be modeled. This is achieved by using default values for insertion or deletion. A default insertion cost $C_I \in [-\infty,0]$ is used as $C(e)$ whenever the input instance does not contain an edge $e$. A default deletion cost $C_D \in [0,\infty ]$ is used as $C(e)$ whenever the input instance does contain an edge $e$ that has no cost associated yet. \ No newline at end of file
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 \documentclass[10pt,a4paper]{article} \usepackage[utf8]{inputenc} \usepackage[english]{babel} \usepackage{amsmath} \usepackage{amsfonts} \usepackage{amssymb} \author{Philipp Spohr} \title{Rough Analysis of Cluster Editing Reduction Rules in Multi-Graphs} \begin{document} \maketitle \section{•} \end{document} \ No newline at end of file
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 \documentclass[10pt,a4paper]{article} \usepackage[utf8]{inputenc} \usepackage[english]{babel} \usepackage{amsmath} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{abstract} \usepackage{hyperref} \usepackage{graphicx} \usepackage{tikz} \usepackage{verbatim} \usepackage{float} \usetikzlibrary{shapes,arrows} \usetikzlibrary{positioning} \hypersetup{ linktoc=all } \author{Philipp Spohr} \title{Developing and evaluating a Cytoscape app for graph-based clustering} \begin{document} \maketitle \cleardoublepage \begin{abstract} This paper describes an implementation of the Yoshiko-alorithm, which clusters data based on the weighted cluster-editing problem, as a plugin for Cytoscape. Cytoscape is a network visualization and analysis tool (insert info) Yoshiko is based on work from (insert info) \end{abstract} \tableofcontents \clearpage \section{Introduction} \section{The Yoshiko-App for Cytoscape} \subsection{Technical Details} \subsubsection{Program Structure} \subsubsection{JNI} \subsection{Algorithm} \input{Chapter/alg_overview} \subsubsection{Data Modeling} \paragraph{Theory} \input{Chapter/dm_theory} \paragraph{Implementation} \input{Chapter/dm_impl} \section{Evaluation of the Yoshiko Algorithm} \section{Outlook} \subsection{Multigraph Analysis} \subsection{Integration in other frameworks} \end{document} \ No newline at end of file
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