Color Coding draft

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Bibliography.bib

@@ -1,20 +1,6 @@
-@book{Sham,
+@phdthesis{cookrage2018,
-   author = "Pak Sham",
+	title = {{RAGE}: {The} {Rage} {Attack} {Graph} {Engine}},
-   title = "Statistics in Human Genetics",
+	author = {Cook, Kyle},
-   publisher = "Arnold",
+	year = {2018},
-   year = 1998,
+	file = {Kyle Cook Thesis:/home/noah/Zotero/storage/2SR28HM2/Kyle Cook Thesis.pdf:application/pdf},
-}
-
-@misc{Scot95,
-  author = "David W. Scott",
-  note = "Personal communication",
-  year = 1995,
-}
-
-
-@BOOK{Mathematica,
-   author = "Stephen Wolfram",
-   title = "The Mathematica Book",
-   publisher = "Cambridge University Press",
-   year = 1996,
 }

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Chapter1.tex

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 \TUchapter{INTRODUCTION}
 \TUsection{First Heading: The Introduction}
-This is the first section of the introduction. For additional
+%This is the first section of the introduction. For additional
-information see \cite{Sham,Scot95} or just for fun you may wish to
+%information see %\cite{Sham,Scot95} or just for fun you may wish to
-read \cite{Mathematica}.
+%read \cite{Mathematica}.
 
 Here is the beginning of a second paragraph.
 

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Chapter2.tex

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-\TUchapter{THE SECOND CHAPTER}
+\TUchapter{RELATED WORKS}
 
 \TUsection{First Heading}
 \par This is the beginning of the second chapter and the first section of the second chapter. The rest of the text in this section is meaningless filler.\footnote{The filler used on this page is of a family called \emph{Lorem Ipsum}. It was generated by http://www.lipsum.com/feed/html on August 18, 2014 at 8:08 pm Central Time. The site  explains the history of \emph{Lorem Ipsum} filler, the reason for using it, and a procedure for generating it.}

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Chapter3.tex

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-\TUchapter{THE SECOND CHAPTER}
+\TUchapter{UTILITY EXTENSIONS TO THE RAGE ATTACK GRAPH GENERATOR}
 
-\TUsection{First Heading}
+\TUsection{Path Walking}
-\par This is the beginning of the second chapter and the first section of the second chapter. The rest of the text in this section is meaningless filler.\footnote{The filler used on this page is of a family called \emph{Lorem Ipsum}. It was generated by http://www.lipsum.com/feed/html on August 18, 2014 at 8:08 pm Central Time. The site  explains the history of \emph{Lorem Ipsum} filler, the reason for using it, and a procedure for generating it.}
+\par Due to the large-scale nature of Attack Graphs, analysis can prove difficult and time-consuming. With some networks reaching millions of states and edges, 
+analyzing the entire network can be overwhelming complex. As a means of simplifying analysis, a potential strategy could be to consider only small subsets of
+the network at a time, rather than feeding the entire network into an analysis algorithm. To aid in this effort, a Path Walking feature was implemented as a
+separate program, and has two primary modes of usage. The goal of this feature is to provide a subset of the network that includes all possible paths from the
+root node to a designated node. The first mode is a manual mode, where a user can input the desired state to walk to, and the program will output a separate
+graph of all possible paths to the specified state. The second mode is an automatic mode, where the program will output seperate subgraphs to all states in
+the network that have qualities of $``compliance$\_$vio = true"$ or $``compliance$\_$vios > 0"$. This often produces multiple subgraphs, that can then be 
+separately fed into an analysis program. 
 
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+Figure \ref{fig:PW} demonstates an output of the Path Walking feature when walking to state 14. In this figure, the primary observable feature is that the
-
+network was reduced from 16 states to 6 states, and 32 edges to 12 edges. The reduction from the original network to the subset varies on the overall connectivity 
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+of the original Attack Graph, but the reduction can aid in simplifying the analysis process if only certain states of the network are to be analyzed.
-
-\TUsection{Second Heading} Second section of the second chapter.
 \begin{figure}[htp]
-\vspace{.2truein} \centerline{Normally a figure would go here.}
+    \includegraphics[width=\linewidth]{"./Chapter3_img/PW.png"}
-    \caption{Title of the Second Figure}
+    \vspace{.2truein} \centerline{}
+        \caption{Path Walking to State 14}
+        \label{fig:PW}
 \end{figure}
-\begin{table}[htp]
+
-\vspace{.2truein} \centerline{Normally a figure would go here.}
+\TUsection{Compound Operators}
-    \caption{Title of the Second Table}
+Many of the networks previously generated by RAGE compromise of states with features that can be fully enumerated. In many of the generated networks, there is an 
-\end{table}
+established set of qualities that will be used, with an established set of values. These typically have included $``compliance$\_$vio=true/false"$,
-\begin{table}[htp]
+$``root=true/false"$, or other general $``true/false"$ values or $``version=X"$ qualities. To expand on the types and complexities of networks that can be
-\vspace{.2truein} \centerline{Normally a figure would go here.}
+generated, compound operators have been added to RAGE. When updating a state, rather than setting a quality to a specific value, the previous value can now
-    \caption{Title of the Third Table}
+be modified by an amount specified through standard compound operators such as $\mathrel{+}=$, $\mathrel{-}=$, $\mathrel{*}=$, or $\mathrel{/}=$.
-\end{table}\\
+
+The work conducted by the author of \cite{cookrage2018} when designing the software architecture included specifications for a quality encoding scheme. As the
+author discusses, qualities have four fields, which include the asset ID, attributes, operator, and value. The operator field is 4 bits, which allows for a total
+of 16 operators. Since the only operator in use at the time was the $``\mathrel{=}"$ operator, the addition of four compound operators does not surpass the 16 operator limit,
+and no encoding scheme changes were necessary. This also allows for additional compound operators to be incorporated in the future.
+
+A few changes were necessary to allow for the addition of compound operators. Before the generation of an Attack Graph begins, all values are stored in a hash
+table. For previous networks generated by RAGE, this was not a difficulty, since all values could be fully enumerated and all possible values were known. When
+using compound operators however, not all values can be fully known. The concept of approximating which exploits will be applicable and what absolute minimum
+or maximum values will be prior to generation is a difficult task, so not all values can be enumerated and stored into the hash table. As a result, on-the-fly
+updates to the hash table needed to be added to the generator. The original key-value scheme for hash tables relied on utilizing the size of the hash table for
+values. Since the order in which updates happen may not always remain consistent (and is especially true in distributed computing environments), it is possible
+for states to receive different hash values with the original hashing scheme. To prevent this, the hashing scheme was adjusted so that the new value of the
+compound operator is inserted into the hash table values if it was not found, rather than the size of the hash table. Previously, there was no safety check
+for the hash table, so if the value was not found, the program would end execution. The assumption that this value can be inserted into the hash table is safe 
+to make, since compound operators are conducted on numeric values, and matches the numeric type of the hash table.
+
+\TUsection{Color Coding}
+As a visual aid for analysis purposes, color coding was another feature implemented as a postprocessing tool for RAGE. When viewing the output graph of RAGE, all states are
+originally identical in appearance, apart from number of edges, edge IDs, and state IDs. To allow for visual differentiation, color coding can be enabled in the run script.
+Color coding currently functions by working through the graph output text file, but it can be extended to read directly from Postgres instead. The feature scans through the
+output file, and locates states that have $``compliance$\_$vios = X"$ (where \textit{X} is a number greater than 0), or $``compliance$\_$vio = true"$. For states that meet these
+properties, the color coding feature will add a color to the graphviz DOT file through the $[color=COL]$ attribute for the given node, where \textit{COL} is assigned based on severity.
+For this version of color coding, severity is determined by the total number of compliance violations, but future versions can alter the severity measure through alternative means.
+Figure \ref{fig:CC} displays an example graph that leverages color coding to easily identify problem states.
+\begin{figure}[htp]
+    \includegraphics[width=\linewidth]{"./Chapter3_img/CC.png"}
+    \vspace{.2truein} \centerline{}
+        \caption{Color Coding a Small Network Based on Violations}
+        \label{fig:CC}
+\end{figure}
+
+\TUsection{Intermediate Database Storage} Fourth section of the third chapter.
+
+\TUsection{Relational Operators} Fifth section of the third chapter.
+

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+\TUsection{Subgraphing Approach} Second section of the second chapter.
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Schrick-Noah_MS-Thesis.bbl

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+Kyle Cook.
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+\newblock PhD thesis, 2018.
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+\contentsline {table}{\numberline {5.1}{\ignorespaces Title of the Second Table}}{13}{}%
+\contentsline {table}{\numberline {5.2}{\ignorespaces Title of the Third Table}}{13}{}%
+\contentsline {table}{\numberline {6.1}{\ignorespaces Title of the Second Table}}{15}{}%
+\contentsline {table}{\numberline {6.2}{\ignorespaces Title of the Third Table}}{15}{}%
+\contentsline {table}{\numberline {7.1}{\ignorespaces Title of the Second Table}}{17}{}%
+\contentsline {table}{\numberline {7.2}{\ignorespaces Title of the Third Table}}{17}{}%
+\contentsline {table}{\numberline {A.1}{\ignorespaces Title of the Only Table in this Appendix.}}{19}{}%
+\contentsline {table}{\numberline {B.1}{\ignorespaces Title of the First Table in this Appendix.}}{20}{}%
+\contentsline {table}{\numberline {B.2}{\ignorespaces Title of the Second Table in this Appendix.}}{21}{}%

Schrick-Noah_MS-Thesis.tex

@@ -90,6 +90,7 @@
 
 \RequirePackage{setspace}
 \usepackage{boxedminipage}
+\usepackage{graphicx}
 
 % Added by Richard D Redner 2017-08-16
 % If, in the List of Tables or List of Figures, the figure/table numbers
@@ -152,8 +153,8 @@
 \sixthmember{Sixth Member}   % as needed
 
 \numofpages{92}                    % number of pages in the document
-\numofchapters=6                   % number of chapters in the document
+\numofchapters=7                   % number of chapters in the document
-\lastchapter{Conclusions}	  % the title of the last numbered chapter
+\lastchapter{Conclusions and Future Works}	  % the title of the last numbered chapter
 \numofabstractwords{29}            % number of words in the abstract
 
 %
@@ -200,8 +201,13 @@ over the place.
 % Main Body of Document
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-\include{Chapter1.sample}
+\include{Chapter1}
-\include{Chapter2.sample}
+\include{Chapter2}
+\include{Chapter3}
+\include{Chapter4}
+\include{Chapter5}
+\include{Chapter6}
+\include{Chapter7}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % BIBLIOGRAPHY
@@ -210,7 +216,7 @@ over the place.
 \addtocontents{toc}{\protect{\hfill \ }}
 \addcontentsline{toc}{section}{\contentsadj NOMENCLATURE}
 \bibliographyp
-\bibliography{MyBibliography.sample}
+\bibliography{Bibliography}
 \bibliographystyle{plain}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -218,5 +224,5 @@ over the place.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 \appendixpages       % prepare for the generation of the appendices
-\include{Appendices.sample}
+\include{Appendices}
 \end{document}

Schrick-Noah_MS-Thesis.toc

@@ -5,8 +5,45 @@
 {\hfill \ }
 \contentsline {section}{\hspace {-\parindent }ACKNOWLEDGEMENTS}{v}{}%
 {\hfill \ }
-\contentsline {section}{\hspace {-\parindent }TABLE OF CONTENTS}{vi}{}%
+\contentsline {section}{\hspace {-\parindent }TABLE OF CONTENTS}{vii}{}%
 {\hfill \ }
-\contentsline {section}{\hspace {-\parindent }LIST OF TABLES}{vii}{}%
+\contentsline {section}{\hspace {-\parindent }LIST OF TABLES}{viii}{}%
 {\hfill \ }
-\contentsline {section}{\hspace {-\parindent }LIST OF FIGURES}{viii}{}%
+\contentsline {section}{\hspace {-\parindent }LIST OF FIGURES}{ix}{}%
+\contentsline {chapter}{\numberline {CHAPTER 1: }{\bf \uppercase {INTRODUCTION}}}{1}{}%
+\contentsline {section}{\numberline {1.1}\bf First Heading: The Introduction}{1}{}%
+\contentsline {section}{\numberline {1.2}\bf Second Heading}{1}{}%
+\contentsline {subsection}{\numberline {1.2.1}\it First Subheading}{1}{}%
+\contentsline {subsection}{\numberline {1.2.2}\it Second Subheading}{1}{}%
+\contentsline {subsubsection}{First Sub-subsection Header}{1}{}%
+\contentsline {chapter}{\numberline {CHAPTER 2: }{\bf \uppercase {RELATED WORKS}}}{3}{}%
+\contentsline {section}{\numberline {2.1}\bf First Heading}{3}{}%
+\contentsline {section}{\numberline {2.2}\bf Second Heading}{4}{}%
+\contentsline {chapter}{\numberline {CHAPTER 3: }{\bf \uppercase {UTILITY EXTENSIONS TO THE RAGE ATTACK GRAPH GENERATOR}}}{5}{}%
+\contentsline {section}{\numberline {3.1}\bf Path Walking}{5}{}%
+\contentsline {section}{\numberline {3.2}\bf Compound Operators}{6}{}%
+\contentsline {section}{\numberline {3.3}\bf Color Coding}{7}{}%
+\contentsline {section}{\numberline {3.4}\bf Intermediate Database Storage}{9}{}%
+\contentsline {section}{\numberline {3.5}\bf Relational Operators}{9}{}%
+\contentsline {chapter}{\numberline {CHAPTER 4: }{\bf \uppercase {SYNCHRONOUS FIRING}}}{10}{}%
+\contentsline {section}{\numberline {4.1}\bf First Heading}{10}{}%
+\contentsline {section}{\numberline {4.2}\bf Second Heading}{11}{}%
+\contentsline {chapter}{\numberline {CHAPTER 5: }{\bf \uppercase {IMPLEMENTATION OF MESSAGE PASSING INTERFACE}}}{12}{}%
+\contentsline {section}{\numberline {5.1}\bf Tasking Approach}{12}{}%
+\contentsline {section}{\numberline {5.2}\bf Subgraphing Approach}{13}{}%
+\contentsline {chapter}{\numberline {CHAPTER 6: }{\bf \uppercase {PERFORMANCE ANALYSIS}}}{14}{}%
+\contentsline {section}{\numberline {6.1}\bf First Heading}{14}{}%
+\contentsline {section}{\numberline {6.2}\bf Second Heading}{15}{}%
+\contentsline {chapter}{\numberline {CHAPTER 7: }{\bf \uppercase {CONCLUSIONS AND FUTURE WORKS}}}{16}{}%
+\contentsline {section}{\numberline {7.1}\bf First Heading}{16}{}%
+\contentsline {section}{\numberline {7.2}\bf Second Heading}{17}{}%
+{\hfill \ }
+\contentsline {section}{\hspace {-\parindent }NOMENCLATURE}{18}{}%
+\addvspace {10pt}
+\contentsline {section}{\hspace {-\parindent }BIBLIOGRAPHY}{18}{}%
+{\hfill \ }
+\contentsline {section}{\hspace {-\parindent }APPENDIX A:\ \ {\bf \uppercase {THE FIRST APPENDIX}} }{19}{}%
+\contentsline {section}{\hspace {-\parindent }APPENDIX B:\ \ {\bf \uppercase {THE SECOND APPENDIX}} }{20}{}%
+\contentsline {section}{\numberline {B.1}\bf A Heading in an Appendix}{20}{}%
+\contentsline {subsection}{\numberline {B.1.1}\it A Subheading in an Appendix}{20}{}%
+\contentsline {subsubsection}{A Sub-subsection in an Appendix}{20}{}%

texput.log

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+ %&-line parsing enabled.
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+
+! Emergency stop.
+<*> exit
+        
+End of file on the terminal!
+
+ 
+Here is how much of TeX's memory you used:
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