Init and half outline done

This commit is contained in:
Tom Zuidberg
2026-04-25 21:49:02 +02:00
parent afd194a678
commit 6ad1ef7115
9 changed files with 9389 additions and 0 deletions

142
paper.tex Normal file
View File

@@ -0,0 +1,142 @@
\documentclass[journal,compsoc,10pt]{IEEEtran}
% Load some possibly useful packages. You can remove the ones you don't need or
% add other packages that you need in your paper.
\usepackage{graphicx} % required to include graphics
\usepackage{amsfonts,amssymb,amsmath} % mathsymbols etc
\usepackage{mathtools} % includes some fixes to amsmath, and adds convenience macros
\usepackage{bm} % make any letter boldface in math
\usepackage{algpseudocode} % aka `algorithmicx`: same look `algorithmic`, but more flexible
\usepackage{array} % for better looking arrays
\usepackage{booktabs} % for better looking tables
\usepackage[usenames]{xcolor} % colors for highlighting etc.
\usepackage{url} % for urls
\usepackage[%pdftitle=, % define the PDF metadata
%pdfauthor=,
colorlinks=true, linkcolor=purple, urlcolor=blue, citecolor=cyan,
anchorcolor=black % make links/references 'clickable' without ugly frames
]{hyperref}
\usepackage{cleveref} % smart references to figures, equations etc.
% some packages which may be useful when drafting, but should be removed before submission
\usepackage{todonotes}
% You can define your own commands. This is useful for shorthands, for example
\newcommand{\EE}{\mathbb{E}}
\newcommand{\RR}{\mathbb{R}}
\newcommand{\eE}{\mathcal{E}}
\newcommand{\gG}{\mathcal{G}}
\newcommand{\nN}{\mathcal{N}}
\newcommand{\lnorm}[1]{\ell_{#1}\text{-norm}}
% Commands are also useful to ensure standardized notation, such as how to display vectors and matrices.
% The point is to replace formatting commands with semantic ones.
% This both makes the source more semantic, and also makes it easier to change formatting choices later
% IMPORTANT: In TeX, all commands share a global namespace. You need to be careful therefore not to overwrite an existing command.
% Use \newcommand to ensure you don't accidentally overwrite an important macro
% Use \renewcommand if you *do* want to overwrite a macro, have checked what the original does,
% and have made sure the redefinition is safe.
\newcommand{\T}{\mathsf{T}} % transpose
\renewcommand{\vec}[1]{\bm{#1}} % redefine \vec to produce boldface instead of adding an arrow
\newcommand{\mat}[1]{\bm{#1}} % define \vec to produce boldface
\newcommand{\ones}{\bm{1}} % all-ones vector
\newcommand{\eye}{\bm{I}} % identity matrix
\newcommand{\ei}{\bm{e}_i} % standard basis vector e_i
\newcommand{\ej}{\bm{e}_j} % standard basis vector e_j
% TIP: Resist the temptation to be too clever with macros
% - \ei and \ej are easier to type than e.g. \ee[i] (note that \e is a low-level command and should not be redefined)
% - While you can define macros in terms of other macros (eg we could define \ei in terms of \vec),
% many journals wont accept this. Recursive macros also produce more frequent and more complicated compilation errors
% Commands like \sin and \exp ensure proper fonts and spacing for math operators.
% Use the dedicated \DeclareMathOperator to define new operators
\DeclareMathOperator{\diag}{diag}
\begin{document}
\title{Influence of update schemes on gene regulatory networks}
% author information
% COMMENT OUT THESE LINES FOR YOUR CONFERENCE SUBMISSION!
\author{Tom Zuidberg \\ 455969}
\maketitle
\thispagestyle{plain}
\pagestyle{plain}
\begin{abstract}
In this paper we will introduce boolean networks (BN) and their relevance to gene regulatory networks (GRN). We will have a closer look on update schemes. Specifically, synchronous, sequential and asynchronous update schemes and their effect on the behavior of BN and GRN respectively.
\end{abstract}
\section{Introduction}00
\subsection{Notation}
\section{Boolean networks}
\section{Update Schemes}
Explain different update schemes:
\begin{itemize}
\item Synchronous scheme - all nodes update at the same time
\item Sequential - close to synchronous. the nodes update in a specific order and take into account the updated input node if that node had been updated before/is positioned earlier in the sequence
\item block sequential - mix of synchronous and sequential. predefined blocks update sequentiall, inside a block the update follows the synchronous scheme
\item asynchronous deterministic - one node is updated per tick following a specific sequence
\item asynchronous generalized - same as asynchronous deterministic with the slight change that within the sequence nodes may appear multiple times.
\end{itemize}
\section{Relevance for Gene Regulatory Networks}
Tie the update schemes and their different outcomes or behavior to GRN.
\section{Conclusion}
\begin{figure*} % The starred version uses both columns; unstarred only one column
\centering
% \includegraphics[width=5in]{edge_vs_hyperedge.png}
% TIP: Ensure the original image file has approximately the right dimensions
% (if using matplotlib, specify correct figure size) so that the image is not rescaled too brutally.
\caption{Boolean example.
% NB: The '~' inserts a non-breaking space, ensuring 'Ref.' is never separated from its number
Simple boolean network example; a graph of the network and most likely a table as well for the updated states $x(t) \rightarrow x(t+1)$
}
\end{figure*}
\begin{figure*} % The starred version uses both columns; unstarred only one column
\centering
\caption{
graph of all possible states for a boolean network using a synchronous update scheme
}
\end{figure*}
\begin{figure*} % The starred version uses both columns; unstarred only one column
\centering
% \includegraphics[width=5in]{edge_vs_hyperedge.png}
% TIP: Ensure the original image file has approximately the right dimensions
% (if using matplotlib, specify correct figure size) so that the image is not rescaled too brutally.
\caption{
example graph of boolean network showcasing grouping of specific nodes.
}
\end{figure*}
% The list of references is provided as `references.bib`
\bibliographystyle{unsrt}
\bibliography{IEEEabrv,references}
\end{document}