146 lines
6.8 KiB
TeX
146 lines
6.8 KiB
TeX
\documentclass[journal,compsoc,10pt]{IEEEtran}
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% Load some possibly useful packages. You can remove the ones you don't need or
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% add other packages that you need in your paper.
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\usepackage{graphicx} % required to include graphics
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\usepackage{amsfonts,amssymb,amsmath} % mathsymbols etc
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\usepackage{mathtools} % includes some fixes to amsmath, and adds convenience macros
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\usepackage{bm} % make any letter boldface in math
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\usepackage{algpseudocode} % aka `algorithmicx`: same look `algorithmic`, but more flexible
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\usepackage{array} % for better looking arrays
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\usepackage{booktabs} % for better looking tables
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\usepackage[usenames]{xcolor} % colors for highlighting etc.
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\usepackage{url} % for urls
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\usepackage[%pdftitle=, % define the PDF metadata
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%pdfauthor=,
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colorlinks=true, linkcolor=purple, urlcolor=blue, citecolor=cyan,
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anchorcolor=black % make links/references 'clickable' without ugly frames
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]{hyperref}
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\usepackage{cleveref} % smart references to figures, equations etc.
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% some packages which may be useful when drafting, but should be removed before submission
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\usepackage{todonotes}
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% You can define your own commands. This is useful for shorthands, for example
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\newcommand{\EE}{\mathbb{E}}
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\newcommand{\RR}{\mathbb{R}}
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\newcommand{\eE}{\mathcal{E}}
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\newcommand{\gG}{\mathcal{G}}
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\newcommand{\nN}{\mathcal{N}}
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\newcommand{\lnorm}[1]{\ell_{#1}\text{-norm}}
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% Commands are also useful to ensure standardized notation, such as how to display vectors and matrices.
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% The point is to replace formatting commands with semantic ones.
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% This both makes the source more semantic, and also makes it easier to change formatting choices later
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% IMPORTANT: In TeX, all commands share a global namespace. You need to be careful therefore not to overwrite an existing command.
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% Use \newcommand to ensure you don't accidentally overwrite an important macro
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% Use \renewcommand if you *do* want to overwrite a macro, have checked what the original does,
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% and have made sure the redefinition is safe.
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\newcommand{\T}{\mathsf{T}} % transpose
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\renewcommand{\vec}[1]{\bm{#1}} % redefine \vec to produce boldface instead of adding an arrow
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\newcommand{\mat}[1]{\bm{#1}} % define \vec to produce boldface
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\newcommand{\ones}{\bm{1}} % all-ones vector
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\newcommand{\eye}{\bm{I}} % identity matrix
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\newcommand{\ei}{\bm{e}_i} % standard basis vector e_i
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\newcommand{\ej}{\bm{e}_j} % standard basis vector e_j
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% TIP: Resist the temptation to be too clever with macros
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% - \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)
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% - While you can define macros in terms of other macros (eg we could define \ei in terms of \vec),
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% many journals won’t accept this. Recursive macros also produce more frequent and more complicated compilation errors
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% Commands like \sin and \exp ensure proper fonts and spacing for math operators.
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% Use the dedicated \DeclareMathOperator to define new operators
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\DeclareMathOperator{\diag}{diag}
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\begin{document}
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\title{Influence of update schemes on gene regulatory networks}
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% author information
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% COMMENT OUT THESE LINES FOR YOUR CONFERENCE SUBMISSION!
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\author{Tom Zuidberg \\ 455969}
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\maketitle
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\thispagestyle{plain}
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\pagestyle{plain}
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\begin{abstract}
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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.
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\end{abstract}
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\section{Introduction}
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\section{Boolean networks}
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Explain Boolean network and what an update scheme is using the synchronous/parallel scheme.
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\subsection{Notation}
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Define clear notation used throughout the paper
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\section{Update Schemes}
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Explain different update schemes including characteristics for behavior especially chaotic behavior.
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\subsection{Synchronous scheme}
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all nodes update at the same time
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\subsection{Sequential scheme}
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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
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\subsection{Block-sequential scheme}
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mix of synchronous and sequential. predefined blocks update sequential, inside a block the update follows the synchronous scheme
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\subsection{Asynchronous deterministic}
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one node is updated per tick following a specific sequence
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\subsection{Asynchronous generalized}
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same as asynchronous deterministic with the slight change that within the sequence nodes may appear multiple times.
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\section{Relevance for Gene Regulatory Networks}
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Tie the update schemes and their different outcomes or behavior to GRN.
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Emphasizing the drawbacks of asynchronous models when applied to GRN e.g. it takes way to long to update a GRN using asynchronous deterministic for it to have an effect; assuming that one update takes a few minutes, when the whole process can take days to complete.\cite{schwab2020concepts}
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\section{Conclusion}
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References: \cite{schwab2020concepts}\cite{aracena2009robustness}\cite{bornholdt2008boolean}\cite{goles2010block}\cite{helikar2011boolean}
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\begin{figure*} % The starred version uses both columns; unstarred only one column
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\centering
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% \includegraphics[width=5in]{edge_vs_hyperedge.png}
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% TIP: Ensure the original image file has approximately the right dimensions
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% (if using matplotlib, specify correct figure size) so that the image is not rescaled too brutally.
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\caption{Boolean example.
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% NB: The '~' inserts a non-breaking space, ensuring 'Ref.' is never separated from its number
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Simple boolean network example; a graph of the network and most likely a table as well for the updated states $x(t) \rightarrow x(t+1)$
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}
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\end{figure*}
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\begin{figure*} % The starred version uses both columns; unstarred only one column
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\centering
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\caption{
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graph of all possible states for a boolean network using a synchronous update scheme
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}
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\end{figure*}
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\begin{figure*} % The starred version uses both columns; unstarred only one column
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\centering
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% \includegraphics[width=5in]{edge_vs_hyperedge.png}
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% TIP: Ensure the original image file has approximately the right dimensions
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% (if using matplotlib, specify correct figure size) so that the image is not rescaled too brutally.
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\caption{
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example graph of boolean network showcasing grouping of specific nodes.
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}
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\end{figure*}
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% The list of references is provided as `references.bib`
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\bibliographystyle{unsrt}
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\bibliography{IEEEabrv,references}
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\end{document}
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