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-% --- Title / Authors --------------------------------------------------------- -% patch \maketitle so that it doesn't center -\patchcmd{\@maketitle}{center}{flushleft}{}{} -\patchcmd{\@maketitle}{center}{flushleft}{}{} -% patch \maketitle so that the font size for the title is normal -\patchcmd{\@maketitle}{\LARGE}{\LARGE\sffamily}{}{} -% patch the patch by authblk so that the author block is flush left -\def\maketitle{{% - \renewenvironment{tabular}[2][] - {\begin{flushleft}} - {\end{flushleft}} - \AB@maketitle}} -\makeatletter -\renewcommand\AB@affilsepx{ \protect\Affilfont} -%\renewcommand\AB@affilnote[1]{{\bfseries #1}\hspace{2pt}} -\renewcommand\AB@affilnote[1]{{\bfseries #1}\hspace{3pt}} -\makeatother -\renewcommand\Authfont{\sffamily\bfseries} -\renewcommand\Affilfont{\sffamily\small\mdseries} -\setlength{\affilsep}{1em} - -\LetLtxMacro{\OldIncludegraphics}{\includegraphics} -\renewcommand{\includegraphics}[2][]{\OldIncludegraphics[width=12cm, #1]{#2}} - - -% --- Document ---------------------------------------------------------------- -\title{[Re] A Generalized Linear Integrate-and-Fire Neural Model Produces - Diverse Spiking Behaviors} - - \usepackage{authblk} - \author[1]{Georgios Detorakis} - \affil[1]{Department of Cognitive Sciences, UC Irvine, - Irvine, CA, USA} - -\date{\vspace{-5mm} - \sffamily \small - \href{mailto:corresponding-author@mail.com}{gdetorak@uci.edu \\ - gdetor@protonmail.com}} - - -\setlength\LTleft{0pt} -\setlength\LTright{0pt} - - -\begin{document} -\maketitle - -\marginpar{ - %\hrule - \sffamily\small - %\vspace{2mm} - {\bfseries Editor}\\ - Name Surname\\ - - {\bfseries Reviewers}\\ - Name Surname\\ - Name Surname\\ - - {\bfseries Received} Sep, 1, 2015\\ - {\bfseries Accepted} Sep, 1, 2015\\ - {\bfseries Published} Sep, 1, 2015\\ - - {\bfseries Licence} \href{http://creativecommons.org/licenses/by/4.0/}{CC-BY} - - \begin{flushleft} - {\bfseries Competing Interests:}\\ - The author has declared that no competing interests exist. - \end{flushleft} - - \hrule - \vspace{3mm} - - \hypersetup{urlcolor=white} - - \vspace{-1mm} - \begin{repobox} - \bfseries\normalsize - \href{http://github.com/rescience/rescience-submission/article}{\faGithubAlt~Article repository} - \end{repobox} - \vspace{-1mm} - \begin{repobox} - \bfseries\normalsize - \href{http://github.com/rescience/rescience-submission/code}{\faGithubAlt~Code repository} - \end{repobox} - \hypersetup{urlcolor=blue} -} - -\begin{rebox} -\sffamily {\bfseries A reference implementation of} -\small -\begin{flushleft} -\begin{itemize} - \item[→] A Generalized Linear Integrate-and-Fire Neural Model Produces - Diverse Spiking Behaviors, Stefan Mihalas and Ernst Niebur, Neural - Computation 21, 704--718, 2009. - \end{itemize}\par -\end{flushleft} -\end{rebox} - - -\section{Introduction}\label{introduction} - -Integrate-and-fire neurons are being used extensively in the field of -neuroscience for modeling spiking behaviors~\cite{dayan:2001}. In this work we -provide a reference implementation of~\cite{mihalas:2009}, where the authors -have introduced a generalization of the leaky integrate-and-fire neuron model. -The Mihalas-Niebur Neuron (MNN) model is a linear integrate-and-fire neuron -model capable of expressing a rich spiking behavior based on a set of -parameters. - -An MNN model expresses tonic and phasic spiking, class $1$ and $2$, spike -frequency adaptation, accommodation, threshold variability, rebound spike, -integrator, input bistability, hyperpolarizing spiking and bursting, tonic, -phasic and rebound bursting, mixed mode, afterpotentials, basal bistability, -preferred frequency and spike latency. -Due to its simplicity, the MNN model has been used in neuromorphic -implementations such as~\cite{folowosele:2011}. - -The model consists of linear differential equations, which describe the membrane -and threshold potentials and internal currents. All the results provided in -\cite{mihalas:2009} have been obtained by using only two internal currents and -thus we use the exact same number of internal currents in this work. The -subthreshold dynamics are defined by a set of linear ordinary differential -equations, while an instantaneous threshold potential controls when the neuron -fires an action potential (spike) in a dynamic way. The ability of the MNN -model to generate -such a diverse spiking behavior is due to the complex update rules. In this -work the MNN model has been implemented in Python (version 3.6.1) using -Numpy (version 1.13.1) and Matplotlib (version 2.0.2) packages. - - - -\section{Methods}\label{methods} - -In order to implement the model described in \cite{mihalas:2009}, we discretized -the dynamical system using the forward Euler integration scheme. The time step -is fixed to $0.1\, \Rm{ms}$ for all the simulations, and the total simulation -time $t_f$ varies according to figure 1 of the original paper. Our -implementation differs from the one in the original paper, since in -\cite{mihalas:2009}, authors numerically solve equation $3.5$ (algebraic -equation) under the constraint imposed by inequality $3.4$ and thus they -compute the spike times. On the other hand, in this work we directly compute -numerically the solution of the dynamical system defined by equations $2.1$ -and $2.2$ in \cite{mihalas:2009} (see tables~\ref{table:2} and~\ref{table:3}). - -We provide all equations and parameters of the model in tables as it has been -suggested by~\cite{nordlie:2009}. -Table~\ref{table:1} provides the summary of the model. Tables~\ref{table:2} -and~\ref{table:3} give the subthreshold dynamics (differential equations) -describing the membrane and the threshold potentials as well as the two internal -currents and the update rules. The parameters for all the simulations are given -in table~\ref{table:4}, while the external current intensities and pulse -duration are provided in table~\ref{table:5}. The parameters in this work are -exactly the same used in the original paper (table 1, pg. $711$). We had to -infer the time intervals and the total simulation times for the pulses since -they are not given explicitly in the original paper. Thus, we extracted the -time intervals from figure $1$ of \cite{mihalas:2009} by visual inspection. -The initial conditions are given in table~\ref{table:6}. - -All simulations ran on a Dell OptiPlex $7040$, equipped with a sixth -generation i$7$ processor, $16\, \Rm{GB}$ of physical memory and running Arch -Linux (x$86\_64$). The total execution time of all simulations was $2.41$ -seconds and the peak consumed memory was $162\, \Rm{MB}$\footnote{Python memory -profiler used (\url{https://pypi.python.org/pypi/memory_profiler}).}\@. - -%% -\begin{table}[!htbp] - \centering - \begin{tabular}{ll} - \thickhline - \multicolumn{2}{c}{Model Summary} \\\thickhline - \rowcolor{Gray} - Populations & No population -- single neuron model \\\rowcolor{LightGray} - Topology & -- \\ \rowcolor{Gray} - Connectivity & -- \\ \rowcolor{LightGray} - Neuron Model & Linear Integrate-and-Fire Neuron \\\rowcolor{Gray} - Channel Models & Linear, first order ODEs \\ \rowcolor{LightGray} - Synapse Model & -- \\ \rowcolor{Gray} - Plasticity & -- \\ \rowcolor{LightGray} - Input & Constant current or rectangular pulses \\\rowcolor{Gray} - Measurements & Membrane potential, phase plane \\ - \thickhline - \end{tabular} - \caption{{\bfseries \sffamily Summary of the model}} - \label{table:1} -\end{table} -%% - -%% -\begin{table}[!htbp] - \centering - \begin{tabular}{p{3.5cm}ll} - \thickhline - \multicolumn{2}{c}{Neuron Model} \\\thickhline - \rowcolor{Gray} - Name & Mihalas-Niebur Neuron (MNN) \\ \rowcolor{LightGray} - Type & Linear Leaky Integrate-and-Fire Neuron \\ \rowcolor{Gray} - Membrane Potential & $ - \begin{aligned} - \frac{\Rm{d}V(t)}{\Rm{d}t} &= \frac{1}{C} \Big(I_e + I_1 + I_2 - G(V(t) - - E_L) \Big) - \end{aligned}$ \\ \rowcolor{LightGray} - Instantaneous Threshold Potential & $ - \begin{aligned} - \frac{\Rm{d}\Theta(t)}{\Rm{d}t} &= a(V(t) - E_L) - b(\Theta(t) - - \Theta_{\infty}) - \end{aligned} $ - \\ \rowcolor{Gray} - Internal Currents & $ - \begin{aligned} - \frac{\Rm{d}I_{1}(t)}{\Rm{d}t} &= -k_1I_1(t)\\ - \frac{\Rm{d}I_{2}(t)}{\Rm{d}t} &= -k_2I_2(t) \\ - \end{aligned} $ - \end{tabular} - \caption{{\bfseries \sffamily Description of the subthreshold dynamics of - Mihalas-Niebur neuron model.} $V(t)$ and $\Theta(t)$ are the membrane and - threshold potentials, respectively. $E_L$ and $\Theta_{\infty}$ are the - reversal potentials for the membrane and the threshold variables, - respectively. $a, b, k_1, k_2$ and $G$ are constant parameters. $I_e$ is - the external current applied on the neuron model.} - \label{table:2} -\end{table} -%% - -\begin{table}[!htbp] - \centering - \begin{tabular}{cc} - \thickhline - \multicolumn{2}{c}{Update rules} \\ \thickhline - Variable & Rule \\ \rowcolor{Gray} - $V(t)$ & $V_r$ \\ \rowcolor{LightGray} - $\Theta(t)$ & $\max\{\Theta_r, \Theta(t) \}$ \\ \rowcolor{Gray} - $I_1(t)$ & $R_1 \times I_1(t) + A_1$ \\ \rowcolor{LightGray} - $I_2(t) $ & $R_2 \times I_2(t) + A_2$ \\\thickhline - \end{tabular} - \caption{{\bfseries \sffamily Update rules.} $V_r$ and $\Theta_r$ - are the reset values for the membrane and threshold potentials, - respectively. $R_1, R_2, A_1$ and $A_2$ are constants.} - \label{table:3} -\end{table} -%% - -%% -\begin{table}[!htbp] - \centering - \begin{tabular}{CCCCC} - \thickhline - \multicolumn{5}{c}{Model Parameters} \\\thickhline - \begin{tabular}[x]{@{}c@{}} Figure \\ \end{tabular} - & \begin{tabular}[x]{@{}c@{}} $a$ \\ $(\Rm{s^{-1}})$ \end{tabular} - & \begin{tabular}[x]{@{}c@{}} $A_1/C$ \\ $(\Rm{V/s})$ \end{tabular} - & \begin{tabular}[x]{@{}c@{}} $A_2/C$ \\ $(\Rm{V/s})$ \end{tabular}& - \begin{tabular}[x]{@{}c@{}} $t_f$ \\ $(\Rm{s})$ \end{tabular} \\ - \thickhline - 1A & $0$ & $0$ & $0$ & $0.2$ \\\rowcolor{Gray} - 1B & $0$ & $0$ & $0$ & $0.5$ \\\rowcolor{LightGray} - 1C & $5$ & $0$ & $0$ & $0.2$ \\\rowcolor{Gray} - 1D & $5$ & $0$ & $0$ & $0.5$ \\\rowcolor{LightGray} - 1E & $5$ & $0$ & $0$ & $1.0$ \\\rowcolor{Gray} - 1F & $5$ & $0$ & $0$ & $0.4$ \\\rowcolor{LightGray} - 1G & $5$ & $0$ & $0$ & $1.0$ \\\rowcolor{Gray} - 1H & $5$ & $0$ & $0$ & $0.3$ \\\rowcolor{LightGray} - 1I & $5$ & $0$ & $0$ & $0.4$ \\\rowcolor{Gray} - 1J & $5$ & $0$ & $0$ & $1.0$ \\\rowcolor{LightGray} - 1K & $30$ & $0$ & $0$ & $0.4$ \\\rowcolor{Gray} - 1L & $30$ & $10$ & $-0.6$ & $0.4$ \\\rowcolor{LightGray} - 1M & $5$ & $10$ & $-0.6$ & $0.5$ \\\rowcolor{Gray} - 1N & $5$ & $10$ & $-0.6$ & $0.5$ \\\rowcolor{LightGray} - 1O & $5$ & $10$ & $-0.6$ & $1.0$ \\\rowcolor{Gray} - 1P & $5$ & $5$ & $-0.3$ & $0.5$ \\\rowcolor{LightGray} - 1Q & $5$ & $5$ & $-0.3$ & $0.2$ \\\rowcolor{Gray} - 1R & $0$ & $8$ & $-0.1$ & $0.2$ \\\rowcolor{LightGray} - 1S & $5$ & $-3$ & $0.5$ & $0.8$ \\\rowcolor{Gray} - 1T & $-80$ & $0$ & $0$ & $0.05$ \\ - \thickhline - \multicolumn{5}{l}{Common Parameters} \\\rowcolor{LightGray} - \thickhline - \multicolumn{5}{p{22.5em}}{ - $b = 10\, \Rm{s^{-1}}$, $G/C = 50\, \Rm{s^{-1}}$, - $k_1 = 200\, \Rm{s^{-1}}$, $k_2 = 20\, \Rm{s^{-1}}$, - $\Theta_{\infty} = -0.05\, \Rm{V}$, - $R_1 = 0$, $R_2 = 1$, $E_l = -0.07\, \Rm{V}$, - $V_r = -0.07\, \Rm{V}$, $\Theta_r = -0.06\, \Rm{V}$. - } - \\\thickhline - \end{tabular} - \caption{{\bfseries \sffamily Simulation Parameters} } - \label{table:4} -\end{table} -%% - -\vspace{-1cm} - -%% -\begin{table}[!htbp] - \centering - \begin{tabular}{CCp{28.2em}} - \thickhline - \multicolumn{3}{c}{Model Parameters} \\ \thickhline - Figure & Type & $I_e/C (\Rm{V/s})$ \\ - \thickhline - 1A & \includegraphics[width=0.1\textwidth]{figs/const.pdf} & $1.5$ \\\rowcolor{Gray} - 1B & \includegraphics[width=0.1\textwidth]{figs/const.pdf} & $1 + 10^{-6}$ \\\rowcolor{LightGray} - 1C & \includegraphics[width=0.1\textwidth]{figs/const.pdf} & $2$ \\\rowcolor{Gray} - 1D &\includegraphics[width=0.1\textwidth]{figs/const.pdf} & $1.5$ \\\rowcolor{LightGray} - 1E &\includegraphics[width=0.1\textwidth]{figs/pulse.pdf} & - $1.5 (0.1 \Rm{s}),\, 0 (0.5\Rm{s}),\, 0.5 (0.1\Rm{s}),\, 1 - (0.1\Rm{s}),\, 1.5 (0.1\Rm{s}),\, 0 (0.1 \Rm{s})$ - \\\rowcolor{Gray} - 1F &\includegraphics[width=0.1\textwidth]{figs/pulse.pdf} & $1.5 (0.02 - \Rm{s}),\, 0 (0.18 \Rm{s}),\, -1.5 (0.025 \Rm{s}),\, 0 (0.025 - \Rm{s}),\, 1.5 (0.025 \Rm{s}),\, 0 (0.125 \Rm{s})$ - \\\rowcolor{LightGray} - 1G & \includegraphics[width=0.1\textwidth]{figs/pulse.pdf} & $0 (0.05 - \Rm{s}),\, -3.5 (0.756 \Rm{s}),\, 0 (0.194 \Rm{s})$ \\\rowcolor{Gray} - 1H & \includegraphics[width=0.1\textwidth]{figs/const.pdf} & $2(1 + - 10^{-6})$ \\\rowcolor{LightGray} - 1I & \includegraphics[width=0.1\textwidth]{figs/pulse.pdf} & - \begin{tabular}[x]{@{}c@{}} - $1.5 (0.02 \Rm{s}),\, 0 (0.01 \Rm{s}),\, 1.5 (0.02 \Rm{s}),\, - 0 (0.25 \Rm{s}),\, 1.5 (0.02 \Rm{s}),\, 0 (0.02 \Rm{s}) $\\ - $ 1.5 (0.02 \Rm{s}),\, 0 (0.04 \Rm{s})$ - \end{tabular} - \\\rowcolor{Gray} - 1J & \includegraphics[width=0.1\textwidth]{figs/pulse.pdf} & $1.5 (0.1 - \Rm{s}),\, 1.7 (0.4 \Rm{s}),\, 1.5 (0.1 \Rm{s}),\, 1.7 (0.4 \Rm{s})$ - \\\rowcolor{LightGray} - 1K & \includegraphics[width=0.1\textwidth]{figs/const.pdf} & $-1$ \\\rowcolor{Gray} - 1L & \includegraphics[width=0.1\textwidth]{figs/const.pdf} & $-1$ \\\rowcolor{LightGray} - 1M & \includegraphics[width=0.1\textwidth]{figs/const.pdf} & $2$ \\\rowcolor{Gray} - 1N & \includegraphics[width=0.1\textwidth]{figs/const.pdf} & $1.5$ \\\rowcolor{LightGray} - 1O &\includegraphics[width=0.1\textwidth]{figs/pulse.pdf} & $0 (0.1 - \Rm{s}),\, -3.5 (0.5 \Rm{s}),\, 0 (0.4 \Rm{s})$ \\\rowcolor{Gray} - 1P & \includegraphics[width=0.1\textwidth]{figs/const.pdf} & $2$ \\\rowcolor{LightGray} - 1Q & \includegraphics[width=0.1\textwidth]{figs/pulse.pdf} & $2 (0.015 - \Rm{s}),\, 0 (0.185 \Rm{s})$ \\\rowcolor{Gray} - 1R & \includegraphics[width=0.1\textwidth]{figs/pulse.pdf}& $5 (0.01 - \Rm{s}),\, 0 (0.09 \Rm{s}),\, 5 (0.01 \Rm{s}),\, 0 (0.09 \Rm{s})$ - \\\rowcolor{LightGray} - 1S & \includegraphics[width=0.1\textwidth]{figs/pulse.pdf}& - \begin{tabular}[x]{@{}c@{}} - $5 (0.005 \Rm{s}),\, 0 (0.005 \Rm{s}),\, 4 (0.005 \Rm{s}),\, 0 (0.385 \Rm{s}),\, - 5 (0.005 \Rm{s}),\, 0 (0.045 \Rm{s}) $\\ - $4 (0.005\Rm{s}),\, 0 (0.345 \Rm{s}) $ - \end{tabular} - \\\rowcolor{Gray} - 1T & \includegraphics[width=0.1\textwidth]{figs/pulse.pdf} & $8 (0.002 \Rm{s}),\, 0 (0.048 \Rm{s})$ \\ - \thickhline - \end{tabular} - \caption{{\bfseries \sffamily External current.} This table provides the - external current for each panel in Figure~\ref{fig:1}. There are two types - of external currents, constants and pulses. In the case of pulses the - duration of each pulse is given in seconds along with its intensity. - } - \label{table:5} -\end{table} -%% -\vspace{-2cm} -%% -\begin{table}[!htbp] - \centering - \begin{tabular}{cc} - \thickhline - \multicolumn{2}{c}{Initial Conditions} \\ \thickhline - Variable & Initial Value \\ - \rowcolor{Gray} - $V(t)$ & $-0.07\, \Rm{V}$ / $-0.03\, \Rm{V}$ (Figure 1H) \\ \rowcolor{LightGray} - $\Theta(t)$ & $-0.05\, \Rm{V}$ / $-0.03\, \Rm{V}$ (Figure 1H) \\ \rowcolor{Gray} - $I_1(t)$ & $0.01\, \Rm{V}$ \\ \rowcolor{LightGray} - $I_2(t) $ & $0.001\, \Rm{V}$ \\ \thickhline - \end{tabular} - \caption{{\bfseries \sffamily Initial conditions.} In all simulations - have been used the same initial conditions, except from the one - illustrated in Figure~\ref{fig:1}H.} - \label{table:6} -\end{table} -%% - -\clearpage - -\section{Results}\label{results} - -All three figures from the original article have been successfully replicated. -All the different spiking behaviors of the model are illustrated in -Figure~\ref{fig:1}, where the black solid line indicates the membrane potential -($V(t)$), the red dashed line illustrates the instantaneous threshold potentials -($\Theta(t)$), and the gray line shows the input to the neuron ($I_e/C$). -The $x$-axis scales in all panels are exactly the same as in the original -paper (indicating the total simulation time ($t_f$), while the $y$-axis scale -differs from the one in the original paper. In this work the $y$-axis scale -is the same same for all the subplots ($[-95, -25]\, \Rm{mV}$), except for -panels G and O ($[-145, -25]\, \Rm{mV}$). - -Figures~\ref{fig:2} and~\ref{fig:3} depict the phase space of the phasic -spiking ($V(t)$ and $\Theta(t)$) and phasic bursting ($V(t)$, -$I_1(t)$, and $I_2(t)$). In both figures the blue curves and the black dots -indicate the trajectory of the system and spike events, respectively. -In Figure~\ref{fig:2} the gray arrows show the evolution of the system -(vector field of the system). Figure~\ref{fig:3} has a different orientation -from the original one but both illustrate the same trajectories and spike -events of the system. -All the figures express the same qualitative behavior as the original -figures in~\cite{mihalas:2009}. - -\begin{figure}[htpb!] - \centering - \includegraphics[width=0.9\textwidth]{figs/Figure01.pdf} - \caption{{\bfseries \sffamily Neural responses of MNN.} Black solid lines - indicate the membrane potential ($V(t)$), the red dashed lines show the - threshold potentials ($\Theta(t)$), and the gray lines the external - currents applied on each case. - {\bfseries \sffamily A} tonic spiking, - {\bfseries \sffamily B} class $1$, - {\bfseries \sffamily C} spike frequency adaptation, - {\bfseries \sffamily D} phasic spiking, - {\bfseries \sffamily E} accommodation, - {\bfseries \sffamily F} threshold variability, - {\bfseries \sffamily G} rebound spike, - {\bfseries \sffamily H} class $2$, - {\bfseries \sffamily I} integrator, - {\bfseries \sffamily J} input bistability, - {\bfseries \sffamily K} hyperpolarization induced spiking, - {\bfseries \sffamily L} hyperpolarization induced bursting, - {\bfseries \sffamily M} tonic bursting, - {\bfseries \sffamily N} phasic bursting, - {\bfseries \sffamily O} rebound burst, - {\bfseries \sffamily P} mixed mode, - {\bfseries \sffamily Q} afterpotentials, - {\bfseries \sffamily R} basal bistability, - {\bfseries \sffamily S} preferred frequency, - {\bfseries \sffamily T} spike latency.} - \label{fig:1} -\end{figure} - -\begin{figure}[htpb!] - \centering - \includegraphics[width=0.6\textwidth]{figs/Figure02.pdf} - \caption{{\bfseries \sffamily Phase space of phasic spiking.} Blue - solid lines indicate the trajectories of the model in the phase spiking - behavior (Figure~\ref{fig:1}D). The dashed line corresponds to $V(t) = - \Theta(t)$, and the black dots represent spike events. The parameters for - this simulation are the same as in Figure~\ref{fig:1}D.} - \label{fig:2} -\end{figure} - -\begin{figure}[htpb!] - \centering - \includegraphics[width=0.8\textwidth]{figs/Figure03.pdf} - \caption{{\bfseries \sffamily Phase space of phasic bursting.} Blue solid - lines represent the trajectories of the system and the black dots indicate - spiking events. The parameters for this simulation are the same as in - Figure~\ref{fig:1}N.} - \label{fig:3} -\end{figure} - -\section{Conclusion}\label{conclusion} - -All figures in~\textcite{mihalas:2009} have been successfully replicated -with high fidelity. Overall, the whole reproducing process was smooth and -without obscure points since most of the parameters are provided in the -original article. Only the time intervals for which the external current is -applied to the model and the initial conditions are not provided explicitly. -Therefore, we had to extract that information from figure $1$ of the original -article. To conclude, the -article~\cite{mihalas:2009} has been successfully reproduced without any -discrepancy. - -{\sffamily \small - \printbibliography[title=References] -} -\end{document}