Generalized Carnevale-Hines algorithm (van Elburg and van Ooyen 2009)

 Download zip file   Auto-launch 
Help downloading and running models
Demo illustrating the behaviour of the integrate-and-fire model in the parameter regime relevant for the generalized event-based Carnevale-Hines integration scheme. The demo includes the improved implementation of the IntFire4 mechanism.
1 . van Elburg RA, van Ooyen A (2009) Generalization of the event-based Carnevale-Hines integration scheme for integrate-and-fire models. Neural Comput 21:1913-30 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Synapse;
Brain Region(s)/Organism:
Cell Type(s): Abstract integrate-and-fire leaky neuron;
Gap Junctions:
Simulation Environment: NEURON;
Model Concept(s): Simplified Models;
Implementer(s): van Elburg, Ronald A.J. [R.van.Elburg at];
Authors:    Original (taum > taui2 > taui1 > taue)   :   M. Hines and N.T. Carnevale
            Improved (taui2 > taue and taui2 > taui1):   R.A.J. van Elburg

Artificial cell with fast exponential decay excitatory current and
slower alpha function like inhibitory current and arbitrary membrane time constant.
Fires when membrane state = 1. On firing, only the membrane state returns to 0

Although the four states, e, i1, i2, m are available, plotting will be
more pleasing if one uses the function E, I, and M

Fast excitatory current, E(t), has single exponential decay with time constant, taue.

Slower inhibitory current, I2(t), is alpha function like and has two time contants,
taui1 and  taui2.

The leaky integrator membrane has time constant taum.
The total current is the input to this integrator.

Cell fires when state m passes 1
and after firing, m = 0.

Require  taui2 > taue and  taui2 > taui1
or in other words ki1 > ki2 and ke > ki2 

States are normalized so that an excitatory weight of 1 produces
a maximum e of 1 and a maximum m of 1
Also an inhibitory weight of -1 produces a maximum i2 of -1
and a maximum m of -1.

Basic equations:
 dE(t)/dt  = -ke*E(t)
 dI1(t)/dt = -ki1*I1(t)
 dI2(t)/dt = -ki2*I2(t) + ai1*I1(t)
 dM(t)/dt  = -km*M(t) + ae*E(t) + ai2*I2(t)

The initial conditions are e, i1, i2, and m

The analytic solution is

E(t) = e*exp(-ke*t)
I1(t) = i1*exp(-ki1*t)
I2(t) = i2*exp(-ki2*t) + bi1*i1*(exp(-ki2*t) - exp(-ki1*t))
M(t) = m * exp(-km*t)
	+ be*e*(exp(-km*t) - exp(-ke*t))
	+ bi2*i2*(exp(-km*t) - exp(-ki2*t))
	+ bi2*bi1*i1 * (exp(-km*t) - exp(-ki2*t))
	- bi2*bi1*i1*(ki2 - km)/(ki1 - km)*(exp(-km*t) - exp(-ki1*t))

The derivation of a lower bound on the first passage time based on Newton 
iteration is possible if we assume that taue<=taui2, i.e. that the 
inhibition outlasts excitation. The validity of the Newton iteration for setting 
a lower bound on threshold passage time follows from a physical analysis of the 
different contributing currents. The parameters taui1 are involved in controlling 
the time course of the growth of the inhibitory current. Therefore the taui1
associated current contributes to a growth of inhibition and can be ignored when trying to find a 
lower bound for the threshold passage time because it contributes only to its delay. 
The other contributions to the membrane potential change are the 
leak current associated with the membrane time constant taum and the 
exponentially decaying (parts) of the synaptic currents. The leak current is 
maximal close to threshold and can therefore only grow when approaching 
threshold. So if we use the present value in a calculation of threshold passage 
time while we are approaching threshold we will underestimate threshold passage 
time. The exponentially decaying (parts) of the synaptic currents consist of an 
excitatory and an inhibitory part, if we assume taue<taui2 we can see 
that the inhibitory parts outlast the excitatory currents and therefore if we 
assume that m changes according to the present values of these currents we 
underestimate threshold passage time. Because the sum of these currents is m'=
dm/dt and Newton iteration states that m(t)~m(t_0)+m'*(t-t_0) we find that 
Newton iteration underestimates threshold passsage time. If the membrane 
potential moves away from threshold toward rest, the excitatory current is 
smaller then leak current and inhibitory currents combined, because it decays 
faster then the inhibitory current it will also at future times not be able to 
overcome the leak current at the present membrane potential and hence not be 
able to rise above it and reach threshold.

A formal proof based on analysis of the exact solution of this mechanism is possible and can be found in:
    R.A.J. van Elburg and A. van Ooyen, `Generalization of the event-based Carnevale-Hines integration scheme
for integrate-and-fire models', Neural Computation, July 2009, Vol. 21, No. 7: 1913-1930. (doi:10.1162/neco.2009.07-08-815 )
and is based on a formal proof for the original version which can be found in:
    Carnevale, N.T.  and Hines, M.L., `The NEURON Book',Cambridge University Press,Cambridge, UK (2006).

	RANGE taue, taui1, taui2, taum, e, i1, i2, m, ae, ai2, ai1
	RANGE nself, nexcite, ninhibit
	GLOBAL eps, taueps

	taue = 5 (ms)      <0,1e9>
	taui1 = 10 (ms)    <0,1e9>
	taui2 = 20 (ms)    <0,1e9>
	taum = 50 (ms)     <0,1e9>
	ib = 0
	eps = 1e-6         <1e-9,0.01>
	taueps = 0.01      <1e-9,1e9>

	e i1 i2 m
	enew i1new i2new mnew
	t0 (ms)
	nself nexcite ninhibit

	ke (1/ms) ki1 (1/ms) ki2 (1/ms) km (1/ms)
	ae (1/ms) ai1 (1/ms) ai2 (1/ms)
	be bi1 bi2
	a b
	tau_swap (ms)
	flag (1)

PROCEDURE newstates(d(ms)) {
	LOCAL ee, ei1, ei2, em
	ee = exp(-ke*d)
	ei1 = exp(-ki1*d)
	ei2= exp(-ki2*d)
	em = exp(-km*d)
	enew = e*ee
	i1new = i1*ei1
	i2new = i2*ei2 + bi1*i1*(ei2 - ei1)
	mnew = m*em
		+ be*e*(em - ee)
		+ (bi2*i2 + a*i1)*(em - ei2)
		- b*i1*(em - ei1)

	newstates(t - t0)
	M = mnew

	newstates(t - t0)
	E = ae*enew

	newstates(t - t0)
	I = ai2*i2new

PROCEDURE update() {
	e = enew
	i1 = i1new
	i2 = i2new
	m = mnew
	t0 = t

PROCEDURE fixprecondition() {
	: and force assertion for correctness of algorithm
	: Preconditions:
    : taue  < taui2 
    : taui1 < taui2
    : To avoid division by zero errors, the need for alpha function [x*exp(-x)] 
    : solutions  and poor convergence we also impose
    : fabs(taux-tauy) >= taueps
    : The checks on the preconditions can lead to 3 consecutive shifts in taum 
    : and a smaller number of shifts in the other parameters to prevent this 
    : shift from bringing taum at or below zero we need to ensure 
    : that we keep sufficient distance from zero.
    if(taui2 < 4*taueps){
    if(taui1 < 3*taueps){
    if(taue < 2*taueps){
    : taue  < taui2  
    if (taue > taui2) { 
        taue = taui2 - taueps 
        printf("Warning: Adjusted taue from %g  to %g  to ensure taue < taui2\n",tau_swap,taue)        
    } else if (taui2-taue < taueps){
        taue = taui2 - taueps 

    : taui1 < taui2, after this taui2 is fixed
	if (taui1 > taui2) {
        printf("Warning: Swapped taui1 and taui2\n")   
    : Avoid division by zero errors and poor convergence and impose
    : fabs(taux-tauy) >= taueps
    if (taui2-taui1 < taueps){          :  taui1 < taui2 --> taui2-taui1 is positive
        taui1 = taui2 - taueps 

    if (taum <= taui2) {
        if (taui2 -taum < taueps){      :  (taum <= taui2) --> taui2 -taum is positive definite
        if (fabs(taui1 -taum) < taueps){
        if (fabs(taui1 -taum) < taueps){
            if(taui1 -taum < 0){
            } else{
        if (fabs(taue -taum) < taueps){
            if(taue -taum < 0){
            } else{
        if (fabs(taui1 -taum) < taueps){
    } else if (taum-taui2 < taueps){    :  (taum > taui2) --> taum -taui2 is positive 

PROCEDURE factors() {
	ke=1/taue  ki1=1/taui1  ki2=1/taui2  km=1/taum

	: normalize so the peak magnitude of m is 1 when single e of 1
	tp = log(km/ke)/(km - ke)
	be = 1/(exp(-km*tp) - exp(-ke*tp))
	ae = be*(ke - km)
        :printf("INITIAL be=%g tp=%g \n", be, tp)
    : normalize so the peak magnitude of i2 is 1 when single i of 1
	tp = log(ki2/ki1)/(ki2 - ki1)
	bi1 = 1/(exp(-ki2*tp) - exp(-ki1*tp))
	ai1 = bi1*(ki1 - ki2)
    :printf("INITIAL bi1=%g tp=%g \n", bi1, tp)
    : normalize so the peak magnitude of m is 1 when single i of 1
	: first set up enough so we can use newstates()
	e = 0
	i1 = 1
	i2 = 0
	m = 0
	bi2 = 1
	ai2 = bi2*(ki2 - km)
	a = bi2*bi1
	b = a*(ki2 - km)/(ki1 - km)
    :find the 0 of dm/dt
	tp = search()
    : now compute normalization factor and reset constants that depend on it
	bi2 = 1/mnew
	ai2 = bi2*(ki2 - km)
	a = bi2*bi1
	b = a*(ki2 - km)/(ki1 - km)
	: now newstates(tp) should set mnew=1
    :printf("INITIAL bi2=%g tp=%g mnew=%g\n", bi2, tp, mnew)
	i1 = 0

FUNCTION deriv(d(ms)) (/ms2) { : proportional, not exact derivative but sign true (provided ki1 > ki2)
    deriv= ( - km *exp( - d*km ) + ki2*exp( - d*ki2))/(ki2 - km) -(( - km*exp( - d*km) + ki1*exp( - d*ki1)))/(ki1 - km )

FUNCTION search() (ms) {
	LOCAL x, t1, t2
	: should only do this when tau's change
    : exponential search for two initial t values for the chord search one factor
    : of 10 separated, with the low value t1 before (deriv(t1) < 0) and the high
    : value t2 after (deriv(t2) > 0) the extremal reached by m due to an isolated
    : i1 current. For this calculation the i1 current is taken to be depolarizing
    : and therefore the extremum is actually a maximum. During the simulation i1 is 
    : constrained to be hyperpolarizing and then the extremum will be a minimum 
    : occuring at the same location.
    if(deriv(t1) < 0  ){
        while ( deriv(t1) < 0 && t1>1e-9 ){
        if (deriv(t1) < 0) { 
    		printf("Error wrong deriv(t1): t1=%g deriv(t1)=%g\n", t1, deriv(t1))
            search = 1e-9
        while (deriv(t2) > 0 && t2<1e9 ){
    	if (deriv(t2) > 0) { 
    		printf("Error wrong deriv(t2): t2=%g deriv(t2)=%g\n", t2, deriv(t2))
    		search = 1e9
    : printf("search  t1=%g x1=%g t2=%g x2=%g\n", t1, deriv(t1), t2, deriv(t2))
    : chord search for the  maximum in m(t) 
    while (t2 - t1 > 1e-6 && flag==0) {
		search = (t1+t2)/2
		x = deriv(search)
		if (x > 0) {
			t1 = search
			t2 = search
        :printf("search  t1=%g x1=%g t2=%g x2=%g\n", t1, deriv(t1), t2, deriv(t2))

	e = 0
	i1 = 0
	i2 = 0
	m = 0
	t0 = t
	net_send(firetimebound(), 1)


    :printf("event %g t=%g e=%g i1=%g i2=%g m=%g\n", flag, t, e, i1, i2, m)
	if (m > 1-eps) { : time to fire
		m = 0
	if (flag == 1) { :self event
		nself = nself + 1
		net_send(firetimebound(), 1)
		if (w > 0) {
			nexcite = nexcite + 1
			e = e + w
			ninhibit = ninhibit + 1
			i1 = i1 + w
        :printf("w=%g e=%g i1=%g\n", w, e, i1)
		net_move(firetimebound() + t)

FUNCTION firetimebound() (ms) {
	LOCAL slope
	slope = -km*m + ae*e + ai2*i2
	if (slope <= 1e-9) {
		firetimebound = 1e9
		firetimebound = (1 - m)/slope

Loading data, please wait...