Python: Writing a small neural network with matrices

Question

I'm trying to simulate a two neuron network in python. It's simple enough to do writing separate equations for each neuron, but since I would like to generalize the code a bit more so that it's easy to increase the number of neurons without rewriting the equations over and over. The two neural network equations are the following:

Basically, I have two Hodgkin-Huxley neurons that are coupled together through the last term in the voltage equations. So what I would like to do is to write a code in such a way so that I can expand the network easily. To do so, I created a vector V for the neuron voltages: [V1, V2], and create a vector X where X models the gating variables m,h, and n. So I would have X = [[m1, h1, n1], [m2, h2, n2]]. However, currently the code is not producing spiking but rather appears the voltage just blows up to infinity. That suggests there's a problem with the gating variables X. The gating variables m, h, and n should always be between 0 and 1, so it looks as if the gating variables are just reaching 1 and staying there which would cause the voltage the blow up. I'm not sure what's causing them to just stay at 1. The code is running and not producing any errors.

import scipy as sp
import numpy as np
import pylab as plt

NN=2 #Number of Neurons in Model

dt=0.01
T = sp.arange(0.0, 1000.0, dt)
nt = len(T)  # total number of time steps

    # Constants
gNa = 120.0 # maximum conducances, in mS/cm^2
gK  =  36.0
gL  =   0.3
ENa =  50.0 # Nernst reversal potentials, in mV
EK  = -77
EL  = -54.387

#Coupling Terms
Vr = 20
w = 1
e11 = e22 = 0
e12 = e21 = 0.1
E = np.array([[e11, e12], [e21, e22]])

#Gating Variable Transition Rates
def alpham(V): return (0.1*V+4.0)/(1.0 - sp.exp(-0.1*V-4.0))
def betam(V):  return 4.0*sp.exp(-(V+65.0) / 18.0)
def alphah(V): return 0.07*sp.exp(-(V+65.0) / 20.0)
def betah(V):  return 1.0/(1.0 + sp.exp(-0.1*V-3.5))
def alphan(V): return (0.01*V+0.55)/(1.0 - sp.exp(-0.1*V-5.5))
def betan(V):  return 0.125*sp.exp(-(V+65.0) / 80.0)
def psp(V,s): return ((5*(1-s))/(1+sp.exp(-(V+3)/8)))-s

#Current Terms
def I_Na(V,x): return gNa * (x[:,0]**3) * x[:,1] * (V - ENa) #x0=m, x1=h, x2=n
def I_K(V,x): return gK * (x[:,2]**4) * (V - EK)
def I_L(V): return gL * (V - EL)
def I_inj(t): return 10.0

#Initial Conditions
V = np.zeros((nt,NN)) #Voltage vector
X = np.zeros((nt,NN,3)) #Gating Variables m,h,n (NN neurons x 3 gating variables)
S = np.zeros((nt,NN)) #Coupling term

dmdt = np.zeros((nt,NN))
dhdt = np.zeros((nt,NN))
dndt = np.zeros((nt,NN))

V[0,:] = -65.0
X[0,:,0] = alpham(V[0,:])/(alpham(V[0,:])+betam(V[0,:])) #m
X[0,:,1] = alphah(V[0,:])/(alphah(V[0,:])+betah(V[0,:])) #h
X[0,:,2] = alphan(V[0,:])/(alphan(V[0,:])+betan(V[0,:])) #n

alef = 5.0/(1+sp.exp(-(V[0,:]+3)/8.0))
S[0,:] = alef/(alef+1)

dmdt[0,:] = alpham(V[0,:])*(1-X[0,:,0])-betam(V[0,:])*X[0,:,0]
dhdt[0,:] = alphah(V[0,:])*(1-X[0,:,1])-betah(V[0,:])*X[0,:,1]
dndt[0,:] = alphan(V[0,:])*(1-X[0,:,2])-betan(V[0,:])*X[0,:,2]

#Euler-Maruyama Integration
for i in xrange(1,nt):
    V[i,:]= V[i-1,:]+dt*(I_inj(i-1)-I_Na(V[i-1,:],X[i-1,:])-I_K(V[i-1,:],X[i-1,:])-I_L(V[i-1,:]))+dt*((Vr-V[i-1,:])/w * np.dot(E,S[i-1,:]))    

    #Gating Variable
    dmdt[i,:] = dmdt[i-1,:] + alpham(V[i-1,:])*(1-X[i-1,:,0])-betam(V[i-1,:])*X[i-1,:,0]
    dhdt[i,:] = dhdt[i-1,:] + alphah(V[i-1,:])*(1-X[i-1,:,1])-betah(V[i-1,:])*X[i-1,:,1]
    dndt[i,:] = dndt[i-1,:] + alphan(V[i-1,:])*(1-X[i-1,:,2])-betan(V[i-1,:])*X[i-1,:,2]
    z = np.array([dmdt[i-1,:],dhdt[i-1,:],dndt[i-1,:]]).T

    #Gating Variable Constraints (0<m,h,n<1)
    X[i,:,0] = max(0,min(X[i,:,0].all(),1))
    X[i,:,1] = max(0,min(X[i,:,1].all(),1))
    X[i,:,2] = max(0,min(X[i,:,2].all(),1))

    #Update Gating Variables
    X[i,:,:]= X[i-1,:,:]+dt*(z)

    #Coupling Term
    S[i,:] = S[i-1,:]+dt*psp(V[i-i,:],S[i-1,:])

V1 = V[:,0]
V2 = V[:,1]

plt.plot(T,V1, 'red')
plt.plot(T,V2, 'blue')

plt.show()

I purposefully am not using odeint to integrate my ODEs because I would like to add stochasticity to the equations later and therefore want to use the Euler method above. Anyway, if anyone can help me figure out how to fix this code so that the expected spiking behavior occurs, that would be fantastic. Thank you!

I would hesitate to tag this with `neural-network` if you are talking about an HH model, which is a biophysical model. — juanpa.arrivillaga, Mar 16 '17 at 19:18
I recommend getting individual pieces of the code to work first, then adding complexity in step wise fashion. Eg consider getting just the passive current working for one neuron, then get spiking for one neuron, then add passive current of second neuron, then spiking behavior for both. Right now the problem could be with the equations or the integration code, and getting things working in step wise fashion should make debugging tractable. — Justas, Mar 16 '17 at 23:19

score 1 · Answer 1 · answered Mar 21 '17 at 20:23

1

Check your input current and also your conductances. If you write your code according to the modernized formalism, it will make your life easier as well, that is dm/dt = (m_inf - m)/tau. Specifically, though, your gating variable integrations aren't working. You're not updating them properly. Check for missing timestep math.

answered Mar 21 '17 at 20:23

Alec Hoyland

11
1

Thanks for the help! It turns out the equations I used for the dmdt, dhdt, and dndt weren't updating correctly. It's fixed now! – Brenton Mar 24 '17 at 03:22

score 1 · Answer 2 · answered Aug 17 '19 at 11:04

Here is what I did to couple to neuron. You can find more details on github : https://www.github.com/nosratullah/HodgkinHuxely

import numpy as np

def HodgkinHuxley(I,preVoltage):

    #holders
    v = []
    m = []
    h = []
    n = []
    s = [] #synaptic channel
    Isynlist = []
    dt = 0.05
    t = np.linspace(0,10,len(I))

    #constants
    Cm = 1.0 #microFarad
    ENa=50 #miliVolt
    EK=-77  #miliVolt
    El=-54 #miliVolt
    E_ampa = 0 #miliVolt
    g_Na=120 #mScm-2
    g_K=36 #mScm-2
    g_l=0.03 #mScm-2
    g_syn = 0.3
    t_d = 2 #ms Decay time
    t_r = 0.4 #ms Raise time
    Tij = 0 #ms time delay
    #Define functions
    def alphaN(v):
        return 0.01*(v+50)/(1-np.exp(-(v+50)/10))

    def betaN(v):
        return 0.125*np.exp(-(v+60)/80)

    def alphaM(v):
        return 0.1*(v+35)/(1-np.exp(-(v+35)/10))

    def betaM(v):
        return 4.0*np.exp(-0.0556*(v+60))

    def alphaH(v):
        return 0.07*np.exp(-0.05*(v+60))

    def betaH(v):
        return 1/(1+np.exp(-(0.1)*(v+30)))

    def H_pre(preV):
        return 1 + np.tanh(preV)

    #Initialize the voltage and the channels :
    v.append(-60)
    m0 = alphaM(v[0])/(alphaM(v[0])+betaM(v[0]))
    n0 = alphaN(v[0])/(alphaN(v[0])+betaN(v[0]))
    h0 = alphaH(v[0])/(alphaH(v[0])+betaH(v[0]))
    #s0 = alpha_s(preVoltage[0])/(alpha_s(preVoltage[0])+beta_s(preVoltage[0]))
    s0 = 0

    #t.append(0)
    m.append(m0)
    n.append(n0)
    h.append(h0)
    s.append(s0)

    if (type(preVoltage)==int):
        preVoltage = np.zeros(len(I)) #check if preVoltage exists or not

    #solving ODE using Euler's method:
    for i in range(1,len(t)):
        m.append(m[i-1] + dt*((alphaM(v[i-1])*(1-m[i-1]))-betaM(v[i-1])*m[i-1]))
        n.append(n[i-1] + dt*((alphaN(v[i-1])*(1-n[i-1]))-betaN(v[i-1])*n[i-1]))
        h.append(h[i-1] + dt*((alphaH(v[i-1])*(1-h[i-1]))-betaH(v[i-1])*h[i-1]))
        s.append(s[i-1] + dt * (H_pre(preVoltage[i-1])*((1-s[i-1]/t_r))-(s[i-1]/t_d)))
        gNa = g_Na * h[i-1]*(m[i-1])**3
        gK = g_K*n[i-1]**4
        gl = g_l
        INa = gNa*(v[i-1]-ENa)
        IK = gK*(v[i-1]-EK)
        Il = gl*(v[i-1]-El)
        #Synaptic Current comes from the pre neuron
        Isyn = -0.1 * s[i-1] * (v[i-1] - E_ampa)
        #making a list for Synaptic currents for plotting
        Isynlist.append(Isyn)
        v.append(v[i-1]+(dt)*((1/Cm)*(I[i-1]-(INa+IK+Il+Isyn))))

    return v,Isynlist


length = 10000
zeroVoltage = np.zeros(length)
#inputCurrent = np.ones(length)*4
#inputCurrent[1000:2000] = 10
#inputCurrent[2000::] = 3
#inputCurrent2 = np.ones(length)*5.46
noisyInput1 = np.ones(length)*7 + np.random.normal(0,3,length)
noisyInput2 = np.ones(length)*5 + np.random.normal(0,3,length)
preVoltage,preSyn = HodgkinHuxley(noisyInput1,zeroVoltage)
postVoltage,postSyn = HodgkinHuxley(noisyInput2,preVoltage)
plt.figure(figsize=(15,10))
plt.plot(preVoltage,'r',label='pre synaptic voltage');
#plt.plot(postVoltage,'b');
plt.plot(postSyn,'g-.',label='synaptic voltage');
plt.plot(postVoltage,'b',label='post synaptic voltage');
#plt.xlim(xmin=0)
plt.ylim(ymax=50)
plt.legend(loc='upper left');
plt.savefig('coupledNeuron.png',dpi=150)
plt.show()

score 0 · Answer 3 · answered Mar 16 '17 at 20:42

Since you have

\dot(x)_j = f(x_j) + \sum_j C_ij g(x_j, x_i)

you can also write your ride hand side like that. x_j is a vector, e.g. (v, m, h, n s).

This oscillator example could be a starting point:

x.shape is n_onsite_variables, n_oscillators

def f(x):
    return np.array([x[1, :], -x[0, :]])


def g(xi, xj):
    return xi[0] - xj[0]

def rhs(x, t, c):
    coupling = np.array([sum(cij*g(xi,xj) for cij, xj in zip(ci, x.T))
                                          for ci, xi in zip(c, x.T)])
    coupling = np.outer(np.arange(2), coupling) # coupling in x''

    return f(x) + coupling

x0 = np.random.random(size=(2, 3))
>>> array([[ 0.74386362,  0.85799588,  0.70501992],
   [ 0.65903405,  0.41575505,  0.93166973]])

def ring(n):
    c = np.eye(n, k=1) + np.eye(n, k=-1)
    c[0, -1] = 1
    c[-1, 0] = 1
    return c

c = ring(3)
x1 = rhs(x0, 0, c)
>>> array([[ 0.65903405,  0.41575505,  0.93166973],
    [-0.81915217, -0.59088767, -0.89683958]])

I am sure this can be improved. Especially if you want a more general coupling.

Python: Writing a small neural network with matrices

3 Answers3