udion / Neurapse

3rd Gen Neural Networks

Current Deep Learning methods (2nd Gen) set very impressive state of the art results, although the building blocks such as convolutions etc are biologically inspired they still are not as efficient as computations happening at many biological neural networks.

Spiking Neural Networks (SNNs) are called 3rd Gen and they attempt to simulate biological neural networks closely. Broadly the framework consists of Spikes, Neurons, Synapses, Networks. IBM launched TrueNorth chip in 2014, Intel announced Loihi in 2017 both are attempts to do neuromorphic computations efficiently on chip.

Neurapse is a package in python which implements some of the fundamental blocks of SNN and is written in a manner so that it can easily be extended and customized for simulation purposes.

Biological neural networks have been studied vastly since the early 19th century. Several neuronal models have been proposed and used in simulations, showing close resemblance of biological neural networks. To study more about Biological neural networks, visit Prof. Gerstner's course on Neuronal Dynamics. This package is an introductory framework for getting started with computational neuroscience.

(This project was started as part of assignments in the course EE 746: Neuromorphic Engineering (Instructor: Prof. Udayan Ganguly) at IIT-Bombay)

Supports

• Neurons : Hodgkin Huxley (HH), Adaptive Exponential Integrate and Fire (AEF) , Leaky integrate and Fire (LIF), IZHIKEVICH
• Synapses: Constant Synapse (No STDP), Plastic Synapses (2 kinds of STDP)
• Networks: Feed Forward using LIF, Dynamic Random Networks(DRN)

Requirements

• Python 3.6+
• numpy
• matplotlib

How to use the framework?

clone or fork this repository by git clone https://github.com/udion/Neurapse. Make sure you have the dependencies given in the requirements.txt (So far it only requires numpy, matplotlib)

Some examples are given with the comments in examples*.py.

Importing a neuron (or jump to Network example)

import numpy as np
import matplotlib.pyplot as plt

import Neurapse.Neurons as Neu #importing Hodgkin-Huxley neuron
import Neurapse.utils.CURRENTS as Cur #to generate currents (Square pulse in this example)

Neurons in SNN frameworks are described using certain parameters such as Capacitance, Resting potentials, Time constants etc

Hodgkin-Huxley neuron in particular has the following parameters :

C = 1e-6
E_Na = 50e-3
E_k = -77e-3
E_l = -55e-3
g_Na = 120e-3
g_k = 36e-3
g_l = 0.3e-3
I0 = 15e-6

Neuron = Neu.HH(C, E_Na, E_k, E_l, g_Na, g_k, g_l)

T = 30e-3 # Time in seconds
delta_t = 1e-5 # quanta in which time updates in seconds
n_t = int(5*T//delta_t)+1 # Total time of simulation is 5*T, hence number of time-steps is n_t

Let's generate the input current and visualise it

Sq1 = Cur.SQUARE_PULSE(t_start=6000, t_end=9000, T=n_t)
I = Sq1.generate() # normalised current i.e maximum amplitude is 1 unit, of shape [1 X T]
I = I0*I # I is input current to the neuron in micro-Ampere 

plt.plot(I)
plt.xlabel('time')
plt.ylabel('applied current')
plt.show() #graph shown below

Let's pass this current to the Neuron (hodgkin-huxley defined above). Neurons have a .compute() function which will give the response of the neuron, given intial condition and input current

# initial conditions of neurons will be of shape [num_neuron X 1], in this case num neurons
# These are the initial conditions of Hodgkin-Huxley, checkout the reading material
# to figure out how to get these, for now enjoy the ride :P
V0 = -0.06515672*np.ones((1,1))
h0 = 0.60159082*np.ones((1,1))
m0 = 0.05196212*np.ones((1,1))
n0 = 0.31527801*np.ones((1,1))

# response of the HH neuron
# V is the membrane potential, m/h/n are the current parameters of HH
V, h, m, n = Neuron.compute(V0, h0, m0, n0, I, delta_t)

# we can get Sodium/Pottasium channel currents using h,m,n
i_Na = g_Na*(m**3)*h*(V-E_Na)
i_k = g_k*(n**4)*(V-E_k)
i_l = g_l*(V-E_l)

We can visualise the responses, say V, i_Na (Sodium channel current), i_k(potassium channel current), leaky current

We can similarly use other neurons (HH models the ion channel currents very well, but is expensive in computation due to coupled differential equations of channel currents). Adaptive Exponential Integrate and Fire (AEF) neuron is one such model which is not as complex as HH but by tweaking the parameters one can get different behaviour of the neurons. exampleAEF.py shows how to use AEF neuron, some responses are

Importing a Network

Fully connected Network with constant weight Synapse (No STDP)

NNetwork_Const class uses LIF neurons to build a fully connected SNN as shown in the diagram. To do so one has to specify the fanout, initial weights, synaptic time delay

import numpy as np
import matplotlib.pyplot as plt
import Neurapse.utils.CURRENTS as Cur
from Neurapse.Networks import NNetwork_Const

Fanout = [[0,1],[0,1],[0,1]]
W = [[3000,3000],[3000,3000],[3000,3000]]
Tau = [[1e-3,8e-3],[5e-3,5e-3],[9e-3,1e-3]]  

Net = NNetwork_Const(Fanout, W, Tau, 3, 2) #defines the network

Since there are 3 input neurons we will make Input currents of shape [3 X n_t] and pass it to the network

I_pre = np.array([
    50e-9*Cur.SQUARE_PULSE(0, 10, 10000).generate(),
    50e-9*Cur.SQUARE_PULSE(40, 50, 10000).generate(),
    50e-9*Cur.SQUARE_PULSE(80, 90, 10000).generate(),
]).reshape(3,-1)

print(I_pre.shape)
V_pre_response, V_post_response, I_sy_list, I_post = Net.compute(I_pre, 1e-4)

Now we can see the response of the 2 post synaptic neurons

 for i in range(2):
    plt.plot(V_post_response[i,:], label='post-{}'.format(i))
plt.legend()
plt.xlabel('time')
plt.ylabel('V')
plt.title('response of the post neurons')

This shows that for the given configuration, post-synaptic neuron 1 spikes and other does not spike, hence this configuration is suitable for identifying the given input pattern

Dynamical Random network with plastic synapses (STDP)

example_DRN.py shows how to use the DRN classes. To read more about the dynamic random classes refer to Polychronization: Computation with Spikes

There are two classes, namely DRN_Const and DRN_Plastic for building a random network of neurons having constant weight synapses and plastic synapses respectively. As for the previous case, the fanout, initial weights and synaptic time delays have to be specified. Here, first N_exci neurons from a list [0, 1, 2, ..., N-1] (indices of neurons) are excitatory neurons and the remaining N_inhi are inhibitory neurons. The excitatory neurons can connect to any other neuron in the pool, while the inhibitory neurons synapse only to other excitatory neurons. Each neuron communicates to a connect_frac * N of unique neurons in the network. As an example, a random network with 20 neurons is shown below. Note, the red edges show inhibitory synapses and blue ones show excitatory synapses.

The raster plot for a dynamic random network (N = 500, T = 2000 ms) changing the synaptic weights adaptively according to modified STDP rule is shown below.

Want to customize or contribute?

Neurapse contains:

• Neurons.py which has different classes of neurons (you can add more!)
• Synapses.py which has a few synapses implementing different STDP mechanisms (you can add more!)
• Networks.py shows how to put together neurons and Synapses to build a network
• utils has various functions to generate currents/spikes etc

Authors

• @suyash67
• @udion

Feel free to submit pull requests