R. Bogacz delivers a detailed and beautifully made tutorial on a subject that can be very difficult to understand, Variational Bayes, as seen from Karl Fristons perspective; Namely invoking the Free-Energy principle to motivate Active Inference. In the last decade, Active Inference has gained traction with the wider neuroscientific community, and recently Karl was measured to be the most influential neuroscientist in the modern era.
I use the same notation as in R. Bogacz. The code implements and refers to equations in the paper, and network graphs were provided by Bogacz himself.
A simple organism is trying to infer the size of a food item. The only source of noisy information is one photoreceptor that signals the light reflected from this item, we denote this . The non-linear function that relates size to photosensory input is assumed to be . We assume that this signal is normally distributed with mean and variance .
We can write of the the likelihood function (probability of a size given a signal ) as
is the normal distribution with mean and variance .
Through learning or evolutionary filtering, the agent has been endowed with priors on the expected size of food items, and therefore expects sizes of food items to normally distributed with mean and where the subscript stands for prior. Formally
To compute the exact distribution of sensory input we can formulate the posterior using Bayes theorem
where the denominator is
and sum the whole range of possible sizes.
The following code implements such an exact solution and plots it.
import numpy as np import seaborn as sns import matplotlib.pyplot as plt from scipy.stats import norm sns.set(style="white", palette="muted", color_codes=True) %matplotlib inline
# non-linear transformation of size to perceived sensory input e.g. g(phi) def sensory_transform(input): sensory_output = np.square(input) return sensory_output
The reason we explicitly define is that we might want to change it later. For now we assume a simple non-linear relation . The following snippet of code assumes values of and plots the posterior distribution.
def exact_bayes(): # variabels v = 2 # real size of item sigma_u = 1 # standard deviation of noisy input v_p = 3 # mean of prior sigma_p = 1 # variance of prior / sensory noise s_range = np.arange(0.01,5,0.01) # range of sensory input s_step = 0.01 # step size # exact bayes (equation 4) numerator = (np.multiply(norm.pdf(s_range,v_p,sigma_p),# prior norm.pdf(v,sensory_transform(s_range),sigma_u))) # likelihood normalisation = np.sum(numerator*s_step) # denominator / model evidence / p(noisy input) (equation 5) posterior = numerator / normalisation # posterior # plot exact bayes plt.figure(figsize=(7.5,2.5)) plt.plot(s_range,posterior) plt.ylabel(r' $p(v | u)$') sns.despine()
Inspecting the graph, we find that approximately maximises the posterior. There are two fundamental problems with this approach
The posterior does not take a standard form, and is thus described by (potentially) infinitely many moments, instead of just simple sufficient statistics, such as the mean and the variance of a gaussian.
The normalisation term that sits in the numerator of Bayes formula
can be complicated and numerical solutions often rely on computationally intense algorithms, such as the Expectation-Maximisation algorithm.
We are interested in a more general way of finding the value that maximises the posterior . This involves maximising the numerator of Bayes equation. As this is independent of the denominator and therefore maximising will maximise the posterior. By taking the logarithm to the numerator we get
and the dynamics can be derived (see notes) to be
The next snippit of code asumes values for and implements the above dynamics to find the value of that maximises the posterior using a manual implementation of the dynamics and iterating using Eulers method.
def simple_dyn(): # variabels v = 2 # real size of item sigma_u = 1 # standard deviation of noisy input v_p = 3 # mean of prior sigma_p = 1 # variance of prior / sensory noise s_range = np.arange(0.01,5,0.01) # range of sensory input s_step = 0.01 # step size # assume that phi maximises the posterior phi = np.zeros(np.size(s_range)) # use Eulers method to find the most likely value of phi for i in range(1,len(s_range)): phi = v_p phi[i] = phi[i - 1] + s_step * ( ( (v_p - phi[i - 1]) / sigma_u ) + ( ( v - sensory_transform(phi[i - 1]) ) / sigma_u ) * (2 * phi[i - 1]) ) # equation 12 # plot convergence plt.figure(figsize=(5,2.5)) plt.plot(s_range,phi) plt.xlabel('Time') plt.ylabel(r' $\phi$') sns.despine()
It is clear that the output converges rapidly to , the value that maximises the posterior.
So we ask the question: What does a minimal and biologically plausible network model that can do such calculations look like?
Firstly, we must specify what exactly biologically plausible means.
A neuron only performs computations on the input it is given, weighted by its synaptic weights.
Synaptic plasticity of one neuron, is only based on the activity of pre-synaptic and post-synaptic activity connecting to that neuron.
Consider the dynamics of a simple network that relies on just two neurons and is coherent with the above requirements of local computation
where and are the prediction errors
that arise from the assumption that the input is normally distributed (again, see Bogaez for derivations).
Below the network dynamics are sketched. Arrows denote excitatory input, circles inhibitory input, and unless specified (), weights of connections are assumed to be one.
The next snippit of code implements those dynamics and thus, the network learns what value of that maximises the posterior.
def learn_phi(): # variabels v = 2 # real size of item sigma_u = 1 # standard deviation of noisy input v_p = 3 # mean of prior sigma_p = 1 # variance of prior / sensory noise s_range = np.arange(0.01,5,0.01) # range of sensory input s_step = 0.01 # step size # preallocate phi = np.zeros(np.size(s_range)) epsilon_e = np.zeros(np.size(s_range)) epsilon_s = np.zeros(np.size(s_range)) # dynamics of prediction errors for size (epsilon_v) and sensory input (epsilon_u) for i in range(1,len(s_range)): phi = v_p # initialise best guess (prior) of size epsilon_e = 0 # initialise prediction error for size epsilon_s = 0 # initialise prediction error for sensory input phi[i] = phi[i-1] + s_step*( -epsilon_e[i-1] + epsilon_s[i-1] * ( 2*(phi[i-1]) ) ) # equation 12 epsilon_e[i] = epsilon_e[i-1] + s_step*( phi[i-1] - v_p - sigma_u * epsilon_e[i-1] ) # equation 13 epsilon_s[i] = epsilon_s[i-1] + s_step*( v - sensory_transform(phi[i-1]) - sigma_p * epsilon_s[i-1] ) # equation 14 # plot network dynamics plt.figure(figsize=(5,2.5)) plt.plot(s_range,phi) plt.plot(s_range,epsilon_e) plt.plot(s_range,epsilon_s) plt.ylabel('Activity') sns.despine()
As the figure shows, the network learns but is slower in converging than when using Eulers method, as the model relies on several other nodes that are inhibits and excites each other, which causes oscillatory behaviour. Both and oscillate and converge to the values where
Which can be understood as the steady-state of the network. This means that minimising prediction errors (by learning the correct parameters) minimises the free energy potential - a tenet in Active Inference.
Recall that we assumed that size was communicated via. a noisy signal assumed to be normally distributed. Above, we outlined a simple sample method for finding the mean value that maximises the posterior .
By expanding this simple model, we can esimate the variance of the normal distribution as well. Considering computation in one single node computing prediction error
where is the variance of the best guess of , . Estimation of can be achieved by adding a interneuron which is connected to the prediction error node, and receives input from this via the connection with weight encoding , such as sketched in the figure below.
The dynamics are described by
which the following snippit of code implements.
def learn_sigma(): # variabels v = 2 # observed homeostatic error sigma_u = 1 # standard deviation of the homeostatic error v_p = 3 # mean of prior homeostatic error / noisy input / simple prior sigma_p = 1 # variance of prior / sensory noise s_range = np.arange(0.01,5,0.01) # range of sensory input s_step = 0.01 # step size # new variabels maxt = 20 # maximum number of iterations trials = 2000 # of trials epi_length = 20 # length of episode alpha = 0.01 # learning rate mean_phi = 5 # the average value that maximises the posterior sigma_phi = 2 # the variance of phi last_phi = 5 # the last observed phi # preallocate sigma = np.zeros(trials) error = np.zeros(trials) e = np.zeros(trials) sigma = 1 # initialise sigma in 1 for j in range(1,trials): error = 0 # initialise error in zero e = 0 # initialise interneuron e in zero phi = np.random.normal(5, np.sqrt(2), 1) # draw a new phi every round for i in range(1,2000): error[i] = error[i-1] + s_step*(phi-last_phi-e[i-1]) # equation 59 e[i] = e[i-1] + s_step*(sigma[j-1]*error[i-1]-e[i-1]) # equation 60 sigma[j] = sigma[j-1] + alpha*(error[-1]*e[-1]-1) # synaptic weight (Sigma) update # plot dynamics of Sigma plt.figure(figsize=(5,2.5)) plt.plot(sigma) plt.xlabel('Time') plt.ylabel(r' $\Sigma$') sns.despine()
Because is constantly varying
phi = np.random.normal(5, np.sqrt(2), 1) never converge to just one value, but instead to approximately 2, the variance of .