Learning Notes, Programming, Python

Stochastic – Particle Filtering & Markov Chain Monte Carlo (MCMC) with python example



A particle can be seen as an evaluation of all random variables in a joint distribution.


\displaystyle  \text{Particle A: } [X=1, Y=2] \\ \\ \text{Particle B: } [X=3, Y=1] \\ \\ \text{where } X, Y \in  \{1, 2, 3\}


MCMC refers to methods for randomly sample particles from a joint distribution with a Markov Chain.

Particle Filtering

Particle Filtering is also termed Sequential Monte Carlo. It refers to the process of repeatedly sampling, cast votes after each iteration based on sampled particles and modify the next sampling based on the votes in order to obtain the probability distribution of some un-observable states.

Formally, let x be the unobservable states and y be the observable states related to x. Suppose we receive observations of y at each time step k, we can write the probability based on a Markov Chain:

\displaystyle X_k|(X_{k-1} =x_{k-1}) \propto p(x_k|x_{k-1})

\displaystyle Y_k|(X_{k} =x_{k}) \propto p(y_k|x_{k})

Based on Chapman-Kolmogorov Equation and Bayes Theorem, the conditional probability distribution of latent states x based on priori knowledge y is:

\displaystyle p(x_k|y_{1:k}) \propto p(y_k|x_k)\int_k p(x_k|x_{k-1})p(x_{k-1}|Y_{1:K-1})

MCMC Methods

Gibbs Sampling

Unknown: Joint distribution P(X_1, X_2, \dots, X_n)

Known: Conditional Probability P(X_i|\vec{X}_{others})

Goal: Obtain an estimation of the joint distribution


  1. Choose an initial value  X^0_i for the variable of interest.
  2. Compute distribution by randomly fixing  “others” variable P(X_j|X_i, \vec{X}_{others}) for some j \neq i
  3. Sample from distribution to get a realization of X_j , then update the conditional probability P(X_i|X_j, \vec{X}_{others}) correspondingly,
  4. Sample the target
  5. Do step 2 to step 3 repeatedly for all j \in [1, n] \neq i for k iterations.

An implementation is given below:

def main():
    This program demonstrates a two-variable Gibbs sampling iteration.

    X(size), Y(size)    Samplers which realize corresponding variables.
    PX, PY              Predefined probability distribution of the two random variable.
                        PX and PY are what we wish to estimate and is often unknown in
    properties          Property of the pdf PX and PY, including the domain, resolution and
                        a norm constant which is for plotting p.m.f
    :return None:
    X, Y, PX, PY, properties = GenerateSamplers()
    w = np.linspace(

    Xcollection = []
    x_k = X(1)  # Initial sampling
    y_0 = Y(1)  # Initial sampling
    PYcX = PY/x_k   # P(Y|X=x_k), should be know from statistical data instead
    PXcY = PX/y_0   # P(X|Y=y_0), should be know from statistical data also
    PYcX /= PYcX.sum() # Normalizing the conditional probabilities
    PXcY /= PXcY.sum()
    for k in xrange(50000):
        PYcX /= x_k # Update conditional probability
        PYcX /= PYcX.sum() # Normalize
        y_k = np.random.choice(w, p=PYcX, size=1) # sample from new probability distribution

        PXcY /= y_k # Update conditional probability
        PXcY /= PXcY.sum() # Normalize
        x_k = np.random.choice(w, p=PXcY, size=1)
        Xcollection.append(x_k) # Record the sample

    # Plotting
    plt.hist(np.array(Xcollection), bins=200, normed=1, alpha=0.5)
    plt.plot(w, PX/properties['normConstant'])

if __name__ == '__main__':

And the GenerateSampler() function:

def GenerateSamplers():
    Creates a pair of random variables, one probability distribution is a
     gaussian mixture, another is a simple gaussian with mean 0 and sd 10.

    Domain of the sample is set to -10 to 10

    :return [lambda: sample1, lambda: sample2:
    # Properties settings
    resolution = 2000 # 2000 partitions between whole domain
    domain = [-10, 10]
    gm = {'means': [-1, 2, -4], 'sds': [0.4, 8, 3], 'weight': [0.1, 0.6, 0.3]}
    gy = {'means': 0, 'sds': 5}

    # define a normed gaussian
    def Gaussian(mean, var, x):
        return 1 / (var * np.sqrt(2 * np.pi)) * np.exp(-0.5 * (x - mean) ** 2 / var ** 2)

    w = np.linspace(domain[0], domain[1], resolution)

    # Generate pdf
    PX = np.sum([gm['weight'][i]*Gaussian(gm['means'][i], gm['sds'][i], w)
                 for i in xrange(len(gm['means']))], axis=0)
    PY = Gaussian(gy['means'], gy['sds'], w)

    # Normalization
    PX /= PX.sum()
    PY /= PY.sum()

    # Create sampler functions
    X = lambda size: np.random.choice(w, p=PX, size=size)
    Y = lambda size: np.random.choice(w, p=PY, size=size)
    properties = {'resolution': resolution, 'domain': domain, 'normConstant': (domain[1] - domain[0])/float(resolution - 1)}
    return X, Y, PX, PY, properties

The result is the following figure, where P(X) is a mixture of gaussians (linear combination of gaussians):



See Also

Stochastic – Stationary Process Stochastic

Stochastic – Poisson Process with Python example

Stochastic – Python Example of a Random Walk Implementation