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I am trying to use write my own stochastic and deterministic variables with pymc3, but old published recipe for pymc2.3 explained how we can parametrize our variables no longer works. For instance I tried to use this direct approach and it failed:

def x_logp(value, x_l, x_h):
    if ((value>x_h) or (value<x_l)):
        return -np.inf
    else:
        return -np.log(x_h-x_l+1)
def x_rand(x_l,x_h):
    return np.round((x_h-x_l)*np.random.random_sample())+x_l

Xpos=pm.stochastic(logp=x_logp,
                   doc="X position of halo center ",
                   observed=False, 
                   trace=True,
                   name='Xpos',
                   random=x_rand,
                   value=25.32,
                   parents={'x_l':0,'x_h'=500},
                   dtype=float64,
                   plot=True,
                   verbose=0)

I got the following error message:

ERROR: AttributeError: 'module' object has no attribute 'Stochastic' [unknown]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: 'module' object has no attribute 'Stochastic'

I am wondering how could I define my own variables with pymc3 without using the available pymc distributions?

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  • $\begingroup$ I think this question is better asked on Stackoverflow $\endgroup$ – Dan Aug 27 '14 at 18:40
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    $\begingroup$ @Dan I asked and nobody replied so far. $\endgroup$ – Dalek Aug 27 '14 at 18:42
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Custom probability densities can be included using pymc.DensityDist(). For the gradient computation to work though, you have to supply your density as a theano function. For example, see https://github.com/pymc-devs/pymc3/blob/master/pymc3/examples/custom_dists.py:

# This model was presented by Jake Vanderplas in his blog post about
# comparing different MCMC packages
# http://jakevdp.github.io/blog/2014/06/14/frequentism-and-bayesianism-4-bayesian-in-python/
#
# While at the core it's just a linear regression, it's a nice
# illustration of using Jeffrey priors and custom density
# distributions in PyMC3.
#
# Adapted to PyMC3 by Thomas Wiecki
import matplotlib.pyplot as plt
import numpy as np
import pymc
import theano.tensor as T
np.random.seed(42)
theta_true = (25, 0.5)
xdata = 100 * np.random.random(20)
ydata = theta_true[0] + theta_true[1] * xdata
# add scatter to points
xdata = np.random.normal(xdata, 10)
ydata = np.random.normal(ydata, 10)
data = {'x': xdata, 'y': ydata}
with pymc.Model() as model:
alpha = pymc.Uniform('intercept', -100, 100)
# Create custom densities
beta = pymc.DensityDist('slope', lambda value: -1.5 * T.log(1 + value**2), testval=0)
sigma = pymc.DensityDist('sigma', lambda value: -T.log(T.abs_(value)), testval=1)
# Create likelihood
like = pymc.Normal('y_est', mu=alpha + beta * xdata, sd=sigma, observed=ydata)
start = pymc.find_MAP()
step = pymc.NUTS(scaling=start) # Instantiate sampler
trace = pymc.sample(10000, step, start=start)

If you can't express you density as a theano compute graph, you have to create a blackbox theano expression using the new as_op decorator. For example: hhttps://github.com/pymc-devs/pymc3/blob/master/pymc3/examples/disaster_model_theano_op.py. Note that this requires Theano from current master branch:

from pymc import *
import theano.tensor as t
from numpy import arange, array, ones, concatenate, empty
from numpy.random import randint
__all__ = ['disasters_data', 'switchpoint', 'early_mean', 'late_mean', 'rate',
'disasters']
# Time series of recorded coal mining disasters in the UK from 1851 to 1962
disasters_data = array([4, 5, 4, 0, 1, 4, 3, 4, 0, 6, 3, 3, 4, 0, 2, 6,
3, 3, 5, 4, 5, 3, 1, 4, 4, 1, 5, 5, 3, 4, 2, 5,
2, 2, 3, 4, 2, 1, 3, 2, 2, 1, 1, 1, 1, 3, 0, 0,
1, 0, 1, 1, 0, 0, 3, 1, 0, 3, 2, 2, 0, 1, 1, 1,
0, 1, 0, 1, 0, 0, 0, 2, 1, 0, 0, 0, 1, 1, 0, 2,
3, 3, 1, 1, 2, 1, 1, 1, 1, 2, 4, 2, 0, 0, 1, 4,
0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1])
years = len(disasters_data)

#here is the trick
@theano.compile.ops.as_op(itypes=[t.lscalar, t.dscalar, t.dscalar],otypes=[t.dvector])
def rateFunc(switchpoint,early_mean, late_mean):
    ''' Concatenate Poisson means '''
    out = empty(years)
    out[:switchpoint] = early_mean
    out[switchpoint:] = late_mean
    return out

with Model() as model:
    # Prior for distribution of switchpoint location
    switchpoint = DiscreteUniform('switchpoint', lower=0, upper=years)
    # Priors for pre- and post-switch mean number of disasters
    early_mean = Exponential('early_mean', lam=1.)
    late_mean = Exponential('late_mean', lam=1.)
    # Allocate appropriate Poisson rates to years before and after current
    # switchpoint location
    idx = arange(years)
    #theano style:
    #rate = switch(switchpoint >= idx, early_mean, late_mean)
    #non-theano style
    rate = rateFunc(switchpoint, early_mean, late_mean)
    # Data likelihood
    disasters = Poisson('disasters', rate, observed=disasters_data)
    # Initial values for stochastic nodes
    start = {'early_mean': 2., 'late_mean': 3.}
    # Use slice sampler for means
    step1 = Slice([early_mean, late_mean])
    # Use Metropolis for switchpoint, since it accomodates discrete variables
    step2 = Metropolis([switchpoint])
    # njobs>1 works only with most recent (mid August 2014) Thenao version:
    # https://github.com/Theano/Theano/pull/2021
    tr = sample(1000, tune=500, start=start, step=[step1, step2],njobs=1)
traceplot(tr)

We might make this as_op part a bit easier in the future.

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