Bayesian hacker chapter1_introduction imp use edward


#1

EDIT: Oops, this is a re-post. See Bayesian hacker chapter 1 use edward.

moved from https://github.com/blei-lab/edward/issues/729.

@cavities

import pymc3 as pm
import theano.tensor as tt

with pm.Model() as model:
    alpha = 1.0/count_data.mean()  # Recall count_data is the
                                   # variable that holds our txt counts
    lambda_1 = pm.Exponential("lambda_1", alpha)
    lambda_2 = pm.Exponential("lambda_2", alpha)
    
    tau = pm.DiscreteUniform("tau", lower=0, upper=n_count_data - 1)

    
with model:
    idx = np.arange(n_count_data) # Index
    lambda_ = pm.math.switch(tau >= idx, lambda_1, lambda_2)
    observation = pm.Poisson("obs", lambda_, observed=count_data)
    step = pm.Metropolis()
    trace = pm.sample(10000, tune=5000,step=step)

and use edward

sess=tf.Session()
alpha_f = 1.0/count_data.mean()


alpha = tf.Variable(alpha_f, name="alpha", dtype=tf.float32)

# init 
lambda_1 = Exponential(alpha)
lambda_2 = Exponential(alpha)
tau = Uniform(low=0.0,high=float(n_count_data - 1))
idx = np.arange(n_count_data)
lambda_ = tf.where(tau>=idx,tf.ones(shape=[n_count_data,],dtype=tf.float32)*lambda_1,tf.ones(shape=[n_count_data,],dtype=tf.float32)*lambda_2)

# error
z = Poisson(lambda_,value=tf.Variable(tf.ones(n_count_data)))

# model
T = 5000  # number of posterior samples
qlambda_1 =  Empirical(params=tf.Variable(tf.zeros([T,n_count_data,1])))
qlambda_2 =  Empirical(params=tf.Variable(tf.zeros([T,n_count_data,1])))
# qlambda_  =  Empirical(params=tf.Variable(tf.zeros([T,n_count_data,1])))


qz = Empirical(params=tf.Variable(tf.random_normal([n_count_data,1])))
inference = ed.HMC({lambda_1:qlambda_1,lambda_2:qlambda_2},data={z:count_data})
inference.run()

TypeError                                 Traceback (most recent call last)
<ipython-input-134-fd551ffe571e> in <module>()
     23 
     24 qz = Empirical(params=tf.Variable(tf.random_normal([n_count_data,1])))
---> 25 inference = ed.HMC({lambda_1:qlambda_1,lambda_2:qlambda_2},data={z:count_data})
     26 inference.run()
     27 

c:\python35\lib\site-packages\edward\inferences\hmc.py in __init__(self, *args, **kwargs)
     48     >>> inference = ed.HMC({z: qz}, data)
     49     """
---> 50     super(HMC, self).__init__(*args, **kwargs)
     51 
     52   def initialize(self, step_size=0.25, n_steps=2, *args, **kwargs):

c:\python35\lib\site-packages\edward\inferences\monte_carlo.py in __init__(self, latent_vars, data)
     87                            "a scalar sample shape.")
     88 
---> 89     super(MonteCarlo, self).__init__(latent_vars, data)
     90 
     91   def initialize(self, *args, **kwargs):

c:\python35\lib\site-packages\edward\inferences\inference.py in __init__(self, latent_vars, data)
     70       data = {}
     71 
---> 72     check_latent_vars(latent_vars)
     73     self.latent_vars = latent_vars
     74 

c:\python35\lib\site-packages\edward\util\random_variables.py in check_latent_vars(latent_vars)
     74     elif not key.shape.is_compatible_with(value.shape):
     75       raise TypeError("Key-value pair in latent_vars does not have same "
---> 76                       "shape: {}, {}".format(key.shape, value.shape))
     77     elif key.dtype != value.dtype:
     78       raise TypeError("Key-value pair in latent_vars does not have same "

TypeError: Key-value pair in latent_vars does not have same shape: (), (74, 1)


ps:url


Bayesian hacker chapter 1 use edward
#2

The error message says that you’re matching latent variables with differing dimensions. For example, you wrote qlambda_1 as an Empirical distribution with shape [n_count_data, 1] to try to approximate a scalar random variable lambda_1.


#3