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Metropolis broadcasting issue #1083

morepoch opened this issue May 5, 2016 · 1 comment


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commented May 5, 2016

I try to use Metropolis sampling method for a simple hierarchical model, following is the code:

import pymc3 as pm
import numpy as np
#%% generate synthetic data
MU_PHI = -10
SD_PHI = 2
MU_THETA = 10.0
NUM_OBS = 60
t_x = np.random.normal(size=(NUM_SUBJ, NUM_OBS))
t_z = np.random.normal(size=(NUM_SUBJ, NUM_OBS))
c_y = np.random.normal(size=(NUM_SUBJ, NUM_OBS))
#%% Model
basic_model = pm.Model()
with basic_model:
    # hyper-parameter
    mu_phi = pm.Normal('mu_phi', mu=MU_PHI, sd=SD_PHI)
    mu_theta = pm.Normal('mu_theta', mu=MU_THETA, sd=SD_THETA)
    # parameter
    phi = pm.Normal('phi', mu=mu_phi, sd=SD_PHI, shape=(NUM_SUBJ, 1))
    theta = pm.Normal('theta', mu=mu_theta, sd=SD_THETA, shape=(NUM_SUBJ, 1))
    # deterministic variable
    mu_c_y = theta - phi
    # observation
    var_c_y = pm.Normal('c_y', mu=mu_c_y, sd=1.0, shape=(NUM_SUBJ, NUM_OBS), observed=c_y)
    start = pm.find_MAP()
    trace = pm.sample(10000, start=start, step=pm.Metropolis())
  • [Case 1] When I directly run the above code, I get the following ValueError:
ValueError: Input dimension mis-match. (input[1].shape[1] = 60, input[3].shape[1] = 1)
Apply node that caused the error: Elemwise{Composite{(i0 + (-sqr((i1 - (i2 - i3)))))}}(TensorConstant{(1L, 1L) o..3787715435}, TensorConstant{[[-0.55792..13113699]]}, Reshape{2}.0, phi_shared)
Toposort index: 7
Inputs types: [TensorType(float64, (True, True)), TensorType(float64, matrix), TensorType(float64, col), TensorType(float64, matrix)]
Inputs shapes: [(1L, 1L), (20L, 60L), (20L, 1L), (20L, 1L)]
Inputs strides: [(8L, 8L), (480L, 8L), (8L, 8L), (8L, 8L)]
Inputs values: [array([[-1.83787715]]), 'not shown', 'not shown', 'not shown']
Outputs clients: [[Sum{acc_dtype=float64}(Elemwise{Composite{(i0 + (-sqr((i1 - (i2 - i3)))))}}.0)]]

I guess it's because theano requires indicating broadcastable dimensions in the graph before compilation, while numpy can do broadcasting at run time.

  • [Case 2] When I modify the "deterministic variable" from
mu_c_y = theta - phi


mu_c_y = phi


mu_c_y = theta

Then there's no error anymore, the sampling goes well. The question is that when the deterministic variable involves two different stochastic variable, there's broadcasting issue, but if only with one, there's no issues.

  • [Case 3] With the original code, if I change to NUTS sampler, the sampling goes well without any issues.

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commented Aug 16, 2019

Closing for inactivity.

@ColCarroll ColCarroll closed this Aug 16, 2019

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