I’ve been trying to learn the basics of modeling distributions, inferring paramaterization from observed data, and imputation but I seem to be at a standstill and cannot resolve the error I am getting. These are the steps that I’ve taken so far:
-
Created a representative distribution for something I am interested in, an inverse gamma with alpha=1.75, beta=.45, and mu=0 (no issues)
-
Draw random samples from representative distribution (no issues)
-
With fully observed data (nothing missing) allow alpha, beta, and mu to vary as follows. Yes I realize the priors and test values are overspecialized but this was just a conceptual test to make sure I had the code correct (no issues here either)
alpha_m=pm.Normal(‘alpha_m’,1.75,.25,testval=1.75)
beta_m=pm.Normal(‘beta_m’,.45,.25,testval=.45)
mu_m=pm.Normal(‘mu_m’,0,.25,testval=0)
x = pm.InverseGamma(‘x’,alpha=alpha_m,beta=beta_m,mu=mu_m,observed=data_full)
-
At this point compared the data generated using bayesian inference (blue), with data drawn from the specified distribution from step 1 (orange), and the true data (green). Results are pretty solid for my purposes so I was happy to move forward. (no issues)
-
Now I tried removing a few values from the observed data and forcing imputation and I can’t get it to work for the life of me, even referencing all the material I could find. (issues start here)
Here I create the mask, where example.csv is the same as data_full above but with random values removed and only a single column.
data = pd.read_csv(“example.csv”)
data=data[‘example’]
data = data.fillna(-999)
data=pd.Series(data)
masked_values = np.ma.masked_array(data, mask=data==-999)
Then the only change I made from the above was
x = pm.InverseGamma(‘x’,alpha=alpha_m,beta=beta_m,mu=mu_m,observed=masked_values)
and I get the following error:
SamplingError: Initial evaluation of model at starting point failed!
Starting values:
{‘alpha_m’: array(1.95737899), ‘beta_m’: array(0.27115254), ‘mu_m’: array(0.60721553), ‘x_missing’: array([-2.56459914e-01, 1.03271340e+00, 5.37146175e-01, 6.33337610e-02,
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1.13071463e+00, -3.68609644e-01, -5.00859329e-01, 6.44641718e-01,
3.02196631e-01, 7.10830251e-01, -6.50745530e-01, -2.75524564e-01,
8.97536559e-01, 3.10161264e-01, -6.28564407e-01, 8.13093317e-01,
3.40975576e-01, -4.06067127e-01, 8.94295936e-01, 1.14401623e+00,
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2.26381114e-01, -7.23113749e-01, -3.71539725e-03, -4.74133583e-01])}
Initial evaluation results:
alpha_m 0.22
beta_m 0.21
mu_m -2.48
x_missing 0.00
x -inf
Name: Log-probability of test_point, dtype: float64
- I tried evaluating some test points because of the strange log probabilities listed in the error. For example the error states the the test point for mu_m is evaluated to -2.48, but when I simply test:
z = pm.Normal.dist(mu=0,sd=.25)
z.logp(0).eval()
I get that it should evaluate to array(0.46735583) so something seems completely wrong.
Any help would be greatly appreciated!