 Conversion rate model: Beta parameters from pm.Uniform

Hi pymc community,

this is my first post here, as my getting to know pymc3…
I posted this question in stackoverflow (python - Conversion rate posterior in pymc3 - Stack Overflow)
but this seems to be the more appropriate place for pymc experts.

I have conversions rates for every Monday over the past year for posts published on my webpage:

YMD n_orders n_views
20200120 5750 191265
20200127 5725 193661
20200203 6182 203081
20200210 6008 189918
20200217 5543 181347

If I take the average of conversions in my dataset (i.e. average over success/trials) I get a conversion of about 0.027. This is the range of my trials and success variables:

success trials
min 1194.0
max 6182.0

Based on the min/max range of my observations I built the following model:

with pm.Model() as comparing_days:
alpha_1 = pm.Uniform('alpha_1', 1000, 10000, shape=1)
beta_1 = pm.Uniform('beta_1', 40000, 250000, shape=1)
p_B = pm.Beta('p_B', alpha=alpha_1, beta=beta_1, shape=1)
obs = pm.Binomial('obs', n=df_cr.trials,
p=p_B, observed=df_cr.success, shape=1)

After running 50K samples (after 1K burn-in) using pm.sample I get the output below

So the alpha and beta parameter go up their max values, doesn’t seem to converge, also during sampling it complains about the low acceptance probability.

What am I doing wrong? Does my model make sense at all?

Welcome!

So first things first. You should ignore all aspects of this result because of the (large number of) presence of divergences (visually indicated by the black tick marks on the x-axis, but pymc3 also would have complained about them at the terminal). Once you see those, the details of the posterior can’t really be interpreted.

Two quick observations about your model. First, your priors over the alpha and beta parameters imply extremely precise/strong beliefs about the value of p_B. Depending on how much data you have available and your specific needs, this may or may not be desirable. Second, uniform priors often cause sampling difficulties because of the bounds that they create at each end of the interval.

Without knowing exactly what your data looks like, my suggestion would be to weaken the priors and probably re-specify the mode so that your parameters characterize the mean and SD of the beta distribution rather than alpha and beta. Because beta distributions have support over [0,1] an uninformative prior over the mean is somewhat easier to select. For the SD, you can choose a prior with support over the positive reals and build in as much confidence as you wish. Something like a gamma prior is fairly conventional for priors on scale parameters in hierarchical models. Here is a sketch of something that may be useful (beware, extremely untested):

with pm.Model() as comparing_days:
mu = pm.Uniform('mu', upper=0, lower=1)
sd = pm.Gamma('sd', alpha=1, beta=10)
p_B = pm.Beta('p_B', mu=mu, sigma=sd)
obs = pm.Binomial('obs', n=df_cr.trials,
p=p_B, observed=df_cr.success)
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Thank you so much @cluhmann!
I tried the following:

with pm.Model() as comparing_days:
mu = pm.Uniform('mu', upper=0.1, lower=0.001)
sd = pm.InverseGamma('sd', alpha=20, beta=0.1)
p_B = pm.Beta('p_B', mu=mu, sigma=sd, shape=1)
obs = pm.Binomial('obs', n=df_cr.trials, p=p_B, observed=df_cr.success, shape=1)

and this convergences much better, 29 divergences in both chains (50K iterations)

Is this number of divergences acceptable? What is an acceptable level of divergences?
Thanks again, this looks much better now!

Zero (unfortunately). Even a single divergence should be a reason for concern.

What can you do? Besides changing your model (or priors, or data) you can also try to increase target_accept in pm.sample(). That sometimes helps the sampler enough to not diverge anymore. But first you should ask yourself if there might be something fundamentally flawed with your model, as that is often the reason why divergences crop up.

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Sad but true! 29 divergences out of 100K draws can likely be taken care of by tweaking the sampling.

It’s massive overkill, but if you (or anyone else) are looking for a deep dive into sampling diagnostics, I would highly recommend Aki’s keynote from PyMCon 2020.

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Hi there,
thank you both @cluhmann and @ricardoV94
I used following:

with pm.Model() as comparing_days:
mu = pm.Uniform('mu', upper=0.1, lower=0.001)
sd = pm.InverseGamma('sd', alpha=25, beta=0.03)
p_B = pm.Beta('p_B', mu=mu, sigma=sd, shape=1)
obs = pm.Binomial('obs', n=df_cr.trials,
p=p_B, observed=df_cr.success, shape=1)

and got

0 divergences!
So this looks good now. Thanks also for the link to Aki’s keynote, I’ll definitely have a look at it.

2 Likes