sample method modifies start dictionary

[lhelleckes]

When specifying start in the sample method, the provided dictionary is modified

Code example

start_dict = {
    'X0_mu': 25
}
with pymc3.Model() as pmodel:
    X0_mu = pymc3.Lognormal('X0_mu', mu=numpy.log(0.25), sd=0.10)
    idata = pymc3.sample(
        tune=100, draws=500,
        start=start_dict,
    )
    
print(start_dict)

Output

{'X0_mu': 25, 'X0_mu_log__': 3.2188758248682006}

Expected behaviour
The method should edit a copy of the original dictionary for reproducibility.

Versions and main components

• PyMC3 Version: 3.11.0
• Python Version: 3.7

[chandan5362]

@lhelleckes , need a little more information,
the output should be only X0_mu : 25 right?

[ricardoV94]

@lhelleckes , need a little more information,
the output should be only X0_mu : 25 right?

Yes, I am pretty sure that's it. We should make a copy before update_start_vals: https://github.com/pymc-devs/pymc3/blob/37ca5ea9b25aa00ed4d460f0fb417712d125d248/pymc3/sampling.py#L428-L433

@chandan5362 Do you want to make a PR?

[michaelosthege]

pm.find_MAP possibly has the same issue.

[chandan5362]

The main factor behind this issue (for both pm.find_MAP , pm.sample) is the function update-start-vals, as it updates the passed arguments (includes transformed variable as well). As It can be seen here.
https://github.com/pymc-devs/pymc3/blob/b77e2d1498a74872ccabc8ea9f51add447e41941/pymc3/util.py#L182-L193
so, one way to get rid of this issue is to use deepcopy (if you agree) or we can go for creating extra variable ( I don't like it though).
If you all agree, then I can create a PR.

[michaelosthege]

Wouldn't it be enough to just re-create the dict like start = { k : v for k, v in start.items() } somewhere in pm.sample and possibly pm.find_MAP?

But you can't do that in update_start_vals because it was designed to modify the pass-by-reference input and has no return value. Unless you change that too.

[ricardoV94]

You also have to handle the case where you have a list of dictionaries (one per chain)