[WIP] Ch6

[canyon289]

No description provided.

[AlexAndorra]

Thank you for this hard and useful work @canyon289 and @aloctavodia !
Ravin, I can help you if you need? Particularly on chapters 6 (Mixture Models) and 7 (Gaussian Processes). I just finished the exercises on these models for Richard McElreath's book, so it's still fresh in my head 😉
Of course, I can also assist on other chapters, but looks like they are quite ready.

[canyon289]

Hey @AlexAndorra would you be open to reviewing as I finish the exercises? Notebooks are hard to work on in parallel but an extra set of eyes would be helpful!

[AlexAndorra]

Sure, would be happy to!
Which chapters are the most pressing for review?

[canyon289]

Any of the ones in PR really. Just a heads up though. Osvaldo and I are reeeaaalllllyyyy slow on this. Like we've taken months, and sometimes take multiple weeks to respond to each other. If were slow with you too please don't be frustrated :)

[AlexAndorra]

Ha ha I totally understand! I'm doing that on my spare time too, which is quite cyclical (but, sadly, rather hard to predict, even with a Bayesian model...).
Will take a look at the PRs ASAP (may have to re-read some chapters first 😝).

[canyon289]

No worries. Thank you for your time. We really appreciate your efforts :)

[AlexAndorra]

Going through the exercises, a first thought is that it would be useful for readers to have the text of the questions, that are in the book, in addition to the answers.
If @aloctavodia is ok with that, I can do a PR to add it to the 4 notebooks already merged. Not sure I'm able to do it on the NBs currently in review though (maybe with the Review NB app?)...

[canyon289]

If @aloctavodia agrees I can add them into the ones in review to make things easier

[AlexAndorra]

That would be great!
Also, allow the Review NB App access to this repo would make the review process easier I think. But I guess we have to wait for our dear Oslvado to do that ;)

[aloctavodia]

Happy to see you both working together, I agree with both of you! :-)
I am slowly transitioning from vacation to going back to work :-)

[AlexAndorra]

Ha ha good to have you back Osvaldo (and also good luck 😉)! I'll do the PR and reviews ASAP then! FYI, I'm doing the transition in the opposite direction 😜 Le ven. 26 juil. 2019 à 21:53, Osvaldo Martin <[email protected]> a écrit :

…

Happy to see you both working together, I agree with both of you! :-) I am slowly transitioning from vacation to going back to work :-) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#40?email_source=notifications&email_token=AHIJMTBRNVR2DZ3EE2CTL6LQBNI3DA5CNFSM4IFZWHQ2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD25RYVQ#issuecomment-515578966>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHIJMTBLKJVKX4RKAD4ZMOTQBNI3DANCNFSM4IFZWHQQ> .

[canyon289]

So either @aloctavodia or @AlexAndorra I could use help! On this section for question 4 to 6 I'm getting a ton of divergences and not really sure what to do about it. Tried increasing tuning and number of samples but no luck :(

[AlexAndorra]

Thank you Ravin! I'll try to take a look this week or the next ;)

[AlexAndorra]

@aloctavodia do you think you could set up the Review NB App on this repo? I think it would make the review process easier ;) Thank you!

[AlexAndorra]

So I managed to take a look at your NB @canyon289 🎉 Here are my (deep) thoughts (sorry it's not very convenient, but without the Review NB app I don't see any other way):

• In general, it looks like all the models needed more informative priors. Iteratively and with some prior predictive checks, I think I found some priors (particularly on the Dirichlet) that allow the models to sample quite smoothly (but it's very probable it's not the best solution and that @aloctavodia will come up with something better)

• Exercise 1: there were a label-switching problem and divergences in the three models (a few for 2 and 3 clusters, a lot for 4 clusters). Adopting more regularizing priors and ordering the means solved it for 2 and 3 clusters, but the 4-cluster one still has a few divergences, despite my numerous attemtps. I suspect it is overparametrized, as it tries to find 4 clusters within 3-cluster data. Here is the modified model:

with pm.Model() as two_components:
        p = pm.Dirichlet("p", a=np.array([10.]*cluster))

        # Each mean of the mixture data has its own estimate of a mean with a fixed SD in this case
        means = pm.Normal("means", mu=np.linspace(vals.min(), vals.max(), cluster), 
                          sd=10., shape=cluster, transform=pm.distributions.transforms.ordered)
        
        # Estimate of the standard deviation of the whole population
        sd = pm.HalfCauchy("sd", 1.)
        y = pm.NormalMixture("y", w=p, mu=means, sd=sd, observed=vals)
        
        trace = pm.sample(1000, tune=5000, cores=2, random_seed=123)

• Exercise 2: I just wanted to note that az.compare(traces) throws me a ValueError: could not broadcast input array from shape (300,1) into shape (300). Is it the same for you? Nothing other than that. The WAIC-LOO comparison still (rightly) ranks the 3-cluster model on top, and the traces look a lot healthier with the new model.

• Execise 4: This one is a real head-scratcher... I tried ordering the means and changing the gamma prior but nothing worked. I think the model is misspecified but I really don't know where...

• Exercise 5: Here, adopting regularizing priors and ordering the means made the model sample smoothly. The traces look better, although they are not perfect - I think the model has trouble distinguishing two species that have very similar probability. Plus, the third species' probability seems to be close to 0. Here is the model:

with pm.Model() as model_mg:
    
    p = pm.Dirichlet('p', a=np.array([5.]*clusters))
    
    means = pm.Normal('means', mu=np.linspace(sepal_length.min(), sepal_length.max(), clusters), 
                      sd=10., shape=clusters, transform=pm.distributions.transforms.ordered)
    
    sd = pm.HalfNormal('sd', sd=10.)
    
    y = pm.NormalMixture('y', w=p, mu=means, sd=sd, observed=sepal_length)
    
    sepal_trace = pm.sample(1000, tune=6000, cores=2, nuts_kwargs={"target_accept": 0.9})

• Exercise 6: Same thing as above, with the same regularizing priors, but I have a question here. If I understood correctly, this model clusters the species based on sepal_width and sepal_length independently (we could actually do two separate models and sample from them independently). Is there a way to use both features at the same time in the same model - i.e cluster the species based both on sepal_width and sepal_length?

[canyon289]

@AlexAndorra Thanks for the feedback here and on ch7

For question 2: I'm using the ArviZ version in the environment.yml file. At one point there was code introduced in ArviZ that created the exception you're referring to but I think its gone now.

For Exercise 6. I'm actually not sure. I thought the way I specified the model is how MultiObserved works in ArviZ. I'll ask on the PyMC discourse to be sure.

As for the rest I appreciate you going through them! I'll implement your suggestions this weekend.

PyMCheers!

[AlexAndorra]

You're welcome Ravin ;)

FYI, I'm using Arivz's latest version (0.4.1), which means a novelty broke this specific code... Do I need to open an issue on Arivz's repo?

For exercise 6, my knowledge stops there on the matter, but I'm curious about the answer. I'll follow your question on Discourse!

[canyon289]

Fixed exercise 2 per Alex's notes. Thank you!