Half GSoC reached

Even though it feels like yesterday, the coding period started nearly a month and a half ago. We have already been coding for more than half of the GSoC coding period time. I have passed the first evaluation, received the first payment and implemented or modified many functions in ArviZ (even created some bugs too…). Therefore, it feels like a good time to review in a little depth my work up to this point, and compare with the timeline proposed.

Finished tasks

According to the proposed timeline, I should have finished up to task T7, and be starting T9. I do not count T8 here because it is basically correcting bugs, which I have already started doing and has no finish date. In general lines, I have followed and fulfilled my initial timeline up until here, but from here on, it will start to diverge as we have considered more interesting to pursue some new goals.

T1-T3: Information Criteria

Hence, I should have finished my work on information criteria (T1-T3: implementation, tests, documentation and examples). And indeed I have. I have modified the API of the information criterion (IC) stats functions loo and waic in three key ways:

  • I have created a custom class ELPDData class so that the return value of IC functions in ArviZ is of this type, which results in a more meaningful printed text to ease interpretation of IC results.
  • I have modified IC functions to use xarray. After this change, the conversion to unlabeled array is not necessary anymore and pointwise IC values are correctly labeled, following the labels found in the log likelihood data from which IC is calculated.
  • In addition to using xarray for calculations, I have also modified how the IC function is applied and broadcasted to each observation allowing to work the whole time not only with labeled data but with multidimensional data. Before this change, the data was reshaped always to a 2D object whose shape was $(N_{samples}, N_{obsevations})$, now, the calculations are performed with objects of shape $(…, N_{samples})$ where the $…$ can be any shape. Rgarding the information criteria related plots, I have added many customization options to plot_khat and implementes a new plotting function plot_elpd, which compares graphically pointwise IC values between 2 or more models. In plot_khat, I added many new coloring and labeling options. From all of them, the most relevant is probably the hover labels (see them below!), which also lead me to implementing a context manager for ipython sessions to temporarily change the backend from inline to an interactive one. Check out how to use it!


T4-T6: Convergence analysis tools

The other block of my proposal were convergence analysis tools. A great deal of tools was published while I was writing the proposal, and they were added to the stats module in ArviZ right before the start of my coding period. I reviewed extensively the pull request that added all these tools and read the papers to get familiar with how they worked and how they were implemented.

In this block, my work consisted in creating plotting functions to allow graphical exploration of all the new convergence analysis tools. These include local, quantile and evolution effective sample size plots and local and quantile Monte-Carlo standard error plots. Both plots leave room for great customization, some examples can be seen below:



T#: Model checking

Moreover, I also implemented Leave One Out (LOO) Probability Integral Transform (PIT) checks, to see if the observed data could have been generated from the model.

LOO-PIT combines the idea of the PIT algorithm, which is that if an observation $x_i$ is generated from a probability density function $f(x)$, then $F(x) = P(x < x_i)$ is distributed as a uniform random variable; with the LOO algorithm idea which is to perform the calculations on $x_i$ with the inference results of fitting all data but $x_i$. Thus, for every $x_i$ in the observed data, $f(x)$ is estimated fitting all data but $x_i$ and then $x_i$ is used to check the PIT uniformity.

This kind of check requires models with a high number of observations, but can detect problems with the model. If the LOO-PIT samples are far from uniformity, it probably means that the observed data could never be generated from the current model.

It also implements the comparison of the empirical cumulative density function (ECDF) with its theoretical value (because we know it must be uniform) and then plot also the theoretical envelope inside of which most uniform ECDFs will end up.


T7: Test on real examples

I created a github repo to generate and store a wide range of Bayesian inference examples, and in addition to the models in ArviZ, I also tested the functions manually on these examples. I do not plan on stopping here however. I will check repos and packages that use ArviZ, PyMC3 or PyStan and analyze the robustness of their workflow. Then, I will try to apply all the functions implemented in these repos and extend the checks performed on the model and the MCMC samples. This could achieve two goals, it could make these algorithms more known and it will most probably help in finding bugs and improving the documentation.

Future work

I have no more work planned on the convergence analysis block, but I do have plans for the other two blocks, implementing the Leave Future Out cross validation in the information criteria block and implementing Simulation Based Calibration in the model checking block. Both algorithms require refitting, which poses a huge challenge for a backend agnostic package like ArviZ without sampling capabilities of its own. I have already started working on some wrappers in order to allow refitting using any user defined backend such as PyStan, PyMC3 of emcee.

In addition, I have also started working on implementing rcParams in ArviZ, following matplotlib’s implementation, in order to allow easier and better configuration of ArviZ defaults.

Finally, of the planned tasks that lie ahead, I will not spend much time on benchmarking (T9), because that would collide with the other ongoing GSoC project to apply Numba to ArviZ algorithms, nor I will write a section in ArviZ resources repo, I will probably post tutorials on how to use ArviZ’s new functions in this blog, following the example of the LOO on transformed data example.