Guillaume Filion

Hi, can you explain what you are trying to do? For instance, what are `test.txt` and `out.fasta`? The patterns are missing from your command lines. Assuming that `test.txt` contains some...

The definition is not specific enough. For instance, in the first example there could be two 2-matches (GAA and TTC) or just one (any of GAAT, AATT, ATTC).

The purpose of this pull request is to harmonize the behavior of masking between the different ways of estimating the gradient of the ELBO (most notably when `has_r_sample` is `False`)....

Hi @ordabayevy! Thanks for taking the time to help me with this. There were issues in the file `tests/infer/test_gradient.py` (mostly in the code for the new tests) and running `make...

@fritzo It seems that you wrote the following comment in [ `pyro/distributions/score_parts.py` ](https://github.com/pyro-ppl/pyro/blob/dev/pyro/distributions/score_parts.py) ``` 71b7d3da0 (Fritz Obermeyer 2018-08-26 10:51:42 -0700 17) def scale_and_mask(self, scale=1.0, mask=None): 71b7d3da0 (Fritz Obermeyer 2018-08-26 10:51:42...

Thanks @fritzo! That's so useful to understand how the code works. I'll start from there and think of ways to address the issues without breaking everything. By the way, I...

I think I understand why the `score.function` terms are not scaled. Let me know if this is correct @fritzo. What you call `log_r` in the code must refer to $\log...

Thanks for confirming @fritzo. Below is a very long post, I don't expect anyone to read it. It is mostly here for reference, to keep track of my rationale. ###...

I have opened pull request https://github.com/pyro-ppl/pyro/pull/3265 with the changes discussed above and some new tests involving gradients with `poutine.mask`.

Hi @fritzo! I had a closer look at the issue and it's a little more complicated than I thought... Are there already some tests for the creation of parameters in...