Join GitHub today
GitHub is home to over 28 million developers working together to host and review code, manage projects, and build software together.
Sign upAdd explanation for the assumption of what counts as signal in BRSA, correct default optimizer of BRSA #337
Conversation
and others
added some commits
Sep 2, 2016
added some commits
Jul 14, 2017
brainiak/reprsimil/brsa.py
Outdated
| Please note that the model assumes that the covariance matrix U which | ||
| all \\beta_i follow is zero-meaned. For more details of its implication, | ||
| see documentation of `.BRSA` | ||
| Parameters | ||
| ---------- | ||
| n_iter : int. Default: 50 |
This comment has been minimized.
This comment has been minimized.
brainiak/reprsimil/brsa.py
Outdated
| under the assumption in BRSA, their similarity is 1; under the assumption | ||
| that only deviation of pattern from average patterns is signal of interest, | ||
| their similarity should be -1. | ||
| Parameters | ||
| ---------- | ||
| n_iter : int. Default: 50 |
This comment has been minimized.
This comment has been minimized.
mihaic
Feb 16, 2018
Contributor
This a good example for why we should not list defaults in docstrings: it creates the need to change values in an additional place, which is frequently forgotten, such as in this PR.
My recommendation: do not list the default in the docstring; it is already visible in the HTML docs in the function definition.
tests/reprsimil/test_brsa.py
Outdated
| @@ -178,7 +178,7 @@ def test_fit(): | ||
| rank = n_C - 1 | ||
| n_nureg = 1 | ||
| brsa = BRSA(rank=rank, n_nureg=n_nureg, tol=2e-3, | ||
| n_iter=4, init_iter=4, auto_nuisance=True) | ||
| n_iter=20, init_iter=4, auto_nuisance=True) |
This comment has been minimized.
This comment has been minimized.
mihaic
Feb 16, 2018
Contributor
Is this the minimum number that works with L-BFGS-B? Just trying to minimize required time for tests.
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
|
@mihaic Yes! I will resubmit today :) |
and others
added some commits
Feb 20, 2018
mihaic
merged commit 03d83c8
into
brainiak:master
Feb 21, 2018
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
lcnature commentedFeb 16, 2018
add notes in the documentation for the different assumption in BRSA from traditional RSA on what counts as signal. Also corrected the mismatch between documentation and actual implementation of the default optimizer. L-BFGS-B appears to require less memory and fits faster in each iteration than BFGS. But it is possible that more iterations are needed because Hessian is approximated, so the default max number of iteration is increased