Add explanation for the assumption of what counts as signal in BRSA, correct default optimizer of BRSA #337
Conversation
30 commits
Sep 2, 2016
and others
added
13 commits
Jul 14, 2017
added …rom 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
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Outdated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 |
mihaic
Feb 16, 2018
Contributor
Same.
Same.
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Outdated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 |
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.
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Outdated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) |
mihaic
Feb 16, 2018
Contributor
Is this the minimum number that works with L-BFGS-B? Just trying to minimize required time for tests.
Is this the minimum number that works with L-BFGS-B? Just trying to minimize required time for tests.
@mihaic Yes! I will resubmit today :) |
4 commits
Feb 20, 2018
and others
added …educed number of iteration in test code and increased that in brsa module.
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.
Suggestions cannot be applied on multi-line comments.
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