Add explanation for the assumption of what counts as signal in BRSA, correct default optimizer of BRSA #337
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and others
added 30 commits
Sep 2, 2016
added 13 commits
Jul 14, 2017
…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
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| 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Outdated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
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| @@ -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.
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@mihaic Yes! I will resubmit today :) |
and others
added 4 commits
Feb 20, 2018
…educed number of iteration in test code and increased that in brsa module.
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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