Add explanation for the assumption of what counts as signal in BRSA, correct default optimizer of BRSA #337
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added 13 commits
July 13, 2017 23:05
…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
mihaic
requested changes
Feb 16, 2018
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` | ||
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| Parameters | ||
| ---------- | ||
| n_iter : int. Default: 50 |
brainiak/reprsimil/brsa.py
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| 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. | ||
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| Parameters | ||
| ---------- | ||
| n_iter : int. Default: 50 |
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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) | |||
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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 :) |
…educed number of iteration in test code and increased that in brsa module.
mihaic
approved these changes
Feb 21, 2018
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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