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Add explanation for the assumption of what counts as signal in BRSA, correct default optimizer of BRSA #337

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merged 47 commits into from Feb 21, 2018

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lcnature commented Feb 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

lcnature and others added some commits Sep 2, 2016

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	new file: brainiak/brsa/test.txt
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	new file: brainiak/brsa/test.txt
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	new file: brainiak/brsa/test.txt
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Mingbo Cai added some commits Jul 14, 2017

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

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mihaic Feb 16, 2018

Contributor

Same.

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

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mihaic Feb 16, 2018

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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.

@@ -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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mihaic Feb 16, 2018

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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 commented Feb 20, 2018

@lcnature, we are preparing a new release to incorporate PR #339. Will you address the comments (they are really simple) today or tomorrow to get this PR in?

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lcnature commented Feb 20, 2018

@mihaic Yes! I will resubmit today :)

Mingbo Cai and others added some commits Feb 20, 2018

Mingbo Cai
removed all description of default parameters, added newsfragments, r…
…educed number of iteration in test code and increased that in brsa module.
Mingbo Cai
Mingbo Cai
@mihaic

mihaic approved these changes Feb 21, 2018

@mihaic mihaic merged commit 03d83c8 into brainiak:master Feb 21, 2018

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