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Add recent work to BRSA - #194

Merged

mihaic merged 154 commits into

brainiak:masterfrom

lcnature:add_transform_brsa

Aug 9, 2017

Merged

Add recent work to BRSA#194
mihaic merged 154 commits into
brainiak:masterfrom
lcnature:add_transform_brsa

Commits on Sep 2, 2016
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Commits on Sep 22, 2016
- Merge remote-tracking branch 'upstream/master'
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Commits on Sep 28, 2016
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Commits on Oct 13, 2016
- Merge remote-tracking branch 'upstream/master'
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Commits on Oct 24, 2016
- Merge remote-tracking branch 'upstream/master'
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Commits on Nov 1, 2016
- Merge remote-tracking branch 'upstream/master'
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- Merge branch 'master' of https://github.com/lcnature/brainiak
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- Merge remote-tracking branch 'refs/remotes/origin/master'
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- Merge remote-tracking branch 'refs/remotes/origin/master'
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- forcing scan_onsets to be integer
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- make scan_onsets integers as well in example
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- Merge branch 'master' into add_transform_brsa
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- Merge pull request #1 from mihaic/add_transform_brsa
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Commits on Nov 21, 2016
- Add transform function
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Commits on Nov 30, 2016
- Adding marginalized version of BRSA
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Commits on Dec 2, 2016
- not finished
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Commits on Dec 16, 2016
- Adding group BRSA
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- minor changes
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- new example for GBRSA
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- correcting a bug of matrix size
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Commits on Dec 22, 2016
- Cleaning brsa.py
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Commits on Jan 10, 2017
- updating local changes made a while ago
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Commits on Jan 23, 2017
- Making transform function not use private variable
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- Merge branch 'master' of https://github.com/IntelPNI/brainiak
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- Merge branch 'master' of https://github.com/IntelPNI/brainiak into add_transform_brsa
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Commits on Jan 26, 2017
- Merge branch 'master' of https://github.com/IntelPNI/brainiak
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Commits on Jan 30, 2017
- Merge branch 'master' of https://github.com/IntelPNI/brainiak
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Commits on Feb 13, 2017
- working on forward step
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- forward step finished
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Commits on Feb 14, 2017
- Added backward step
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Commits on Feb 22, 2017
- working on score function
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Commits on Feb 23, 2017
- finishing the score function
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Commits on Feb 27, 2017
- Finished the score and transform functions for both BRSA and GBRSA. Corrected a bug in dealing with spatial noise (sigma was unnecessarilty multipled when calculating beta
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Commits on Mar 1, 2017
- one commit before trying autopep8
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Commits on Mar 2, 2017
- passed checks
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Commits on Mar 4, 2017
- finished
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- stripped the example notebookx
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- merge
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- add gest_gbrsa.py
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- cleaned test code
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- adding some comments
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Commits on Mar 8, 2017
- changes in accordance to the comments
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- add reference to BRSA within GBRSA
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- add back one test to increase coverage of test
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- correcting test_brsa.py
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- adding one blank line to score()
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- trying to further reduce test time
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- adding more blank lines...
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- Fix Sphinx errors
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- Merge pull request #2 from mihaic/add_transform_brsa_fix_sphinx
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- add requirements for brsa example
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- change back to accepting only strong for nureg_method
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Commits on Mar 10, 2017
- change to argument tau2_prior
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Commits on Mar 11, 2017
- basically no change to test again
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Commits on Mar 12, 2017
- debugging test failure
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- removed print()
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- test what is different on the server
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- test server
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- resubmit
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- changed gen_DF
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- changed all use of scipy.linalg.block_diag due to different behavior of it on different machines
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- changes to the docstring
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- uncomment out one test
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Commits on Mar 14, 2017
- Made description of the prior_var_GP* functions more generic, changed some docstrings and reduced testing time
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Commits on Mar 15, 2017
- cut the docstring for prior_GP_var_half_cauchy
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- correct a typo
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Commits on Mar 17, 2017
- change docstring of prior_GP_var_half_cauchy
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Commits on Mar 18, 2017
- changed score() to make sure scan_onsets is initialized to an array of integers
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Commits on Mar 20, 2017
- Additional change to utils.gen_design to make sure that the generated design matrix has a reasonable range. Also make it using temporal resolution of 0.01 s as default to control the time of comput…
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Commits on Mar 22, 2017
- Merge remote-tracking branch 'remotes/upstream/master'
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- changed example names and simplified _prepare_DF
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- Merge branch 'master' into add_transform_brsa
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- changed docstrings related to priors of tau
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- changed docstrings related to priors of tau
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Commits on Mar 23, 2017
- changing default of PCA to whiten the output
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- fixed issue with scan_onsets in GBRSA.score() and changed some text in gbrsa example
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Commits on Mar 24, 2017
- added two prior functions to __all__ of brsa.py. Changed default annealing speed. Added check for n_nureg when auto_nureg is True. Store the log likelihood for training data as private variable for…
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- remove blank line
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- move the location of input checking in GBRSA
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Commits on Mar 31, 2017
- correcting typo
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Commits on Apr 4, 2017
- add one check for scan_onsets in _fit_RSA_marginalized_null
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Commits on Apr 11, 2017
- Merge branch 'master' into add_transform_brsa
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Commits on Apr 12, 2017
- Merge branch 'add_transform_brsa' of https://github.com/lcnature/brainiak into add_transform_brsa
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- Merge remote-tracking branch 'upstream/master'
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- Merge branch 'master' into add_transform_brsa
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- Add automatic determination of nuisance regressor numbers based on BIC
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Commits on Apr 13, 2017
- correcting a but introduced to test_brsa.py
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- changed number of observations to n_T*n_V
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Commits on Apr 19, 2017
- changed some recommendations in the example of (g)brsa
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Commits on May 31, 2017
- Merge branch 'master' into add_transform_brsa
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- adding Ncomp_SVHT_MG_DLD_approx to brsa.py, and a few other changes from test_gbrsa branch, including half_log_det
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- fixed a bug
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Commits on Jun 4, 2017
- incorporating some changes in test_gbrsa into add_transform_brsa while the latter is still being reviewed. This preview_gbrsa version will be out for users to try before the full PR is finished
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- remove redundant sentence in docstring of GBRSA
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- reducing complexity of _fit_RSA_marginalized
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Commits on Jun 6, 2017
- changed the default method for estimating number of nuisance regressors to be the one by Gavish and Donoho, changed the prior of SNR to exponential distribution. Cleaned up some unused comments
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- increase test code coverage for reprsimil
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Commits on Jun 8, 2017
- add the two Ncomp functions to the modules listed in __all__ of reprsimil
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- Merge remote-tracking branch 'upstream/master' into add_transform_brsa
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- correct docstrings of Ncomp functions
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Commits on Jun 9, 2017
- fix a bug introduced in the previous version
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- added test for estimating n_nureg_
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Commits on Jun 19, 2017
- add checking for NaN after performing zscore, by adding a customized _zscore function
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- _zscore does not solve the problem. If there is no fluctuation in some voxels, fixing them all to 0 still cannot pass tests in ICA. So we will leave it for the users to exclude such voxels
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Commits on Jun 27, 2017
- implementing some of the suggested changes in pull request
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Commits on Jun 28, 2017
- partial update thanksto some of the comments
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- fixing docstring problem
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- continue debugging docstring
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- trying to figure out what is wrong with docstring
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- still debugging docstring
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Commits on Jun 29, 2017
- Merge remote-tracking branch 'upstream/master' into add_transform_brsa
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- fix trailing underscore issue
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- remove filtering of warnings
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- remove import of warnings in brsa
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- stripped brsa example outputs
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Commits on Jun 30, 2017
- more changes according to the code review
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Commits on Jul 5, 2017
- add more explanation to GP_inten
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- Changed the default optimizer of GBRSA back to BFGS. This is because practically I found that although L-BFGS-B runs faster for the same number of iteration, it appears to take more iterations in t…
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Commits on Jul 8, 2017
- make sure n_nureg_ is integer in BRSA
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Commits on Jul 10, 2017
- Changed the parameter name DC_single to baseline_single, and changed its default to False. A fix of bug happening when auto_nuisance=False and n_nureg is left unset.
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Commits on Jul 12, 2017
- changed default of nureg_method to PCA
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- add checking for SNR_prior
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- add comment in _set_SNR_grids
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- corrected for formatting of the comment
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Commits on Jul 13, 2017
- Merge remote-tracking branch 'upstream/master'
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Commits on Jul 14, 2017
- Merge remote-tracking branch 'upstream/master'
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- merged the change in upstream/master
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Commits on Jul 20, 2017
Commits on Jul 31, 2017
- Merge remote-tracking branch 'remotes/upstream/master'
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- Merge branch 'master' into add_transform_brsa
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- added feature description for this pull-request
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Commits on Aug 9, 2017
- addressed recent comment of brsa, moved CoM_exp function from reprsimil.brsa to utils.utils, and changed the default of n_nureg from opt to None, and added description of the extension of BRSA work…
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- added one sentence
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- changing one line to pass run-checks
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- replaced the phrase "refreshing noise" by "innovation noise"
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- changed some typo and docstrings
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- Merge branch 'master' into add_transform_brsa
  mihaic
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Commits

Commits on Sep 2, 2016

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Commits on Feb 27, 2017

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Commits on Apr 19, 2017