New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Add recent work to BRSA #194
Merged
Merged
Changes from all commits
Commits
Show all changes
154 commits
Select commit
Hold shift + click to select a range
e4ab872
a
06c869a
deleted: brsa/test.txt
9b0819c
Merge remote-tracking branch 'upstream/master'
7766c2b
Merge remote-tracking branch 'upstream/master'
89dc1e1
Merge remote-tracking branch 'upstream/master'
ea5b572
Merge remote-tracking branch 'upstream/master'
f65a42f
Merge remote-tracking branch 'upstream/master'
ea7b002
a
ad3af51
deleted: brsa/test.txt
4fec06f
Merge branch 'master' of https://github.com/lcnature/brainiak
66277e6
a
1b6127a
deleted: brsa/test.txt
4b1a794
a
2ded8db
deleted: brsa/test.txt
9ac940d
Merge remote-tracking branch 'refs/remotes/origin/master'
66ebf5f
a
6a24344
deleted: brsa/test.txt
746f66e
a
9fad12b
deleted: brsa/test.txt
92a199b
a
5265476
deleted: brsa/test.txt
3acf09f
a
bc49c16
deleted: brsa/test.txt
973bd92
Merge remote-tracking branch 'refs/remotes/origin/master'
f288c31
forcing scan_onsets to be integer
accb974
make scan_onsets integers as well in example
eed8ee8
Merge branch 'master' into add_transform_brsa
mihaic 0e7029f
Merge pull request #1 from mihaic/add_transform_brsa
lcnature 057deb0
Add transform function
e02d5a0
Adding marginalized version of BRSA
ceed81d
not finished
dab73e7
Adding group BRSA
16b5933
minor changes
aa8a540
new example for GBRSA
8e0eca4
correcting a bug of matrix size
4dd6b16
Cleaning brsa.py
c23ac2d
updating local changes made a while ago
1b87212
Making transform function not use private variable
8289f44
Merge branch 'master' of https://github.com/IntelPNI/brainiak
a5f9836
Merge branch 'master' of https://github.com/IntelPNI/brainiak into ad…
ab2fc0f
Merge branch 'master' of https://github.com/IntelPNI/brainiak
21ae9b6
Merge branch 'master' of https://github.com/IntelPNI/brainiak
7ca085e
working on forward step
f93fab9
forward step finished
2968cd1
Added backward step
64b58ed
working on score function
4d74871
finishing the score function
9655042
Finished the score and transform functions for both BRSA and GBRSA. C…
1cea980
one commit before trying autopep8
778ac7d
passed checks
eaafbd2
finished
149c37e
stripped the example notebookx
d6d4e97
merge
756c8df
add gest_gbrsa.py
a2309ce
cleaned test code
ec2ab08
adding some comments
e284a48
changes in accordance to the comments
f861056
add reference to BRSA within GBRSA
4c78752
add back one test to increase coverage of test
324ee0e
correcting test_brsa.py
7f7aecf
adding one blank line to score()
53d0a49
trying to further reduce test time
0cac292
adding more blank lines...
bf4c646
Fix Sphinx errors
mihaic ca7ead1
Merge pull request #2 from mihaic/add_transform_brsa_fix_sphinx
lcnature 4dc630f
add requirements for brsa example
9716eb4
change back to accepting only strong for nureg_method
5c2b5e4
change to argument tau2_prior
18e9db5
basically no change to test again
ada6841
debugging test failure
3fabc50
removed print()
6bef0a1
test what is different on the server
0974850
test server
1b3dc06
resubmit
7687ebe
changed gen_DF
a168632
changed all use of scipy.linalg.block_diag due to different behavior …
6eebc78
changes to the docstring
81cd751
uncomment out one test
1498229
Made description of the prior_var_GP* functions more generic, changed…
3784bfd
cut the docstring for prior_GP_var_half_cauchy
4ff14f8
correct a typo
99b55a1
change docstring of prior_GP_var_half_cauchy
b0dbd82
changed score() to make sure scan_onsets is initialized to an array o…
d1b9501
Additional change to utils.gen_design to make sure that the generated…
979cd82
Merge remote-tracking branch 'remotes/upstream/master'
8dcf274
changed example names and simplified _prepare_DF
d6c6cb8
Merge branch 'master' into add_transform_brsa
lcnature 1139445
changed docstrings related to priors of tau
bd3bc01
changed docstrings related to priors of tau
4f78da8
changing default of PCA to whiten the output
e92ef57
fixed issue with scan_onsets in GBRSA.score() and changed some text i…
944f0e1
added two prior functions to __all__ of brsa.py. Changed default anne…
ece81da
remove blank line
2acd7b6
move the location of input checking in GBRSA
fe9f954
correcting typo
7c57abd
add one check for scan_onsets in _fit_RSA_marginalized_null
733812f
Merge branch 'master' into add_transform_brsa
lcnature d250e29
Merge branch 'add_transform_brsa' of https://github.com/lcnature/brai…
741b9ee
Merge remote-tracking branch 'upstream/master'
bc29bf1
Merge branch 'master' into add_transform_brsa
cd28f83
Add automatic determination of nuisance regressor numbers based on BIC
c24d70e
correcting a but introduced to test_brsa.py
5ada11e
changed number of observations to n_T*n_V
1188d53
changed some recommendations in the example of (g)brsa
4664daf
Merge branch 'master' into add_transform_brsa
lcnature 7e9dbe7
adding Ncomp_SVHT_MG_DLD_approx to brsa.py, and a few other changes f…
db2990d
fixed a bug
30e3085
incorporating some changes in test_gbrsa into add_transform_brsa whil…
1506c45
remove redundant sentence in docstring of GBRSA
b7097f7
reducing complexity of _fit_RSA_marginalized
50f8820
changed the default method for estimating number of nuisance regresso…
92bd91f
increase test code coverage for reprsimil
c225f15
add the two Ncomp functions to the modules listed in __all__ of reprs…
2cf748b
Merge remote-tracking branch 'upstream/master' into add_transform_brsa
ea56834
correct docstrings of Ncomp functions
93cc5c5
fix a bug introduced in the previous version
6201378
added test for estimating n_nureg_
b2576ad
add checking for NaN after performing zscore, by adding a customized …
c672dee
_zscore does not solve the problem. If there is no fluctuation in som…
3cbad44
implementing some of the suggested changes in pull request
1b388fb
partial update thanksto some of the comments
73703f2
fixing docstring problem
e9909ec
continue debugging docstring
9689b99
trying to figure out what is wrong with docstring
85d3ac4
still debugging docstring
70afe3c
Merge remote-tracking branch 'upstream/master' into add_transform_brsa
7ac0f17
fix trailing underscore issue
a414f4f
remove filtering of warnings
3189ac6
remove import of warnings in brsa
42e823b
stripped brsa example outputs
068ced1
more changes according to the code review
060c706
add more explanation to GP_inten
28e799a
Changed the default optimizer of GBRSA back to BFGS. This is because …
dbbfdb8
make sure n_nureg_ is integer in BRSA
1ccab03
Changed the parameter name DC_single to baseline_single, and changed …
3fb031f
changed default of nureg_method to PCA
0c47ede
add checking for SNR_prior
37f4b22
add comment in _set_SNR_grids
60593af
corrected for formatting of the comment
5c87f1e
Merge remote-tracking branch 'upstream/master'
34af3ac
Merge remote-tracking branch 'upstream/master'
b918ccb
merged the change in upstream/master
c34745c
fixed some docstring according to the PR. Isolated the work of creati…
2e4bb88
renamed test_grid_flatten to test_grid_flatten_num_int
1545313
in test_grid_flatten_num_int() of test_gbrsa.py(), condense all codes…
8dd02ca
Merge remote-tracking branch 'remotes/upstream/master'
5177839
Merge branch 'master' into add_transform_brsa
9b6ed41
added feature description for this pull-request
af9fe57
addressed recent comment of brsa, moved CoM_exp function from reprsim…
e9b41cc
added one sentence
d5872a2
changing one line to pass run-checks
60f04e5
replaced the phrase "refreshing noise" by "innovation noise"
c131485
changed some typo and docstrings
b665e6b
Merge branch 'master' into add_transform_brsa
mihaic File filter
Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
There are no files selected for viewing
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,2 @@ | ||
reprsimil: add Group Bayesian RSA, add transform (decoding) and score (model selection) functions, add automatic determination of the number of necessary nuisance regressors. | ||
utils: modified gen_design to make the generated design matrix approximately scaled in amplitudes. |
Oops, something went wrong.
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.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
scale
is missing.There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
fixed