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Add Bayesian RSA to the package (reprsimil) #98

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merged 63 commits into from Sep 22, 2016

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@lcnature
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lcnature commented Sep 7, 2016

Bayesian RSA stands for Bayesian representational similarity analysis.
The code should be functional.
Planned updates for the upcoming weeks:
(1) add an example as a python notebook
(2) upload supplementary file including the derivation of the gradient of log likelihood
(3) capability of modeling the spatial correlation of noise

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Can one of the admins verify this patch?

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buildbot-princeton commented Sep 7, 2016

Can one of the admins verify this patch?

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Can one of the admins verify this patch?

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buildbot-princeton commented Sep 7, 2016

Can one of the admins verify this patch?

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Add to whitelist.

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mihaic commented Sep 7, 2016

Add to whitelist.

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mihaic Sep 7, 2016

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Thank you for the PR, @lcnature.

Could you please recommend someone who is familiar with your work and can assess the neuroscience validity of the code?

Also, is pr-check passing for you? I tried on my computer and run-checks is failing just like on Jenkins because of trailing whitespace:

brainiak/reprsimil/brsa.py:23:31: W291 trailing whitespace
brainiak/reprsimil/brsa.py:123:14: W291 trailing whitespace
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mihaic commented Sep 7, 2016

Thank you for the PR, @lcnature.

Could you please recommend someone who is familiar with your work and can assess the neuroscience validity of the code?

Also, is pr-check passing for you? I tried on my computer and run-checks is failing just like on Jenkins because of trailing whitespace:

brainiak/reprsimil/brsa.py:23:31: W291 trailing whitespace
brainiak/reprsimil/brsa.py:123:14: W291 trailing whitespace
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lcnature Sep 8, 2016

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Sorry @mihaic . I made some changes to the docstring after it passed the last time.
The trailing whitespace was fixed but now I have errors about unexpected indentation in docstring, which I cannot find why.

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lcnature commented Sep 8, 2016

Sorry @mihaic . I made some changes to the docstring after it passed the last time.
The trailing whitespace was fixed but now I have errors about unexpected indentation in docstring, which I cannot find why.

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mihaic Sep 8, 2016

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That's perfectly OK. You can make as many commits you want, there is no issue with having test failures. :)

The line number in the doc building errors are very misleading (see issue #42).

You need an empty line before "Parameters".

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mihaic commented Sep 8, 2016

That's perfectly OK. You can make as many commits you want, there is no issue with having test failures. :)

The line number in the doc building errors are very misleading (see issue #42).

You need an empty line before "Parameters".

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Thanks @mshvartsman who has kindly agreed to review. I will let you know after I upload more documentation of the maths.

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lcnature commented Sep 8, 2016

Thanks @mshvartsman who has kindly agreed to review. I will let you know after I upload more documentation of the maths.

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@mihaic How can I know why the check with macos failed?

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lcnature commented Sep 8, 2016

@mihaic How can I know why the check with macos failed?

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@lcnature Within Princeton network, you can click the Details to see. It looks like it is an import error related to FCMA, which is weird because FCMA is not yet merged. @mihaic may have some idea about this?

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yidawang commented Sep 8, 2016

@lcnature Within Princeton network, you can click the Details to see. It looks like it is an import error related to FCMA, which is weird because FCMA is not yet merged. @mihaic may have some idea about this?

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lcnature Sep 8, 2016

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@yidawang In fact I do not have read permission -- access denied even after logging in.

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lcnature commented Sep 8, 2016

@yidawang In fact I do not have read permission -- access denied even after logging in.

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@lcnature I don't even know there are permission settings out there. In the "console output" I can see the code tries to import brainiak.fcma.cython_blas which is not supposed to be in the current codebase.

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yidawang commented Sep 8, 2016

@lcnature I don't even know there are permission settings out there. In the "console output" I can see the code tries to import brainiak.fcma.cython_blas which is not supposed to be in the current codebase.

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Retest this please.

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mihaic commented Sep 8, 2016

Retest this please.

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The error was caused by leftovers from previous PR builds, which were preventing the documentation from building. So not related to the new code. I added a clean step to the builder (I am sure I had added it before and it magically disappeared...) to prevent this from happening again.

Unfortunately, the Jenkins results are only visible to people with Jenkins accounts. I will talk to the admin to see if we can make the results public.

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mihaic commented Sep 8, 2016

The error was caused by leftovers from previous PR builds, which were preventing the documentation from building. So not related to the new code. I added a clean step to the builder (I am sure I had added it before and it magically disappeared...) to prevent this from happening again.

Unfortunately, the Jenkins results are only visible to people with Jenkins accounts. I will talk to the admin to see if we can make the results public.

Spatial correlation will be included in a future version.
"""
def __init__(

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Looks like there are some parameters here (intern_smooth_range, space_smooth_range, etc) that are not documented up in the docstring. If I understand the standard correctly, all exposed parameters (e.g. arguments to __init__) should be documented.

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Looks like there are some parameters here (intern_smooth_range, space_smooth_range, etc) that are not documented up in the docstring. If I understand the standard correctly, all exposed parameters (e.g. arguments to __init__) should be documented.

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lcnature Sep 8, 2016

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Thanks Mike! I will add them! Those are parameters added later and I forgot
to add documentation.

Mingbo Cai

On Thu, Sep 8, 2016 at 1:39 PM, Michael Shvartsman <notifications@github.com

wrote:

In brainiak/reprsimil/brsa.py
#98 (comment):

  • lGPspace_ : number, only if GP_space or GP_inten is True
  •    the length scale of Gaussian Process prior of log(SNR)
    
  • bGP_ : number, only if GP_space or GP_inten is True.
  •    the standard deviation of the GP prior
    
  • lGPinten_: number, only if GP_inten is True
  •    the length scale in fMRI intensity of the GP prior of log(SNR)
    
  • Notes

  • The current version assumes noise is independent across voxels.
  • Real data typically has spatial correlation in noise.
  • This assumption might still introduce some bias in the result.
  • Spatial correlation will be included in a future version.
  • """
  • def init(

Looks like there are some parameters here (intern_smooth_range,
space_smooth_range, etc) that are not documented up in the docstring. If I
understand the standard correctly, all exposed parameters (e.g. arguments
to init_) should be documented.


You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/IntelPNI/brainiak/pull/98/files/1f5775a6846235c51d7c65be2e22eae6cdec5444#r78053771,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AHZ3TXs1FwywlNuQwu1-cgF-TbXEiMklks5qoEg_gaJpZM4J3eAD
.

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lcnature Sep 8, 2016

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Thanks Mike! I will add them! Those are parameters added later and I forgot
to add documentation.

Mingbo Cai

On Thu, Sep 8, 2016 at 1:39 PM, Michael Shvartsman <notifications@github.com

wrote:

In brainiak/reprsimil/brsa.py
#98 (comment):

  • lGPspace_ : number, only if GP_space or GP_inten is True
  •    the length scale of Gaussian Process prior of log(SNR)
    
  • bGP_ : number, only if GP_space or GP_inten is True.
  •    the standard deviation of the GP prior
    
  • lGPinten_: number, only if GP_inten is True
  •    the length scale in fMRI intensity of the GP prior of log(SNR)
    
  • Notes

  • The current version assumes noise is independent across voxels.
  • Real data typically has spatial correlation in noise.
  • This assumption might still introduce some bias in the result.
  • Spatial correlation will be included in a future version.
  • """
  • def init(

Looks like there are some parameters here (intern_smooth_range,
space_smooth_range, etc) that are not documented up in the docstring. If I
understand the standard correctly, all exposed parameters (e.g. arguments
to init_) should be documented.


You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/IntelPNI/brainiak/pull/98/files/1f5775a6846235c51d7c65be2e22eae6cdec5444#r78053771,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AHZ3TXs1FwywlNuQwu1-cgF-TbXEiMklks5qoEg_gaJpZM4J3eAD
.

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mshvartsman Sep 16, 2016

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👍

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👍

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lcnature Sep 20, 2016

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@mihaic I cannot tell what causes a failure in Travid CI test:
https://travis-ci.org/IntelPNI/brainiak/jobs/161177341

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lcnature commented Sep 20, 2016

@mihaic I cannot tell what causes a failure in Travid CI test:
https://travis-ci.org/IntelPNI/brainiak/jobs/161177341

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@lcnature No clue. The error was only on MacOS. The tests passed on MacOS on Jenkins, so I restarted the Travis test.

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mihaic commented Sep 20, 2016

@lcnature No clue. The error was only on MacOS. The tests passed on MacOS on Jenkins, so I restarted the Travis test.

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mihaic Sep 20, 2016

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@lcnature More evidence that the best approach for solving computer errors is restarting. :)

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mihaic commented Sep 20, 2016

@lcnature More evidence that the best approach for solving computer errors is restarting. :)

@lcnature lcnature closed this Sep 20, 2016

@lcnature lcnature reopened this Sep 20, 2016

@mshvartsman

I think ready to go out there and get its tires kicked.

Show outdated Hide outdated brainiak/utils/utils.py
Show outdated Hide outdated brainiak/utils/utils.py
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lcnature Sep 21, 2016

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This time travis-CI throws some details for its failure. It looks like some problem with pytest iteslf.

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lcnature commented Sep 21, 2016

This time travis-CI throws some details for its failure. It looks like some problem with pytest iteslf.

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mihaic Sep 21, 2016

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@lcnature Please update the branch so I can merge it.

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mihaic commented Sep 21, 2016

@lcnature Please update the branch so I can merge it.

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mihaic approved these changes Sep 21, 2016

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@mihaic Thanks Mihai, I updated and travis-CI failed again...

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lcnature commented Sep 22, 2016

@mihaic Thanks Mihai, I updated and travis-CI failed again...

@mihaic mihaic merged commit 669f041 into brainiak:master Sep 22, 2016

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continuous-integration/travis-ci/pr The Travis CI build failed
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@lcnature Thank you very much for your contribution and for addressing the issues that came up during the review (thanks for pointing them out, @mshvartsman).
We will be looking into the Travis failure.

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mihaic commented Sep 22, 2016

@lcnature Thank you very much for your contribution and for addressing the issues that came up during the review (thanks for pointing them out, @mshvartsman).
We will be looking into the Travis failure.

@lcnature lcnature deleted the lcnature:add_brsa branch Sep 22, 2016

yidawang added a commit to yidawang/brainiak that referenced this pull request Sep 27, 2016

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