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Deterministic SRM #102

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merged 17 commits into from Sep 21, 2016

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@TuKo
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TuKo commented Sep 14, 2016

Added the Deterministic Shared Response Model to Functional Alignment methods:

  • Added tests
  • Modified examples (python & notebook) to run with both Probabilistic and Deterministic SRM.
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mihaic Sep 14, 2016

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@cameronphchen Could you please review this PR?

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mihaic commented Sep 14, 2016

@cameronphchen Could you please review this PR?

This implementation is based on the following publications:
The implementations are based on the following publications:

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mihaic Sep 14, 2016

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Could you please change the second reference to our Arxiv paper?
https://arxiv.org/abs/1608.04647

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mihaic Sep 14, 2016

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Could you please change the second reference to our Arxiv paper?
https://arxiv.org/abs/1608.04647

TuKo added some commits Sep 14, 2016

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mihaic approved these changes Sep 14, 2016

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cameronphchen Sep 14, 2016

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@mihaic @TuKo Sure, I'll review this.

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cameronphchen commented Sep 14, 2016

@mihaic @TuKo Sure, I'll review this.

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Thanks Javier!! Overall it looks good to me. I have added a comment on a new test case and some other minor comments.

Show outdated Hide outdated brainiak/funcalign/srm.py
number of samples must be the same across subjects.
The Deterministic Shared Response Model is approximated using the
Block Coordinate Descent (BCD) algorithm proposed in [Chen2015]_.

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cameronphchen Sep 15, 2016

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Can we remove the _ after [Chen2015]?

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cameronphchen Sep 15, 2016

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Can we remove the _ after [Chen2015]?

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mihaic Sep 15, 2016

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That creates a link in the HTML version:
http://pythonhosted.org/brainiak/brainiak.funcalign.html

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mihaic Sep 15, 2016

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That creates a link in the HTML version:
http://pythonhosted.org/brainiak/brainiak.funcalign.html

X : list of 2D arrays, element i has shape=[voxels_i, samples]
Each element in the list contains the fMRI data of one subject.
y : not used

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cameronphchen Sep 15, 2016

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same here, if y is not used, why not remove it?

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cameronphchen Sep 15, 2016

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same here, if y is not used, why not remove it?

Show outdated Hide outdated brainiak/funcalign/srm.py
Show outdated Hide outdated brainiak/funcalign/srm.py
Show outdated Hide outdated tests/funcalign/test_srm.py
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TuKo Sep 20, 2016

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@cameronphchen, please check the modifications and let us know if everything is fine.

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TuKo commented Sep 20, 2016

@cameronphchen, please check the modifications and let us know if everything is fine.

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LGTM. Thanks for the revision!

@mihaic mihaic merged commit e010328 into brainiak:master Sep 21, 2016

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@TuKo TuKo deleted the TuKo:deterministicsrm branch Sep 28, 2016

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