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Add MIDA, CoIRLS, distribution plot, and brain example #246

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merged 55 commits into from Aug 1, 2022
Merged

Add MIDA, CoIRLS, distribution plot, and brain example #246

merged 55 commits into from Aug 1, 2022

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shuo-zhou
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@shuo-zhou shuo-zhou commented Oct 21, 2021 •
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Fixes #173.

Description

  • An example for multi-site brain fMRI classification.
  • A toy example of domain adaptation.
  • PyTorch version>=1.10.0
  • Refactor: kale.embed.mpca -> kale.embed.factorization
  • New features:
    • kale.embde.factorization.MIDA
    • kale.interpret.visualize.distplot_1d
    • kale.pipeline.multi_domain_adapter.CoIRLS

Status

Ready

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Breaking change (fix or new feature that would cause existing functionality to change).
  • New tests added to cover the changes.
  • In-line docstrings updated.
  • Source for documentation at docs manually updated for new API.

@shuo-zhou shuo-zhou marked this pull request as draft October 21, 2021 12:45
@shuo-zhou shuo-zhou added the work-in-progress Work in progress that should NOT be merged label Nov 20, 2021
@haipinglu
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@sz144 I hope to work with you to resolve and merge this PR after merging #284. Share the issues remaining with the team today.

haipinglu
haipinglu reviewed Jul 27, 2022
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examples/autism_detection/config.py Outdated
@@ -0,0 +1,39 @@
"""
Default configurations for cardiac MRI data (ShefPAH) processing and classification
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@haipinglu haipinglu Jul 27, 2022 •
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Have you checked your code/comment? Are you sure this config is about cardiac? The filename says autism.

haipinglu
haipinglu reviewed Jul 27, 2022
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examples/autism_detection/config.py Outdated
# -----------------------------------------------------------------------------
_C.DATASET = CN()
_C.DATASET.ROOT = "../data"
_C.DATASET.PIPELINE = "cpac"
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@haipinglu haipinglu Jul 27, 2022 •
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Any reference to help users to read further? Particularly, available options.

haipinglu
haipinglu reviewed Jul 27, 2022
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examples/autism_detection/config.py
_C.DATASET = CN()
_C.DATASET.ROOT = "../data"
_C.DATASET.PIPELINE = "cpac"
_C.DATASET.ATLAS = "rois_cc200"
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@haipinglu haipinglu Jul 27, 2022 •
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Any reference (as a comment)?
Possible to provide (as a comment) available options?

haipinglu
haipinglu reviewed Jul 27, 2022
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examples/toy_domain_adaptation/main.py Outdated
from kale.pipeline.multi_domain_adapter import _CoIRLS


def plot_scores_dist(ys_score, yt_score, title=None):
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@haipinglu haipinglu Jul 27, 2022 •
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Is this reusable for problems of the same nature? If yes, then it should go to core API, e.g. visualization.

haipinglu
haipinglu reviewed Jul 27, 2022
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examples/video_loading/README.md Outdated
- [4. Alternate Video Frame Sampling Methods](#4-alternate-video-frame-sampling-methods)
- [5. Using VideoFrameDataset for training](#5-using-videoframedataset-for-training)
- [6. Allowing Multiple Labels per Sample](#6-allowing-multiple-labels-per-sample)
- [5. Conclusion](#5-conclusion)
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Why change this and with two 5s and 6s?

haipinglu
haipinglu reviewed Jul 28, 2022
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kale/embed/decomposition.py Outdated
Haiping Lu, K.N. Plataniotis, and A.N. Venetsanopoulos, "MPCA: Multilinear Principal Component Analysis of Tensor
Objects", IEEE Transactions on Neural Networks, Vol. 19, No. 1, Page: 18-39, January 2008. For initial Matlab
implementation, please go to https://uk.mathworks.com/matlabcentral/fileexchange/26168.
"""Python implementation of tensor decomposition approach Multilinear Principal Component Analysis (MPCA)
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As said, factorization should be better than decomposition.
Also, have you updated the docs?

@shuo-zhou shuo-zhou added new feature New feature/module (including request) and removed work-in-progress Work in progress that should NOT be merged labels Jul 28, 2022
@shuo-zhou shuo-zhou requested a review from haipinglu July 31, 2022 18:54
haipinglu
haipinglu reviewed Jul 31, 2022
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haipinglu
haipinglu requested changes Jul 31, 2022
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Great job.
Only some minor issues remain to be fixed (see comments). Once done, it can be merged. Many thanks.

@haipinglu haipinglu changed the title Brain example Add brain example Aug 1, 2022
@haipinglu haipinglu changed the title Add brain example Add MIDA, CoIRLS, distribution plot, and brain example Aug 1, 2022
@haipinglu haipinglu merged commit 7342dd3 into pykale:main Aug 1, 2022
@shuo-zhou shuo-zhou deleted the brain-example branch August 2, 2022 00:39
@github-actions github-actions bot mentioned this pull request Aug 11, 2022
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Construct an example on brain fMRI classification
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@shuo-zhou @haipinglu @xianyuanliu @bobturneruk @peizhenbai @codecov-commenter