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Add BreastInvasiveCarcinoma dataset #7905

Merged
merged 19 commits into from
Sep 2, 2023
Merged

Add BreastInvasiveCarcinoma dataset #7905

merged 19 commits into from
Sep 2, 2023

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Favourj-bit
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This is a dataset that was generated by integrating the breast cancer (BRCA TCGA) dataset from the cBioPortal (cbioportal.org) and a biological network for node connections from Pathway Commons (www.pathwaycommons.org). The dataset contains the gene features of each patient and the overall survival time (in months) of each patient, which are the labels.

@Favourj-bit
Added breast_cancer_graph_dataset
c7e7035 
This is a dataset that was generated by integrating the breast cancer (BRCA TCGA) dataset from the cBioPortal (cbioportal.org) and a biological network for node connections from Pathway Commons (www.pathwaycommons.org). The dataset contains the gene features of each patient and the overall survival time (in months) of each patient, which are the labels.
@Favourj-bit Favourj-bit requested a review from wsad1 as a code owner August 19, 2023 10:26
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codecov bot commented Aug 19, 2023 •
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Codecov Report

Merging #7905 (1e557bb) into master (6847849) will decrease coverage by 0.73%.
The diff coverage is n/a.

❗ Current head 1e557bb differs from pull request most recent head 41ec8c5. Consider uploading reports for the commit 41ec8c5 to get more accurate results

@@            Coverage Diff             @@
##           master    #7905      +/-   ##
==========================================
- Coverage   90.25%   89.52%   -0.73%     
==========================================
  Files         459      459              
  Lines       26954    26951       -3     
==========================================
- Hits        24328    24129     -199     
- Misses       2626     2822     +196

see 31 files with indirect coverage changes

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@Favourj-bit Favourj-bit changed the title Added breast_cancer_graph_dataset Added breast_invasive_carcinoma_brca.py Aug 21, 2023
@rusty1s rusty1s changed the title Added breast_invasive_carcinoma_brca.py Add BreastInvasiveCarcinoma dataset Aug 21, 2023
akihironitta
akihironitta reviewed Aug 26, 2023
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Thank you for adding this dataset! I've just directly made some changes to your PR, but please have a look and feel free to revert them if necessary :)

torch_geometric/datasets/brca_tgca.py Outdated
Comment on lines 17 to 22
r"""The breast cancer (BRCA TCGA) dataset from `cBioPortal
<https://www.cbioportal.org>`_ and the biological network for node
connections from `Pathway Commons <https://www.pathwaycommons.org>`_.
The dataset contains the gene features of each patient in graph_features
and the overall survival time (in months) of each patient,
which are the labels.
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Could you check the docstring change as I've just removed some redundant sentences? Also, it'd be ncie if you could describe what nodes and edges represent to help new users understand this dataset. (example: https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.datasets.KarateClub.html#torch_geometric.datasets.KarateClub)

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Hi @akihironitta
Thank you for your review. I noticed that you removed the link that directs to the repository where it shows how the data was created and modelling with the data. I think this is an important information that should be included, and during my discussion with @rusty1s , he mentioned i could include this in the docstring.
I'll be adding this back, but apart from that, I'm okay with the other changes

@rusty1s rusty1s enabled auto-merge (squash) September 2, 2023 11:43
@rusty1s rusty1s merged commit 9f33615 into pyg-team:master Sep 2, 2023
JakubPietrakIntel pushed a commit that referenced this pull request Sep 27, 2023
@Favourj-bit @pre-commit-ci
@akihironitta @rusty1s @JakubPietrakIntel
Add BreastInvasiveCarcinoma dataset (#7905)
f962189 
This is a dataset that was generated by integrating the breast cancer
(BRCA TCGA) dataset from the cBioPortal (cbioportal.org) and a
biological network for node connections from Pathway Commons
(www.pathwaycommons.org). The dataset contains the gene features of each
patient and the overall survival time (in months) of each patient, which
are the labels.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Akihiro Nitta <nitta@akihironitta.com>
Co-authored-by: Matthias Fey <matthias.fey@tu-dortmund.de>
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@akihironitta akihironitta akihironitta left review comments

@rusty1s rusty1s rusty1s approved these changes

@wsad1 wsad1 Awaiting requested review from wsad1 wsad1 is a code owner

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