Use 2015 data & remove holdout set #5
Merged
Conversation
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
d33bs
reviewed
Dec 7, 2022
There was a problem hiding this comment.
Nice job! I left a few comments and suggestions with this review. Please don't hesitate to let me know if you have any questions or if I may clarify at all.
I also wanted to follow up with a general question:
- I noticed that notebook files
2.train_model/train_model.ipynband4.interpret_model/interpret_model.ipynbdid not have nbconverted.pypair files. Should those be included with this PR?
Co-authored-by: Dave Bunten <[email protected]>
…iling_model into use-2015-data
|
Thank you for the review @d33bs! Notebook files |
|
Accidentally merged this PR without approval, but @d33bs and I discussed that everything was good to merge. |
roshankern
added a commit
that referenced
this pull request
Dec 12, 2022
* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <[email protected]> * PR fixes * module docstrings Co-authored-by: Dave Bunten <[email protected]> * add PR curves * get PR curves/data * update docs, recreate py files * greg recommendations Co-authored-by: Dave Bunten <[email protected]>
roshankern
added a commit
that referenced
this pull request
Jan 4, 2023
* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <[email protected]> * PR fixes * module docstrings Co-authored-by: Dave Bunten <[email protected]> * validation module * correlation matrix * reviz * reformat * pearson correlation * spearman correlation * documentation * documentation * docs * docs, rerun * docs * docs * Update 5.validate_model/validate_model.sh Co-authored-by: Dave Bunten <[email protected]> * Update utils/validate_utils.py Co-authored-by: Dave Bunten <[email protected]> * raw link clarification * Update utils/validate_utils.py Co-authored-by: Dave Bunten <[email protected]> * Update utils/validate_utils.py Co-authored-by: Dave Bunten <[email protected]> * Update utils/validate_utils.py Co-authored-by: Dave Bunten <[email protected]> * conditional to remove x, y columns * clarify perturbation rename * black formatting Co-authored-by: Dave Bunten <[email protected]>
roshankern
added a commit
that referenced
this pull request
Feb 6, 2023
* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <[email protected]> * PR fixes * module docstrings Co-authored-by: Dave Bunten <[email protected]> * move class PR curves * use typing tuple return hint * use tuple * confusion matrix evaluation * rename cm files * update documentation * code documentation * get model scores * undo last commit * update documentation * use correct env * dave suggestions --------- Co-authored-by: Dave Bunten <[email protected]>
roshankern
added a commit
that referenced
this pull request
Feb 7, 2023
* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <[email protected]> * PR fixes * module docstrings Co-authored-by: Dave Bunten <[email protected]> * add score util * add/run notebook * update documentation/formatting * update documentation * black formatting * rename function * compile tidy data * update documentation, dave suggestions --------- Co-authored-by: Dave Bunten <[email protected]>
roshankern
added a commit
that referenced
this pull request
Feb 10, 2023
* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <[email protected]> * PR fixes * module docstrings Co-authored-by: Dave Bunten <[email protected]> * create single cell images module * rename_module * finish module * remove sample images from PR * Co-authored-by: Jenna Tomkinson <[email protected]> * documentation * documentation * dave suggestions * Update utils/single_cell_utils.py Co-authored-by: Dave Bunten <[email protected]> --------- Co-authored-by: Dave Bunten <[email protected]>
roshankern
added a commit
that referenced
this pull request
Feb 10, 2023
* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <[email protected]> * PR fixes * module docstrings Co-authored-by: Dave Bunten <[email protected]> * upload files --------- Co-authored-by: Dave Bunten <[email protected]>
roshankern
added a commit
that referenced
this pull request
Feb 13, 2023
* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <[email protected]> * PR fixes * module docstrings Co-authored-by: Dave Bunten <[email protected]> * save interpretations * docs, recreate py file * fix typo * PR suggestions --------- Co-authored-by: Dave Bunten <[email protected]>
roshankern
added a commit
that referenced
this pull request
Feb 14, 2023
* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <[email protected]> * PR fixes * module docstrings Co-authored-by: Dave Bunten <[email protected]> * get predictions * delete unused file, compiled predictions * rerun evaluate module * docs * dave suggestions --------- Co-authored-by: Dave Bunten <[email protected]>
roshankern
added a commit
that referenced
this pull request
Feb 17, 2023
* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <[email protected]> * PR fixes * module docstrings Co-authored-by: Dave Bunten <[email protected]> * restructure PR curves notebook * dave suggestions --------- Co-authored-by: Dave Bunten <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
This PR is ready for review! This PR incorporates a newer version of mitocheck_data, downloading the 2015 MitoCheck dataset and merging it with the older dataset. The pipeline is then rerun with this expanded dataset.
The "holdout" dataset is also removed, leaving only the training and testing data subsets. Our logic here is that the application of the final phenotypic profiling model to other datasets (ex Cell Health) will validate the model in the same way a holdout dataset would.