share xgboost code with scarches_xgb #16
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Author
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Ping @LuckyMD :) |
Owner
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ahhh, this is useful. I was planning on doing this as well ^^. Thanks. |
Author
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You're welcome! Don't think I can merge this into your branch but feel free to merge if you're happy with this. |
Owner
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I will check in more detail exactly what you removed and then merge :) |
* use just one batch of pancreas data * keep_techs or [...]
Co-authored-by: openproblems-bio <[email protected]> Co-authored-by: Scott Gigante <[email protected]>
* add openproblems-cli test instructions * fix typo * include aws cli in instructions * make KEY_NAME more obvious * document describe and shutdown * use jq to get status * split aws instructions into separate md * Add AWS profile to EC2 instructions, fix launching command * Update EC2.md * Reference docker * lint * ubuntu requires su * ubuntu requires su Co-authored-by: Scott Gigante <[email protected]> Co-authored-by: Nikolay Markov <[email protected]> Co-authored-by: Scott Gigante <[email protected]>
Updates the requirements on [rpy2](https://github.com/rpy2/rpy2) to permit the latest version. - [Release notes](https://github.com/rpy2/rpy2/releases) - [Changelog](https://github.com/rpy2/rpy2/blob/master/NEWS) - [Commits](https://github.com/rpy2/rpy2/commits) --- updated-dependencies: - dependency-name: rpy2 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <[email protected]>
Co-authored-by: openproblems-bio <[email protected]> Co-authored-by: Scott Gigante <[email protected]>
…o#658) Updates the requirements on [sagemaker](https://github.com/aws/sagemaker-python-sdk) to permit the latest version. - [Release notes](https://github.com/aws/sagemaker-python-sdk/releases) - [Changelog](https://github.com/aws/sagemaker-python-sdk/blob/master/CHANGELOG.md) - [Commits](aws/sagemaker-python-sdk@v2.113.0...v2.116.0) --- updated-dependencies: - dependency-name: sagemaker dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <[email protected]>
Co-authored-by: openproblems-bio <[email protected]> Co-authored-by: Scott Gigante <[email protected]>
…ems-bio#661) Updates the requirements on [torch](https://github.com/pytorch/pytorch) to permit the latest version. - [Release notes](https://github.com/pytorch/pytorch/releases) - [Changelog](https://github.com/pytorch/pytorch/blob/master/RELEASE.md) - [Commits](pytorch/pytorch@v1.12.0-rc1...v1.13.0) --- updated-dependencies: - dependency-name: torch dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <[email protected]>
* add short metric descriptions to README * pre-commit * move metrics in subtask readmes * pre-commit * reformated graph metrics * change format of READMEs in all batch integration subtasks * pre-commit * line breaks * more line breaks * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: LuckyMD <[email protected]>
* retry failed request * another one
* use v1.10 benchmark * just pull the images * update full benchmark to v1.10
* fix DR baselines * add density test * fix dataset prep * bugfix * can't have >500 comps * ignore missing parametricumap * typo * account for arpack convergence
…penproblems-bio#823) * metrics check if input is baseline * pre-commit * check if embedding or nn graph present for baselines * rest of baseline checks * silhouette baseline check * refactor * refacotr embed * set is_baseline after method to prevent overwrite * set is_baseline in sample method --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <[email protected]>
* Changes in destVI code (openproblems-bio#826) Co-authored-by: Scott Gigante <[email protected]> * pre-commit --------- Co-authored-by: Can Ergen <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* new common baselines and cross import * pre-commit * addressing comments * pre-commit * fix wrong import * wrong import * pre-commit * wrong import 2 * pre-commit --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* jitter baseline patch * celltype_random_embedding_w/o_jitter * Split jitter and no jitter * import --------- Co-authored-by: Scott Gigante <[email protected]>
) * add reverse order/regular order Try to match the magic code format for decorators and implementation of reverse norm * Update __init__.py * pre-commit * Update alra.py * Update alra.py * pre-commit * Fix method names * Update alra.py * function names should be lowercase * Update alra.R * X is unused * Fix bug * Revert 77302de * pre-commit * Actually pass sqrt in sqrt norm methods --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <[email protected]>
* precompute nn ranking on full data * bugfix * bugfix2 * fix sample_dataset * just subsample it * Remove nan check
* add method and metric summaries * Update auprc.py
* shorten method descriptions * Update auprc.py * pre-commit --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* parse metadata in new format * typo # ci skip * ignore workdir * remove selectively * temp * bugfix # ci skip * fix ref # ci skip * more temp # ci skip * don't remove tasks # ci skip # publish * pretty print # ci skip # publish * move get_sha to utils * add get_sha to workflow_utils * push meta to experimental website * monitor separate;y * don't build images for website * id -> task_id * add description if missing * only publish explicitly * test website # publish * fix ref # publish * untemp * remove patch # publish * clean up readmes # publish * also publish the bib * remove experimental website repo * remove unnecessary diff * add code url to function metadata # publish * set base to main # publish * code_url was already taken # publish
* temp * add get_sha to workflow_utils * refactor results # ci skip * fixes # ci skip * install gitpython * upload new results path * # publish * test process * test process # publish * test process # publish * temp * test process # publish * Revert "temp" This reverts commit 5ccbdfa. * temp # publish * pre-commit * remove experimental website repo --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* only update sha on changes * handle git hash of functions * comment git_hash function * pre-commit * ignore another warning --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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