Add PerturbationDataValidator #672
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Zethson
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Oct 16, 2024
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Zethson
commented
- Adds a first implementation of PerturbationDataValidator
- Switches RTD to UV
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
…e/perturbation_data_validator
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
stefanpeidli
added a commit
that referenced
this pull request
Feb 7, 2025
* Set legend anchor as parameter (#660) * Fix missing space * Remove explicit anndata in dependencies (#666) * Incorporate use case tutorials (#665) * Fixed DEG layer retrieval * Use-case tutorial icons * Restructure tutorial page * Subgroup tutorials * Improve KNN label_transfer in PerturbationSpace (#658) * Add uncertainty score in KNN label_transfer in PerturbationSpace Certainty is quantified as the fraction of nearest neighbors belonging to the classified (i.e. the most abundant) label compared to the total number of nearest neighbors. * Update pre-commit-config.yaml Replaces yanked dependency of mypy "types-pkg-resources" with "types-setuptools" as recommended: https://pypi.org/project/types-pkg-resources/ * Improve label imputation in PerturbationSpace class Key changes: - Now uses KNN graph in adata: saves cost and increases consistency - Vectorized operations instead of expensive for loop - Distance weighting for KNN imputation - Quantifies uncertainty as local KNN label entropy * Fixed plotting for mixscape.plot_barplot and sccoda.plot_effects_barplot (#667) * Augur scsim warnings (#670) * Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Add PerturbationDataValidator (#672) * Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> * Add super draft of pertpy validator Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Nested try Signed-off-by: zethson <[email protected]> * validator in test Signed-off-by: zethson <[email protected]> * try uv for rtd Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv fix Signed-off-by: zethson <[email protected]> * mb sphinx fix for validator Signed-off-by: zethson <[email protected]> * docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Latest OS for RTD * Remove curator again Signed-off-by: zethson <[email protected]> * Fix jax random array (#686) * Fix jax random array Signed-off-by: zethson <[email protected]> * Fix further jax warnings Signed-off-by: zethson <[email protected]> * Fix edger Signed-off-by: zethson <[email protected]> * Fix choice Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Switch to formulaic-contrasts (#682) * Switch to formulaic-contrasts * Cleanup * removing design matrix workaround (#691) Co-authored-by: Emma Dann <[email protected]> * Fix PyDESeq2 * Update tests * fix typo in gitignore * Remove contrast dataclass, which isnt used anywhere * Fix edgeR rpy2 tests (#692) * fix broken rpy2 edger tests * updated edger tests * Fix tests (scipy) Signed-off-by: zethson <[email protected]> * submodule Signed-off-by: zethson <[email protected]> * Remove unused code Signed-off-by: zethson <[email protected]> * type hints Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: zethson <[email protected]> * Release 0.9.5 Signed-off-by: zethson <[email protected]> * Prepare 0.10.0 Signed-off-by: zethson <[email protected]> * Added Mixscape seeds and test (#683) Co-authored-by: Lukas Heumos <[email protected]> * Fix probability data type (#696) Signed-off-by: Lukas Heumos <[email protected]> * Optimize MeanVarDistributionDistance (#697) * Fix probability data type Signed-off-by: Lukas Heumos <[email protected]> * Optimize mean_var distance Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Optimize test speed (#699) * Try buildjet Signed-off-by: Lukas Heumos <[email protected]> * Try buildjet large Signed-off-by: Lukas Heumos <[email protected]> * speed up predict_differential_prioritization Signed-off-by: Lukas Heumos <[email protected]> * speed up tests Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Lower bound for scikit-learn (#701) Signed-off-by: Lukas Heumos <[email protected]> * Fix type annotation Signed-off-by: Lukas Heumos <[email protected]> * Fix empty figure returns when show=True in plotting functions (#703) * Removed show parameter * Adapt plotting API for Augur, Coda, Dialogue * Adapted plotting API for Milo, Mixscape, scgen * Add joblib * Remove joblib --------- Co-authored-by: Lukas Heumos <[email protected]> * Fix scikit-learn intendation Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: zethson <[email protected]> Signed-off-by: Lukas Heumos <[email protected]> Co-authored-by: Lilly May <[email protected]> Co-authored-by: Lukas Heumos <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]>
stefanpeidli
added a commit
that referenced
this pull request
Feb 7, 2025
* Set legend anchor as parameter (#660) * Fix missing space * Remove explicit anndata in dependencies (#666) * Incorporate use case tutorials (#665) * Fixed DEG layer retrieval * Use-case tutorial icons * Restructure tutorial page * Subgroup tutorials * Improve KNN label_transfer in PerturbationSpace (#658) * Add uncertainty score in KNN label_transfer in PerturbationSpace Certainty is quantified as the fraction of nearest neighbors belonging to the classified (i.e. the most abundant) label compared to the total number of nearest neighbors. * Update pre-commit-config.yaml Replaces yanked dependency of mypy "types-pkg-resources" with "types-setuptools" as recommended: https://pypi.org/project/types-pkg-resources/ * Improve label imputation in PerturbationSpace class Key changes: - Now uses KNN graph in adata: saves cost and increases consistency - Vectorized operations instead of expensive for loop - Distance weighting for KNN imputation - Quantifies uncertainty as local KNN label entropy * Fixed plotting for mixscape.plot_barplot and sccoda.plot_effects_barplot (#667) * Augur scsim warnings (#670) * Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Add PerturbationDataValidator (#672) * Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> * Add super draft of pertpy validator Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Nested try Signed-off-by: zethson <[email protected]> * validator in test Signed-off-by: zethson <[email protected]> * try uv for rtd Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv fix Signed-off-by: zethson <[email protected]> * mb sphinx fix for validator Signed-off-by: zethson <[email protected]> * docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Latest OS for RTD * Remove curator again Signed-off-by: zethson <[email protected]> * Fix jax random array (#686) * Fix jax random array Signed-off-by: zethson <[email protected]> * Fix further jax warnings Signed-off-by: zethson <[email protected]> * Fix edger Signed-off-by: zethson <[email protected]> * Fix choice Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Switch to formulaic-contrasts (#682) * Switch to formulaic-contrasts * Cleanup * removing design matrix workaround (#691) Co-authored-by: Emma Dann <[email protected]> * Fix PyDESeq2 * Update tests * fix typo in gitignore * Remove contrast dataclass, which isnt used anywhere * Fix edgeR rpy2 tests (#692) * fix broken rpy2 edger tests * updated edger tests * Fix tests (scipy) Signed-off-by: zethson <[email protected]> * submodule Signed-off-by: zethson <[email protected]> * Remove unused code Signed-off-by: zethson <[email protected]> * type hints Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: zethson <[email protected]> * Release 0.9.5 Signed-off-by: zethson <[email protected]> * Prepare 0.10.0 Signed-off-by: zethson <[email protected]> * Added Mixscape seeds and test (#683) Co-authored-by: Lukas Heumos <[email protected]> * Fix probability data type (#696) Signed-off-by: Lukas Heumos <[email protected]> * Optimize MeanVarDistributionDistance (#697) * Fix probability data type Signed-off-by: Lukas Heumos <[email protected]> * Optimize mean_var distance Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Optimize test speed (#699) * Try buildjet Signed-off-by: Lukas Heumos <[email protected]> * Try buildjet large Signed-off-by: Lukas Heumos <[email protected]> * speed up predict_differential_prioritization Signed-off-by: Lukas Heumos <[email protected]> * speed up tests Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Lower bound for scikit-learn (#701) Signed-off-by: Lukas Heumos <[email protected]> * Fix type annotation Signed-off-by: Lukas Heumos <[email protected]> * Fix empty figure returns when show=True in plotting functions (#703) * Removed show parameter * Adapt plotting API for Augur, Coda, Dialogue * Adapted plotting API for Milo, Mixscape, scgen * Add joblib * Remove joblib --------- Co-authored-by: Lukas Heumos <[email protected]> * Fix scikit-learn intendation Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: zethson <[email protected]> Signed-off-by: Lukas Heumos <[email protected]> Co-authored-by: Lilly May <[email protected]> Co-authored-by: Lukas Heumos <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]>
Zethson
added a commit
that referenced
this pull request
Feb 20, 2025
* Implement mixture models for guide assignment Key additions: - Added a base abstract class "MixtureModel" with numpyro - Added a first mixture model "Poisson_Gauss_Mixture" - New function "assign_mixture_model" in GuideAssignment class * Merge main into branch (#705) * Set legend anchor as parameter (#660) * Fix missing space * Remove explicit anndata in dependencies (#666) * Incorporate use case tutorials (#665) * Fixed DEG layer retrieval * Use-case tutorial icons * Restructure tutorial page * Subgroup tutorials * Improve KNN label_transfer in PerturbationSpace (#658) * Add uncertainty score in KNN label_transfer in PerturbationSpace Certainty is quantified as the fraction of nearest neighbors belonging to the classified (i.e. the most abundant) label compared to the total number of nearest neighbors. * Update pre-commit-config.yaml Replaces yanked dependency of mypy "types-pkg-resources" with "types-setuptools" as recommended: https://pypi.org/project/types-pkg-resources/ * Improve label imputation in PerturbationSpace class Key changes: - Now uses KNN graph in adata: saves cost and increases consistency - Vectorized operations instead of expensive for loop - Distance weighting for KNN imputation - Quantifies uncertainty as local KNN label entropy * Fixed plotting for mixscape.plot_barplot and sccoda.plot_effects_barplot (#667) * Augur scsim warnings (#670) * Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Add PerturbationDataValidator (#672) * Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> * Add super draft of pertpy validator Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Nested try Signed-off-by: zethson <[email protected]> * validator in test Signed-off-by: zethson <[email protected]> * try uv for rtd Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv fix Signed-off-by: zethson <[email protected]> * mb sphinx fix for validator Signed-off-by: zethson <[email protected]> * docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Latest OS for RTD * Remove curator again Signed-off-by: zethson <[email protected]> * Fix jax random array (#686) * Fix jax random array Signed-off-by: zethson <[email protected]> * Fix further jax warnings Signed-off-by: zethson <[email protected]> * Fix edger Signed-off-by: zethson <[email protected]> * Fix choice Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Switch to formulaic-contrasts (#682) * Switch to formulaic-contrasts * Cleanup * removing design matrix workaround (#691) Co-authored-by: Emma Dann <[email protected]> * Fix PyDESeq2 * Update tests * fix typo in gitignore * Remove contrast dataclass, which isnt used anywhere * Fix edgeR rpy2 tests (#692) * fix broken rpy2 edger tests * updated edger tests * Fix tests (scipy) Signed-off-by: zethson <[email protected]> * submodule Signed-off-by: zethson <[email protected]> * Remove unused code Signed-off-by: zethson <[email protected]> * type hints Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: zethson <[email protected]> * Release 0.9.5 Signed-off-by: zethson <[email protected]> * Prepare 0.10.0 Signed-off-by: zethson <[email protected]> * Added Mixscape seeds and test (#683) Co-authored-by: Lukas Heumos <[email protected]> * Fix probability data type (#696) Signed-off-by: Lukas Heumos <[email protected]> * Optimize MeanVarDistributionDistance (#697) * Fix probability data type Signed-off-by: Lukas Heumos <[email protected]> * Optimize mean_var distance Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Optimize test speed (#699) * Try buildjet Signed-off-by: Lukas Heumos <[email protected]> * Try buildjet large Signed-off-by: Lukas Heumos <[email protected]> * speed up predict_differential_prioritization Signed-off-by: Lukas Heumos <[email protected]> * speed up tests Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Lower bound for scikit-learn (#701) Signed-off-by: Lukas Heumos <[email protected]> * Fix type annotation Signed-off-by: Lukas Heumos <[email protected]> * Fix empty figure returns when show=True in plotting functions (#703) * Removed show parameter * Adapt plotting API for Augur, Coda, Dialogue * Adapted plotting API for Milo, Mixscape, scgen * Add joblib * Remove joblib --------- Co-authored-by: Lukas Heumos <[email protected]> * Fix scikit-learn intendation Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: zethson <[email protected]> Signed-off-by: Lukas Heumos <[email protected]> Co-authored-by: Lilly May <[email protected]> Co-authored-by: Lukas Heumos <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]> * Merge main into branch (#706) * Set legend anchor as parameter (#660) * Fix missing space * Remove explicit anndata in dependencies (#666) * Incorporate use case tutorials (#665) * Fixed DEG layer retrieval * Use-case tutorial icons * Restructure tutorial page * Subgroup tutorials * Improve KNN label_transfer in PerturbationSpace (#658) * Add uncertainty score in KNN label_transfer in PerturbationSpace Certainty is quantified as the fraction of nearest neighbors belonging to the classified (i.e. the most abundant) label compared to the total number of nearest neighbors. * Update pre-commit-config.yaml Replaces yanked dependency of mypy "types-pkg-resources" with "types-setuptools" as recommended: https://pypi.org/project/types-pkg-resources/ * Improve label imputation in PerturbationSpace class Key changes: - Now uses KNN graph in adata: saves cost and increases consistency - Vectorized operations instead of expensive for loop - Distance weighting for KNN imputation - Quantifies uncertainty as local KNN label entropy * Fixed plotting for mixscape.plot_barplot and sccoda.plot_effects_barplot (#667) * Augur scsim warnings (#670) * Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Add PerturbationDataValidator (#672) * Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> * Add super draft of pertpy validator Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Nested try Signed-off-by: zethson <[email protected]> * validator in test Signed-off-by: zethson <[email protected]> * try uv for rtd Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv fix Signed-off-by: zethson <[email protected]> * mb sphinx fix for validator Signed-off-by: zethson <[email protected]> * docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Latest OS for RTD * Remove curator again Signed-off-by: zethson <[email protected]> * Fix jax random array (#686) * Fix jax random array Signed-off-by: zethson <[email protected]> * Fix further jax warnings Signed-off-by: zethson <[email protected]> * Fix edger Signed-off-by: zethson <[email protected]> * Fix choice Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> * Switch to formulaic-contrasts (#682) * Switch to formulaic-contrasts * Cleanup * removing design matrix workaround (#691) Co-authored-by: Emma Dann <[email protected]> * Fix PyDESeq2 * Update tests * fix typo in gitignore * Remove contrast dataclass, which isnt used anywhere * Fix edgeR rpy2 tests (#692) * fix broken rpy2 edger tests * updated edger tests * Fix tests (scipy) Signed-off-by: zethson <[email protected]> * submodule Signed-off-by: zethson <[email protected]> * Remove unused code Signed-off-by: zethson <[email protected]> * type hints Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: zethson <[email protected]> * Release 0.9.5 Signed-off-by: zethson <[email protected]> * Prepare 0.10.0 Signed-off-by: zethson <[email protected]> * Added Mixscape seeds and test (#683) Co-authored-by: Lukas Heumos <[email protected]> * Fix probability data type (#696) Signed-off-by: Lukas Heumos <[email protected]> * Optimize MeanVarDistributionDistance (#697) * Fix probability data type Signed-off-by: Lukas Heumos <[email protected]> * Optimize mean_var distance Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Optimize test speed (#699) * Try buildjet Signed-off-by: Lukas Heumos <[email protected]> * Try buildjet large Signed-off-by: Lukas Heumos <[email protected]> * speed up predict_differential_prioritization Signed-off-by: Lukas Heumos <[email protected]> * speed up tests Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]> * Lower bound for scikit-learn (#701) Signed-off-by: Lukas Heumos <[email protected]> * Fix type annotation Signed-off-by: Lukas Heumos <[email protected]> * Fix empty figure returns when show=True in plotting functions (#703) * Removed show parameter * Adapt plotting API for Augur, Coda, Dialogue * Adapted plotting API for Milo, Mixscape, scgen * Add joblib * Remove joblib --------- Co-authored-by: Lukas Heumos <[email protected]> * Fix scikit-learn intendation Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: zethson <[email protected]> Signed-off-by: Lukas Heumos <[email protected]> Co-authored-by: Lilly May <[email protected]> Co-authored-by: Lukas Heumos <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]> * Refactor guide assignment logic and enhance mixture model parameters * Cleanup MixtureModel class * Enhance guide assignment validation and error handling in GuideAssignment class * Update dev nb * Add test for grna_mixture_model * Remove dev nb * Update notebook for guide assignment * Update guide assignment notebooks * Apply suggestions from code review Review comments by @Zethson Co-authored-by: Lukas Heumos <[email protected]> * Improve code to fit review suggestions - Added lots of type hints and return types - Improved naming of variables - Added and removed a few comments - Added user warnings if a guide is not expressed at all * Fix sloppy data dimensions for numpyro Previously data was (N,1) dim. Now applying ravel, and changed numpyro plates accordingly for correct batching. * Update test_grna_assignment.py We changed "Negative" to "negative" :) * Polish Signed-off-by: Lukas Heumos <[email protected]> * Polish Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: zethson <[email protected]> Signed-off-by: Lukas Heumos <[email protected]> Co-authored-by: Lilly May <[email protected]> Co-authored-by: Lukas Heumos <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]>
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