Module and scripts for evaluating representations (#156)

* docstring * move scripts from contrastive_scripts to viscy/scripts * organize files in applications/contrastive_phenotyping * delete unused evaluation code * more cleanup * refactor evaluation metrics for translation task * refactor viscy.evaluation -> viscy.translation.evaluation_metrics and viscy.representation.evaluation * WIP: representation evaluation module * WIP: representation eval - docstrings in numpy format * WIP: more documentation * refactor: feature_extractor moved to viscy.representation.evaluation * lint * bug fix * refactored common computations and dataset * add imbalance-learn dependecy to metrics * refactor classification of embeddings * organize viscy.representation.evaluation * ruff * Soorya's plotting script * WIP: combine two versions of plot_embeddings.py * simplify representation.viscy.evaluation - move LCA to its own module * refactor of viscy.representation.evaluation * refactored and tested PCA and UMAP plots --------- Co-authored-by: Soorya Pradeep <[email protected]>
mehta-lab · Sep 10, 2024 · 634b955 · 634b955
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diff --git a/applications/contrastive_phenotyping/contrastive_cli/computed_features.py b/applications/contrastive_phenotyping/contrastive_cli/computed_features.py
diff --git a/applications/contrastive_phenotyping/contrastive_cli/figures/figure4/classify_feb.py b/applications/contrastive_phenotyping/contrastive_cli/figures/figure4/classify_feb.py
diff --git a/applications/contrastive_phenotyping/contrastive_scripts/demo_fit.py b/applications/contrastive_phenotyping/contrastive_scripts/demo_fit.py