Code

Insights module and SHAPInsight#391

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AdrianSosic merged 102 commits intoemdgroup:mainemdgroup/baybe:mainfrom Alex6022:feature/shap-utilsAlex6022/baybe:feature/shap-utilsCopy head branch name to clipboardJan 20, 2025

+745-35

Commits

Commits on Sep 29, 2024

• Optional import of shap package.

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• 1st implementation of SHAP utilities in experimental space and with procedural approach.

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Commits on Oct 1, 2024

• Implementation option to perform SHAP either in computational or experimental searchspace representation.

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Commits on Oct 3, 2024

• SHAP package implementation in diagnostics utility, complete tests and plotting methods.

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• Tests for explainer utilities and generalization for all explainers in SHAP package.

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• Implemented plotting with non-shap attributions.

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Commits on Oct 4, 2024

• Refactored diagnostics test and optimized handling of maple explainers.

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• Shortened plotting method names.

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• Merge branch 'emdgroup:main' into feature/shap-utils

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• Cleanup for PR

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Commits on Oct 23, 2024

• Renamed diangostics package, enabled optional shap import

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• Merge branch 'emdgroup:main' into feature/shap-utils

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Commits on Oct 27, 2024

• Refactoring of test_diagnostics.py

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Commits on Oct 28, 2024

• Merge branch 'emdgroup:main' into feature/shap-utils

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• Merge branch 'feature/shap-utils' of https://github.com/Alex6022/baybe into feature/shap-utils

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• Merge branch 'feature/shap-utils' of https://github.com/Alex6022/baybe into feature/shap-utils

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• Fixed changelog merging error

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Commits on Nov 1, 2024

• Update pyproject.toml

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• Rework import flag

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• Update mypy.ini

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• Rework tests

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Commits on Nov 18, 2024

• Generalized explanation for all shap explainer types, refactoring of optional dependencies, diagnostics subpackage.

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• Merge branch 'feature/shap-utils' of https://github.com/Alex6022/baybe into feature/shap-utils

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Commits on Nov 19, 2024

• Reworked tests from feedback, Cleanup for Review

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Commits on Nov 20, 2024

• Further cleanup

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Commits on Dec 9, 2024

• Renaming of "diagnostics" package into "insights", Addition of Insight and SHAPInsight classes, refactoring of SHAP functions into SHAPInsight class.

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Commits on Dec 10, 2024

• Moved explainer maps from testing of shap functionality to shap, allowing explainers to be specified via strings. General cleanup for PR.

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• Merge branch 'main' of https://github.com/emdgroup/baybe into feature/shap-utils

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• Cleanup of CONTRIBUTORS.md

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Commits on Dec 27, 2024

• Minor reformatting

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• Package housekeeping

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• Merge branch 'main' into feature/shap-utils

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Commits on Jan 2, 2025

• Rework classes

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• Update tests

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Commits on Jan 3, 2025

• Enhance error message

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• Add special handling for Lime

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Commits on Jan 6, 2025

• Rename bg_data to background_data

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• Add missing validators

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• Fix type annotations

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• Replace unnecessary post init call

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• Remove unnecessary guard clause

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• Turn method guard clause into proper attribute validator

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• Improve model function definition

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Commits on Jan 7, 2025

• Refactor plot methods to return plt.Axes if plots not shown directly. Removed "force" from SUPPORTED_SHAP_PLOTS.

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• Merge branch 'feature/shap-utils' of https://github.com/Alex6022/baybe into feature/shap-utils

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• Drop Insights base class

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• Turn explanation property into explain method

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• Pass data to be explained as method argument

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• Extract explainer factory function

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• Add from_surrogate constructor

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Commits on Jan 8, 2025

• Refactor class attributes

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• Drop duplicate input validation

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• Refactor plotting

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• Define default explainer class

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• Make data to be explained optional

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• Drop converter utility

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Commits on Jan 9, 2025

• Refactor explainer sets

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• Add column permutation test

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• Make test pass by permuting columns

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• Rework docstrings

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• Avoid unnecessary data copy

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• Fix optional dependency handling

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• Use shap's optional dependency group

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• Update lockfile

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• Update README.md

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• Refactor insights/__init__.py

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• Update README.md

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• Refactor insights/__init__.py

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• Add missing sphinx-paramlinks doc dependency

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• Update lockfile

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• Fix BayBE spelling

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Commits on Jan 10, 2025

• fixup! Rework docstrings

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• Fix mypy issues

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Commits on Jan 12, 2025

• Merge branch 'feature/shap-utils' of https://github.com/Alex6022/baybe into feature/shap-utils

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• Fixed permutation of explanation object. Reintroduced ValueError when initiliazing SHAPInsight from campaign without measurements.

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Commits on Jan 13, 2025

• Simplify set union

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• Rename df method argument to data

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• Removed double docstring

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• Test cleanup

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• Improved comments and docstring

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• Filter data to measurement parameters only when initializing from recommender

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Commits on Jan 14, 2025

• Validate that explainer is of accepted type

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• Avoid test collection import errors due to optional dependencies

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• Drop try-except branch for unsupported explainers types

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• Refactor explainer incompatibility handling using type validation

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• Move content of temporary test file by overriding fixtures locally

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• Fix type check

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• Replace xfail with skip

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• Refine permutation workaround

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• Update lockfile

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• Fix sphinx references

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• Improve docstrings

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• Reintroduce recommender validation guard clause

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• Make use_comp_rep flag keyword-only

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• Adjust batteries included text in README

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• Move import statement to avoid test fail

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Commits on Jan 20, 2025

• Rephrase bullet point

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• Enable force plot

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• Fix kwargs type hints

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• Apply suggestions from code review

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• Expand tests

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• Use context for expected failures

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