0.13.0

What's Changed

Added

• extras group for installing all dependencies required for optional features
• Support for NumPy 2.0+
• ParetoObjective class for Pareto optimization of multiple targets and corresponding
  qNoisyExpectedHypervolumeImprovement / qLogNoisyExpectedHypervolumeImprovement /
  qLogNParEGO acquisition functions
• Composite surrogates now drop rows containing NaNs (separately for each target),
  effectively enabling partial measurements
• SubstanceParameter, CustomDiscreteParameter and CategoricalParameter now also
  support restricting the search space via active_values, while values continue to
  identify allowed measurement inputs
• Campaign.posterior_stats and Surrogate.posterior_stats as convenience methods for
  providing statistical measures about the target predictions of a given set of
  candidates
• acquisition_values and joint_acquisition_value convenience methods to
  Campaign and BayesianRecommender for computing acquisition values
• Campaign.get_acquisition_function and BayesianRecommender.get_acquisition_function
  convenience methods for retrieving the underlying acquisition function
• AcquisitionFunction.evaluate convenience method for computing acquisition values
  from candidates in experimental representation
• qPSTD acquisition function
• BCUT2D encoding for SubstanceParameter
• SHAPInsight now supports the waterfall plot type
• Cardinality constraints sections to the user guide
• ContinuousCardinalityConstraint is now compatible with BotorchRecommender
• Attribute max_n_subspaces to BotorchRecommender, allowing to control
  optimization behavior in the presence of cardinality constraints
• Surrogate.replicate method for making single-target surrogate models multi-target
  compatible
• CompositeSurrogate class for composing multi-target surrogates from single-target
  surrogates
• is_multi_output attribute to Objective
• supports_multi_output attribute/property to Surrogate/AcquisitionFunction
• n_outputs property to Objective
• Attribute relative_threshold and method get_absolute_thresholds to
  ContinuousCardinalityConstraint for handling inactivity ranges
• Utilities inactive_parameter_combinations andn_inactive_parameter_combinations
  to both ContinuousCardinalityConstraintand SubspaceContinuous for iterating
  over cardinality-constrained parameter sets
• Utilities activate_parameter and is_cardinality_fulfilled for enforcing and
  validating cardinality constraints
• Utility is_inactive for determining if parameters are inactive
• A MinimumCardinalityViolatedWarning is triggered when minimum cardinality
  constraints are violated
• Stored benchmarking results now include the Python environment and version

Changed

• Targets are now allowed to contain NaN, deferring potential failure to attempted
  recommendation instead of data ingestion
• For label-like parameters, SubspaceDiscrete now only includes parameter values
  that are in active_values
• The default value for sequential_continuous in BotorchRecommender has been
  changed to True
• SHAPInsight now allows explanation input that has additional columns compared to
  the background data (will be ignored)
• Acquisition function indicator is_mc has been removed in favor of new indicators
  supports_batching and supports_pending_experiments
• fuzzy_row_match now uses vectorized operations, resulting in a speedup of matching
  measurements to the search space between 4x and 40x
• Model scaling now uses the parameter bounds instead of the search space bounds
• benchmarks module now accepts a list of domains to be executed
• Construction of BoTorch acquisition functions has been redesigned from ground up
• ngboost is now an optional dependency
• setuptools-scm is now an optional dependency, used for improved version inference
• create_example_plots, to_string and indent have been relocated within utils

Fixed

• Incorrect optimization direction with PSTD with a single minimization target
• Provide version fallback in case scm fails to infer version during installation

Removed

• fuzzy_row_match will no longer warn about entries not matching to the search space
• funcy dependency
• scikit-learn-extra dependency by integrating relevant code parts into baybe

Expired Deprecations (from 0.9.*)

• baybe.objective namespace
• acquisition_function_cls constructor parameter for BayesianRecommender
• VarUCB and qVarUCB acquisition functions

Merged Pull Requests

• Fix Substance Encodings by @Scienfitz in #474
• Add Python environment and version metadata to benchmark results by @fabianliebig in #476
• Serialize python env and version data by @fabianliebig in #478
• Refactor benchmark architecture by @AdrianSosic in #477
• Refactor ACQF indicators by @Scienfitz in #479
• XFail bugged test case by @Scienfitz in #481
• Fix SHAP Plot Tests by @Scienfitz in #486
• Rework validation for measurements and pending_experiments by @Scienfitz in #456
• Negative beta values by @AdrianSosic in #488
• Minor SHAP improvements by @Scienfitz in #494
• Increase timeout for benchmark test to 1440 minutes (24 hours) by @fabianliebig in #498
• Add logging to indicate currently running benchmark and its runtime by @fabianliebig in #499
• Vectorize fuzzy_row_match by @Scienfitz in #489
• Disable pre-commit.ci autofixing by @AdrianSosic in #501
• Pareto optimization by @AdrianSosic in #475
• Botorch with cardinality constraint via sampling by @Waschenbacher in #301
• Fix Pareto example plot export by @AdrianSosic in #505
• Fix serialization errors on 3.12 by @AdrianSosic in #506
• User guide for cardinality constraints by @AdrianSosic in #496
• Generalize active_values by @Scienfitz in #495
• Pipeline benchmark parallelization by @fabianliebig in #502
• Xfail bugged SHAP plot tests by @Scienfitz in #510
• Fix converter typing by @AdrianSosic in #511
• Acquisition function builder by @AdrianSosic in #490
• Add Campaign.posterior_stats by @Scienfitz in #504
• Provide version fallback in case scm fails to infer version during installation by @dasmy in #524
• Fix lockfile creation for uv>=0.6.0 by @AdrianSosic in #527
• Drop funcy dependency by @AdrianSosic in #528
• Add qLogNParEGO by @Scienfitz in #532
• More hypervolume acquisition functions by @AdrianSosic in #507
• Make ngboost optional by @AdrianSosic in #529
• Posterior Stats: Catch No Measurements Case by @Scienfitz in #536
• Make scikit-learn-extra optional by @AdrianSosic in #530
• Make setuptools-scm optional by @AdrianSosic in #526
• Enable Pareto and MATCH by @Scienfitz in #537
• Acquisition utility method by @AdrianSosic in #509
• Remove xfail for fixed SHAP case by @Scienfitz in #540
• Expire 0.9.* deprecations by @AdrianSosic in #497
• Enable Partial Measurements by @Scienfitz in #514
• Integrate KMedoids by @Scienfitz in #538
• Bump dev tools versions by @AdrianSosic in #503
• Release 0.13.0 by @AdrianSosic in #541

New Contributors

• @dasmy made their first contribution in #524

Full Changelog: 0.12.2...0.13.0