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BayBE documentation

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Version: 0.11.4

Documentation

Readme
User Guide
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Examples
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- Basics
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  - Campaign
  - Recommenders
- Searchspaces
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- Constraints Discrete
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  - Exclusion
  - Mixture
  - Product/Sum
  - Dependency
  - Custom
- Constraints Continuous
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  - Linear
  - Hybrid Space
- Multi Target
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  - Desirability
- Serialization
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- Custom Surrogates
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  - Surrogate Params
  - Custom Pretrained
- Backtesting
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- Custom Hooks
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- Multi Armed Bandit
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  - Bernoulli Multi Armed Bandit
- Transfer Learning
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  - Backtesting
  - Basic Transfer Learning

baybe
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- baybe.acquisition
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  - baybe.acquisition.acqfs
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  - baybe.acquisition.base
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    - AcquisitionFunction
  - baybe.acquisition.partial
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    - PartialAcquisitionFunction
  - baybe.acquisition.utils
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    - baybe.acquisition.utils.convert_acqf
    - baybe.acquisition.utils.str_to_acqf
- baybe.campaign
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  - Campaign
- baybe.constraints
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  - baybe.constraints.base
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  - baybe.constraints.conditions
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  - baybe.constraints.continuous
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    - ContinuousCardinalityConstraint
    - ContinuousLinearConstraint
  - baybe.constraints.deprecation
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  - baybe.constraints.discrete
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  - baybe.constraints.validation
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    - baybe.constraints.validation.validate_cardinality_constraints_are_nonoverlapping
    - baybe.constraints.validation.validate_constraints
- baybe.exceptions
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- baybe.kernels
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  - baybe.kernels.base
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  - baybe.kernels.basic
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  - baybe.kernels.composite
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- baybe.objective
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  - baybe.objective.Objective
- baybe.objectives
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  - baybe.objectives.base
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    - baybe.objectives.base.to_objective
    - Objective
  - baybe.objectives.deprecation
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    - baybe.objectives.deprecation.structure_objective
  - baybe.objectives.desirability
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    - baybe.objectives.desirability.scalarize
    - DesirabilityObjective
  - baybe.objectives.enum
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    - Scalarizer
  - baybe.objectives.single
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    - SingleTargetObjective
- baybe.parameters
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  - baybe.parameters.base
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  - baybe.parameters.categorical
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    - CategoricalParameter
    - TaskParameter
  - baybe.parameters.custom
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    - CustomDiscreteParameter
  - baybe.parameters.enum
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  - baybe.parameters.numerical
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    - NumericalContinuousParameter
    - NumericalDiscreteParameter
  - baybe.parameters.substance
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    - baybe.parameters.substance.Smiles
    - SubstanceParameter
  - baybe.parameters.utils
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    - baybe.parameters.utils.get_parameters_from_dataframe
    - baybe.parameters.utils.sort_parameters
  - baybe.parameters.validation
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- baybe.priors
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  - baybe.priors.base
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    - Prior
  - baybe.priors.basic
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- baybe.recommenders
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  - baybe.recommenders.base
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    - RecommenderProtocol
  - baybe.recommenders.meta
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    - baybe.recommenders.meta.base
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      - MetaRecommender
    - baybe.recommenders.meta.sequential
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  - baybe.recommenders.naive
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    - NaiveHybridSpaceRecommender
  - baybe.recommenders.pure
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    - baybe.recommenders.pure.base
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      - PureRecommender
    - baybe.recommenders.pure.bayesian
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      - baybe.recommenders.pure.bayesian.base
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        BayesianRecommender
      - baybe.recommenders.pure.bayesian.botorch
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        BotorchRecommender
      - baybe.recommenders.pure.bayesian.sequential_greedy
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        baybe.recommenders.pure.bayesian.sequential_greedy.SequentialGreedyRecommender
    - baybe.recommenders.pure.nonpredictive
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      - baybe.recommenders.pure.nonpredictive.base
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        NonPredictiveRecommender
      - baybe.recommenders.pure.nonpredictive.clustering
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        GaussianMixtureClusteringRecommender
        
        KMeansClusteringRecommender
        
        PAMClusteringRecommender
        
        SKLearnClusteringRecommender
      - baybe.recommenders.pure.nonpredictive.sampling
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        FPSRecommender
        
        RandomRecommender
- baybe.searchspace
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  - baybe.searchspace.continuous
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    - SubspaceContinuous
  - baybe.searchspace.core
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  - baybe.searchspace.discrete
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  - baybe.searchspace.validation
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- baybe.serialization
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  - baybe.serialization.core
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  - baybe.serialization.mixin
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    - SerialMixin
  - baybe.serialization.utils
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    - baybe.serialization.utils.deserialize_dataframe
    - baybe.serialization.utils.serialize_dataframe
- baybe.simulation
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  - baybe.simulation.core
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    - baybe.simulation.core.simulate_experiment
  - baybe.simulation.lookup
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    - baybe.simulation.lookup.look_up_targets
  - baybe.simulation.scenarios
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    - baybe.simulation.scenarios.simulate_scenarios
  - baybe.simulation.transfer_learning
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    - baybe.simulation.transfer_learning.simulate_transfer_learning
- baybe.surrogates
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  - baybe.surrogates.bandit
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    - BetaBernoulliMultiArmedBanditSurrogate
  - baybe.surrogates.base
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  - baybe.surrogates.custom
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    - baybe.surrogates.custom.register_custom_architecture
    - CustomONNXSurrogate
  - baybe.surrogates.gaussian_process
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    - baybe.surrogates.gaussian_process.core
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      - GaussianProcessSurrogate
    - baybe.surrogates.gaussian_process.kernel_factory
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    - baybe.surrogates.gaussian_process.presets
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        baybe.surrogates.gaussian_process.presets.core.make_gp_from_preset
        
        GaussianProcessPreset
      - baybe.surrogates.gaussian_process.presets.default
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        DefaultKernelFactory
      - baybe.surrogates.gaussian_process.presets.edbo
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        EDBOKernelFactory
  - baybe.surrogates.linear
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    - BayesianLinearSurrogate
  - baybe.surrogates.naive
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    - MeanPredictionSurrogate
  - baybe.surrogates.ngboost
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    - NGBoostSurrogate
  - baybe.surrogates.random_forest
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    - RandomForestSurrogate
  - baybe.surrogates.utils
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  - baybe.surrogates.validation
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    - baybe.surrogates.validation.get_model_params_validator
    - baybe.surrogates.validation.validate_custom_architecture_cls
- baybe.targets
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  - baybe.targets.base
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    - Target
  - baybe.targets.binary
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    - baybe.targets.binary.ChoiceValue
    - BinaryTarget
  - baybe.targets.enum
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    - TargetMode
    - TargetTransformation
  - baybe.targets.numerical
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    - NumericalTarget
  - baybe.targets.transforms
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- baybe.telemetry
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- baybe.utils
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  - baybe.utils.augmentation
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    - baybe.utils.augmentation.df_apply_dependency_augmentation
    - baybe.utils.augmentation.df_apply_permutation_augmentation
  - baybe.utils.basic
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  - baybe.utils.boolean
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  - baybe.utils.botorch_wrapper
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    - baybe.utils.botorch_wrapper.botorch_function_wrapper
  - baybe.utils.chemistry
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  - baybe.utils.conversion
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    - baybe.utils.conversion.fraction_to_float
    - baybe.utils.conversion.nonstring_to_tuple
  - baybe.utils.dataframe
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  - baybe.utils.interval
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  - baybe.utils.memory
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    - baybe.utils.memory.bytes_to_human_readable
  - baybe.utils.numerical
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  - baybe.utils.plotting
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  - baybe.utils.random
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    - baybe.utils.random.set_random_seed
    - baybe.utils.random.temporary_seed
  - baybe.utils.sampling_algorithms
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  - baybe.utils.scaling
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    - ColumnTransformer
  - baybe.utils.torch
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    - baybe.utils.torch.VARNAME_TORCH_USE_SINGLE_PRECISION
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  - baybe.utils.validation
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Misc

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Contributors
Known Issues
Changelog
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Backtesting¶

These examples demonstrate BayBE’s Backtesting capabilities.

Multi Target
Custom Analytical
Full Lookup
Botorch Analytical
Hybrid
Full Initial Data
Impute Mode

Example for full simulation loop using the multi target mode for custom analytic

Example for surrogate model with a custom pretrained model

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