Index

A

add_logging_args() (in module batchie.log_config) add_observations() (batchie.core.BayesianModel method) add_score() (batchie.core.ScoresHolder method) (batchie.scoring.main.ChunkedScoresHolder method)

add_theta() (batchie.core.ThetaHolder method) add_value() (batchie.core.DistanceMatrix method) (batchie.distance_calculation.ChunkedDistanceMatrix method) alpha (batchie.models.sparse_combo.SparseDrugComboMCMCSample attribute)

B

batchie.common module batchie.core module batchie.data module batchie.distance.mse module batchie.distance_calculation module batchie.fast_mvn module batchie.introspection module batchie.log_config module batchie.models.sparse_combo module batchie.models.sparse_combo_interaction module

batchie.policies.k_per_sample module batchie.retrospective module batchie.sampling module batchie.scoring.gaussian_dbal module batchie.scoring.main module batchie.scoring.rand module batchie.scoring.size module batchie.synergy module BatchieEnsemblePlateSmoother (class in batchie.retrospective) BayesianModel (class in batchie.core) bliss() (batchie.models.sparse_combo.LegacySparseDrugComboImpl method)

C

calculate_mse() (in module batchie.retrospective) calculate_pairwise_distance_matrix_on_predictions() (in module batchie.distance_calculation) calculate_synergy() (in module batchie.synergy) ChunkedDistanceMatrix (class in batchie.distance_calculation) ChunkedScoresHolder (class in batchie.scoring.main) combine() (batchie.core.ThetaHolder method) (batchie.data.Screen method) (batchie.data.ScreenBase method) (batchie.data.ScreenSubset method) (batchie.distance_calculation.ChunkedDistanceMatrix method) (batchie.scoring.main.ChunkedScoresHolder method) concat() (batchie.core.ThetaHolder class method) (batchie.data.Screen class method) (batchie.data.ScreenSubset class method) (batchie.distance_calculation.ChunkedDistanceMatrix class method) (batchie.scoring.main.ChunkedScoresHolder class method)

configure_logging() (in module batchie.log_config) consume() (in module batchie.distance_calculation) control_treatment_name (batchie.data.ScreenSubset property) copy_array_with_control_treatments_set_to_zero() (in module batchie.common) create_instance() (in module batchie.introspection) create_plate_balanced_holdout_set_among_masked_plates() (in module batchie.retrospective) create_random_holdout() (in module batchie.retrospective) create_single_treatment_effect_array() (in module batchie.data) create_single_treatment_effect_map() (in module batchie.data)

D

dbal_fast_gauss_scoring_vectorized() (in module batchie.scoring.gaussian_dbal) dbal_fast_gaussian_scoring_heteroscedastic() (in module batchie.scoring.gaussian_dbal) dbal_fast_gaussian_scoring_homoscedastic() (in module batchie.scoring.gaussian_dbal) distance() (batchie.core.DistanceMetric method) (batchie.distance.mse.MSEDistance method)

DistanceMatrix (class in batchie.core) DistanceMetric (class in batchie.core) doses_for_treatment() (batchie.data.ExperimentSpace method)

E

encode_1d_array_to_0_indexed_ids() (in module batchie.data) encode_obs() (batchie.models.sparse_combo.LegacySparseDrugComboImpl method) (batchie.models.sparse_combo_interaction.LegacySparseDrugComboInteractionImpl method) encode_treatment_arrays_to_0_indexed_ids() (in module batchie.data)

equals() (batchie.core.Theta method) ess_pars() (batchie.models.sparse_combo.LegacySparseDrugComboImpl method) evaluate() (batchie.core.Metric method) evaluate_all() (batchie.core.Metric method) ExperimentSpace (class in batchie.data)

F

filter_dataset_to_treatments_that_appear_in_at_least_one_combo() (in module batchie.data) filter_dataset_to_unique_treatments() (in module batchie.data) filter_eligible_plates() (batchie.core.PlatePolicy method) (batchie.policies.k_per_sample.KPerSamplePlatePolicy method)

FixedSizeSmoother (class in batchie.retrospective) from_dicts() (batchie.core.Theta class method) (batchie.models.sparse_combo.SparseDrugComboMCMCSample class method) (batchie.models.sparse_combo_interaction.SparseDrugComboInteractionMCMCSample class method) from_screen() (batchie.data.ExperimentSpace class method)

G

GaussianDBALScorer (class in batchie.scoring.gaussian_dbal) generate_and_unmask_initial_plate() (batchie.core.InitialRetrospectivePlateGenerator method) generate_combination_at_sorted_index() (in module batchie.scoring.gaussian_dbal) generate_plates() (batchie.core.RetrospectivePlateGenerator method) get() (batchie.models.sparse_combo.LegacySparseDrugComboImpl method) get_class() (in module batchie.introspection) get_combination_at_sorted_index() (in module batchie.scoring.gaussian_dbal) get_lower_triangular_indices_chunk() (in module batchie.distance_calculation)

get_model_state() (batchie.core.MCMCModel method) (batchie.models.sparse_combo.SparseDrugCombo method) (batchie.models.sparse_combo_interaction.SparseDrugComboInteraction method) get_number_of_lower_triangular_indices() (in module batchie.distance_calculation) get_plate() (batchie.data.Screen method) get_required_init_args_with_annotations() (in module batchie.introspection) get_score() (batchie.core.ScoresHolder method) (batchie.scoring.main.ChunkedScoresHolder method) get_theta() (batchie.core.ThetaHolder method)

I

InitialRetrospectivePlateGenerator (class in batchie.core) interactions_to_logits() (in module batchie.models.sparse_combo) invert() (batchie.data.ScreenSubset method)

is_complete (batchie.core.ThetaHolder property) is_complete() (batchie.distance_calculation.ChunkedDistanceMatrix method) is_observed (batchie.data.ScreenBase property)

K

KPerSamplePlatePolicy (class in batchie.policies.k_per_sample)

L

LegacySparseDrugComboImpl (class in batchie.models.sparse_combo) LegacySparseDrugComboInteractionImpl (class in batchie.models.sparse_combo_interaction) load() (batchie.core.DistanceMatrix class method) (batchie.core.SimulationTracker class method) (batchie.distance_calculation.ChunkedDistanceMatrix class method)

load_h5() (batchie.core.ThetaHolder static method) (batchie.data.ExperimentSpace class method) (batchie.data.Screen static method) (batchie.scoring.main.ChunkedScoresHolder class method) lower_triangular_indices() (in module batchie.distance_calculation)

M

mask_screen() (in module batchie.retrospective) mcmc_step() (batchie.models.sparse_combo.LegacySparseDrugComboImpl method) (batchie.models.sparse_combo_interaction.LegacySparseDrugComboInteractionImpl method) MCMCModel (class in batchie.core) merge() (batchie.data.Plate method) MergeMinPlateSmoother (class in batchie.retrospective) MergeTopBottomPlateSmoother (class in batchie.retrospective) Metric (class in batchie.core) module batchie.common batchie.core batchie.data batchie.distance.mse batchie.distance_calculation batchie.fast_mvn batchie.introspection batchie.log_config batchie.models.sparse_combo batchie.models.sparse_combo_interaction batchie.policies.k_per_sample batchie.retrospective batchie.sampling batchie.scoring.gaussian_dbal batchie.scoring.main batchie.scoring.rand batchie.scoring.size batchie.synergy

MSEDistance (class in batchie.distance.mse)

N

n_obs() (batchie.core.BayesianModel method) (batchie.models.sparse_combo.LegacySparseDrugComboImpl method) (batchie.models.sparse_combo.SparseDrugCombo method) (batchie.models.sparse_combo_interaction.LegacySparseDrugComboInteractionImpl method) (batchie.models.sparse_combo_interaction.SparseDrugComboInteraction method) n_plates (batchie.data.ScreenBase property) n_thetas (batchie.core.ThetaHolder property)

n_unique_doses (batchie.data.ExperimentSpace property) n_unique_samples (batchie.data.ExperimentSpace property) (batchie.data.ScreenBase property) n_unique_treatment_types (batchie.data.ExperimentSpace property) n_unique_treatments (batchie.data.ExperimentSpace property) (batchie.data.ScreenBase property) NPlatePerCellLineSmoother (class in batchie.retrospective) numpy_array_is_0_indexed_integers() (in module batchie.data)

O

observation_mask (batchie.data.Screen property) (batchie.data.ScreenBase property) (batchie.data.ScreenSubset property)

observations (batchie.data.Screen property) (batchie.data.ScreenBase property) (batchie.data.ScreenSubset property) OptimalSizeSmoother (class in batchie.retrospective)

P

pad_ragged_arrays_to_dense_array() (in module batchie.scoring.gaussian_dbal) PairwisePlateGenerator (class in batchie.retrospective) Plate (class in batchie.data) plate_id (batchie.data.Plate property) plate_id_with_minimum_score() (batchie.core.ScoresHolder method) (batchie.scoring.main.ChunkedScoresHolder method) plate_ids (batchie.data.Screen property) (batchie.data.ScreenBase property) (batchie.data.ScreenSubset property) plate_mapping (batchie.data.Screen property) (batchie.data.ScreenBase property) (batchie.data.ScreenSubset property) plate_name (batchie.data.Plate property) PlatePermutationPlateGenerator (class in batchie.retrospective) PlatePolicy (class in batchie.core) plates (batchie.data.Screen property) precision (batchie.models.sparse_combo.SparseDrugComboMCMCSample attribute) (batchie.models.sparse_combo_interaction.SparseDrugComboInteractionMCMCSample attribute)

predict() (batchie.models.sparse_combo.LegacySparseDrugComboImpl method) (in module batchie.models.sparse_combo) predict_conditional_mean() (batchie.core.Theta method) (batchie.models.sparse_combo.SparseDrugComboMCMCSample method) (batchie.models.sparse_combo_interaction.SparseDrugComboInteractionMCMCSample method) predict_conditional_variance() (batchie.core.Theta method) (batchie.models.sparse_combo.SparseDrugComboMCMCSample method) (batchie.models.sparse_combo_interaction.SparseDrugComboInteractionMCMCSample method) predict_single_drug() (batchie.models.sparse_combo.LegacySparseDrugComboImpl method) (in module batchie.models.sparse_combo) predict_viability() (batchie.core.Theta method) (batchie.models.sparse_combo.SparseDrugComboMCMCSample method) (batchie.models.sparse_combo_interaction.SparseDrugComboInteractionMCMCSample method) private_parameters_dict() (batchie.core.Theta method) (batchie.models.sparse_combo.SparseDrugComboMCMCSample method) (batchie.models.sparse_combo_interaction.SparseDrugComboInteractionMCMCSample method)

R

RandomScorer (class in batchie.scoring.rand) reset_model() (batchie.core.BayesianModel method) (batchie.models.sparse_combo.LegacySparseDrugComboImpl method) (batchie.models.sparse_combo.SparseDrugCombo method) (batchie.models.sparse_combo_interaction.LegacySparseDrugComboInteractionImpl method) (batchie.models.sparse_combo_interaction.SparseDrugComboInteraction method)

RetrospectivePlateGenerator (class in batchie.core) RetrospectivePlateSmoother (class in batchie.core) reveal_plates() (in module batchie.retrospective) rng (batchie.core.BayesianModel property) (batchie.models.sparse_combo.SparseDrugCombo property) (batchie.models.sparse_combo_interaction.SparseDrugComboInteraction property)

S

sample() (batchie.core.VIModel method) (in module batchie.sampling) sample_id_from_sample_name() (batchie.data.ExperimentSpace method) sample_ids (batchie.data.Screen property) (batchie.data.ScreenBase property) (batchie.data.ScreenSubset property) sample_mapping (batchie.data.Screen property) (batchie.data.ScreenBase property) (batchie.data.ScreenSubset property) sample_mvn_from_precision() (in module batchie.fast_mvn) sample_name_from_sample_id() (batchie.data.ExperimentSpace method) sample_names (batchie.data.Screen property) (batchie.data.ScreenBase property) (batchie.data.ScreenSubset property) sample_space_size (batchie.data.ScreenBase property) SampleSegregatingPermutationPlateGenerator (class in batchie.retrospective) save() (batchie.core.DistanceMatrix method) (batchie.core.SimulationTracker method) (batchie.distance_calculation.ChunkedDistanceMatrix method) save_h5() (batchie.core.ThetaHolder method) (batchie.data.ExperimentSpace method) (batchie.data.Screen method) (batchie.scoring.main.ChunkedScoresHolder method) score() (batchie.core.Scorer method) (batchie.scoring.gaussian_dbal.GaussianDBALScorer method) (batchie.scoring.rand.RandomScorer method) (batchie.scoring.size.SizeScorer method) score_chunk() (in module batchie.scoring.main) Scorer (class in batchie.core) ScoresHolder (class in batchie.core)

Screen (class in batchie.data) ScreenBase (class in batchie.data) ScreenSubset (class in batchie.data) select_next_plate() (in module batchie.scoring.main) select_unique_zipped_numpy_arrays() (in module batchie.common) set_observed() (batchie.data.Screen method) set_rng() (batchie.core.BayesianModel method) (batchie.models.sparse_combo.SparseDrugCombo method) (batchie.models.sparse_combo_interaction.SparseDrugComboInteraction method) shared_parameters_dict() (batchie.core.Theta method) (batchie.models.sparse_combo_interaction.SparseDrugComboInteractionMCMCSample method) SimulationTracker (class in batchie.core) single_effect_lookup (batchie.models.sparse_combo_interaction.SparseDrugComboInteractionMCMCSample attribute) single_treatment_effects (batchie.data.Screen property) (batchie.data.ScreenBase property) (batchie.data.ScreenSubset property) size (batchie.data.ScreenBase property) SizeScorer (class in batchie.scoring.size) smooth_plates() (batchie.core.RetrospectivePlateSmoother method) SparseCoverPlateGenerator (class in batchie.retrospective) SparseDrugCombo (class in batchie.models.sparse_combo) SparseDrugComboInteraction (class in batchie.models.sparse_combo_interaction) SparseDrugComboInteractionMCMCSample (class in batchie.models.sparse_combo_interaction) SparseDrugComboMCMCSample (class in batchie.models.sparse_combo) step() (batchie.core.MCMCModel method) (batchie.models.sparse_combo.SparseDrugCombo method) (batchie.models.sparse_combo_interaction.SparseDrugComboInteraction method) subset() (batchie.data.Screen method) (batchie.data.ScreenSubset method) subset_observed() (batchie.data.Screen method) subset_unobserved() (batchie.data.Screen method)

T

Theta (class in batchie.core) ThetaHolder (class in batchie.core) to_dense() (batchie.core.DistanceMatrix method) (batchie.distance_calculation.ChunkedDistanceMatrix method) to_screen() (batchie.data.ScreenSubset method) treatment_arity (batchie.data.ScreenBase property) treatment_doses (batchie.data.Screen property) (batchie.data.ScreenBase property) (batchie.data.ScreenSubset property) treatment_ids (batchie.data.Screen property) (batchie.data.ScreenBase property) (batchie.data.ScreenSubset property)

treatment_ids_from_treatment_name() (batchie.data.ExperimentSpace method) treatment_mapping (batchie.data.Screen property) (batchie.data.ScreenBase property) (batchie.data.ScreenSubset property) treatment_names (batchie.data.Screen property) (batchie.data.ScreenBase property) (batchie.data.ScreenSubset property) treatment_space_size (batchie.data.ScreenBase property)

U

unique_plate_ids (batchie.data.ScreenBase property) unique_sample_ids (batchie.data.ScreenBase property)

unique_treatments (batchie.data.ScreenBase property) unmask_screen() (in module batchie.retrospective)

V

V0 (batchie.models.sparse_combo.SparseDrugComboMCMCSample attribute) V1 (batchie.models.sparse_combo.SparseDrugComboMCMCSample attribute)

V2 (batchie.models.sparse_combo.SparseDrugComboMCMCSample attribute) (batchie.models.sparse_combo_interaction.SparseDrugComboInteractionMCMCSample attribute) VIModel (class in batchie.core)

W

W (batchie.models.sparse_combo.SparseDrugComboMCMCSample attribute) (batchie.models.sparse_combo_interaction.SparseDrugComboInteractionMCMCSample attribute)

W0 (batchie.models.sparse_combo.SparseDrugComboMCMCSample attribute)