Index

_

__call__() (BOBE.CobayaLikelihood method) (BOBE.kernels.Kernel method), [1] (BOBE.Likelihood method) (BOBE.likelihood.CobayaLikelihood method), [1] (BOBE.likelihood.Likelihood method), [1] __init__() (BOBE.acquisition.AcquisitionFunction method), [1] (BOBE.acquisition.EI method), [1] (BOBE.acquisition.LogEI method), [1] (BOBE.acquisition.WeightedIntegratedPosteriorBase method), [1] (BOBE.bo.BOBE method), [1] (BOBE.BOBE method) (BOBE.BOBEResults method) (BOBE.BOBESummaryPlotter method) (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.CobayaLikelihood method) (BOBE.EI method) (BOBE.GP method) (BOBE.gp.GP method), [1] (BOBE.GPwithClassifier method) (BOBE.kernels.Kernel method), [1] (BOBE.Likelihood method) (BOBE.likelihood.CobayaLikelihood method), [1] (BOBE.likelihood.Likelihood method), [1] (BOBE.LogEI method) (BOBE.pool.MPI_Pool method) (BOBE.utils.log.LevelFilter method) (BOBE.utils.plot.BOBESummaryPlotter method) (BOBE.utils.results.BOBEResults method)

A

acq_optimize (BOBE.acquisition.AcquisitionFunction attribute), [1]

Acquisition Function AcquisitionFunction (class in BOBE.acquisition), [1]

B

Bayesian Evidence Bayesian Optimization BOBE module BOBE (class in BOBE) (class in BOBE.bo), [1] BOBE.acquisition module, [1] BOBE.bo module BOBE.clf module, [1] BOBE.clf_gp module BOBE.gp module BOBE.kernels module BOBE.likelihood module

BOBE.optim module, [1] BOBE.pool module BOBE.samplers module BOBE.utils.core module BOBE.utils.log module BOBE.utils.plot module BOBE.utils.seed module BOBEResults (class in BOBE) (class in BOBE.utils.results) BOBESummaryPlotter (class in BOBE) (class in BOBE.utils.plot)

C

check_convergence_ei() (BOBE.bo.BOBE method), [1] (BOBE.BOBE method) check_convergence_logz() (BOBE.bo.BOBE method), [1] (BOBE.BOBE method) check_max_evals_and_gpsize() (BOBE.bo.BOBE method), [1] (BOBE.BOBE method) clear_jax_caches() (BOBE.pool.MPI_Pool method) clf_data_size (BOBE.clf_gp.GPwithClassifier property), [1] (BOBE.GPwithClassifier property) close() (BOBE.pool.MPI_Pool method) Cobaya CobayaLikelihood (class in BOBE) (class in BOBE.likelihood), [1]

compute_integrals() (in module BOBE.samplers), [1] copy() (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.GP method) (BOBE.gp.GP method), [1] (BOBE.GPwithClassifier method) covariance() (BOBE.kernels.Kernel method), [1] (BOBE.kernels.MaternKernel method), [1] (BOBE.kernels.RBFKernel method), [1] create_summary_dashboard() (BOBE.BOBESummaryPlotter method) (BOBE.utils.plot.BOBESummaryPlotter method) create_summary_plots() (in module BOBE.utils.plot)

D

Deep Sigmoidal Location Process (DSLP)

diagonal() (BOBE.kernels.Kernel method), [1] DummyDistribution (class in BOBE.gp)

E

EI (class in BOBE) (class in BOBE.acquisition), [1] end_timing() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method)

ensure_reproducibility() (in module BOBE.utils.seed) evaluate_likelihood() (BOBE.bo.BOBE method), [1] (BOBE.BOBE method) Expected Improvement (EI)

F

fantasy_var() (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.GP method) (BOBE.gp.GP method), [1] (BOBE.GPwithClassifier method) fast_update_cholesky() (in module BOBE.gp) filter() (BOBE.utils.log.LevelFilter method) finalise_results() (BOBE.bo.BOBE method), [1] (BOBE.BOBE method) finalize() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) fit() (BOBE.GP method) (BOBE.gp.GP method), [1]

from_state_dict() (BOBE.clf_gp.GPwithClassifier class method), [1] (BOBE.GP class method) (BOBE.gp.GP class method), [1] (BOBE.GPwithClassifier class method) fun() (BOBE.acquisition.AcquisitionFunction method), [1] (BOBE.acquisition.EI method), [1] (BOBE.acquisition.LogEI method), [1] (BOBE.acquisition.WIPStd method), [1] (BOBE.acquisition.WIPV method), [1] (BOBE.EI method) (BOBE.LogEI method) (BOBE.WIPStd method) (BOBE.WIPV method)

G

Gaussian Process (GP) get_acquisition_data() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) get_best_loglike_data() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) get_cobaya_initial_points() (BOBE.pool.MPI_Pool method) get_data_format_examples() (in module BOBE.utils.plot) get_dimension_based_defaults() (in module BOBE) (in module BOBE.bo) get_ellipsoid_predict_proba_fn() (in module BOBE.clf), [1] get_getdist_samples() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) get_global_seed() (in module BOBE.utils.seed) get_gp_data() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) get_hyperparams() (BOBE.GP method) (BOBE.gp.GP method), [1] get_jax_key() (in module BOBE.utils.seed) get_last_iteration() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) get_logger() (in module BOBE) (in module BOBE.utils.log) get_mc_points() (in module BOBE.acquisition), [1] get_mc_samples() (in module BOBE.acquisition), [1] get_new_jax_key() (in module BOBE.utils.seed)

get_next_batch() (BOBE.acquisition.AcquisitionFunction method), [1] (BOBE.bo.BOBE method), [1] (BOBE.BOBE method) get_next_point() (BOBE.acquisition.AcquisitionFunction method), [1] (BOBE.acquisition.EI method), [1] (BOBE.acquisition.WeightedIntegratedPosteriorBase method), [1] (BOBE.EI method) get_nn_predict_proba_fn() (in module BOBE.clf), [1] get_numpy_rng() (in module BOBE.utils.seed) get_random_point() (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.GP method) (BOBE.gp.GP method), [1] (BOBE.GPwithClassifier method) get_results_dict() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) get_svm_predict_proba_fn() (in module BOBE.clf), [1] get_threshold_for_nsigma() (in module BOBE.utils.core) get_timing_summary() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) GP (class in BOBE) (class in BOBE.gp), [1] gp_fit() (BOBE.pool.MPI_Pool method) gp_mll() (in module BOBE.gp) GPwithClassifier (class in BOBE) (class in BOBE.clf_gp), [1]

H

hyperparams_dict() (BOBE.GP method) (BOBE.gp.GP method), [1]

I

is_cluster_environment() (in module BOBE.utils.core)

is_resuming() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method)

J

JAX

K

Kernel (class in BOBE.kernels), [1] kernel() (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.GPwithClassifier method)

kernel_variance (BOBE.kernels.Kernel attribute), [1] kl_divergence_gaussian() (in module BOBE.utils.core) kl_divergence_samples() (in module BOBE.utils.core)

L

lengthscales (BOBE.kernels.Kernel attribute), [1] LevelFilter (class in BOBE.utils.log) Likelihood (class in BOBE) (class in BOBE.likelihood), [1] load() (BOBE.clf_gp.GPwithClassifier class method), [1] (BOBE.GP class method) (BOBE.gp.GP class method), [1] (BOBE.GPwithClassifier class method)

load_gp_file() (in module BOBE.bo) load_gp_statedict() (in module BOBE.bo) load_results() (BOBE.BOBEResults class method) (BOBE.utils.results.BOBEResults class method) Log Evidence log_prob() (BOBE.gp.DummyDistribution method) LogEI (class in BOBE) (class in BOBE.acquisition), [1]

M

make_distribution() (in module BOBE.gp) Marginal Likelihood MaternKernel (class in BOBE.kernels), [1] module BOBE BOBE.acquisition, [1] BOBE.bo BOBE.clf, [1] BOBE.clf_gp BOBE.gp BOBE.kernels BOBE.likelihood BOBE.optim, [1] BOBE.pool BOBE.samplers BOBE.utils.core BOBE.utils.log BOBE.utils.plot BOBE.utils.seed

MPI_Pool (class in BOBE.pool)

N

name (BOBE.acquisition.AcquisitionFunction attribute), [1], [2], [3] (BOBE.acquisition.EI attribute), [1] (BOBE.acquisition.LogEI attribute), [1] (BOBE.acquisition.WIPStd attribute), [1] (BOBE.acquisition.WIPV attribute), [1] (BOBE.EI attribute) (BOBE.LogEI attribute) (BOBE.WIPStd attribute) (BOBE.WIPV attribute)

neg_mll() (BOBE.GP method) (BOBE.gp.GP method), [1] Nested Sampling nested_sampling_Dy() (in module BOBE.samplers), [1] noise (BOBE.kernels.Kernel attribute), [1] npoints (BOBE.clf_gp.GPwithClassifier property), [1] (BOBE.GP property) (BOBE.gp.GP property), [1] (BOBE.GPwithClassifier property) NumPyro

O

optimize_optax() (in module BOBE.optim), [1] optimize_optax_vmap() (in module BOBE.optim), [1]

optimize_scipy() (in module BOBE.optim), [1] optimizer (BOBE.acquisition.AcquisitionFunction attribute), [1] optimizer_options (BOBE.acquisition.AcquisitionFunction attribute), [1]

P

plot_acquisition_evolution() (BOBE.BOBESummaryPlotter method) (BOBE.utils.plot.BOBESummaryPlotter method) plot_best_loglike_evolution() (BOBE.BOBESummaryPlotter method) (BOBE.utils.plot.BOBESummaryPlotter method) plot_convergence_diagnostics() (BOBE.BOBESummaryPlotter method) (BOBE.utils.plot.BOBESummaryPlotter method) plot_evidence_evolution() (BOBE.BOBESummaryPlotter method) (BOBE.utils.plot.BOBESummaryPlotter method) plot_final_samples() (in module BOBE.utils.plot) plot_gp_hyperparameters() (BOBE.BOBESummaryPlotter method) (BOBE.utils.plot.BOBESummaryPlotter method) plot_gp_kernel_variance() (BOBE.BOBESummaryPlotter method) (BOBE.utils.plot.BOBESummaryPlotter method) plot_gp_lengthscales() (BOBE.BOBESummaryPlotter method) (BOBE.utils.plot.BOBESummaryPlotter method) plot_kl_divergences() (BOBE.BOBESummaryPlotter method) (BOBE.utils.plot.BOBESummaryPlotter method) plot_parameter_evolution() (BOBE.BOBESummaryPlotter method) (BOBE.utils.plot.BOBESummaryPlotter method) plot_summary_stats() (BOBE.BOBESummaryPlotter method) (BOBE.utils.plot.BOBESummaryPlotter method) plot_timing_breakdown() (BOBE.BOBESummaryPlotter method) (BOBE.utils.plot.BOBESummaryPlotter method) Posterior

predict_batched() (BOBE.GP method) (BOBE.gp.GP method), [1] predict_mean_batched() (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.GP method) (BOBE.gp.GP method), [1] (BOBE.GPwithClassifier method) predict_mean_single() (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.GP method) (BOBE.gp.GP method), [1] (BOBE.GPwithClassifier method) predict_single() (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.GP method) (BOBE.gp.GP method), [1] (BOBE.GPwithClassifier method) predict_var_batched() (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.GP method) (BOBE.gp.GP method), [1] (BOBE.GPwithClassifier method) predict_var_single() (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.GP method) (BOBE.gp.GP method), [1] (BOBE.GPwithClassifier method) Prior prior_transform() (in module BOBE.samplers), [1]

R

RBFKernel (class in BOBE.kernels), [1] recompute_cholesky() (BOBE.GP method) (BOBE.gp.GP method), [1] renormalise_log_weights() (in module BOBE.utils.core) resample_equal() (in module BOBE.utils.core) run() (BOBE.bo.BOBE method), [1] (BOBE.BOBE method) run_EI() (BOBE.bo.BOBE method), [1] (BOBE.BOBE method)

run_map_objective() (BOBE.pool.MPI_Pool method) run_weighted_integrated_posterior() (BOBE.bo.BOBE method), [1] (BOBE.BOBE method) run_WIPStd() (BOBE.bo.BOBE method), [1] (BOBE.BOBE method) run_WIPV() (BOBE.bo.BOBE method), [1] (BOBE.BOBE method)

S

saas_prior_logprob() (in module BOBE.gp) sample_GP_NUTS() (in module BOBE.samplers), [1] save() (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.GP method) (BOBE.gp.GP method), [1] (BOBE.GPwithClassifier method) save_all_formats() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) save_all_plots() (BOBE.BOBESummaryPlotter method) (BOBE.utils.plot.BOBESummaryPlotter method) save_chain_files() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) save_intermediate() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) save_main_results() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) save_minimum_files() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) save_summary_stats() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) save_timing_data() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method)

scale_from_unit() (in module BOBE) (in module BOBE.utils.core) scale_to_unit() (in module BOBE) (in module BOBE.utils.core) set_global_seed() (in module BOBE.utils.seed) setup_logging() (in module BOBE) (in module BOBE.utils.log) Sparse Axis-Aligned Subspace (SAAS) split_jax_key() (in module BOBE.utils.seed) split_vmap() (in module BOBE.utils.core) sq_dist() (BOBE.kernels.Kernel method), [1] start_timing() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) state_dict() (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.GP method) (BOBE.gp.GP method), [1] (BOBE.GPwithClassifier method) suppress_stdout_stderr() (in module BOBE.utils.core) Surrogate Model svm_predict() (in module BOBE.clf), [1] svm_predict_proba() (in module BOBE.clf), [1]

T

TASK_ACQUISITION_OPT (BOBE.pool.MPI_Pool attribute) TASK_CLEAR_JAX_CACHES (BOBE.pool.MPI_Pool attribute) TASK_COBAYA_INIT (BOBE.pool.MPI_Pool attribute) TASK_EXIT (BOBE.pool.MPI_Pool attribute) TASK_GP_FIT (BOBE.pool.MPI_Pool attribute) TASK_INIT (BOBE.pool.MPI_Pool attribute) TASK_OBJECTIVE_EVAL (BOBE.pool.MPI_Pool attribute) train_classifier() (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.GPwithClassifier method)

train_ellipsoid() (in module BOBE.clf), [1] train_ellipsoid_classifier() (in module BOBE.clf), [1] train_ellipsoid_multiple_restarts() (in module BOBE.clf), [1] train_nn() (in module BOBE.clf), [1] train_nn_classifier() (in module BOBE.clf), [1] train_nn_multiple_restarts() (in module BOBE.clf), [1] train_svm_classifier() (in module BOBE.clf), [1] train_with_restarts() (in module BOBE.clf), [1]

U

update() (BOBE.clf_gp.GPwithClassifier method), [1] (BOBE.GP method) (BOBE.gp.GP method), [1] (BOBE.GPwithClassifier method) update_acquisition() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) update_best_loglike() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) update_convergence() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method)

update_gp() (BOBE.bo.BOBE method), [1] (BOBE.BOBE method) update_gp_hyperparams() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) update_hyperparams() (BOBE.GP method) (BOBE.gp.GP method), [1] (BOBE.kernels.Kernel method), [1] update_kl_divergences() (BOBE.BOBEResults method) (BOBE.utils.results.BOBEResults method) update_verbosity() (in module BOBE.utils.log)

W

Weighted Integrated Posterior Variance (WIPV) WeightedIntegratedPosteriorBase (class in BOBE.acquisition), [1] WIPStd (class in BOBE) (class in BOBE.acquisition), [1]

WIPV (class in BOBE) (class in BOBE.acquisition), [1] worker_wait() (BOBE.pool.MPI_Pool method)