Index

A

add_autodiff() (in module eulerpi.core.model)

allPoints (SparseGrid attribute) ArtificialModelInterface (class in eulerpi.core.model)

B

basic_model_check() (in module eulerpi.core.model_check) basis_1d() (in module eulerpi.core.sparsegrid) basis_nd() (in module eulerpi.core.sparsegrid)

bw() (Exponential method) (Linear method) (LinearODE method) (X2Model method)

C

CaffeineSBMLModel (class in eulerpi.examples.sbml.sbml_caffeine_model) calc_forward() (TemperatureWithFixedParams method) calc_gram_determinant() (in module eulerpi.core.transformations) calc_jacobian() (TemperatureWithFixedParams method) calc_kernel_width() (in module eulerpi.core.kde) calc_walker_acceptance() (in module eulerpi.core.sampling) CENTRAL_PARAM (CaffeineSBMLModel attribute) (Corona attribute) (Exponential attribute) (ExternalPlant attribute) (Heat attribute) (HeatArtificial attribute) (JaxPlant attribute) (Linear attribute) (LinearODE attribute) (MentenSBMLModel attribute) (Temperature attribute) (X2Model attribute)

CHEBYSHEV (DenseGridType attribute) compute_all_points() (SparseGrid method) compute_coefficients() (SparseGrid method) compute_index_list4top_down_sparse_grid_traverse() (SparseGrid method) compute_integral() (SparseGrid method) compute_n_points() (SparseGrid method) Corona (class in eulerpi.examples.corona.corona) CoronaArtificial (class in eulerpi.examples.corona.corona) count_emcee_sub_runs() (ResultManager method) CrashModel (class in tests.test_logging) create_application_folder_structure() (ResultManager method) create_slice_folder_structure() (ResultManager method) Custom (DataTransformationType attribute)

D

data_dim (Corona attribute) (CrashModel attribute) (Exponential attribute) (ExternalPlant attribute) (Heat attribute) (JaxPlant attribute) (Linear attribute) (LinearODE attribute) (Model attribute) (SBMLModel property) (Temperature attribute) (X2Model attribute)

DataIdentity (class in eulerpi.core.data_transformation) DataNormalizer (class in eulerpi.core.data_transformation) DataPCA (class in eulerpi.core.data_transformation) DataTransformation (class in eulerpi.core.data_transformation) DataTransformationType (class in eulerpi.core.data_transformation_types) DEBUGFORMATTER (in module eulerpi) delete_application_folder_structure() (ResultManager method) delete_slice_folder_structure() (ResultManager method) DENSE_GRID (InferenceType attribute) DenseGridType (class in eulerpi.core.dense_grid_types) dim (SparseGrid attribute) do_matrix_multiplication() (in module tests.test_jax)

E

EQUIDISTANT (DenseGridType attribute) eulerpi module eulerpi.core.data_transformation module eulerpi.core.data_transformation_types module eulerpi.core.dense_grid module eulerpi.core.dense_grid_types module eulerpi.core.inference module eulerpi.core.inference_types module eulerpi.core.kde module eulerpi.core.model module eulerpi.core.model_check module eulerpi.core.plotting module eulerpi.core.result_manager module eulerpi.core.sampling module eulerpi.core.sparsegrid module eulerpi.core.transformations module eulerpi.examples module

eulerpi.examples.corona module eulerpi.examples.corona.corona module eulerpi.examples.cpp.python_reference_plants module eulerpi.examples.heat module eulerpi.examples.heat.heat module eulerpi.examples.sbml.sbml_caffeine_model module eulerpi.examples.sbml.sbml_menten_model module eulerpi.examples.simple_models module eulerpi.examples.temperature module eulerpi.examples.temperature.temperature module eulerpi.jax_extension module eval_function() (Subspace method) eval_function_sg() (SparseGrid method) eval_kde_cauchy() (in module eulerpi.core.kde) eval_kde_gauss() (in module eulerpi.core.kde) eval_log_transformed_density() (in module eulerpi.core.transformations) evaluate_density() (in module eulerpi.core.transformations) evaluate_on_grid_chunk() (in module eulerpi.core.dense_grid) evaluate_on_sparse_grid() (in module eulerpi.core.sparsegrid) evaluation_points (Heat attribute) Examples() (in module tests.test_examples) Exponential (class in eulerpi.examples.simple_models) ExternalPlant (class in eulerpi.examples.cpp.python_reference_plants)

F

forward() (Corona class method) (CrashModel method) (Exponential class method) (ExternalPlant method) (Heat class method) (JaxPlant class method) (Linear class method) (LinearODE class method) (Model method) (SBMLModel method) (Temperature method) (TemperatureWithFixedParams method) (X2Model class method)

forward_and_jacobian() (JaxModel method) (Model method) (SBMLModel method) forward_method() (JaxModel static method) from_data() (DataNormalizer class method) (DataPCA class method) from_transformation() (DataNormalizer class method) full_model_check() (in module eulerpi.core.model_check) fw() (Exponential method) (Linear method) (LinearODE method) (X2Model method)

G

generate_artificial_data() (ArtificialModelInterface method) generate_artificial_params() (ArtificialModelInterface method) (CaffeineSBMLModel method) (CoronaArtificial method) (ExternalPlant method) (HeatArtificial method) (JaxPlant method) (Linear method) (LinearODE method) (MentenSBMLModel method) (TemperatureArtificial method) (X2Model method)

generate_chebyshev_grid() (in module eulerpi.core.dense_grid) generate_regular_grid() (in module eulerpi.core.dense_grid) get_application_path() (ResultManager method) get_example_name() (in module tests.test_examples) get_slice_name() (ResultManager method) get_slice_path() (ResultManager method)

H

Heat (class in eulerpi.examples.heat.heat)

heat_rhs() (in module eulerpi.examples.heat.heat) HeatArtificial (class in eulerpi.examples.heat.heat)

I

Identity (DataTransformationType attribute) indices_from_ids() (SBMLModel static method) inference() (in module eulerpi.core.inference) inference_dense_grid() (in module eulerpi.core.dense_grid) inference_mcmc() (in module eulerpi.core.sampling) inference_model_check() (in module eulerpi.core.model_check) inference_sparse_grid() (in module eulerpi.core.sparsegrid)

InferenceType (class in eulerpi.core.inference_types) INFOFORMATTER (in module eulerpi) init_fw_and_bw() (JaxModel class method) integrate() (in module tests.test_inference) (in module tests.test_kde) is_amici_available() (in module eulerpi.core.model) is_artificial() (Model method)

J

jacobian() (CrashModel method) (DataIdentity method) (DataNormalizer method) (DataPCA method) (DataTransformation method) (ExternalPlant method) (JaxModel method) (Model method) (SBMLModel method) (Temperature method) (TemperatureWithFixedParams method)

JaxModel (class in eulerpi.core.model) JaxPlant (class in eulerpi.examples.cpp.python_reference_plants)

K

kde_data_test_set() (in module tests.test_kde)

kernel_estimators() (in module tests.test_kde)

L

levels2index (SparseGrid attribute) Linear (class in eulerpi.examples.simple_models) LinearODE (class in eulerpi.examples.simple_models)

load_amici_model_and_solver() (SBMLModel method) load_inference_results() (ResultManager method) load_slice_inference_results() (ResultManager method)

M

max_level_sum (SparseGrid attribute) MCMC (InferenceType attribute) MentenSBMLModel (class in eulerpi.examples.sbml.sbml_menten_model) meshgrid2matrix() (in module eulerpi.core.sparsegrid) Model (class in eulerpi.core.model) model_name (ResultManager attribute) module eulerpi eulerpi.core.data_transformation eulerpi.core.data_transformation_types eulerpi.core.dense_grid eulerpi.core.dense_grid_types eulerpi.core.inference eulerpi.core.inference_types eulerpi.core.kde eulerpi.core.model eulerpi.core.model_check eulerpi.core.plotting eulerpi.core.result_manager eulerpi.core.sampling eulerpi.core.sparsegrid eulerpi.core.transformations eulerpi.examples eulerpi.examples.corona eulerpi.examples.corona.corona eulerpi.examples.cpp.python_reference_plants eulerpi.examples.heat eulerpi.examples.heat.heat eulerpi.examples.sbml.sbml_caffeine_model eulerpi.examples.sbml.sbml_menten_model eulerpi.examples.simple_models eulerpi.examples.temperature eulerpi.examples.temperature.temperature eulerpi.jax_extension tests tests.conftest tests.profiling tests.test_data_transformation tests.test_dense_grid tests.test_examples tests.test_fixed_params tests.test_heat tests.test_inference tests.test_jax tests.test_kde tests.test_logging tests.test_model_check tests.test_pickling tests.test_plotting tests.test_simple_models tests.test_slices tests.test_transformations

N

n_points (SparseGrid attribute) Normalize (DataTransformationType attribute)

nSubspaces (SparseGrid attribute) num_grid_points (Heat attribute) (HeatArtificial attribute)

P

param_dim (Corona attribute) (CrashModel attribute) (Exponential attribute) (ExternalPlant attribute) (Heat attribute) (JaxPlant attribute) (Linear attribute) (LinearODE attribute) (Model attribute) (SBMLModel property) (Temperature attribute) (X2Model attribute) param_is_within_domain() (Heat method) (Model method) PARAM_LIMITS (CaffeineSBMLModel attribute) (Corona attribute) (CoronaArtificial attribute) (Exponential attribute) (ExternalPlant attribute) (Heat attribute) (HeatArtificial attribute) (JaxPlant attribute) (Linear attribute) (LinearODE attribute) (MentenSBMLModel attribute) (Temperature attribute) (X2Model attribute)

pass_contributions2higher_levels() (Subspace method) PCA (DataTransformationType attribute) perform_simulation() (Heat class method) plate_length (Heat attribute) profiling_with_slices() (in module tests.profiling) pytest_sessionstart() (in module tests.conftest)

R

refine_subspace() (SparseGrid method) ResultManager (class in eulerpi.core.result_manager) run_dense_grid_evaluation() (in module eulerpi.core.dense_grid)

run_emcee_once() (in module eulerpi.core.sampling) run_emcee_sampling() (in module eulerpi.core.sampling) run_name (ResultManager attribute)

S

sample_violin_plot() (in module eulerpi.core.plotting) save_inference_information() (ResultManager method) save_overall() (ResultManager method) save_run() (ResultManager method) SBMLModel (class in eulerpi.core.model)

setSensitivities() (SBMLModel method) SPARSE_GRID (InferenceType attribute) SparseGrid (class in eulerpi.core.sparsegrid) Subspace (class in eulerpi.core.sparsegrid) subspace_list (SparseGrid attribute)

T

t_end (Heat attribute) temp_name() (in module tests.test_fixed_params) Temperature (class in eulerpi.examples.temperature.temperature) TemperatureArtificial (class in eulerpi.examples.temperature.temperature) TemperatureWithFixedParams (class in eulerpi.examples.temperature.temperature) test_calc_gram_determinant() (in module tests.test_transformations) test_calc_kernel_width() (in module tests.test_kde) test_DataIdentity() (in module tests.test_data_transformation) test_DataNormalizer() (in module tests.test_data_transformation) test_DataPCA() (in module tests.test_data_transformation) test_dense_grid() (in module tests.test_dense_grid) test_evaluate_density() (in module tests.test_transformations) test_examples() (in module tests.test_examples) test_fixed_params() (in module tests.test_fixed_params) test_full_model_check() (in module tests.test_model_check) test_heat_artificial() (in module tests.test_heat) test_heat_jacobian() (in module tests.test_heat) test_heat_model() (in module tests.test_heat) test_inference_mcmc_dense_exact() (in module tests.test_inference) test_jax_cpu() (in module tests.test_jax) test_jax_gpu() (in module tests.test_jax) test_KDE_batch() (in module tests.test_kde) test_kde_convergence_gauss() (in module tests.test_kde) test_KDE_data() (in module tests.test_kde) test_kde_gauss() (in module tests.test_kde) test_logs_error_evaluate_density() (in module tests.test_logging) test_model_requirements() (in module tests.test_examples) test_pickling_model() (in module tests.test_pickling) test_sample_plotting() (in module tests.test_plotting) test_slices() (in module tests.test_slices) test_thinning_and_burn_in() (in module tests.test_inference) test_transformationExponential() (in module tests.test_simple_models) test_transformationLinear() (in module tests.test_simple_models) test_transformationODELinear() (in module tests.test_simple_models) tests module tests.conftest module

tests.profiling module tests.test_data_transformation module tests.test_dense_grid module tests.test_examples module tests.test_fixed_params module tests.test_heat module tests.test_inference module tests.test_jax module tests.test_kde module tests.test_logging module tests.test_model_check module tests.test_pickling module tests.test_plotting module tests.test_simple_models module tests.test_slices module tests.test_transformations module transform() (DataIdentity method) (DataNormalizer method) (DataPCA method) (DataTransformation method) TRUE_PARAM_LIMITS (LinearODE attribute)

V

value_and_jacfwd() (in module eulerpi.jax_extension) value_and_jacrev() (in module eulerpi.jax_extension) vj() (Exponential method) (Linear method) (LinearODE method) (X2Model method)

X

X2Model (class in tests.test_transformations)