Index

A

add_autodiff() (in module eulerpi.core.models.jax_model) AffineTransformation (class in eulerpi.core.data_transformations)

allPoints (SparseGrid attribute) ArtificialModelInterface (class in eulerpi.core.models) (class in eulerpi.core.models.artificial_model_interface)

B

BaseModel (class in eulerpi.core.models) (class in eulerpi.core.models.base_model) 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)

D

data_dim (BaseModel attribute), [1] (Corona attribute) (CrashModel attribute) (Exponential attribute) (ExternalPlant attribute) (Heat attribute) (JaxPlant attribute) (Linear attribute) (LinearODE attribute) (SBMLModel property), [1] (Temperature attribute) (X2Model attribute)

DataIdentity (class in eulerpi.core.data_transformations) DataNormalization (class in eulerpi.core.data_transformations) DataPCA (class in eulerpi.core.data_transformations) DataTransformation (class in eulerpi.core.data_transformations) 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.core.data_transformations 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_check module eulerpi.core.models module eulerpi.core.models.artificial_model_interface module eulerpi.core.models.base_model module eulerpi.core.models.jax_extension module eulerpi.core.models.jax_model module eulerpi.core.models.sbml_model 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 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() (BaseModel method), [1] (Corona class method) (CrashModel method) (Exponential class method) (ExternalPlant method) (Heat class method) (JaxPlant class method) (Linear class method) (LinearODE class method) (SBMLModel method), [1] (Temperature method) (TemperatureWithFixedParams method) (X2Model class method)

forward_and_jacobian() (BaseModel method), [1] (JaxModel method), [1] (SBMLModel method), [1] forward_method() (JaxModel static method), [1] forward_vectorized() (BaseModel method), [1] (JaxModel method), [1] full_model_check() (in module eulerpi.core.model_check) fw() (Exponential method) (Linear method) (LinearODE method) (X2Model method)

G

generate_artificial_data() (ArtificialModelInterface method), [1] generate_artificial_params() (ArtificialModelInterface method), [1] (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

indices_from_ids() (SBMLModel static method), [1] 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) init_fw_and_bw() (JaxModel class method), [1] integrate() (in module tests.test_inference) (in module tests.test_kde) is_amici_available() (in module eulerpi.core.models.sbml_model)

J

jacobian() (AffineTransformation method) (BaseModel method), [1] (CrashModel method) (DataIdentity method) (DataPCA method) (DataTransformation method) (ExternalPlant method) (JaxModel method), [1] (SBMLModel method), [1] (Temperature method) (TemperatureWithFixedParams method)

JaxModel (class in eulerpi.core.models) (class in eulerpi.core.models.jax_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), [1] 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 (in module eulerpi.core.models) model_name (ResultManager attribute) module eulerpi.core.data_transformations eulerpi.core.dense_grid eulerpi.core.dense_grid_types eulerpi.core.inference eulerpi.core.inference_types eulerpi.core.kde eulerpi.core.model_check eulerpi.core.models eulerpi.core.models.artificial_model_interface eulerpi.core.models.base_model eulerpi.core.models.jax_extension eulerpi.core.models.jax_model eulerpi.core.models.sbml_model 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 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) nSubspaces (SparseGrid attribute)

num_grid_points (Heat attribute) (HeatArtificial attribute)

P

param_dim (BaseModel attribute), [1] (Corona attribute) (CrashModel attribute) (Exponential attribute) (ExternalPlant attribute) (Heat attribute) (JaxPlant attribute) (Linear attribute) (LinearODE attribute) (SBMLModel property), [1] (Temperature attribute) (X2Model attribute) param_is_within_domain() (BaseModel method), [1] (Heat 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) 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.models) (class in eulerpi.core.models.sbml_model)

setSensitivities() (SBMLModel method), [1] 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_AffineTransformation() (in module tests.test_data_transformation) 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_DataNormalization() (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() (AffineTransformation method) (DataIdentity method) (DataPCA method) (DataTransformation method) TRUE_PARAM_LIMITS (LinearODE attribute)

V

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

X

X2Model (class in tests.test_transformations)