Index A | B | C | D | E | F | G | J | K | L | M | O | P | Q | R | S | T | U A acceptance() (mhn.mcmc.mcmc.MCMC method) AUTO (mhn.optimizers.Device attribute) B bits_fixed_n() (in module mhn.model) build_q() (in module mhn.full_state_space.ModelConstruction) build_regularized_gradient_func() (in module mhn.training.penalties_cmhn) (in module mhn.training.penalties_omhn) build_regularized_score_func() (in module mhn.training.penalties_cmhn) (in module mhn.training.penalties_omhn) C cholesky (mhn.mcmc.kernels.smMALAResult attribute) cMHN (class in mhn.model) (mhn.optimizers.MHNType attribute) cMHNOptimizer (class in mhn.optimizers) compute_inverse() (in module mhn.full_state_space.PerformanceCriticalCode) compute_marginal_likelihood() (mhn.model.cMHN method) (mhn.model.oMHN method) compute_next_event_probs() (in module mhn.utilities) (mhn.model.cMHN method) (mhn.model.oMHN method) compute_restricted_inverse() (in module mhn.training.likelihood_cmhn) count_ones64() (in module mhn.training.likelihood_cmhn) CPU (mhn.optimizers.Device attribute) cpu_gradient_and_score() (in module mhn.training.likelihood_cmhn) (in module mhn.training.likelihood_omhn) cpu_score() (in module mhn.training.likelihood_cmhn) (in module mhn.training.likelihood_omhn) create_indep_model() (in module mhn.training.state_containers) cuda_available() (in module mhn) (in module mhn.training.likelihood_cmhn) cuda_compute_inverse() (in module mhn.full_state_space.Likelihood) cuda_fisher() (in module mhn.full_state_space.Likelihood) cuda_gradient_and_score() (in module mhn.full_state_space.Likelihood) (in module mhn.training.likelihood_cmhn) (in module mhn.training.likelihood_omhn) CUDAError cython_fisher() (in module mhn.full_state_space.fisher) cython_gradient_and_score() (in module mhn.training.likelihood_cmhn) D data_to_pD() (in module mhn.full_state_space.UtilityFunctions) det_sqrt (mhn.mcmc.kernels.smMALAResult attribute) Device (class in mhn.optimizers) E ess() (mhn.mcmc.mcmc.MCMC method) events (mhn.model.cMHN attribute) (mhn.model.oMHN attribute) F finite_sample() (in module mhn.full_state_space.UtilityFunctions) fisher() (in module mhn.full_state_space.fisher) G G (mhn.mcmc.kernels.smMALAResult attribute) generate_pTh() (in module mhn.full_state_space.Likelihood) get_data_properties() (mhn.optimizers.cMHNOptimizer method) (mhn.optimizers.oMHNOptimizer method) get_data_shape() (mhn.training.state_containers.StateAgeContainer method) (mhn.training.state_containers.StateContainer method) get_equivalent_classical_mhn() (mhn.model.oMHN method) get_max_mutation_num() (mhn.training.state_containers.StateAgeContainer method) (mhn.training.state_containers.StateContainer method) get_params() (mhn.mcmc.kernels.MALAKernel method) (mhn.mcmc.kernels.RWMKernel method) (mhn.mcmc.kernels.smMALAKernel method) get_restr_diag() (mhn.model.cMHN method) (mhn.model.oMHN method) gillespie() (in module mhn.utilities) gillespie_timed() (in module mhn.utilities) GPU (mhn.optimizers.Device attribute) grad() (in module mhn.full_state_space.Likelihood) grad_and_log_likelihood (mhn.mcmc.kernels.Kernel attribute) (mhn.mcmc.kernels.MALAKernel attribute) (mhn.mcmc.kernels.RWMKernel attribute) (mhn.mcmc.kernels.smMALAKernel attribute) grad_reg() (in module mhn.full_state_space.RegularizedOptimization) gradient (mhn.mcmc.kernels.smMALAResult attribute) gradient_and_score() (in module mhn.training.likelihood_cmhn) (in module mhn.training.likelihood_omhn) J jacobi() (in module mhn.full_state_space.Likelihood) K Kernel (class in mhn.mcmc.kernels) KL_div() (in module mhn.full_state_space.UtilityFunctions) kron_vec() (in module mhn.full_state_space.PerformanceCriticalCode) L L1 (mhn.optimizers.Penalty attribute) L1() (in module mhn.full_state_space.RegularizedOptimization) l1() (in module mhn.training.penalties_cmhn) (in module mhn.training.penalties_omhn) L1_() (in module mhn.full_state_space.RegularizedOptimization) l1_() (in module mhn.training.penalties_cmhn) (in module mhn.training.penalties_omhn) L2 (mhn.optimizers.Penalty attribute) l2() (in module mhn.training.penalties_cmhn) (in module mhn.training.penalties_omhn) l2_() (in module mhn.training.penalties_cmhn) (in module mhn.training.penalties_omhn) lambda_from_cv() (mhn.optimizers.cMHNOptimizer method) (mhn.optimizers.oMHNOptimizer method) learn_indep() (in module mhn.full_state_space.ModelConstruction) learn_MHN() (in module mhn.full_state_space.RegularizedOptimization) learn_mhn() (in module mhn.training.regularized_optimization) likeliest_order() (mhn.model.cMHN method) (mhn.model.oMHN method) load() (mhn.model.cMHN class method) (mhn.model.oMHN class method) load_data_from_csv() (mhn.optimizers.cMHNOptimizer method) (mhn.optimizers.oMHNOptimizer method) load_data_matrix() (mhn.optimizers.cMHNOptimizer method) (mhn.optimizers.oMHNOptimizer method) log_accept() (mhn.mcmc.kernels.MALAKernel method) (mhn.mcmc.kernels.RWMKernel method) (mhn.mcmc.kernels.smMALAKernel method) log_likelihood (mhn.mcmc.kernels.MALAResult attribute) (mhn.mcmc.kernels.RWMResult attribute) (mhn.mcmc.kernels.smMALAResult attribute) log_prior (mhn.mcmc.kernels.Kernel attribute) (mhn.mcmc.kernels.MALAKernel attribute) (mhn.mcmc.kernels.MALAResult attribute) (mhn.mcmc.kernels.RWMKernel attribute) (mhn.mcmc.kernels.RWMResult attribute) (mhn.mcmc.kernels.smMALAKernel attribute) (mhn.mcmc.kernels.smMALAResult attribute) log_prior_grad (mhn.mcmc.kernels.MALAKernel attribute) (mhn.mcmc.kernels.smMALAKernel attribute) log_prior_hessian (mhn.mcmc.kernels.smMALAKernel attribute) log_q() (mhn.mcmc.kernels.MALAKernel method) (mhn.mcmc.kernels.smMALAKernel method) log_theta (mhn.model.cMHN attribute) (mhn.model.oMHN attribute) M m_likeliest_orders() (mhn.model.cMHN method) (mhn.model.oMHN method) MALAKernel (class in mhn.mcmc.kernels) MALAResult (class in mhn.mcmc.kernels) MCMC (class in mhn.mcmc.mcmc) meta (mhn.model.cMHN attribute) (mhn.model.oMHN attribute) mhn.CUDA_AVAILABLE (built-in variable) mhn.CUDA_NOT_AVAILABLE (built-in variable) mhn.CUDA_NOT_FUNCTIONAL (built-in variable) mhn.full_state_space.fisher module mhn.full_state_space.Likelihood module mhn.full_state_space.ModelConstruction module mhn.full_state_space.PerformanceCriticalCode module mhn.full_state_space.RegularizedOptimization module mhn.full_state_space.UtilityFunctions module mhn.mcmc.kernels module mhn.mcmc.mcmc module mhn.model module mhn.optimizers module mhn.training module mhn.training.likelihood_cmhn module mhn.training.likelihood_cmhn.CUDA_AVAILABLE (in module mhn.training.likelihood_cmhn) mhn.training.likelihood_cmhn.CUDA_NOT_AVAILABLE (in module mhn.training.likelihood_cmhn) mhn.training.likelihood_cmhn.CUDA_NOT_FUNCTIONAL (in module mhn.training.likelihood_cmhn) mhn.training.likelihood_omhn module mhn.training.penalties_cmhn module mhn.training.penalties_omhn module mhn.training.regularized_optimization module mhn.training.state_containers module mhn.utilities module MHNType (class in mhn.optimizers) module mhn.full_state_space.fisher mhn.full_state_space.Likelihood mhn.full_state_space.ModelConstruction mhn.full_state_space.PerformanceCriticalCode mhn.full_state_space.RegularizedOptimization mhn.full_state_space.UtilityFunctions mhn.mcmc.kernels mhn.mcmc.mcmc mhn.model mhn.optimizers mhn.training mhn.training.likelihood_cmhn mhn.training.likelihood_omhn mhn.training.penalties_cmhn mhn.training.penalties_omhn mhn.training.regularized_optimization mhn.training.state_containers mhn.utilities mu (mhn.mcmc.kernels.MALAResult attribute) (mhn.mcmc.kernels.smMALAResult attribute) O oMHN (class in mhn.model) (mhn.optimizers.MHNType attribute) omhn_fisher() (in module mhn.full_state_space.fisher) oMHNOptimizer (class in mhn.optimizers) one_step() (mhn.mcmc.kernels.MALAKernel method) (mhn.mcmc.kernels.RWMKernel method) (mhn.mcmc.kernels.smMALAKernel method) Optimizer (class in mhn.optimizers) order_likelihood() (mhn.model.cMHN method) (mhn.model.oMHN method) P Penalty (class in mhn.optimizers) penalty (mhn.optimizers.cMHNOptimizer property) (mhn.optimizers.oMHNOptimizer property) plot() (mhn.model.cMHN method) (mhn.model.oMHN method) plot_order_tree() (mhn.model.cMHN method) (mhn.model.oMHN method) plot_orders() (mhn.model.cMHN method) (mhn.model.oMHN method) propose() (mhn.mcmc.kernels.MALAKernel method) (mhn.mcmc.kernels.RWMKernel method) (mhn.mcmc.kernels.smMALAKernel method) Q q_diag() (in module mhn.full_state_space.ModelConstruction) q_subdiag() (in module mhn.full_state_space.ModelConstruction) q_vec() (in module mhn.full_state_space.Likelihood) R random_theta() (in module mhn.full_state_space.ModelConstruction) result (mhn.optimizers.cMHNOptimizer property) (mhn.optimizers.oMHNOptimizer property) rhat() (mhn.mcmc.mcmc.MCMC method) rng (mhn.mcmc.kernels.Kernel attribute) (mhn.mcmc.kernels.MALAKernel attribute) (mhn.mcmc.kernels.RWMKernel attribute) (mhn.mcmc.kernels.smMALAKernel attribute) run() (mhn.mcmc.mcmc.MCMC method) RWMKernel (class in mhn.mcmc.kernels) RWMResult (class in mhn.mcmc.kernels) S sample_artificial_data() (in module mhn.utilities) (mhn.model.cMHN method) (mhn.model.oMHN method) sample_trajectories() (mhn.model.cMHN method) (mhn.model.oMHN method) save() (mhn.model.cMHN method) (mhn.model.oMHN method) save_progress() (mhn.optimizers.cMHNOptimizer method) (mhn.optimizers.oMHNOptimizer method) scale (mhn.mcmc.kernels.RWMKernel attribute) score() (in module mhn.full_state_space.Likelihood) score_reg() (in module mhn.full_state_space.RegularizedOptimization) set_callback_func() (mhn.optimizers.cMHNOptimizer method) (mhn.optimizers.oMHNOptimizer method) set_device() (mhn.optimizers.cMHNOptimizer method) (mhn.optimizers.oMHNOptimizer method) set_init_theta() (mhn.optimizers.cMHNOptimizer method) (mhn.optimizers.oMHNOptimizer method) set_penalty() (mhn.optimizers.cMHNOptimizer method) (mhn.optimizers.oMHNOptimizer method) set_seed() (in module mhn) (in module mhn.utilities) shape (mhn.mcmc.kernels.Kernel attribute) (mhn.mcmc.kernels.MALAKernel attribute) (mhn.mcmc.kernels.RWMKernel attribute) (mhn.mcmc.kernels.smMALAKernel attribute) smMALAKernel (class in mhn.mcmc.kernels) smMALAResult (class in mhn.mcmc.kernels) state_to_int() (in module mhn.full_state_space.UtilityFunctions) StateAgeContainer (class in mhn.training.state_containers) StateContainer (class in mhn.training.state_containers) step_size (mhn.mcmc.kernels.MALAKernel attribute) (mhn.mcmc.kernels.smMALAKernel attribute) SYM_SPARSE (mhn.optimizers.Penalty attribute) sym_sparse() (in module mhn.training.penalties_cmhn) (in module mhn.training.penalties_omhn) sym_sparse_deriv() (in module mhn.training.penalties_cmhn) (in module mhn.training.penalties_omhn) T train() (mhn.optimizers.cMHNOptimizer method) (mhn.optimizers.oMHNOptimizer method) training_data (mhn.optimizers.cMHNOptimizer property) (mhn.optimizers.oMHNOptimizer property) tune_stepsize() (mhn.mcmc.mcmc.MCMC method) U use_cuda (mhn.mcmc.kernels.smMALAKernel attribute)