Index A | B | C | E | F | G | H | I | K | L | M | N | O | P | R | S | T | Z A analyse_reseau() (in module CardamomOT.tools.plot_networks) ApproxODE (class in CardamomOT.inference.simulations) B base_kon() (in module CardamomOT.inference.network) base_kon_torch() (in module CardamomOT.inference.network_final) build_kon_fn() (in module CardamomOT.inference.degradations) BurstyPDMP (class in CardamomOT.inference.simulations) C CardamomOT module CardamomOT.config module CardamomOT.inference module CardamomOT.inference.degradations module CardamomOT.inference.mixture module CardamomOT.inference.network module CardamomOT.inference.network_final module CardamomOT.inference.pretreatment module CardamomOT.inference.proliferations module CardamomOT.inference.simulations module CardamomOT.inference.trajectory module CardamomOT.model module CardamomOT.model.base module CardamomOT.tools module CardamomOT.tools.plot_networks module CardamomOT.tools.plot_results_kov module CardamomOT.tools.plot_results_sim module compare_cell_types() (in module CardamomOT.tools.plot_results_kov) compare_trajectories_umap() (in module CardamomOT.inference.degradations) compute_aic_for_params() (in module CardamomOT.inference.mixture) compute_aic_for_params_scaled() (in module CardamomOT.inference.mixture) compute_loss() (CardamomOT.inference.network_final.GRNInference method) compute_main_loss() (in module CardamomOT.inference.network_final) core_binarization() (CardamomOT.model.base.NetworkModel method) core_inference() (in module CardamomOT.inference.network) E elasticnet_loss() (in module CardamomOT.inference.network_final) em_vectorized_nb_zinb() (in module CardamomOT.inference.mixture) em_vectorized_nb_zinb_scaled() (in module CardamomOT.inference.mixture) estim_gamma_poisson() (in module CardamomOT.inference.mixture) estimate_trajectories() (CardamomOT.model.base.NetworkModel method) estimate_trajectories_given_model() (CardamomOT.model.base.NetworkModel method) F filter_network_fancy() (in module CardamomOT.inference.trajectory) find_next_prot() (in module CardamomOT.inference.trajectory) find_next_prot_mixed() (in module CardamomOT.inference.trajectory) fit_mixture() (CardamomOT.model.base.NetworkModel method) fit_mixture_test() (CardamomOT.model.base.NetworkModel method) fit_network() (CardamomOT.model.base.NetworkModel method) fit_scale_theta() (in module CardamomOT.inference.degradations) flow() (in module CardamomOT.inference.simulations) forward() (CardamomOT.inference.degradations.GeneRegulatoryODE_softmax method) (CardamomOT.inference.network_final.GRNInference method) G GeneRegulatoryODE_softmax (class in CardamomOT.inference.degradations) get_default_parameters() (in module CardamomOT.config) get_project_directories() (in module CardamomOT.config) grad_correc() (in module CardamomOT.inference.network) grad_theta() (in module CardamomOT.inference.network) GRNInference (class in CardamomOT.inference.network_final) H hard_em() (in module CardamomOT.inference.mixture) hard_em_scaled() (in module CardamomOT.inference.mixture) I infer_kinetics_preserve_mean_values_assignment() (in module CardamomOT.inference.mixture) infer_kinetics_scaled() (in module CardamomOT.inference.mixture) infer_kinetics_temporal() (in module CardamomOT.inference.mixture) infer_kinetics_temporal_scaled() (in module CardamomOT.inference.mixture) infer_ratio_d0_d1_full() (in module CardamomOT.inference.degradations) infer_ratio_d0_d1_unitary() (in module CardamomOT.inference.degradations) infer_test() (CardamomOT.model.base.NetworkModel method) inference_degradation_prot() (in module CardamomOT.inference.degradations) inference_network() (in module CardamomOT.inference.network) inference_network_pytorch() (in module CardamomOT.inference.network_final) inference_pytorch() (in module CardamomOT.inference.network_final) K KonCorrectionMLP (class in CardamomOT.inference.degradations) L l2_loss() (in module CardamomOT.inference.network_final) loop_trajectories() (CardamomOT.model.base.NetworkModel method) M main_loop_inference() (in module CardamomOT.inference.network) module CardamomOT CardamomOT.config CardamomOT.inference CardamomOT.inference.degradations CardamomOT.inference.mixture CardamomOT.inference.network CardamomOT.inference.network_final CardamomOT.inference.pretreatment CardamomOT.inference.proliferations CardamomOT.inference.simulations CardamomOT.inference.trajectory CardamomOT.model CardamomOT.model.base CardamomOT.tools CardamomOT.tools.plot_networks CardamomOT.tools.plot_results_kov CardamomOT.tools.plot_results_sim N nb_logpmf_vectorized() (in module CardamomOT.inference.mixture) neg_log_likelihood_logits() (in module CardamomOT.inference.mixture) NetworkModel (class in CardamomOT.model.base) O objective() (in module CardamomOT.inference.network) objective_refinement() (in module CardamomOT.inference.network) P plot_network() (in module CardamomOT.tools.plot_networks) plot_results_prot() (in module CardamomOT.tools.plot_results_sim) plot_results_rna_clean() (in module CardamomOT.tools.plot_results_sim) plot_results_rna_mixture() (in module CardamomOT.tools.plot_results_sim) plot_results_sim_kov() (in module CardamomOT.tools.plot_results_kov) predict() (CardamomOT.inference.proliferations.ProliferationMLP method) predict_resp() (in module CardamomOT.inference.mixture) predict_trajectory() (in module CardamomOT.inference.degradations) ProliferationMLP (class in CardamomOT.inference.proliferations) R refine_inference() (in module CardamomOT.inference.network) refine_network_degradations() (CardamomOT.model.base.NetworkModel method) reseau_top_regulateurs() (in module CardamomOT.tools.plot_networks) S set_ratio_interpolation() (CardamomOT.inference.degradations.GeneRegulatoryODE_softmax method) simulate_network() (CardamomOT.model.base.NetworkModel method) simulate_next_prot_ode() (in module CardamomOT.inference.simulations) simulate_next_prot_pdmp() (in module CardamomOT.inference.simulations) simulate_trajectories_full() (CardamomOT.model.base.NetworkModel method) simulate_trajectories_unitary() (CardamomOT.model.base.NetworkModel method) Simulation (class in CardamomOT.inference.simulations) simulation() (CardamomOT.inference.simulations.ApproxODE method) (CardamomOT.inference.simulations.BurstyPDMP method) simulation_with_growth() (CardamomOT.inference.simulations.BurstyPDMP method) smoothed_l1_loss() (in module CardamomOT.inference.network_final) step() (CardamomOT.inference.simulations.BurstyPDMP method) step_ode() (in module CardamomOT.inference.simulations) T train_proliferation_mlp() (in module CardamomOT.inference.proliferations) Z zinb_logpmf_vectorized() (in module CardamomOT.inference.mixture)