Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Z A add_module() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) agg_param() (in module pseudodynamics.functions.eval_funs), [1] all_gather() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) AllTimepoint_MeshGrid (class in pseudodynamics.reader) annotate_trajectory() (pseudodynamics.models._density_transport.DT_analysis method) apply() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) area_loss() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) assign_nearest_cell() (in module pseudodynamics.functions.eval_funs), [1] association_test() (pseudodynamics.de_test._association_test.AssociationTest method) (pseudodynamics.de_test._association_test.PseudotimeRestrictedAssociationTest method), [1], [2] AssociationTest (class in pseudodynamics.de_test._association_test), [1] associationTest() (pseudodynamics.de_test._base.BetweenLineageTest method) augment_cdf() (in module pseudodynamics.functions.reader_funs) automatic_optimization (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) B backward() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) behavior_curves() (in module pseudodynamics.plotting_fns.curve_plot) BetweenLineageTest (class in pseudodynamics.de_test._base) bfloat16() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) boundary_density_at() (in module pseudodynamics.functions.reader_funs) buffers() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) C call_super_init (pseudodynamics.models._density_transport.Density_Transfer attribute) (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) (pseudodynamics.models.MLP_models.MLP_surrogate attribute) (pseudodynamics.models.Spline_models.CubicSpline attribute) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline attribute) cellstate_drift() (pseudodynamics.models._density_transport.Density_Transfer method) celltype_proportion() (in module pseudodynamics.plotting_fns.density_plot) cfm_velocity_loss() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method), [1], [2] CHECKPOINT_HYPER_PARAMS_KEY (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) CHECKPOINT_HYPER_PARAMS_NAME (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) CHECKPOINT_HYPER_PARAMS_TYPE (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) children() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) clip_gradients() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) clustermap() (pseudodynamics.models._density_transport.DT_analysis method) compile() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) compute_density() (pseudodynamics.reader.HigDim_AnnDS method), [1], [2] (pseudodynamics.reader.TwoTimpepoint_AnnDS method) compute_guassian_u() (in module pseudodynamics.functions.reader_funs) compute_mellon_timesense_u() (in module pseudodynamics.functions.reader_funs), [1] compute_volume() (pseudodynamics.reader.HigDim_AnnDS method), [1], [2] (pseudodynamics.reader.TwoTimpepoint_AnnDS method) configure_callbacks() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) configure_gradient_clipping() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) configure_model() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) configure_optimizers() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) (pseudodynamics.models._pde_informed_params.pde_singlebranch_twotimepoints method) configure_sharded_model() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) constrain_v() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) continuous_params() (in module pseudodynamics.functions.eval_funs), [1] contour_animation() (in module pseudodynamics.plotting_fns.param_plot) cpu() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) CubicSpline (class in pseudodynamics.models.Spline_models) cuda() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) current_epoch (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) D density_by_time() (in module pseudodynamics.plotting_fns.curve_plot) density_loss() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) density_shortterm_simulation() (in module pseudodynamics.functions.eval_funs), [1] Density_Transfer (class in pseudodynamics.models._density_transport), [1] density_transfer() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) device (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) device_mesh (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) DifferentialExpressionTest (class in pseudodynamics.de_test._base) diffusion_entropy_loss() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) diffusion_variance_loss() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) distribution_loss() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) double() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) DT_analysis (class in pseudodynamics.models._density_transport) dtype (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) Duds_AnnDS (class in pseudodynamics.reader) Duds_AnnDS_fastmode (class in pseudodynamics.reader) dump_patches (pseudodynamics.models._density_transport.Density_Transfer attribute) (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) (pseudodynamics.models.MLP_models.MLP_surrogate attribute) (pseudodynamics.models.Spline_models.CubicSpline attribute) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline attribute) E equation() (pseudodynamics.models._pde_informed_params.log_pde_params method), [1], [2] (pseudodynamics.models._pde_informed_params.logrithmic_pde method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) (pseudodynamics.models._pde_informed_params.pde_u_free method) eval() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) evaluate_1d_density() (in module pseudodynamics.functions.reader_funs) evaluate_2d_mesh_density() (in module pseudodynamics.functions.reader_funs) evaluate_u_ds() (in module pseudodynamics.functions.reader_funs) example_input_array (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) ExperimentConfig (class in pseudodynamics._config), [1] extra_repr() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) F fabric (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) find_lastest_ckpt() (pseudodynamics._config.ExperimentConfig method), [1], [2] fit_gam_simple() (in module pseudodynamics.de_test._base) fitGAM() (in module pseudodynamics.de_test._base), [1] float() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) forward() (pseudodynamics.models._density_transport.Density_Transfer method), [1], [2] (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_neighborloss method) (pseudodynamics.models._pde_informed_params.pde_params method), [1], [2] (pseudodynamics.models._pde_informed_params.pde_singlebranch_twotimepoints method) (pseudodynamics.models._pde_informed_params.pde_u_free method) (pseudodynamics.models.MLP_models.MLP_surrogate method), [1] (pseudodynamics.models.Spline_models.CubicSpline method), [1] (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method), [1] forward_density_loss() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) forward_get_params() (in module pseudodynamics.functions.eval_funs) forward_simulation() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) freeze() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) from_json() (pseudodynamics._config.ExperimentConfig method), [1], [2] G get_args() (pseudodynamics._config.ExperimentConfig method) get_buffer() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) get_extra_state() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) get_parameter() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) get_pseudobulk() (in module pseudodynamics.functions.reader_funs) get_pseudobulk_vector() (pseudodynamics.reader.TwoTimpepoint_AnnDS_fastmode method) get_submodule() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) get_u() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) global_rank (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) global_step (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) gradient_of() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) H h_poly() (pseudodynamics.models.Spline_models.CubicSpline method), [1] half() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) heatmap_cell_proportions() (pseudodynamics.models._density_transport.DT_analysis method) hierarchical_clustering() (pseudodynamics.models._density_transport.DT_analysis method) HigDim_AnnDS (class in pseudodynamics.reader), [1] hparams (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) hparams_initial (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) I ipu() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) K KLD_density() (in module pseudodynamics.functions.eval_funs), [1] L Lambda1() (in module pseudodynamics.functions.reader_funs) Lambda2() (in module pseudodynamics.functions.reader_funs) load_from_checkpoint() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) load_gamfit() (in module pseudodynamics.de_test._base) load_model() (in module pseudodynamics.functions.reader_funs) load_result() (pseudodynamics.models._density_transport.DT_analysis method) load_state_dict() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) local_rank (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) log() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) log_dict() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) log_pde_params (class in pseudodynamics.models._pde_informed_params), [1] log_transform() (pseudodynamics.models._density_transport.DT_analysis method) logger (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) loggers (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) logrithmic_pde (class in pseudodynamics.models._pde_informed_params) loss_fn() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) lr_scheduler_step() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) lr_schedulers() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) M make_coord_adata() (in module pseudodynamics.functions.reader_funs), [1] manual_backward() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) MeshGrid_AnnDS (class in pseudodynamics.reader) meshgrid_density_by_time() (in module pseudodynamics.plotting_fns.curve_plot) MeshGrid_DS (class in pseudodynamics.reader) MeshGrid_logDS (class in pseudodynamics.reader) MeshGrid_Resample (class in pseudodynamics.reader) MLP_surrogate (class in pseudodynamics.models.MLP_models) mmd_laplace() (in module pseudodynamics.functions.eval_funs) module pseudodynamics._config, [1] pseudodynamics.de_test pseudodynamics.de_test._association_test pseudodynamics.de_test._base pseudodynamics.functions pseudodynamics.functions.eval_funs pseudodynamics.functions.reader_funs pseudodynamics.models pseudodynamics.models._density_transport pseudodynamics.models._pde_informed_params pseudodynamics.plotting_fns pseudodynamics.plotting_fns.curve_plot pseudodynamics.plotting_fns.density_plot pseudodynamics.plotting_fns.param_plot pseudodynamics.reader, [1] modules() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) mtia() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) mul() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) MultiDim_CubicSpline (class in pseudodynamics.models.Spline_models) N named_buffers() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) named_children() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) named_modules() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) named_parameters() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) O ode_func() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method), [1], [2] (pseudodynamics.models._pde_informed_params.pde_u_free method) on_after_backward() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_after_batch_transfer() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_before_backward() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_before_batch_transfer() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_before_optimizer_step() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_before_zero_grad() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_fit_end() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_fit_start() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_gpu (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) on_load_checkpoint() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_predict_batch_end() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_predict_batch_start() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_predict_end() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_predict_epoch_end() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_predict_epoch_start() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_predict_model_eval() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_predict_start() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_save_checkpoint() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_test_batch_end() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_test_batch_start() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_test_end() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_test_epoch_end() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_test_epoch_start() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_test_model_eval() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_test_model_train() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_test_start() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_train_batch_end() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_train_batch_start() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_train_end() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_train_epoch_end() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_train_epoch_start() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_train_start() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_validation_batch_end() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_validation_batch_start() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_validation_end() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_validation_epoch_end() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_validation_epoch_start() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_validation_model_eval() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_validation_model_train() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_validation_model_zero_grad() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) on_validation_start() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) optimizer_step() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) optimizer_zero_grad() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) optimizers() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) P parameters() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) params_in_umap() (in module pseudodynamics.plotting_fns.param_plot), [1] pde_neighborloss (class in pseudodynamics.models._pde_informed_params) pde_params (class in pseudodynamics.models._pde_informed_params), [1] pde_params_base (class in pseudodynamics.models._pde_informed_params) pde_params_fastmode (class in pseudodynamics.models._pde_informed_params) pde_params_meshgrid (class in pseudodynamics.models._pde_informed_params) pde_singlebranch_twotimepoints (class in pseudodynamics.models._pde_informed_params) pde_u_free (class in pseudodynamics.models._pde_informed_params) Pdyn_ExtractDataset (class in pseudodynamics.reader) plot_gene_trends() (in module pseudodynamics.plotting_fns.param_plot), [1] plot_u_dt() (pseudodynamics.models._pde_informed_params.pde_singlebranch_twotimepoints method) population_loss() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) pred_to_nday() (in module pseudodynamics.functions.reader_funs) predict_dataloader() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) predict_nabla_v() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) predict_param() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) predict_step() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) prepare_data() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) print() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) process_gene_chunk() (in module pseudodynamics.de_test._base) project_params_to_pseudotime() (in module pseudodynamics.functions.eval_funs), [1] pseudodynamics._config module, [1] pseudodynamics.de_test module pseudodynamics.de_test._association_test module pseudodynamics.de_test._base module pseudodynamics.functions module pseudodynamics.functions.eval_funs module pseudodynamics.functions.reader_funs module pseudodynamics.models module pseudodynamics.models._density_transport module pseudodynamics.models._pde_informed_params module pseudodynamics.plotting_fns module pseudodynamics.plotting_fns.curve_plot module pseudodynamics.plotting_fns.density_plot module pseudodynamics.plotting_fns.param_plot module pseudodynamics.reader module, [1] PseudotimeRestrictedAssociationTest (class in pseudodynamics.de_test._association_test), [1] R Random_ExtractDataset (class in pseudodynamics.reader) random_train_val_test_split() (pseudodynamics.reader.TwoTimpepoint_AnnDS method), [1], [2] register_backward_hook() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) register_buffer() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) register_forward_hook() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) register_forward_pre_hook() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) register_full_backward_hook() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) register_full_backward_pre_hook() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) register_load_state_dict_post_hook() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) register_load_state_dict_pre_hook() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) register_module() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) register_parameter() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) register_state_dict_post_hook() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) register_state_dict_pre_hook() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) remove_ignored_hparams() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) requires_grad_() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) resampling_animation_meshgrid() (in module pseudodynamics.plotting_fns.density_plot) resampling_animation_umap() (in module pseudodynamics.plotting_fns.density_plot) resampling_by_density() (pseudodynamics.reader.HigDim_AnnDS method) (pseudodynamics.reader.TwoTimpepoint_AnnDS method) residual_loss() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method), [1], [2] restrict_D() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) run_association_test_parallel() (in module pseudodynamics.de_test._association_test) run_fitGAM_parallel() (in module pseudodynamics.de_test._base) S sample_deltax() (in module pseudodynamics.functions.reader_funs) sample_deltax_from_knn() (in module pseudodynamics.functions.reader_funs), [1] sample_deltax_from_transition() (in module pseudodynamics.functions.reader_funs) save() (pseudodynamics._config.ExperimentConfig method), [1], [2] save_gamfit() (in module pseudodynamics.de_test._base) save_hyperparameters() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) scale_dpt() (in module pseudodynamics.functions.reader_funs) set_extra_state() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) set_submodule() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) setup() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) share_memory() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) Simple_DS (class in pseudodynamics.reader) SingleBranch_AnnDS (class in pseudodynamics.reader) state_dict() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) statify_flow() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method), [1], [2] store_attr() (pseudodynamics._config.ExperimentConfig method) stratified_ode() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method), [1], [2] strict_loading (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) subset_dataset() (pseudodynamics.reader.TwoTimpepoint_AnnDS method), [1], [2] summarize_cell_proportions() (pseudodynamics.models._density_transport.DT_analysis method) super_resolution_pseudobulk() (in module pseudodynamics.functions.reader_funs) Syn_DS (class in pseudodynamics.reader) T T_destination (pseudodynamics.models._density_transport.Density_Transfer attribute) (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) (pseudodynamics.models.MLP_models.MLP_surrogate attribute) (pseudodynamics.models.Spline_models.CubicSpline attribute) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline attribute) teardown() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) test_dataloader() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) test_step() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) to() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) to_dict() (pseudodynamics._config.ExperimentConfig method), [1], [2] to_empty() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) to_onnx() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) to_tensorrt() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) to_torchscript() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) toggle_optimizer() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) toggled_optimizer() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) trace_div() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models._pde_informed_params.pde_params_base method) train() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) train_dataloader() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) train_test_split_adata() (in module pseudodynamics.functions.reader_funs) trainer (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) training (pseudodynamics.models._density_transport.Density_Transfer attribute) (pseudodynamics.models._pde_informed_params.log_pde_params attribute) (pseudodynamics.models._pde_informed_params.pde_params attribute) (pseudodynamics.models.MLP_models.MLP_surrogate attribute) (pseudodynamics.models.Spline_models.CubicSpline attribute) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline attribute) training_step() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_neighborloss method) (pseudodynamics.models._pde_informed_params.pde_params method), [1], [2] (pseudodynamics.models._pde_informed_params.pde_params_fastmode method) (pseudodynamics.models._pde_informed_params.pde_params_meshgrid method) (pseudodynamics.models._pde_informed_params.pde_singlebranch_twotimepoints method) (pseudodynamics.models._pde_informed_params.pde_u_free method) transfer_batch_to_device() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) transition_by_batch() (pseudodynamics.models._density_transport.Density_Transfer method), [1], [2] truncated_clustermap() (in module pseudodynamics.plotting_fns.param_plot) TwoTimepoint_MeshGrid (class in pseudodynamics.reader) TwoTimpepoint_AnnDS (class in pseudodynamics.reader), [1] TwoTimpepoint_AnnDS_fastmode (class in pseudodynamics.reader) type() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) U umap_by_time() (in module pseudodynamics.plotting_fns.density_plot) unfreeze() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) untoggle_optimizer() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) V val_dataloader() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) validation_step() (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method), [1], [2] (pseudodynamics.models._pde_informed_params.pde_singlebranch_twotimepoints method) velocity() (pseudodynamics.models._density_transport.Density_Transfer method) W W_distance() (in module pseudodynamics.functions.eval_funs), [1] W_log_distance() (in module pseudodynamics.functions.eval_funs) X xpu() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method) Z zero_grad() (pseudodynamics.models._density_transport.Density_Transfer method) (pseudodynamics.models._pde_informed_params.log_pde_params method) (pseudodynamics.models._pde_informed_params.pde_params method) (pseudodynamics.models.MLP_models.MLP_surrogate method) (pseudodynamics.models.Spline_models.CubicSpline method) (pseudodynamics.models.Spline_models.MultiDim_CubicSpline method)