Index

_

__call__() (scdiffeq.io.HParams method) (scdiffeq.tools._simulation.Simulation method) __config__() (scdiffeq.core._scdiffeq.scDiffEq method) __configure__() (scdiffeq.io.HParams method) __delattr__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __dir__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __eq__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __format__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __ge__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __getattribute__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __getitem__() (scdiffeq.io.HParams method) (scdiffeq.io.Project method) __getstate__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __gt__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __hash__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __init__() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) (scdiffeq.core._scdiffeq.scDiffEq method) (scdiffeq.core.lightning_models._lightning_ode.LightningODE method) (scdiffeq.core.lightning_models._lightning_ode_fixed_potential.LightningODE_FixedPotential method) (scdiffeq.core.lightning_models._lightning_sde.LightningSDE method) (scdiffeq.core.lightning_models._lightning_sde_fixed_potential.LightningSDE_FixedPotential method) (scdiffeq.core.lightning_models._lightning_sde_fixed_potential_regularized_velocity_ratio.LightningSDE_FixedPotential_RegularizedVelocityRatio method) (scdiffeq.io.Checkpoint method) (scdiffeq.io.HParams method) (scdiffeq.io.Project method) (scdiffeq.io.Version method) (scdiffeq.tools._knn.kNN method) (scdiffeq.tools._simulation.Simulation method) __init_subclass__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __le__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __lt__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn)

__ne__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __new__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __parse__() (scdiffeq.core._scdiffeq.scDiffEq method) (scdiffeq.tools._simulation.Simulation method) __reduce__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __reduce_ex__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __repr__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) (scdiffeq.core._scdiffeq.scDiffEq method) (scdiffeq.io.Checkpoint method) (scdiffeq.io.HParams method) (scdiffeq.io.Version method) (scdiffeq.tools._knn.kNN method) __setattr__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __sizeof__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __str__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __subclasshook__() (in module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging), [1] (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) __update__() (scdiffeq.core._scdiffeq.scDiffEq method) (scdiffeq.tools._simulation.Simulation method) _adjust_step_size() (scdiffeq.core._scdiffeq.scDiffEq method) _attrs (scdiffeq.io.HParams attribute) _build() (scdiffeq.tools._knn.kNN method) _compute_magnitude_f() (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) _compute_magnitude_g() (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) _configure_CSVLogger() (scdiffeq.core._scdiffeq.scDiffEq method) _configure_decoder() (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) _configure_encoder() (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) _configure_lightning_model() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) _configure_name() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) _configure_torch_modules() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) _configure_trainer_generator() (scdiffeq.core._scdiffeq.scDiffEq method) _count_values() (scdiffeq.tools._knn.kNN method) _dynamic_enforcement() (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) _groupby (scdiffeq.io.Version attribute) _initialize__attrs() (scdiffeq.core._scdiffeq.scDiffEq method) _INTEGRATOR() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) _L2Norm (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) _max_count() (scdiffeq.tools._knn.kNN method) _path (scdiffeq.io.Version attribute) _read() (scdiffeq.io.HParams method) _set_version_path_attributes() (scdiffeq.io.Project method) _sum_normalize() (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) _to_adata_sim() (scdiffeq.tools._simulation.Simulation method) _update_lit_diffeq_hparams() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) _velocity_ratio_loss() (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) _yaml_file (scdiffeq.io.HParams attribute) _yaml_path (scdiffeq.io.HParams attribute)

A

adata (scdiffeq.tools._knn.kNN attribute) aggregate() (scdiffeq.tools._knn.kNN method)

annotate_cell_fate() (in module scdiffeq.tools._annotate_cell_fate) annotate_cell_state() (in module scdiffeq.tools._annotate_cell_state)

C

Checkpoint (class in scdiffeq.io) ckpt (scdiffeq.io.Checkpoint property) ckpts (scdiffeq.io.Version property) compute_sinkhorn_divergence() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq)

configure_data() (scdiffeq.core._scdiffeq.scDiffEq method) configure_kNN() (scdiffeq.core._scdiffeq.scDiffEq method) configure_model() (scdiffeq.core._scdiffeq.scDiffEq method) configure_optimizers() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) count() (scdiffeq.tools._knn.kNN method)

D

decode() (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn)

diffusion() (scdiffeq.core._scdiffeq.scDiffEq method) drift() (scdiffeq.core._scdiffeq.scDiffEq method)

E

encode() (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn)

epoch (scdiffeq.io.Checkpoint property)

F

F_hat (scdiffeq.io.Checkpoint property) fit() (scdiffeq.core._scdiffeq.scDiffEq method) forward() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) (scdiffeq.tools._simulation.Simulation method)

freeze() (scdiffeq.core._scdiffeq.scDiffEq method)

H

HParams (class in scdiffeq.io)

hparams (scdiffeq.io.Version property) human_hematopoiesis() (in module scdiffeq.datasets._human_hematopoiesis)

I

idx (scdiffeq.tools._simulation.Simulation property)

index (scdiffeq.tools._knn.kNN property) integrate() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq)

K

kNN (class in scdiffeq.tools._knn) (scdiffeq.core._scdiffeq.scDiffEq property)

L

larry() (in module scdiffeq.datasets._larry_in_vitro) LightningODE (class in scdiffeq.core.lightning_models._lightning_ode) LightningODE_FixedPotential (class in scdiffeq.core.lightning_models._lightning_ode_fixed_potential) LightningSDE (class in scdiffeq.core.lightning_models._lightning_sde)

LightningSDE_FixedPotential (class in scdiffeq.core.lightning_models._lightning_sde_fixed_potential) LightningSDE_FixedPotential_RegularizedVelocityRatio (class in scdiffeq.core.lightning_models._lightning_sde_fixed_potential_regularized_velocity_ratio) load() (scdiffeq.core._scdiffeq.scDiffEq method) logger (scdiffeq.core._scdiffeq.scDiffEq property)

M

metrics (scdiffeq.core._scdiffeq.scDiffEq property) metrics_df (scdiffeq.io.Version property) metrics_groupby (scdiffeq.io.Project attribute) module scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging, [1] scdiffeq.core._scdiffeq scdiffeq.core.lightning_models._lightning_ode scdiffeq.core.lightning_models._lightning_ode_fixed_potential scdiffeq.core.lightning_models._lightning_sde_fixed_potential scdiffeq.core.lightning_models._lightning_sde_fixed_potential_regularized_velocity_ratio scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn

multi_aggregate() (scdiffeq.tools._knn.kNN method)

N

n_dim (scdiffeq.tools._knn.kNN property) n_neighbors (scdiffeq.tools._knn.kNN attribute) n_obs (scdiffeq.tools._knn.kNN property)

None (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn)

P

pancreatic_endocrinogenesis() (in module scdiffeq.datasets._pancreatic_endocrinogenesis) path (scdiffeq.io.Checkpoint property) (scdiffeq.io.Project attribute) per_epoch_metrics (scdiffeq.io.Version property) potential() (scdiffeq.core._scdiffeq.scDiffEq method)

predict_step() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) PRETRAIN() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) pretrain() (scdiffeq.core._scdiffeq.scDiffEq method) pretrain_step() (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn) Project (class in scdiffeq.io)

Q

query() (scdiffeq.tools._knn.kNN method)

R

read_h5ad() (in module scdiffeq.io._data._read_h5ad)

read_pickle() (in module scdiffeq.io._data._pickle_io) reconstruction_loss (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn)

S

scDiffEq (class in scdiffeq.core._scdiffeq) scdiffeq.callbacks._stochastic_weight_averaging.StochasticWeightAveraging module, [1] scdiffeq.core._scdiffeq module scdiffeq.core.lightning_models._lightning_ode module scdiffeq.core.lightning_models._lightning_ode_fixed_potential module scdiffeq.core.lightning_models._lightning_sde_fixed_potential module scdiffeq.core.lightning_models._lightning_sde_fixed_potential_regularized_velocity_ratio module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq module scdiffeq.core.lightning_models.base._batch_processor.BatchProcessor module

scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn module scdiffeq.core.lightning_models.mix_ins._sde_mix_in.SDEMixIn module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn module simulate() (in module scdiffeq.tools._simulation) (scdiffeq.core._scdiffeq.scDiffEq method) Simulation (class in scdiffeq.tools._simulation) space (scdiffeq.tools._knn.kNN attribute) step() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.mix_ins._base_forward_mix_in.BaseForwardMixIn) (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn) (in module scdiffeq.core.lightning_models.mix_ins._vae_mix_in.VAEMixIn)

T

t (scdiffeq.tools._simulation.Simulation property) test_step() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq)

to() (scdiffeq.core._scdiffeq.scDiffEq method) train() (scdiffeq.core._scdiffeq.scDiffEq method) training_step() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq)

U

use_key (scdiffeq.tools._knn.kNN attribute)

V

validation_step() (in module scdiffeq.core.lightning_models.base._base_lightning_diffeq.BaseLightningDiffEq) (in module scdiffeq.core.lightning_models.mix_ins._potential_mix_in.PotentialMixIn) velocity_ratio_loss_transform() (in module scdiffeq.core.lightning_models.mix_ins._regularized_velocity_ratio_mix_in.RegularizedVelocityRatioMixIn)

velocity_stream() (in module scdiffeq.plotting._velocity_stream) Version (class in scdiffeq.io) version (scdiffeq.core._scdiffeq.scDiffEq property) (scdiffeq.io.Checkpoint property)

W

write_pickle() (in module scdiffeq.io._data._pickle_io)

X

X (scdiffeq.tools._knn.kNN property)

Z

Z0 (scdiffeq.tools._simulation.Simulation property)