Index

A

activation() (stories.potentials.MLPPotential method)

adata (stories.tools.DataLoader attribute)

B

batch_size (stories.tools.DataLoader attribute)

C

compute_potential() (in module stories.tools)

compute_velocity() (in module stories.tools)

D

DataLoader (class in stories.tools)

debias (stories.spacetime.SpaceTime attribute) default_checkpoint_manager() (in module stories.tools)

E

epsilon (stories.spacetime.SpaceTime attribute)

ExplicitStep (class in stories.steps.explicit)

F

features (stories.potentials.MLPPotential attribute)

fit() (stories.spacetime.SpaceTime method)

I

ICNNImplicitStep (class in stories.steps.icnn_implicit)

inference_step() (stories.steps.explicit.ExplicitStep method) (stories.steps.icnn_implicit.ICNNImplicitStep method)

L

linear_loss() (in module stories.loss)

log_callback (stories.spacetime.SpaceTime attribute) loss_fn() (in module stories.loss)

M

make_train_val_split() (stories.tools.DataLoader method) MLPPotential (class in stories.potentials) module stories.loss stories.potentials stories.spacetime stories.steps.explicit stories.steps.icnn_implicit stories.tools

N

n_steps (stories.spacetime.SpaceTime attribute)

name (stories.potentials.MLPPotential attribute) next() (stories.tools.DataLoader method)

O

omics_key (stories.tools.DataLoader attribute)

P

parent (stories.potentials.MLPPotential attribute) plot_gene_trends() (in module stories.tools) plot_losses() (in module stories.tools)

plot_single_gene_trend() (in module stories.tools) plot_velocity() (in module stories.tools) potential (stories.spacetime.SpaceTime attribute) proximal_step (stories.spacetime.SpaceTime attribute)

Q

quadratic (stories.spacetime.SpaceTime attribute)

quadratic_loss() (in module stories.loss) quadratic_weight (stories.spacetime.SpaceTime attribute)

R

regress_genes() (in module stories.tools)

S

scope (stories.potentials.MLPPotential attribute) select_driver_genes() (in module stories.tools) space_key (stories.tools.DataLoader attribute) SpaceTime (class in stories.spacetime) stories.loss module stories.potentials module

stories.spacetime module stories.steps.explicit module stories.steps.icnn_implicit module stories.tools module

T

teacher_forcing (stories.spacetime.SpaceTime attribute) tf_enrich() (in module stories.tools) time_key (stories.tools.DataLoader attribute) train_or_val() (stories.tools.DataLoader method)

train_val_split (stories.tools.DataLoader attribute) training_step() (stories.steps.explicit.ExplicitStep method) (stories.steps.icnn_implicit.ICNNImplicitStep method) transform() (stories.spacetime.SpaceTime method)

W

weight_key (stories.tools.DataLoader attribute)