Index

A

add_eval_loss() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) add_phenotypes_to_df() (multidms.Model method) (multidms.model.Model method)

all_mutations (multidms.model_collection.ModelCollection property) (multidms.ModelCollection property) arrays (multidms.Data property) (multidms.data.Data property)

B

binarymaps (multidms.Data property) (multidms.data.Data property)

bundle_idxs (multidms.Data property) (multidms.data.Data property)

C

color_gradient_hex() (in module multidms.plot) conditions (multidms.Data property) (multidms.data.Data property) (multidms.model_collection.ModelCollection property) (multidms.ModelCollection property) converged (multidms.Model property) (multidms.model.Model property)

convergence_trajectory_df (multidms.Model property) (multidms.model.Model property) convergence_trajectory_df() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) convert_subs_wrt_ref_seq() (multidms.Data method) (multidms.data.Data method) count_loss() (in module multidms.jaxmodels)

D

Data (class in multidms) (class in multidms.data) (class in multidms.jaxmodels)

data (multidms.Model property) (multidms.model.Model property) difference_matrix() (in module multidms.utils)

E

eval_loss() (multidms.Model method) (multidms.model.Model method)

explode_params_dict() (in module multidms.utils)

F

fit() (in module multidms.jaxmodels) (multidms.Model method) (multidms.model.Model method) fit_models() (in module multidms) (in module multidms.model_collection)

fit_one_model() (in module multidms.model_collection) from_multidms() (multidms.jaxmodels.Data static method) from_params() (multidms.jaxmodels.Latent static method) functional_score_loss() (in module multidms.jaxmodels) functional_scores (multidms.jaxmodels.Data attribute)

G

ge_landscape() (in module multidms.plot) get_ge_curve() (multidms.Model method) (multidms.model.Model method) get_ge_landscape_df() (multidms.Model method) (multidms.model.Model method)

get_mutations_df() (multidms.Model method) (multidms.model.Model method) get_variants_df() (multidms.Model method) (multidms.model.Model method) global_epistasis (multidms.jaxmodels.Model attribute) GlobalEpistasis (class in multidms.jaxmodels)

I

Identity (class in multidms.jaxmodels)

L

Latent (class in multidms.jaxmodels) logθ (multidms.jaxmodels.Model attribute)

loss_df() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method)

M

Model (class in multidms) (class in multidms.jaxmodels) (class in multidms.model) ModelCollection (class in multidms) (class in multidms.model_collection) ModelCollectionFitError module multidms multidms.data multidms.jaxmodels multidms.model multidms.model_collection multidms.plot multidms.utils multidms module multidms.data module multidms.jaxmodels module

multidms.model module multidms.model_collection module multidms.plot module multidms.utils module mut_param_dataset_correlation() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) mut_param_heatmap() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) mut_param_traceplot() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) mutations (multidms.Data property) (multidms.data.Data property) mutations_df (multidms.Data property) (multidms.data.Data property) mutparser (multidms.Data property) (multidms.data.Data property) my_concat() (in module multidms.utils)

N

name (multidms.Data property) (multidms.data.Data property) non_identical_mutations (multidms.Data property) (multidms.data.Data property)

non_identical_sites (multidms.Data property) (multidms.data.Data property)

P

params (multidms.Model property) (multidms.model.Model property) parse_mut (multidms.Data property) (multidms.data.Data property) parse_muts (multidms.Data property) (multidms.data.Data property) plot_func_score_boxplot() (multidms.Data method) (multidms.data.Data method)

plot_times_seen_hist() (multidms.Data method) (multidms.data.Data method) post_count_wt (multidms.jaxmodels.Data attribute) post_counts (multidms.jaxmodels.Data attribute) pre_count_wt (multidms.jaxmodels.Data attribute) pre_counts (multidms.jaxmodels.Data attribute) predict_post_count() (multidms.jaxmodels.Model method) predict_score() (multidms.jaxmodels.Model method)

R

reference (multidms.Data property) (multidms.data.Data property) (multidms.model_collection.ModelCollection property) (multidms.ModelCollection property)

reference_condition (multidms.jaxmodels.Model attribute) reference_index (multidms.Data property) (multidms.data.Data property) reference_sequence_conditions (multidms.Data property) (multidms.data.Data property)

S

shared_mutations (multidms.model_collection.ModelCollection property) (multidms.ModelCollection property) shift_sparsity() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) Sigmoid (class in multidms.jaxmodels) single_mut_encodings (multidms.Data property) (multidms.data.Data property) site_map (multidms.Data property) (multidms.data.Data property)

site_map_union (multidms.model_collection.ModelCollection property) (multidms.ModelCollection property) split_apply_combine_muts() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) split_sub() (in module multidms.utils) split_subs() (in module multidms.utils) stack_fit_models() (in module multidms.model_collection)

T

targets (multidms.Data property) (multidms.data.Data property)

training_loss (multidms.Model property) (multidms.model.Model property) transform() (in module multidms.utils)

V

variants_df (multidms.Data property) (multidms.data.Data property)

W

warmstart() (multidms.jaxmodels.Latent static method)

wildtype_latent (multidms.Model property) (multidms.model.Model property)

X

X (multidms.jaxmodels.Data attribute)

x_wt (multidms.jaxmodels.Data attribute)

Z

zeros() (multidms.jaxmodels.Latent static method)

Α

α (multidms.jaxmodels.Model attribute)

Β

β (multidms.jaxmodels.Latent attribute)

β0 (multidms.jaxmodels.Latent attribute)

Φ

φ (multidms.jaxmodels.Model attribute)