Index

A

AutoCoEmbeddingGenerator (class in cellmaps_coembedding.runner)

B

batch_all_triplet_loss() (in module cellmaps_coembedding.muse_sc.triplet_loss)

batch_hard_triplet_loss() (in module cellmaps_coembedding.muse_sc.triplet_loss)

C

canberra_similarity() (in module cellmaps_coembedding.muse_sc.df_utils) cellmaps_coembedding module cellmaps_coembedding.cellmaps_coembeddingcmd module cellmaps_coembedding.exceptions module cellmaps_coembedding.muse_sc module cellmaps_coembedding.muse_sc.architecture module

cellmaps_coembedding.muse_sc.df_utils module cellmaps_coembedding.muse_sc.file_utils module cellmaps_coembedding.muse_sc.triplet_loss module cellmaps_coembedding.runner module CellmapsCoEmbedder (class in cellmaps_coembedding.runner) CellmapsCoEmbeddingError check_symmetric() (in module cellmaps_coembedding.muse_sc.df_utils) cosine_similarity_scaled() (in module cellmaps_coembedding.muse_sc.df_utils)

D

DROPOUT (cellmaps_coembedding.runner.EmbeddingGenerator attribute)

E

EmbeddingGenerator (class in cellmaps_coembedding.runner)

euclidean_similarity() (in module cellmaps_coembedding.muse_sc.df_utils)

F

FakeCoEmbeddingGenerator (class in cellmaps_coembedding.runner)

forward() (cellmaps_coembedding.muse_sc.architecture.structured_embedding method) fraction_triplets() (in module cellmaps_coembedding.muse_sc.triplet_loss)

G

generate_readme() (cellmaps_coembedding.runner.CellmapsCoEmbedder method) get_coembedding_file() (cellmaps_coembedding.runner.CellmapsCoEmbedder method) get_dimensions() (cellmaps_coembedding.runner.EmbeddingGenerator method) get_embedding_inputdirs() (cellmaps_coembedding.runner.EmbeddingGenerator method)

get_next_embedding() (cellmaps_coembedding.runner.EmbeddingGenerator method) (cellmaps_coembedding.runner.FakeCoEmbeddingGenerator method) (cellmaps_coembedding.runner.MuseCoEmbeddingGenerator method) (cellmaps_coembedding.runner.ProteinGPSCoEmbeddingGenerator method)

I

init_weights() (in module cellmaps_coembedding.muse_sc.architecture)

init_weights_d() (in module cellmaps_coembedding.muse_sc.architecture)

J

JACKKNIFE_PERCENT (cellmaps_coembedding.runner.EmbeddingGenerator attribute)

K

kendall_scaled() (in module cellmaps_coembedding.muse_sc.df_utils)

L

LATENT_DIMENSIONS (cellmaps_coembedding.runner.EmbeddingGenerator attribute)

load_obj() (in module cellmaps_coembedding.muse_sc.file_utils)

M

main() (in module cellmaps_coembedding.cellmaps_coembeddingcmd) make_matrix_from_labels() (in module cellmaps_coembedding.muse_sc) manhattan_similarity() (in module cellmaps_coembedding.muse_sc.df_utils) module cellmaps_coembedding cellmaps_coembedding.cellmaps_coembeddingcmd cellmaps_coembedding.exceptions cellmaps_coembedding.muse_sc cellmaps_coembedding.muse_sc.architecture cellmaps_coembedding.muse_sc.df_utils cellmaps_coembedding.muse_sc.file_utils cellmaps_coembedding.muse_sc.triplet_loss cellmaps_coembedding.runner

muse_fit_predict() (in module cellmaps_coembedding.muse_sc) MuseCoEmbeddingGenerator (class in cellmaps_coembedding.runner)

N

N_EPOCHS (cellmaps_coembedding.runner.EmbeddingGenerator attribute)

N_EPOCHS_INIT (cellmaps_coembedding.runner.MuseCoEmbeddingGenerator attribute)

P

pearson_scaled() (in module cellmaps_coembedding.muse_sc.df_utils)

Protein_Dataset (class in cellmaps_coembedding.muse_sc.architecture) ProteinGPSCoEmbeddingGenerator (class in cellmaps_coembedding.runner)

R

run() (cellmaps_coembedding.runner.CellmapsCoEmbedder method)

S

save_obj() (in module cellmaps_coembedding.muse_sc.file_utils)

spearman_scaled() (in module cellmaps_coembedding.muse_sc.df_utils) structured_embedding (class in cellmaps_coembedding.muse_sc.architecture)

T

ToTensor (class in cellmaps_coembedding.muse_sc.architecture)

train_model() (in module cellmaps_coembedding.muse_sc)

U

upper_tri_values() (in module cellmaps_coembedding.muse_sc.df_utils)

W

write_result_to_file() (in module cellmaps_coembedding.muse_sc)

Z

znorm() (in module cellmaps_coembedding.muse_sc.df_utils)