Index

_

__init__() (sparank.data.InferenceDataset method) (sparank.data.MemmapDataset method) (sparank.ExpConfig method) (sparank.ModalityConfig method) (sparank.modules.DeconvCrossEntropy method) (sparank.modules.FusionLayer method) (sparank.modules.NTXentLoss method) (sparank.modules.SpotRankTransformer method) (sparank.SimulationConfig method) (sparank.SpaRank method) (sparank.training.Trainer method)

B

batch_key (sparank.ExpConfig attribute) (sparank.SimulationConfig attribute)

batch_request_size (sparank.SimulationConfig attribute) batch_size (sparank.ExpConfig attribute) build_vocab() (in module sparank.data)

C

cell_sample_method (sparank.SimulationConfig attribute) cells_max (sparank.SimulationConfig attribute) cells_mean (sparank.SimulationConfig attribute) cells_min (sparank.SimulationConfig attribute) cells_std (sparank.SimulationConfig attribute) celltype_key (sparank.ExpConfig attribute)

cl_dropout_rate (sparank.ModalityConfig attribute) cl_temperature (sparank.ExpConfig attribute) cl_weight (sparank.ExpConfig attribute) cls_weight (sparank.ExpConfig attribute) context_dim (sparank.ExpConfig attribute) context_key (sparank.ExpConfig attribute)

D

DeconvCrossEntropy (class in sparank.modules) depth (sparank.ExpConfig attribute) (sparank.ModalityConfig attribute)

dim (sparank.ExpConfig attribute) dropout (sparank.ExpConfig attribute)

E

epochs (sparank.ExpConfig attribute)

ExpConfig (class in sparank)

F

find_sc_markers() (in module sparank.data) fit() (sparank.SpaRank method) (sparank.training.Trainer method) forward() (sparank.modules.DeconvCrossEntropy method) (sparank.modules.FusionLayer method) (sparank.modules.NTXentLoss method) (sparank.modules.SpotRankTransformer method)

forward_cl() (sparank.modules.SpotRankTransformer method) forward_mrp() (sparank.modules.SpotRankTransformer method) forward_with_gates() (sparank.modules.SpotRankTransformer method) fusion_type (sparank.ExpConfig attribute) FusionLayer (class in sparank.modules)

G

get_modality() (sparank.ExpConfig method)

H

heads (sparank.ExpConfig attribute) (sparank.ModalityConfig attribute)

I

InferenceDataset (class in sparank.data)

K

k_feat (sparank.ModalityConfig attribute)

L

load() (sparank.ExpConfig class method) (sparank.SpaRank class method)

lr (sparank.ExpConfig attribute)

M

MemmapDataset (class in sparank.data) mlp_dim (sparank.ExpConfig attribute) modalities (sparank.ExpConfig attribute)

modality_names (sparank.ExpConfig property) ModalityConfig (class in sparank) mrp_mask_rate (sparank.ModalityConfig attribute) mrp_weight (sparank.ExpConfig attribute)

N

n_modalities (sparank.ExpConfig property) n_threads (sparank.SimulationConfig attribute) name (sparank.ModalityConfig attribute)

normalize_rna() (in module sparank.data) NTXentLoss (class in sparank.modules) num_workers (sparank.ExpConfig attribute)

P

predict() (sparank.SpaRank method)

prepare() (sparank.SpaRank method)

R

register_modality() (sparank.SpaRank method)

register_mudata() (sparank.SpaRank method)

S

save() (sparank.ExpConfig method) (sparank.SpaRank method) save_dir (sparank.ExpConfig attribute) sim_buffer (sparank.SimulationConfig attribute)

simulate() (in module sparank.data) simulation (sparank.ExpConfig attribute) SimulationConfig (class in sparank) SpaRank (class in sparank) SpotRankTransformer (class in sparank.modules)

T

tokenize_batch() (in module sparank.data) top_k (sparank.ModalityConfig attribute)

total_samples (sparank.SimulationConfig attribute) total_seq_len (sparank.ExpConfig property) Trainer (class in sparank.training)

U

use_cl (sparank.ExpConfig property)

use_context (sparank.ExpConfig property) use_mrp (sparank.ExpConfig property)