Index

C

Classifier (class in geneformer.classifier)

E

EmbExtractor (class in geneformer.emb_extractor) evaluate_model() (Classifier method)

evaluate_saved_model() (Classifier method) extract_embs() (EmbExtractor method)

G

geneformer.classifier module geneformer.emb_extractor module geneformer.in_silico_perturber module geneformer.in_silico_perturber_stats module

geneformer.mtl_classifier module geneformer.tokenizer module get_state_embs() (EmbExtractor method) get_stats() (InSilicoPerturberStats method)

H

hyperopt_classifier() (Classifier method)

I

InSilicoPerturber (class in geneformer.in_silico_perturber)

InSilicoPerturberStats (class in geneformer.in_silico_perturber_stats)

L

load_and_evaluate_test_model() (MTLClassifier method)

M

module geneformer.classifier geneformer.emb_extractor geneformer.in_silico_perturber geneformer.in_silico_perturber_stats geneformer.mtl_classifier geneformer.tokenizer

MTLClassifier (class in geneformer.mtl_classifier)

P

perturb_data() (InSilicoPerturber method) plot_conf_mat() (Classifier method) plot_embs() (EmbExtractor method)

plot_predictions() (Classifier method) plot_roc() (Classifier method) prepare_data() (Classifier method)

R

run_manual_tuning() (MTLClassifier method)

run_optuna_study() (MTLClassifier method)

T

tokenize_data() (TranscriptomeTokenizer method) train_all_data() (Classifier method)

train_classifier() (Classifier method) TranscriptomeTokenizer (class in geneformer.tokenizer)

V

validate() (Classifier method)