Index

A

AssignPcluster() (in module tirank.TrainPre)

B

BulkDataset (class in tirank.Dataloader)

C

calculate_binomial_gene_pairs() (tirank.GPextractor.GenePairExtractor method) calculate_populations_meanRank() (in module tirank.SCSTpreprocess) calculate_regression_gene_pairs() (tirank.GPextractor.GenePairExtractor method) calculate_survival_gene_pairs() (tirank.GPextractor.GenePairExtractor method) check_bulk() (in module tirank.LoadData) ClassscorePredictor (class in tirank.Model) Clustering() (in module tirank.SCSTpreprocess) collate_fn() (tirank.Imageprocessing.ImageDataset static method) compute_similarity() (in module tirank.SCSTpreprocess) ConvStem (class in tirank.Imageprocessing)

cosine_loss() (in module tirank.Loss) cox_loss() (in module tirank.Loss) create_boxplot() (in module tirank.Visualization) create_comparison_density_plot() (in module tirank.Visualization) create_density_plot() (in module tirank.Visualization) create_hist_plot() (in module tirank.Visualization) create_tensor() (in module tirank.Visualization) crop_images() (in module tirank.Imageprocessing) CrossEntropy_loss() (in module tirank.Loss) ctranspath() (in module tirank.Imageprocessing)

D

DEG_analysis() (in module tirank.Visualization)

DEG_volcano() (in module tirank.Visualization) DenseNetEncoderModel (class in tirank.Model)

E

evaluate_on_test_data() (in module tirank.Visualization)

extract_candidate_genes() (tirank.GPextractor.GenePairExtractor method)

F

filter_gene_pairs() (tirank.GPextractor.GenePairExtractor method) FilteringAnndata() (in module tirank.SCSTpreprocess) forward() (tirank.Imageprocessing.ConvStem method) (tirank.Model.ClassscorePredictor method) (tirank.Model.DenseNetEncoderModel method) (tirank.Model.MLPEncoderModel method) (tirank.Model.PathologyPredictor method) (tirank.Model.PositionalEncoding method) (tirank.Model.RegscorePredictor method) (tirank.Model.RiskscorePredictor method) (tirank.Model.TiRankModel method) (tirank.Model.TransformerEncoderModel method)

G

gaussian_kernel() (in module tirank.Loss) GenePairExtractor (class in tirank.GPextractor)

generate_val() (in module tirank.Dataloader) get_best_model() (in module tirank.TrainPre) GetPathoClass() (in module tirank.Imageprocessing)

I

IdenHub() (in module tirank.TrainPre) ImageDataset (class in tirank.Imageprocessing) infer_by_pretrain() (in module tirank.Imageprocessing)

init_weights() (tirank.Model.TiRankModel method) (tirank.Model.TransformerEncoderModel method) initial_model_para() (in module tirank.Model) is_imbalanced() (in module tirank.SCSTpreprocess)

L

load_bulk_clinical() (in module tirank.LoadData) load_bulk_exp() (in module tirank.LoadData) load_data() (tirank.GPextractor.GenePairExtractor method)

load_sc_data() (in module tirank.LoadData) load_st_data() (in module tirank.LoadData) Logtransformation() (in module tirank.SCSTpreprocess)

M

merge_datasets() (in module tirank.SCSTpreprocess) MLPEncoderModel (class in tirank.Model)

mmd_loss() (in module tirank.Loss) model_predict() (in module tirank.Visualization) MSE_loss() (in module tirank.Loss)

N

Normalization() (in module tirank.SCSTpreprocess)

normalize_data() (in module tirank.SCSTpreprocess)

O

objective() (in module tirank.TrainPre)

P

PackData() (in module tirank.Dataloader) PathologyPredictor (class in tirank.Model) Pathway_Enrichment() (in module tirank.Visualization) Pcluster() (in module tirank.TrainPre) perform_sampling_on_RNAseq() (in module tirank.SCSTpreprocess) permute_once() (in module tirank.TrainPre) plot_genepair() (in module tirank.Visualization) plot_label_distribution_among_conditions() (in module tirank.Visualization)

plot_loss() (in module tirank.Visualization) plot_patho_class_heatmap() (in module tirank.Imageprocessing) plot_score_distribution() (in module tirank.Visualization) plot_score_umap() (in module tirank.Visualization) plot_STmap() (in module tirank.Visualization) PositionalEncoding (class in tirank.Model) Predict() (in module tirank.TrainPre) process_embeddings() (in module tirank.Imageprocessing) prototype_loss() (in module tirank.Loss)

R

RegscorePredictor (class in tirank.Model) regularization_loss() (in module tirank.Loss) Reject_With_GMM_Bio() (in module tirank.TrainPre)

Reject_With_GMM_Reg() (in module tirank.TrainPre) Reject_With_StrictNumber() (in module tirank.TrainPre) RiskscorePredictor (class in tirank.Model) run_extraction() (tirank.GPextractor.GenePairExtractor method)

S

save_data() (tirank.GPextractor.GenePairExtractor method) scale_coordinate() (in module tirank.Imageprocessing) SCDataset (class in tirank.Dataloader)

setup_seed() (in module tirank.Model) split_gene_pairs() (tirank.GPextractor.GenePairExtractor method) STDataset (class in tirank.Dataloader)

T

TiRankModel (class in tirank.Model) Train_one_epoch() (in module tirank.TrainPre) transfer_exp_profile() (in module tirank.LoadData) transform_bulk_gene_pairs() (tirank.GPextractor.GenePairExtractor method)

transform_single_cell_gene_pairs() (tirank.GPextractor.GenePairExtractor method) transform_test_exp() (in module tirank.Dataloader) TransformerEncoderModel (class in tirank.Model) tune_hyperparameters() (in module tirank.TrainPre)

V

Validate_model() (in module tirank.TrainPre)

view_dataframe() (in module tirank.LoadData)