Index

_

__init__() (univi.ClassHeadConfig method) (univi.config.TokenizerConfig method) (univi.config.TransformerConfig method) (univi.data.MultiModalDataset method) (univi.ModalityConfig method) (univi.preprocessing.ADTPreprocessor method) (univi.preprocessing.ATACPreprocessor method) (univi.preprocessing.RNAPreprocessor method) (univi.refinement.RefinementConfig method) (univi.refinement.UniVIRefiner method) (univi.trainer.UniVITrainer method) (univi.TrainingConfig method) (univi.UniVIConfig method) (univi.UniVIMultiModalVAE method)

A

add_classification_head() (univi.UniVIMultiModalVAE method) add_lsc17_scores() (in module univi.evaluation)

ADTPreprocessor (class in univi.preprocessing) align_paired_obs_names() (in module univi.data) ATACPreprocessor (class in univi.preprocessing)

B

build_univi_inputs_from_scnmt_triplet() (in module univi.datasets)

C

ClassHeadConfig (class in univi) collate_multimodal_xy_recon() (in module univi.data) compare_raw_vs_denoised_umap_features() (in module univi.plotting) compare_raw_vs_pred_umap_features() (in module univi.plotting)

compute_foscttm() (in module univi.evaluation) compute_match_recall_at_k() (in module univi.evaluation) compute_modality_entropy() (in module univi.evaluation) compute_modality_mixing() (in module univi.evaluation) cross_modal_predict() (in module univi.evaluation)

D

dataset_info() (in module univi.datasets)

denoise_adata() (in module univi.evaluation)

E

encode_adata() (in module univi.evaluation) encode_fused_adata_pair() (in module univi.evaluation) encode_modality() (univi.trainer.UniVITrainer method) encode_moe_gates_from_tensors() (in module univi.evaluation)

evaluate() (univi.refinement.UniVIRefiner method) evaluate_alignment() (in module univi.evaluation) evaluate_cross_reconstruction() (in module univi.evaluation) export_dataset() (in module univi.datasets)

F

fetch() (in module univi.datasets) fit() (univi.refinement.UniVIRefiner method)

fit_label_latent_gaussians() (in module univi.evaluation) freeze_decoders() (univi.UniVIMultiModalVAE method) freeze_encoders() (univi.UniVIMultiModalVAE method)

G

generate_from_latent() (in module univi.evaluation)

get_data_dir() (in module univi.datasets)

H

hao_citeseq_pbmc() (in module univi.datasets)

L

label_transfer_knn() (in module univi.evaluation) list_datasets() (in module univi.datasets) load() (in module univi.datasets)

load_checkpoint() (in module univi.utils.io) load_reference() (in module univi.workflows) load_scnmt_gastrulation_genebody_triplet() (in module univi.datasets)

M

make_loader() (in module univi.workflows) ModalityConfig (class in univi)

mse_per_feature() (in module univi.evaluation) MultiModalDataset (class in univi.data)

P

pbmc_multiome_10k() (in module univi.datasets) pearson_corr_per_feature() (in module univi.evaluation) plot_confusion_matrix() (in module univi.plotting) plot_featurewise_reconstruction_scatter() (in module univi.plotting)

plot_moe_gate_summary() (in module univi.plotting) plot_reconstruction_error_summary() (in module univi.plotting) predict_feature_perturbation() (in module univi.perturbation) predict_heads_adata (in module univi.refinement)

R

reconstruction_metrics() (in module univi.evaluation) RefinementConfig (class in univi.refinement)

register_dataset() (in module univi.datasets) restore_checkpoint() (in module univi.utils.io) RNAPreprocessor (class in univi.preprocessing)

S

sample_latent_by_label() (in module univi.evaluation) save_checkpoint() (in module univi.utils.io) save_reference() (in module univi.workflows) scnmt_gastrulation() (in module univi.datasets)

set_seed() (in module univi.utils.seed) set_style() (in module univi.plotting) split_by_label() (in module univi.preprocessing) stack_embeddings() (in module univi.workflows)

T

TokenizerConfig (class in univi.config) train() (univi.UniVIMultiModalVAE method)

TrainingConfig (class in univi) TransformerConfig (class in univi.config)

U

umap() (in module univi.plotting) umap_by_modality() (in module univi.plotting) unfreeze_decoders() (univi.UniVIMultiModalVAE method) unfreeze_encoders() (univi.UniVIMultiModalVAE method)

UniVIConfig (class in univi) UniVIMultiModalVAE (class in univi) UniVIRefiner (class in univi.refinement) UniVITrainer (class in univi.trainer)

W

write_gates_to_obs() (in module univi.plotting)