Index A | B | C | D | E | F | G | L | M | N | O | P | R | S | T | V | W A accelerator (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) adata_to_df_with_embed() (in module gravity.data.preprocessing) arrow_grid (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) arrow_scale (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) assert_gene_order_matches() (in module gravity.data.preprocessing) attention_dir (gravity.CellStageConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) attention_output (gravity.CellStageConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) attention_topk (gravity.CellStageConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) B batch_size (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) C CellStageConfig (class in gravity) (class in gravity.train.cell_stage) checkpoint_name (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) compute_batc() (in module gravity) configure_optimizers() (gravity.FullModelCellWise method) (gravity.FullModelGeneWise method) D devices (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) E embedding_size (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) epochs (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) estimate_future_positions() (in module gravity) (in module gravity.tools.future) export_intermediate_from_h5ad() (in module gravity) (in module gravity.data.preprocessing) F ffn_dimension (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) forward() (gravity.FullModelCellWise method) (gravity.FullModelGeneWise method) FullModelCellWise (class in gravity) FullModelGeneWise (class in gravity) future_positions (gravity.GeneStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) future_positions_name (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) future_tau (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) G gene_order_path (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) gene_subset (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) GeneStageConfig (class in gravity) (class in gravity.train.gene_stage) get_verbose() (in module gravity) gradient_clip_val (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) gravity module gravity.data.preprocessing module gravity.pipeline module gravity.tools.future module gravity.train.cell_stage module gravity.train.gene_stage module L learning_rate (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) load_cell_stage_dataset() (in module gravity.data.preprocessing) load_gene_order() (in module gravity) (in module gravity.data.preprocessing) load_gene_stage_dataset() (in module gravity.data.preprocessing) log_every_n_steps (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) log_verbose() (in module gravity) M make_plot (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) middle_csv (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) middle_csv_name (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) model_dimension (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) module gravity gravity.data.preprocessing gravity.pipeline gravity.tools.future gravity.train.cell_stage gravity.train.gene_stage N n_neg_neighbors (gravity.CellStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) n_pos_neighbors (gravity.CellStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) num_workers (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) O on_test_epoch_end() (gravity.FullModelCellWise method) (gravity.FullModelGeneWise method) output_dir (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) P PipelineConfig (class in gravity) (class in gravity.pipeline) plot_color (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) plot_gene (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) plot_genes (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) plot_velocity_cell() (in module gravity) plot_velocity_gene() (in module gravity) precision (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) preprocess_counts() (in module gravity) (in module gravity.data.preprocessing) pretrained_checkpoint (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) prior_network (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) progress_bar (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) R rank_tf_scores() (in module gravity) raw_counts (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) resolve_gene_order() (in module gravity) (in module gravity.data.preprocessing) run_pipeline() (in module gravity) (in module gravity.pipeline) S seed (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) set_verbose() (in module gravity) stage1_checkpoint (gravity.GeneStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) stage1_checkpoint_name (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) stage1_csv (gravity.CellStageConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) stage1_csv_name (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) stage1_epochs (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) stage1_lr (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) stage1_pretrained_checkpoint (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) stage2_checkpoint_name (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) stage2_csv (gravity.GeneStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) stage2_csv_name (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) stage2_epochs (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) stage2_lr (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) stage2_pretrained_checkpoint (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) strategy (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) T test_step() (gravity.FullModelCellWise method) (gravity.FullModelGeneWise method) train_cell_stage() (in module gravity) (in module gravity.train.cell_stage) train_gene_stage() (in module gravity) (in module gravity.train.gene_stage) training_step() (gravity.FullModelCellWise method) (gravity.FullModelGeneWise method) V val_fraction (gravity.CellStageConfig attribute) (gravity.GeneStageConfig attribute) (gravity.train.cell_stage.CellStageConfig attribute) (gravity.train.gene_stage.GeneStageConfig attribute) val_fraction_stage1 (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) val_fraction_stage2 (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute) W workdir (gravity.pipeline.PipelineConfig attribute) (gravity.PipelineConfig attribute)