Index

Symbols

--version methylnet-embed command line option methylnet-interpret command line option methylnet-predict command line option methylnet-test command line option methylnet-torque command line option methylnet-visualize command line option -a, --abs_val methylnet-interpret-regenerate_top_cpgs command line option -a, --additional_command <additional_command> methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -a, --additions <additions> methylnet-torque-run_torque_job command line option -a, --all_cpgs_pickle <all_cpgs_pickle> methylnet-interpret-interpret_biology command line option -a, --average_mechanism <average_mechanism> methylnet-predict-classification_report command line option -abs, --absolute methylnet-interpret-return_shap_values command line option -b, --beta <beta> methylnet-embed-perform_embedding command line option -b, --set_beta <set_beta> methylnet-embed-launch_hyperparameter_scan command line option -bce, --bce_loss methylnet-embed-perform_embedding command line option -bs, --batch_size <batch_size> methylnet-embed-perform_embedding command line option methylnet-interpret-produce_shapley_data command line option methylnet-predict-make_new_predictions command line option methylnet-predict-make_prediction command line option -c, --cell_types <cell_types> methylnet-interpret-plot_all_lola_outputs command line option methylnet-interpret-plot_lola_output command line option -c, --class_names <class_names> methylnet-interpret-shapley_jaccard command line option -c, --classes <classes> methylnet-interpret-interpret_biology command line option methylnet-interpret-plot_top_cpgs command line option methylnet-interpret-return_shap_values command line option -c, --col <col> methylnet-interpret-bin_regression_shaps command line option methylnet-interpret-extract_methylation_array command line option methylnet-interpret-order_results_by_col command line option -c, --command <command> methylnet-torque-run_torque_job command line option -c, --cuda methylnet-embed-perform_embedding command line option methylnet-interpret-produce_shapley_data command line option methylnet-predict-make_new_predictions command line option methylnet-predict-make_prediction command line option -c, --job_chunk_size <job_chunk_size> methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -c, --pheno_col <pheno_col> methylnet-interpret-interpret_embedding_classes command line option -cat, --categorical methylnet-predict-launch_hyperparameter_scan command line option methylnet-predict-make_new_predictions command line option methylnet-predict-make_prediction command line option -cc, --cross_class methylnet-interpret-produce_shapley_data command line option -cgs, --cpg_set <cpg_set> methylnet-interpret-interpret_biology command line option -ci, --class_intersect methylnet-interpret-interpret_biology command line option -cl, --pred_class <pred_class> methylnet-interpret-produce_shapley_data command line option -cn, --cell_names <cell_names> methylnet-interpret-produce_shapley_data command line option -co, --classes_only methylnet-interpret-extract_methylation_array command line option -co, --cooccurrence methylnet-interpret-shapley_jaccard command line option -col, --collections <collections> methylnet-interpret-interpret_biology command line option -col, --interest_col <interest_col> methylnet-interpret-produce_shapley_data command line option -conv, --convolutional methylnet-embed-perform_embedding command line option -cp, --crossover_p <crossover_p> methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -cu, --cuda methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -d, --decay <decay> methylnet-embed-perform_embedding command line option methylnet-predict-make_prediction command line option -d, --depletion methylnet-interpret-interpret_biology command line option -d, --description_col <description_col> methylnet-interpret-plot_all_lola_outputs command line option methylnet-interpret-plot_lola_output command line option -do, --disease_only methylnet-predict-make_prediction command line option -dp, --dropout_p <dropout_p> methylnet-predict-make_prediction command line option -dsd, --dump_shap_data methylnet-interpret-produce_shapley_data command line option -e, --categorical_encoder <categorical_encoder> methylnet-interpret-produce_shapley_data command line option methylnet-predict-classification_report command line option methylnet-predict-make_new_predictions command line option -e, --n_epochs <n_epochs> methylnet-embed-perform_embedding command line option methylnet-predict-make_prediction command line option -eta, --eta_min <eta_min> methylnet-embed-perform_embedding command line option methylnet-predict-make_prediction command line option -ex, --extract_library methylnet-interpret-interpret_biology command line option -fs, --feature_selection methylnet-interpret-produce_shapley_data command line option -g, --generate_input methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -g, --global_vals methylnet-interpret-extract_methylation_array command line option -g, --top_global methylnet-interpret-interpret_biology command line option -gn, --gpu_node <gpu_node> methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -gpu, --gpu <gpu> methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -gpu, --use_gpu methylnet-torque-run_torque_job command line option -grid, --hyperparameter_yaml <hyperparameter_yaml> methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -gsea, --gsea_analyses <gsea_analyses> methylnet-interpret-interpret_biology command line option -gsp, --gsea_pickle <gsea_pickle> methylnet-interpret-interpret_biology command line option -hcsv, --hyperparameter_input_csv <hyperparameter_input_csv> methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -hist, --output_histogram methylnet-interpret-return_shap_values command line option -hl, --hyperparameter_log <hyperparameter_log> methylnet-embed-perform_embedding command line option methylnet-predict-make_prediction command line option -hl, --hyperparameter_output_log <hyperparameter_output_log> methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -hlt, --hidden_layer_encoder_topology <hidden_layer_encoder_topology> methylnet-embed-perform_embedding command line option -hlt, --hidden_layer_topology <hidden_layer_topology> methylnet-predict-make_prediction command line option -hs, --height_kernel_sizes <height_kernel_sizes> methylnet-embed-perform_embedding command line option -i, --embedding_methyl_array_pkl <embedding_methyl_array_pkl> methylnet-interpret-interpret_embedding_classes command line option -i, --include_individuals methylnet-interpret-shapley_jaccard command line option -i, --individuals <individuals> methylnet-interpret-interpret_biology command line option methylnet-interpret-plot_top_cpgs command line option methylnet-interpret-return_shap_values command line option methylnet-interpret-view_methylation_top_cpgs command line option -i, --input_csv <input_csv> methylnet-interpret-order_results_by_col command line option -i, --train_pkl <train_pkl> methylnet-embed-perform_embedding command line option methylnet-interpret-produce_shapley_data command line option methylnet-predict-make_prediction command line option -ic, --interest_cols <interest_cols> methylnet-predict-launch_hyperparameter_scan command line option methylnet-predict-make_new_predictions command line option methylnet-predict-make_prediction command line option -ind, --individual <individual> methylnet-interpret-produce_shapley_data command line option -int, --intersection methylnet-interpret-interpret_biology command line option -j, --job_name <job_name> methylnet-embed-perform_embedding command line option methylnet-predict-make_prediction command line option -j, --n_jobs <n_jobs> methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -kl, --kl_warm_up <kl_warm_up> methylnet-embed-perform_embedding command line option -l, --head_lola_dir <head_lola_dir> methylnet-interpret-plot_all_lola_outputs command line option -l, --lola_csv <lola_csv> methylnet-interpret-plot_lola_output command line option -l, --lola_db <lola_db> methylnet-interpret-interpret_biology command line option -l, --loss_reduction <loss_reduction> methylnet-embed-perform_embedding command line option methylnet-predict-make_prediction command line option

-lo, --length_output <length_output> methylnet-interpret-interpret_biology command line option -log, --log_transform methylnet-interpret-return_shap_values command line option -lr, --learning_rate <learning_rate> methylnet-embed-perform_embedding command line option -lr_mlp, --learning_rate_mlp <learning_rate_mlp> methylnet-predict-make_prediction command line option -lr_vae, --learning_rate_vae <learning_rate_vae> methylnet-predict-make_prediction command line option -m, --max_gap <max_gap> methylnet-interpret-interpret_biology command line option -m, --metric <metric> methylnet-interpret-interpret_embedding_classes command line option -m, --model_pickle <model_pickle> methylnet-interpret-produce_shapley_data command line option methylnet-predict-make_new_predictions command line option -m, --t_mult <t_mult> methylnet-embed-perform_embedding command line option methylnet-predict-make_prediction command line option -mc, --model_complexity_factor <model_complexity_factor> methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -mth, --method <method> methylnet-interpret-produce_shapley_data command line option -n, --n_bins <n_bins> methylnet-interpret-bin_regression_shaps command line option -n, --n_extract <n_extract> methylnet-interpret-extract_methylation_array command line option -n, --n_jobs_relaunch <n_jobs_relaunch> methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -n, --n_latent <n_latent> methylnet-embed-perform_embedding command line option -n, --n_workers <n_workers> methylnet-interpret-interpret_biology command line option -n, --neg_val methylnet-interpret-regenerate_top_cpgs command line option -n, --ngpu <ngpu> methylnet-torque-run_torque_job command line option -nf, --n_top_features <n_top_features> methylnet-interpret-produce_shapley_data command line option methylnet-interpret-reduce_top_cpgs command line option methylnet-interpret-regenerate_top_cpgs command line option -nh, --nohup methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -ns, --n_samples <n_samples> methylnet-interpret-produce_shapley_data command line option -o, --output_csv <output_csv> methylnet-interpret-interpret_embedding_classes command line option methylnet-interpret-order_results_by_col command line option -o, --output_dir <output_dir> methylnet-embed-perform_embedding command line option methylnet-interpret-extract_methylation_array command line option methylnet-interpret-grab_lola_db_cache command line option methylnet-interpret-interpret_biology command line option methylnet-interpret-plot_top_cpgs command line option methylnet-interpret-produce_shapley_data command line option methylnet-interpret-return_shap_values command line option methylnet-interpret-shapley_jaccard command line option methylnet-interpret-split_hyper_hypo_methylation command line option methylnet-interpret-view_methylation_top_cpgs command line option methylnet-predict-classification_report command line option methylnet-predict-make_new_predictions command line option methylnet-predict-make_prediction command line option methylnet-predict-regression_report command line option -o, --output_pkl <output_pkl> methylnet-interpret-reduce_top_cpgs command line option methylnet-interpret-regenerate_top_cpgs command line option -o, --outputfilename <outputfilename> methylnet-visualize-plot_roc_curve command line option methylnet-visualize-plot_training_curve command line option -o, --plot_output_dir <plot_output_dir> methylnet-interpret-plot_all_lola_outputs command line option methylnet-interpret-plot_lola_output command line option -op, --output_pval_csv <output_pval_csv> methylnet-interpret-interpret_embedding_classes command line option -opt, --optimize_n_cpgs methylnet-interpret-shapley_jaccard command line option -os, --output_shap_pkl <output_shap_pkl> methylnet-interpret-bin_regression_shaps command line option -ot, --output_test_pkl <output_test_pkl> methylnet-interpret-bin_regression_shaps command line option -ov, --overall methylnet-interpret-shapley_jaccard command line option -ov, --overlap_test methylnet-interpret-interpret_biology command line option -ov, --overwrite methylnet-interpret-plot_all_lola_outputs command line option -q, --queue <queue> methylnet-torque-run_torque_job command line option -r, --n_random_representative <n_random_representative> methylnet-interpret-produce_shapley_data command line option -r, --reset_all methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -r, --results_csv <results_csv> methylnet-interpret-produce_shapley_data command line option -r, --results_pickle <results_pickle> methylnet-predict-classification_report command line option methylnet-predict-regression_report command line option -r, --roc_curve_csv <roc_curve_csv> methylnet-visualize-plot_roc_curve command line option -rc, --residual_cutoff <residual_cutoff> methylnet-interpret-produce_shapley_data command line option -rt, --n_random_representative_test <n_random_representative_test> methylnet-interpret-produce_shapley_data command line option -s, --scheduler <scheduler> methylnet-embed-perform_embedding command line option methylnet-predict-make_prediction command line option -s, --shapley_data <shapley_data> methylnet-interpret-bin_regression_shaps command line option methylnet-interpret-extract_methylation_array command line option methylnet-interpret-list_classes command line option methylnet-interpret-list_individuals command line option methylnet-interpret-plot_top_cpgs command line option methylnet-interpret-reduce_top_cpgs command line option methylnet-interpret-regenerate_top_cpgs command line option methylnet-interpret-return_shap_values command line option methylnet-interpret-shapley_jaccard command line option methylnet-interpret-split_hyper_hypo_methylation command line option methylnet-interpret-view_methylation_top_cpgs command line option -s, --shapley_data_list <shapley_data_list> methylnet-interpret-interpret_biology command line option -sc, --stratify_column <stratify_column> methylnet-embed-launch_hyperparameter_scan command line option methylnet-embed-perform_embedding command line option -sft, --add_softmax methylnet-predict-launch_hyperparameter_scan command line option methylnet-predict-make_prediction command line option -ss, --set_subtraction methylnet-interpret-interpret_biology command line option -ssbs, --shap_sample_batch_size <shap_sample_batch_size> methylnet-interpret-produce_shapley_data command line option -sym, --symmetric methylnet-interpret-order_results_by_col command line option -t, --t_max <t_max> methylnet-embed-perform_embedding command line option methylnet-predict-make_prediction command line option -t, --test_pkl <test_pkl> methylnet-interpret-bin_regression_shaps command line option methylnet-interpret-extract_methylation_array command line option methylnet-interpret-order_results_by_col command line option methylnet-interpret-produce_shapley_data command line option methylnet-interpret-split_hyper_hypo_methylation command line option methylnet-interpret-view_methylation_top_cpgs command line option -t, --time <time> methylnet-torque-run_torque_job command line option -t, --torque methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -t, --training_curve_file <training_curve_file> methylnet-visualize-plot_training_curve command line option -t, --trim <trim> methylnet-interpret-interpret_embedding_classes command line option -thr, --threshold <threshold> methylnet-interpret-split_hyper_hypo_methylation command line option methylnet-visualize-plot_training_curve command line option -top, --top_outputs <top_outputs> methylnet-interpret-produce_shapley_data command line option -tp, --test_pkl <test_pkl> methylnet-predict-make_new_predictions command line option methylnet-predict-make_prediction command line option -v, --add_validation_set methylnet-embed-perform_embedding command line option methylnet-predict-make_prediction command line option -v, --val_loss_column <val_loss_column> methylnet-embed-launch_hyperparameter_scan command line option methylnet-predict-launch_hyperparameter_scan command line option -v, --val_pkl <val_pkl> methylnet-interpret-produce_shapley_data command line option -vae, --input_vae_pkl <input_vae_pkl> methylnet-predict-make_prediction command line option -vae, --vae_interpret methylnet-interpret-produce_shapley_data command line option -vae, --vae_train methylnet-visualize-plot_training_curve command line option -vp, --val_pkl <val_pkl> methylnet-embed-perform_embedding command line option methylnet-predict-make_prediction command line option -w, --analysis <analysis> methylnet-interpret-interpret_biology command line option -w, --n_workers <n_workers> methylnet-embed-perform_embedding command line option methylnet-interpret-produce_shapley_data command line option methylnet-predict-make_new_predictions command line option methylnet-predict-make_prediction command line option -wd, --weight_decay <weight_decay> methylnet-embed-perform_embedding command line option methylnet-predict-make_prediction command line option -ws, --width_kernel_sizes <width_kernel_sizes> methylnet-embed-perform_embedding command line option

A

add_abs_value_classes() (methylnet.interpretation_classes.ShapleyDataExplorer method) add_bin_continuous_classes() (methylnet.interpretation_classes.ShapleyDataExplorer method) add_class() (methylnet.interpretation_classes.ShapleyData method) add_global_importance() (methylnet.interpretation_classes.ShapleyData method)

add_validation_set() (methylnet.models.AutoEncoder method) (methylnet.models.MLPFinetuneVAE method) assemble_replace_dict() (in module methylnet.torque_jobs) assemble_run_torque() (in module methylnet.torque_jobs) AutoEncoder (class in methylnet.models)

B

BioInterpreter (class in methylnet.interpretation_classes)

build_explainer() (methylnet.interpretation_classes.CpGExplainer method)

C

calculate_p_values() (methylnet.interpretation_classes.DistanceMatrixCompute method) cat() (in module methylnet.datasets) classifier_assign_scores_to_shap_data() (methylnet.interpretation_classes.CpGExplainer method) coarse_scan() (in module methylnet.hyperparameter_scans)

compute_distances() (methylnet.interpretation_classes.DistanceMatrixCompute method) cooccurrence_fn() (in module methylnet.interpretation_classes) CosineAnnealingWithRestartsLR (class in methylnet.schedulers) CpGExplainer (class in methylnet.interpretation_classes)

D

decode() (methylnet.models.TybaltTitusVAE method) (methylnet.models.VAE_MLP method)

DistanceMatrixCompute (class in methylnet.interpretation_classes)

E

encode() (methylnet.models.TybaltTitusVAE method) extract_class() (methylnet.interpretation_classes.ShapleyDataExplorer method)

extract_individual() (methylnet.interpretation_classes.ShapleyDataExplorer method) extract_methylation_array() (methylnet.interpretation_classes.ShapleyDataExplorer method)

F

feature_select() (methylnet.interpretation_classes.CpGExplainer method) find_top_jobs() (in module methylnet.hyperparameter_scans) fit() (methylnet.models.AutoEncoder method) (methylnet.models.MLPFinetuneVAE method) fit_transform() (methylnet.models.AutoEncoder method) forward() (methylnet.models.TybaltTitusVAE method) (methylnet.models.VAE_MLP method)

forward_embed() (methylnet.models.VAE_MLP method) forward_predict() (methylnet.models.TybaltTitusVAE method) (methylnet.models.VAE_MLP method) from_explainer() (methylnet.interpretation_classes.CpGExplainer class method) from_pickle() (methylnet.interpretation_classes.ShapleyData class method)

G

generate() (methylnet.datasets.Transformer method) generate_topology() (in module methylnet.hyperparameter_scans) get_latent_z() (methylnet.models.TybaltTitusVAE method)

get_lr() (methylnet.schedulers.Scheduler method) get_methylation_dataset() (in module methylnet.datasets) get_nearby_cpg_shapleys() (methylnet.interpretation_classes.BioInterpreter method) gometh() (methylnet.interpretation_classes.BioInterpreter method)

J

jaccard_similarity() (in module methylnet.interpretation_classes)

jaccard_similarity_top_cpgs() (methylnet.interpretation_classes.ShapleyDataExplorer method)

L

limit_number_top_cpgs() (methylnet.interpretation_classes.ShapleyDataExplorer method)

list_classes() (methylnet.interpretation_classes.ShapleyDataExplorer method) list_individuals() (methylnet.interpretation_classes.ShapleyDataExplorer method)

M

main_prediction_function() (in module methylnet.interpretation_classes) MethylationDataSet (class in methylnet.datasets) MethylationGenerationDataSet (class in methylnet.datasets) MethylationPredictionDataSet (class in methylnet.datasets) methylnet-embed command line option --version methylnet-embed-launch_hyperparameter_scan command line option -a, --additional_command <additional_command> -b, --set_beta <set_beta> -c, --job_chunk_size <job_chunk_size> -cp, --crossover_p <crossover_p> -cu, --cuda -g, --generate_input -gn, --gpu_node <gpu_node> -gpu, --gpu <gpu> -grid, --hyperparameter_yaml <hyperparameter_yaml> -hcsv, --hyperparameter_input_csv <hyperparameter_input_csv> -hl, --hyperparameter_output_log <hyperparameter_output_log> -j, --n_jobs <n_jobs> -mc, --model_complexity_factor <model_complexity_factor> -n, --n_jobs_relaunch <n_jobs_relaunch> -nh, --nohup -r, --reset_all -sc, --stratify_column <stratify_column> -t, --torque -v, --val_loss_column <val_loss_column> methylnet-embed-perform_embedding command line option -b, --beta <beta> -bce, --bce_loss -bs, --batch_size <batch_size> -c, --cuda -conv, --convolutional -d, --decay <decay> -e, --n_epochs <n_epochs> -eta, --eta_min <eta_min> -hl, --hyperparameter_log <hyperparameter_log> -hlt, --hidden_layer_encoder_topology <hidden_layer_encoder_topology> -hs, --height_kernel_sizes <height_kernel_sizes> -i, --train_pkl <train_pkl> -j, --job_name <job_name> -kl, --kl_warm_up <kl_warm_up> -l, --loss_reduction <loss_reduction> -lr, --learning_rate <learning_rate> -m, --t_mult <t_mult> -n, --n_latent <n_latent> -o, --output_dir <output_dir> -s, --scheduler <scheduler> -sc, --stratify_column <stratify_column> -t, --t_max <t_max> -v, --add_validation_set -vp, --val_pkl <val_pkl> -w, --n_workers <n_workers> -wd, --weight_decay <weight_decay> -ws, --width_kernel_sizes <width_kernel_sizes> methylnet-interpret command line option --version methylnet-interpret-bin_regression_shaps command line option -c, --col <col> -n, --n_bins <n_bins> -os, --output_shap_pkl <output_shap_pkl> -ot, --output_test_pkl <output_test_pkl> -s, --shapley_data <shapley_data> -t, --test_pkl <test_pkl> methylnet-interpret-extract_methylation_array command line option -c, --col <col> -co, --classes_only -g, --global_vals -n, --n_extract <n_extract> -o, --output_dir <output_dir> -s, --shapley_data <shapley_data> -t, --test_pkl <test_pkl> methylnet-interpret-grab_lola_db_cache command line option -o, --output_dir <output_dir> methylnet-interpret-interpret_biology command line option -a, --all_cpgs_pickle <all_cpgs_pickle> -c, --classes <classes> -cgs, --cpg_set <cpg_set> -ci, --class_intersect -col, --collections <collections> -d, --depletion -ex, --extract_library -g, --top_global -gsea, --gsea_analyses <gsea_analyses> -gsp, --gsea_pickle <gsea_pickle> -i, --individuals <individuals> -int, --intersection -l, --lola_db <lola_db> -lo, --length_output <length_output> -m, --max_gap <max_gap> -n, --n_workers <n_workers> -o, --output_dir <output_dir> -ov, --overlap_test -s, --shapley_data_list <shapley_data_list> -ss, --set_subtraction -w, --analysis <analysis> methylnet-interpret-interpret_embedding_classes command line option -c, --pheno_col <pheno_col> -i, --embedding_methyl_array_pkl <embedding_methyl_array_pkl> -m, --metric <metric> -o, --output_csv <output_csv> -op, --output_pval_csv <output_pval_csv> -t, --trim <trim> methylnet-interpret-list_classes command line option -s, --shapley_data <shapley_data> methylnet-interpret-list_individuals command line option -s, --shapley_data <shapley_data> methylnet-interpret-order_results_by_col command line option -c, --col <col> -i, --input_csv <input_csv> -o, --output_csv <output_csv> -sym, --symmetric -t, --test_pkl <test_pkl> methylnet-interpret-plot_all_lola_outputs command line option -c, --cell_types <cell_types> -d, --description_col <description_col> -l, --head_lola_dir <head_lola_dir> -o, --plot_output_dir <plot_output_dir> -ov, --overwrite methylnet-interpret-plot_lola_output command line option -c, --cell_types <cell_types> -d, --description_col <description_col> -l, --lola_csv <lola_csv> -o, --plot_output_dir <plot_output_dir> methylnet-interpret-plot_top_cpgs command line option -c, --classes <classes> -i, --individuals <individuals> -o, --output_dir <output_dir> -s, --shapley_data <shapley_data> methylnet-interpret-produce_shapley_data command line option -bs, --batch_size <batch_size> -c, --cuda -cc, --cross_class -cl, --pred_class <pred_class> -cn, --cell_names <cell_names> -col, --interest_col <interest_col> -dsd, --dump_shap_data -e, --categorical_encoder <categorical_encoder> -fs, --feature_selection -i, --train_pkl <train_pkl> -ind, --individual <individual> -m, --model_pickle <model_pickle> -mth, --method <method> -nf, --n_top_features <n_top_features> -ns, --n_samples <n_samples> -o, --output_dir <output_dir> -r, --n_random_representative <n_random_representative> -r, --results_csv <results_csv> -rc, --residual_cutoff <residual_cutoff> -rt, --n_random_representative_test <n_random_representative_test> -ssbs, --shap_sample_batch_size <shap_sample_batch_size> -t, --test_pkl <test_pkl> -top, --top_outputs <top_outputs> -v, --val_pkl <val_pkl> -vae, --vae_interpret -w, --n_workers <n_workers>

methylnet-interpret-reduce_top_cpgs command line option -nf, --n_top_features <n_top_features> -o, --output_pkl <output_pkl> -s, --shapley_data <shapley_data> methylnet-interpret-regenerate_top_cpgs command line option -a, --abs_val -n, --neg_val -nf, --n_top_features <n_top_features> -o, --output_pkl <output_pkl> -s, --shapley_data <shapley_data> methylnet-interpret-return_shap_values command line option -abs, --absolute -c, --classes <classes> -hist, --output_histogram -i, --individuals <individuals> -log, --log_transform -o, --output_dir <output_dir> -s, --shapley_data <shapley_data> methylnet-interpret-shapley_jaccard command line option -c, --class_names <class_names> -co, --cooccurrence -i, --include_individuals -o, --output_dir <output_dir> -opt, --optimize_n_cpgs -ov, --overall -s, --shapley_data <shapley_data> methylnet-interpret-split_hyper_hypo_methylation command line option -o, --output_dir <output_dir> -s, --shapley_data <shapley_data> -t, --test_pkl <test_pkl> -thr, --threshold <threshold> methylnet-interpret-view_methylation_top_cpgs command line option -i, --individuals <individuals> -o, --output_dir <output_dir> -s, --shapley_data <shapley_data> -t, --test_pkl <test_pkl> methylnet-predict command line option --version methylnet-predict-classification_report command line option -a, --average_mechanism <average_mechanism> -e, --categorical_encoder <categorical_encoder> -o, --output_dir <output_dir> -r, --results_pickle <results_pickle> methylnet-predict-launch_hyperparameter_scan command line option -a, --additional_command <additional_command> -c, --job_chunk_size <job_chunk_size> -cat, --categorical -cp, --crossover_p <crossover_p> -cu, --cuda -g, --generate_input -gn, --gpu_node <gpu_node> -gpu, --gpu <gpu> -grid, --hyperparameter_yaml <hyperparameter_yaml> -hcsv, --hyperparameter_input_csv <hyperparameter_input_csv> -hl, --hyperparameter_output_log <hyperparameter_output_log> -ic, --interest_cols <interest_cols> -j, --n_jobs <n_jobs> -mc, --model_complexity_factor <model_complexity_factor> -n, --n_jobs_relaunch <n_jobs_relaunch> -nh, --nohup -r, --reset_all -sft, --add_softmax -t, --torque -v, --val_loss_column <val_loss_column> methylnet-predict-make_new_predictions command line option -bs, --batch_size <batch_size> -c, --cuda -cat, --categorical -e, --categorical_encoder <categorical_encoder> -ic, --interest_cols <interest_cols> -m, --model_pickle <model_pickle> -o, --output_dir <output_dir> -tp, --test_pkl <test_pkl> -w, --n_workers <n_workers> methylnet-predict-make_prediction command line option -bs, --batch_size <batch_size> -c, --cuda -cat, --categorical -d, --decay <decay> -do, --disease_only -dp, --dropout_p <dropout_p> -e, --n_epochs <n_epochs> -eta, --eta_min <eta_min> -hl, --hyperparameter_log <hyperparameter_log> -hlt, --hidden_layer_topology <hidden_layer_topology> -i, --train_pkl <train_pkl> -ic, --interest_cols <interest_cols> -j, --job_name <job_name> -l, --loss_reduction <loss_reduction> -lr_mlp, --learning_rate_mlp <learning_rate_mlp> -lr_vae, --learning_rate_vae <learning_rate_vae> -m, --t_mult <t_mult> -o, --output_dir <output_dir> -s, --scheduler <scheduler> -sft, --add_softmax -t, --t_max <t_max> -tp, --test_pkl <test_pkl> -v, --add_validation_set -vae, --input_vae_pkl <input_vae_pkl> -vp, --val_pkl <val_pkl> -w, --n_workers <n_workers> -wd, --weight_decay <weight_decay> methylnet-predict-regression_report command line option -o, --output_dir <output_dir> -r, --results_pickle <results_pickle> methylnet-test command line option --version methylnet-torque command line option --version methylnet-torque-run_torque_job command line option -a, --additions <additions> -c, --command <command> -gpu, --use_gpu -n, --ngpu <ngpu> -q, --queue <queue> -t, --time <time> methylnet-visualize command line option --version methylnet-visualize-plot_roc_curve command line option -o, --outputfilename <outputfilename> -r, --roc_curve_csv <roc_curve_csv> methylnet-visualize-plot_training_curve command line option -o, --outputfilename <outputfilename> -t, --training_curve_file <training_curve_file> -thr, --threshold <threshold> -vae, --vae_train methylnet.datasets (module) methylnet.hyperparameter_scans (module) methylnet.interpretation_classes (module) methylnet.models (module) methylnet.plotter (module) methylnet.schedulers (module) methylnet.torque_jobs (module) MLPFinetuneVAE (class in methylnet.models)

P

Plot (class in methylnet.plotter) plot_cpgs() (methylnet.interpretation_classes.PlotCircos method) plot_lola_output_() (in module methylnet.interpretation_classes) PlotCircos (class in methylnet.interpretation_classes)

Plotter (class in methylnet.plotter) PlotTransformer (class in methylnet.plotter) predict() (methylnet.models.MLPFinetuneVAE method) project_vae() (in module methylnet.models)

R

RawBetaArrayDataSet (class in methylnet.datasets) regenerate_individual_shap_values() (methylnet.interpretation_classes.ShapleyDataExplorer method) regressor_assign_scores_to_shap_data() (methylnet.interpretation_classes.CpGExplainer method) replace_grid() (in module methylnet.hyperparameter_scans) return_binned_shapley_data() (methylnet.interpretation_classes.ShapleyDataExplorer method) return_cpg_sets() (methylnet.interpretation_classes.ShapleyDataExplorer method) return_dataloader_construct() (in module methylnet.interpretation_classes) return_distances() (methylnet.interpretation_classes.DistanceMatrixCompute method) return_global_importance_cpgs() (methylnet.interpretation_classes.ShapleyDataExplorer method)

return_overlap_score() (methylnet.interpretation_classes.BioInterpreter method) return_p_values() (methylnet.interpretation_classes.DistanceMatrixCompute method) return_predict_function() (in module methylnet.interpretation_classes) return_shap_values() (in module methylnet.interpretation_classes) return_shapley_data_by_methylation_status() (methylnet.interpretation_classes.ShapleyDataExplorer method) return_shapley_predictions() (methylnet.interpretation_classes.CpGExplainer method) return_shapley_scores() (methylnet.interpretation_classes.CpGExplainer method) return_top_cpgs() (methylnet.interpretation_classes.ShapleyDataExplorer method) run_lola() (methylnet.interpretation_classes.BioInterpreter method) run_torque_job_() (in module methylnet.torque_jobs)

S

sample_z() (methylnet.models.TybaltTitusVAE method) Scheduler (class in methylnet.schedulers) ShapleyData (class in methylnet.interpretation_classes)

ShapleyDataExplorer (class in methylnet.interpretation_classes) stack() (in module methylnet.datasets) step() (methylnet.schedulers.Scheduler method)

T

test_mlp() (in module methylnet.models) to_methyl_array() (methylnet.datasets.MethylationDataSet method) to_pickle() (methylnet.interpretation_classes.ShapleyData method) to_tensor() (in module methylnet.interpretation_classes) toggle_latent_z() (methylnet.models.VAE_MLP method)

train_decoder_() (in module methylnet.models) train_mlp() (in module methylnet.models) train_vae() (in module methylnet.models) transform() (methylnet.models.AutoEncoder method) Transformer (class in methylnet.datasets) TybaltTitusVAE (class in methylnet.models)

V

vae_loss() (in module methylnet.models) VAE_MLP (class in methylnet.models) val_decoder_() (in module methylnet.models)

val_mlp() (in module methylnet.models) val_vae() (in module methylnet.models) view_methylation() (methylnet.interpretation_classes.ShapleyDataExplorer method)