Index

_

__version__ (in module ddn3) _add_node_to_a_circle() (in module ddn3.visualize) _angles_in_ellipse() (in module ddn3.visualize) _create_nx_graph() (in module ddn3.visualize)

_get_edge_list() (in module ddn3.tools_export) _get_pos_one_part() (in module ddn3.visualize) _get_pos_two_parts() (in module ddn3.visualize) _plot_network_helper() (in module ddn3.visualize) _regression_one_node() (in module ddn3.parameter_tuning)

A

alpha1 (ddn3.parameter_tuning.DDNParameterSearch attribute)

alpha2 (ddn3.parameter_tuning.DDNParameterSearch attribute)

B

base (in module tools_r) bcd_corr() (in module ddn3.bcd)

bcd_org() (in module ddn3.bcd) bcd_org_old() (in module ddn3.bcd) bcd_residual() (in module ddn3.bcd)

C

calculate_regression() (in module ddn3.parameter_tuning) collect_curves() (in module plot_simulation) concatenate_data() (in module ddn3.tools)

count_edges_P_N() (in module plot_simulation) create_cov_prec_mat() (in module ddn3.simulation) create_pair_graph() (in module ddn3.simulation) cv_two_lambda() (in module ddn3.parameter_tuning)

D

dat1 (ddn3.parameter_tuning.DDNParameterSearch attribute) dat2 (ddn3.parameter_tuning.DDNParameterSearch attribute) ddn() (in module ddn3.ddn) ddn3 module ddn3.bcd module ddn3.ddn module ddn3.parameter_tuning module ddn3.performance module ddn3.pipeline module ddn3.simulation module ddn3.solver module ddn3.strong_rule module

ddn3.tools module ddn3.tools_export module ddn3.visualize module ddn_obj_fun() (in module ddn3.tools) ddn_parallel() (in module ddn3.ddn) ddn_pipeline() (in module ddn3.pipeline) DDNParameterSearch (class in ddn3.parameter_tuning) dingo (in module tools_r) draw1() (in module plot_simulation) draw_f1() (in module plot_simulation) draw_f1_balance() (in module plot_simulation) draw_f1_feature_num() (in module plot_simulation) draw_network_for_ddn() (in module ddn3.visualize) draw_roc() (in module plot_simulation) draw_roc_balance() (in module plot_simulation) draw_roc_feature_num() (in module plot_simulation)

E

err_scale (ddn3.parameter_tuning.DDNParameterSearch attribute)

F

fit() (ddn3.parameter_tuning.DDNParameterSearch method)

G

gen_mv() (in module ddn3.tools) gen_sample_two_conditions() (in module ddn3.simulation) get_best_f2() (in module plot_simulation) get_common_diff_net_topo() (in module ddn3.tools) get_diff_comm_net_for_plot() (in module ddn3.tools_export) get_edge_subset_by_name() (in module ddn3.tools_export) get_error_measure_two_theta() (in module ddn3.performance) get_f1() (in module ddn3.performance) get_f1_mat() (in module plot_simulation) get_ground_truth_edge_count() (in module plot_simulation)

get_lambda1_mb() (in module ddn3.parameter_tuning) get_lambda2_bai() (in module ddn3.parameter_tuning) get_lambda_one_se_1d() (in module ddn3.parameter_tuning) get_lambdas_one_se_2d() (in module ddn3.parameter_tuning) get_net_topo_from_mat() (in module ddn3.tools) get_node_subset_by_name() (in module ddn3.tools_export) get_node_type_and_label_multi_parts() (in module ddn3.tools_export) get_node_type_and_label_two_parts() (in module ddn3.tools_export) get_range_large() (in module plot_simulation) glasso (in module tools_r)

H

huge (in module tools_r)

huge_omega() (in module simulation_r)

J

jgl (in module tools_r)

L

l1_lst (ddn3.parameter_tuning.DDNParameterSearch attribute)

l2_lst (ddn3.parameter_tuning.DDNParameterSearch attribute) lasso() (in module ddn3.strong_rule)

M

make_multi_scale_free() (in module simulation_r) make_two_from_one() (in module simulation_r) make_two_from_one_by_removing() (in module simulation_r) module ddn3 ddn3.bcd ddn3.ddn ddn3.parameter_tuning ddn3.performance ddn3.pipeline ddn3.simulation ddn3.solver ddn3.strong_rule ddn3.tools ddn3.tools_export ddn3.visualize plot_simulation scan_r simulation_r tools_r

N

n (ddn3.parameter_tuning.DDNParameterSearch attribute) n_cv (ddn3.parameter_tuning.DDNParameterSearch attribute)

np2r1d() (in module tools_r) np2r2d() (in module tools_r)

P

p (ddn3.parameter_tuning.DDNParameterSearch attribute) plot_average_f1() (in module plot_simulation) plot_curve() (in module plot_simulation) plot_curve_with_noise() (in module plot_simulation) plot_ddn_jgl_res() (in module plot_simulation) plot_ddn_jgl_simple() (in module plot_simulation)

plot_ddn_jgl_simple1() (in module plot_simulation) plot_error_1d() (in module ddn3.parameter_tuning) plot_error_2d() (in module ddn3.parameter_tuning) plot_simulation module prep_sim_from_two_omega() (in module ddn3.simulation)

R

ratio_val (ddn3.parameter_tuning.DDNParameterSearch attribute) run_corr() (in module ddn3.solver) run_cv_bai() (ddn3.parameter_tuning.DDNParameterSearch method) run_cv_joint() (ddn3.parameter_tuning.DDNParameterSearch method) run_cv_sequential() (ddn3.parameter_tuning.DDNParameterSearch method)

run_mb_bai() (ddn3.parameter_tuning.DDNParameterSearch method) run_mb_cv() (ddn3.parameter_tuning.DDNParameterSearch method) run_org() (in module ddn3.solver) run_resi() (in module ddn3.solver) run_strongrule() (in module ddn3.solver)

S

scan_ddn() (in module scan_r) scan_dingo() (in module scan_r) scan_erro_measure_dingo() (in module ddn3.performance) scan_error_measure() (in module ddn3.performance) scan_jgl() (in module scan_r) scan_r module

scan_wrap_ddn_jgl() (in module scan_r) simple_data() (in module ddn3.simulation) simulation_r module solve2d() (in module ddn3.bcd) standardize_data() (in module ddn3.tools) strong_rule() (in module ddn3.strong_rule)

T

tools_r module

U

utils (in module tools_r)