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--- a +++ b/docs/_build/html/genindex.html @@ -0,0 +1,747 @@ + + +<!DOCTYPE html> +<html class="writer-html5" lang="en" > +<head> + <meta charset="utf-8" /> + + <meta name="viewport" content="width=device-width, initial-scale=1.0" /> + + <title>Index — DeepProg documentation</title> + + + + <link rel="stylesheet" href="_static/css/theme.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + + + + + + + + + + <!--[if lt IE 9]> + <script src="_static/js/html5shiv.min.js"></script> + <![endif]--> + + + <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> + <script src="_static/jquery.js"></script> + <script src="_static/underscore.js"></script> + <script src="_static/doctools.js"></script> + <script src="_static/language_data.js"></script> + + <script type="text/javascript" src="_static/js/theme.js"></script> + + + <link rel="index" title="Index" href="#" /> + <link rel="search" title="Search" href="search.html" /> +</head> + +<body class="wy-body-for-nav"> + + + <div class="wy-grid-for-nav"> + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search" > + + + + <a href="index.html" class="icon icon-home"> DeepProg + + + + </a> + + + + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> +</div> + + + </div> + + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + + + + <ul> +<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li> +<li class="toctree-l1"><a class="reference internal" href="usage.html">Tutorial: Simple DeepProg model</a></li> +<li class="toctree-l1"><a class="reference internal" href="usage_ensemble.html">Tutorial: Ensemble of DeepProg model</a></li> +<li class="toctree-l1"><a class="reference internal" href="usage_advanced.html">Tutorial: Advanced usage of DeepProg model</a></li> +<li class="toctree-l1"><a class="reference internal" href="case_study.html">Case study: Analyzing TCGA HCC dataset</a></li> +<li class="toctree-l1"><a class="reference internal" href="usage_tuning.html">Tutorial: Tuning DeepProg</a></li> +<li class="toctree-l1"><a class="reference internal" href="LICENSE.html">License</a></li> +<li class="toctree-l1"><a class="reference internal" href="api/simdeep.html">simdeep package</a></li> +</ul> + + + + </div> + + </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" aria-label="top navigation"> + + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="index.html">DeepProg</a> + + </nav> + + + <div class="wy-nav-content"> + + <div class="rst-content"> + + + + + + + + + + + + + + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + + <ul class="wy-breadcrumbs"> + + <li><a href="index.html" class="icon icon-home"></a> »</li> + + <li>Index</li> + + + <li class="wy-breadcrumbs-aside"> + + + + </li> + + </ul> + + + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> + + +<h1 id="index">Index</h1> + +<div class="genindex-jumpbox"> + <a href="#C"><strong>C</strong></a> + | <a href="#D"><strong>D</strong></a> + | <a href="#E"><strong>E</strong></a> + | <a href="#F"><strong>F</strong></a> + | <a href="#L"><strong>L</strong></a> + | <a href="#M"><strong>M</strong></a> + | <a href="#N"><strong>N</strong></a> + | <a href="#P"><strong>P</strong></a> + | <a href="#R"><strong>R</strong></a> + | <a href="#S"><strong>S</strong></a> + | <a href="#T"><strong>T</strong></a> + | <a href="#V"><strong>V</strong></a> + | <a href="#W"><strong>W</strong></a> + +</div> +<h2 id="C">C</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.c_index">c_index() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.c_index_from_python">c_index_from_python() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.c_index_from_r">c_index_from_r() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.c_index_multiple">c_index_multiple() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.c_index_multiple_from_python">c_index_multiple_from_python() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.c_index_multiple_from_r">c_index_multiple_from_r() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.collect_cindex_for_full_dataset">collect_cindex_for_full_dataset() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.collect_cindex_for_test_dataset">collect_cindex_for_test_dataset() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.collect_cindex_for_test_fold">collect_cindex_for_test_fold() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.collect_cindex_for_training_dataset">collect_cindex_for_training_dataset() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.collect_number_of_features_per_omic">collect_number_of_features_per_omic() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.collect_pvalue_on_full_dataset">collect_pvalue_on_full_dataset() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.collect_pvalue_on_test_dataset">collect_pvalue_on_test_dataset() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.collect_pvalue_on_test_fold">collect_pvalue_on_test_fold() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.collect_pvalue_on_training_dataset">collect_pvalue_on_training_dataset() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase.compile_models">compile_models() (simdeep.deepmodel_base.DeepBase method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.compute_c_indexes_for_full_dataset">compute_c_indexes_for_full_dataset() (simdeep.simdeep_analysis.SimDeep method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.compute_c_indexes_for_full_dataset">(simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + </ul></li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.compute_c_indexes_for_test_dataset">compute_c_indexes_for_test_dataset() (simdeep.simdeep_analysis.SimDeep method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.compute_c_indexes_for_test_dataset">(simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + </ul></li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.compute_c_indexes_for_test_fold_dataset">compute_c_indexes_for_test_fold_dataset() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.compute_c_indexes_for_training_dataset">compute_c_indexes_for_training_dataset() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.compute_c_indexes_multiple_for_test_dataset">compute_c_indexes_multiple_for_test_dataset() (simdeep.simdeep_analysis.SimDeep method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.compute_c_indexes_multiple_for_test_dataset">(simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + </ul></li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.compute_c_indexes_multiple_for_test_fold_dataset">compute_c_indexes_multiple_for_test_fold_dataset() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.compute_clusters_consistency_for_full_labels">compute_clusters_consistency_for_full_labels() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.compute_clusters_consistency_for_test_labels">compute_clusters_consistency_for_test_labels() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.compute_feature_scores">compute_feature_scores() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.compute_feature_scores_per_cluster">compute_feature_scores_per_cluster() (simdeep.simdeep_analysis.SimDeep method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.compute_feature_scores_per_cluster">(simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + </ul></li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.compute_pvalue_for_merged_test_fold">compute_pvalue_for_merged_test_fold() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.compute_survival_feature_scores_per_cluster">compute_survival_feature_scores_per_cluster() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase.construct_autoencoders">construct_autoencoders() (simdeep.deepmodel_base.DeepBase method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase.construct_supervized_network">construct_supervized_network() (simdeep.deepmodel_base.DeepBase method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.convert_metadata_frame_to_matrix">convert_metadata_frame_to_matrix() (in module simdeep.survival_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.convert_to_rmatrix">convert_to_rmatrix() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.CorrelationReducer">CorrelationReducer (class in simdeep.survival_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.coxph">coxph() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.coxph_from_python">coxph_from_python() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.coxph_from_r">coxph_from_r() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.create_a_cv_split">create_a_cv_split() (simdeep.extract_data.LoadData method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase.create_autoencoders">create_autoencoders() (simdeep.deepmodel_base.DeepBase method)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="D">D</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase">DeepBase (class in simdeep.deepmodel_base)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="E">E</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase.embedding_predict">embedding_predict() (simdeep.deepmodel_base.DeepBase method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase.encoder_input_shape">encoder_input_shape() (simdeep.deepmodel_base.DeepBase method)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase.encoder_predict">encoder_predict() (simdeep.deepmodel_base.DeepBase method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.evalutate_cluster_performance">evalutate_cluster_performance() (simdeep.simdeep_analysis.SimDeep method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.evalutate_cluster_performance">(simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + </ul></li> + </ul></td> +</tr></table> + +<h2 id="F">F</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.simdeep_utils.feature_selection_usage_type">feature_selection_usage_type() (in module simdeep.simdeep_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.fit">fit() (simdeep.simdeep_analysis.SimDeep method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.fit">(simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.CorrelationReducer.fit">(simdeep.survival_utils.CorrelationReducer method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.VarianceReducer.fit">(simdeep.survival_utils.VarianceReducer method)</a> +</li> + </ul></li> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase.fit_alternative_embedding">fit_alternative_embedding() (simdeep.deepmodel_base.DeepBase method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase.fit_autoencoders">fit_autoencoders() (simdeep.deepmodel_base.DeepBase method)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.fit_classification_model">fit_classification_model() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.fit_classification_test_model">fit_classification_test_model() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.fit_on_pretrained_label_file">fit_on_pretrained_label_file() (simdeep.simdeep_analysis.SimDeep method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.fit_on_pretrained_label_file">(simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + </ul></li> + <li><a href="api/simdeep.html#simdeep.survival_utils.CorrelationReducer.fit_transform">fit_transform() (simdeep.survival_utils.CorrelationReducer method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.survival_utils.MadScaler.fit_transform">(simdeep.survival_utils.MadScaler method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.RankNorm.fit_transform">(simdeep.survival_utils.RankNorm method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.VarianceReducer.fit_transform">(simdeep.survival_utils.VarianceReducer method)</a> +</li> + </ul></li> + </ul></td> +</tr></table> + +<h2 id="L">L</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.load_array">load_array() (simdeep.extract_data.LoadData method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.load_data_from_tsv">load_data_from_tsv() (in module simdeep.survival_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase.load_encoders">load_encoders() (simdeep.deepmodel_base.DeepBase method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.load_entrezID_to_ensg">load_entrezID_to_ensg() (in module simdeep.survival_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_utils.load_labels_file">load_labels_file() (in module simdeep.simdeep_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.load_matrix_full">load_matrix_full() (simdeep.extract_data.LoadData method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.load_matrix_test">load_matrix_test() (simdeep.extract_data.LoadData method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.load_matrix_test_fold">load_matrix_test_fold() (simdeep.extract_data.LoadData method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.load_meta_data">load_meta_data() (simdeep.extract_data.LoadData method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.load_meta_data_test">load_meta_data_test() (simdeep.extract_data.LoadData method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_utils.load_model">load_model() (in module simdeep.simdeep_utils)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.load_new_test_dataset">load_new_test_dataset() (simdeep.extract_data.LoadData method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.load_new_test_dataset">(simdeep.simdeep_analysis.SimDeep method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.load_new_test_dataset">(simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + </ul></li> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.load_survival">load_survival() (simdeep.extract_data.LoadData method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.load_survival_file">load_survival_file() (in module simdeep.survival_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.load_survival_test">load_survival_test() (simdeep.extract_data.LoadData method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase.load_test_dataset">load_test_dataset() (simdeep.deepmodel_base.DeepBase method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase.load_training_dataset">load_training_dataset() (simdeep.deepmodel_base.DeepBase method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData">LoadData (class in simdeep.extract_data)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.look_for_prediction_nodes">look_for_prediction_nodes() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.look_for_survival_nodes">look_for_survival_nodes() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="M">M</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.survival_utils.MadScaler">MadScaler (class in simdeep.survival_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.main">main() (in module simdeep.coxph_from_r)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.main">(in module simdeep.deepmodel_base)</a> +</li> + </ul></li> + <li><a href="api/simdeep.html#simdeep.plot_utils.make_color_dict">make_color_dict() (in module simdeep.plot_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.plot_utils.make_color_dict_from_r">make_color_dict_from_r() (in module simdeep.plot_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.plot_utils.make_color_list">make_color_list() (in module simdeep.plot_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_utils.metadata_usage_type">metadata_usage_type() (in module simdeep.simdeep_utils)</a> +</li> + <li> + module + + <ul> + <li><a href="api/simdeep.html#module-simdeep">simdeep</a> +</li> + <li><a href="api/simdeep.html#module-simdeep.config">simdeep.config</a> +</li> + <li><a href="api/simdeep.html#module-simdeep.coxph_from_r">simdeep.coxph_from_r</a> +</li> + <li><a href="api/simdeep.html#module-simdeep.deepmodel_base">simdeep.deepmodel_base</a> +</li> + <li><a href="api/simdeep.html#module-simdeep.extract_data">simdeep.extract_data</a> +</li> + <li><a href="api/simdeep.html#module-simdeep.plot_utils">simdeep.plot_utils</a> +</li> + <li><a href="api/simdeep.html#module-simdeep.simdeep_analysis">simdeep.simdeep_analysis</a> +</li> + <li><a href="api/simdeep.html#module-simdeep.simdeep_boosting">simdeep.simdeep_boosting</a> +</li> + <li><a href="api/simdeep.html#module-simdeep.simdeep_distributed">simdeep.simdeep_distributed</a> +</li> + <li><a href="api/simdeep.html#module-simdeep.simdeep_multiple_dataset">simdeep.simdeep_multiple_dataset</a> +</li> + <li><a href="api/simdeep.html#module-simdeep.simdeep_utils">simdeep.simdeep_utils</a> +</li> + <li><a href="api/simdeep.html#module-simdeep.survival_utils">simdeep.survival_utils</a> +</li> + </ul></li> + </ul></td> +</tr></table> + +<h2 id="N">N</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.normalize_training_array">normalize_training_array() (simdeep.extract_data.LoadData method)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="P">P</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.partial_fit">partial_fit() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.plot_kernel_for_test_sets">plot_kernel_for_test_sets() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.plot_utils.plot_kernel_plots">plot_kernel_plots() (in module simdeep.plot_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.plot_supervised_kernel_for_test_sets">plot_supervised_kernel_for_test_sets() (simdeep.simdeep_analysis.SimDeep method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.plot_supervised_kernel_for_test_sets">(simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + </ul></li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.plot_supervised_predicted_labels_for_test_sets">plot_supervised_predicted_labels_for_test_sets() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.predict_labels">predict_labels() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.predict_labels_on_full_dataset">predict_labels_on_full_dataset() (simdeep.simdeep_analysis.SimDeep method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.predict_labels_on_full_dataset">(simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + </ul></li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.predict_labels_on_test_dataset">predict_labels_on_test_dataset() (simdeep.simdeep_analysis.SimDeep method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.predict_labels_on_test_dataset">(simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + </ul></li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.predict_labels_on_test_fold">predict_labels_on_test_fold() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.predict_labels_using_external_labels">predict_labels_using_external_labels() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.predict_nodes_activities">predict_nodes_activities() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.predict_with_coxph_glmnet">predict_with_coxph_glmnet() (in module simdeep.coxph_from_r)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="R">R</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.survival_utils.RankCorrNorm">RankCorrNorm (class in simdeep.survival_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.RankNorm">RankNorm (class in simdeep.survival_utils)</a> +</li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.reorder_matrix_array">reorder_matrix_array() (simdeep.extract_data.LoadData method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.return_intersection_indexes">return_intersection_indexes() (in module simdeep.survival_utils)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="S">S</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.survival_utils.SampleReducer.sample_to_keep">sample_to_keep() (simdeep.survival_utils.SampleReducer method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.plot_utils.SampleHTML">SampleHTML (class in simdeep.plot_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.SampleReducer">SampleReducer (class in simdeep.survival_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.save_cv_models_classes">save_cv_models_classes() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.deepmodel_base.DeepBase.save_encoders">save_encoders() (simdeep.deepmodel_base.DeepBase method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.save_matrix">save_matrix() (in module simdeep.survival_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_utils.save_model">save_model() (in module simdeep.simdeep_utils)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.save_models_classes">save_models_classes() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.save_ref_matrix">save_ref_matrix() (simdeep.extract_data.LoadData method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.save_test_models_classes">save_test_models_classes() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.select_best_classif_params">select_best_classif_params() (in module simdeep.survival_utils)</a> +</li> + <li> + simdeep + + <ul> + <li><a href="api/simdeep.html#module-simdeep">module</a> +</li> + </ul></li> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep">SimDeep (class in simdeep.simdeep_analysis)</a> +</li> + <li> + simdeep.config + + <ul> + <li><a href="api/simdeep.html#module-simdeep.config">module</a> +</li> + </ul></li> + <li> + simdeep.coxph_from_r + + <ul> + <li><a href="api/simdeep.html#module-simdeep.coxph_from_r">module</a> +</li> + </ul></li> + <li> + simdeep.deepmodel_base + + <ul> + <li><a href="api/simdeep.html#module-simdeep.deepmodel_base">module</a> +</li> + </ul></li> + <li> + simdeep.extract_data + + <ul> + <li><a href="api/simdeep.html#module-simdeep.extract_data">module</a> +</li> + </ul></li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li> + simdeep.plot_utils + + <ul> + <li><a href="api/simdeep.html#module-simdeep.plot_utils">module</a> +</li> + </ul></li> + <li> + simdeep.simdeep_analysis + + <ul> + <li><a href="api/simdeep.html#module-simdeep.simdeep_analysis">module</a> +</li> + </ul></li> + <li> + simdeep.simdeep_boosting + + <ul> + <li><a href="api/simdeep.html#module-simdeep.simdeep_boosting">module</a> +</li> + </ul></li> + <li> + simdeep.simdeep_distributed + + <ul> + <li><a href="api/simdeep.html#module-simdeep.simdeep_distributed">module</a> +</li> + </ul></li> + <li> + simdeep.simdeep_multiple_dataset + + <ul> + <li><a href="api/simdeep.html#module-simdeep.simdeep_multiple_dataset">module</a> +</li> + </ul></li> + <li> + simdeep.simdeep_utils + + <ul> + <li><a href="api/simdeep.html#module-simdeep.simdeep_utils">module</a> +</li> + </ul></li> + <li> + simdeep.survival_utils + + <ul> + <li><a href="api/simdeep.html#module-simdeep.survival_utils">module</a> +</li> + </ul></li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting">SimDeepBoosting (class in simdeep.simdeep_boosting)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_multiple_dataset.SimDeepMultiple">SimDeepMultiple (class in simdeep.simdeep_multiple_dataset)</a> +</li> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.subset_training_sets">subset_training_sets() (simdeep.extract_data.LoadData method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.surv_mean">surv_mean() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.surv_mean_from_python">surv_mean_from_python() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.surv_mean_from_r">surv_mean_from_r() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.surv_median">surv_median() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.surv_median_from_python">surv_median_from_python() (in module simdeep.coxph_from_r)</a> +</li> + <li><a href="api/simdeep.html#simdeep.coxph_from_r.surv_median_from_r">surv_median_from_r() (in module simdeep.coxph_from_r)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="T">T</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.survival_utils.CorrelationReducer.transform">transform() (simdeep.survival_utils.CorrelationReducer method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.survival_utils.VarianceReducer.transform">(simdeep.survival_utils.VarianceReducer method)</a> +</li> + </ul></li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.extract_data.LoadData.transform_matrices">transform_matrices() (simdeep.extract_data.LoadData method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.survival_utils.translate_index">translate_index() (in module simdeep.survival_utils)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="V">V</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.survival_utils.VarianceReducer">VarianceReducer (class in simdeep.survival_utils)</a> +</li> + </ul></td> +</tr></table> + +<h2 id="W">W</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.write_feature_score_per_cluster">write_feature_score_per_cluster() (simdeep.simdeep_analysis.SimDeep method)</a> + + <ul> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.write_feature_score_per_cluster">(simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + </ul></li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/simdeep.html#simdeep.simdeep_analysis.SimDeep.write_feature_scores">write_feature_scores() (simdeep.simdeep_analysis.SimDeep method)</a> +</li> + <li><a href="api/simdeep.html#simdeep.simdeep_boosting.SimDeepBoosting.write_logs">write_logs() (simdeep.simdeep_boosting.SimDeepBoosting method)</a> +</li> + </ul></td> +</tr></table> + + + + </div> + + </div> + <footer> + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2019, Olivier Poirion. + + </p> + </div> + + + + Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a + + <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a> + + provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + </div> + </div> + + </section> + + </div> + + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.Navigation.enable(true); 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