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+<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>
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+<h1 id="index">Index</h1>
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+<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>
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+ | <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>
+        &#169; Copyright 2019, Olivier Poirion.
+
+    </p>
+  </div>
+    
+    
+    
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+    
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