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PROTAC-Degradation-Predictor |
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<h1 id="index">Index</h1> |
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<div class="genindex-jumpbox"> |
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<a href="#A"><strong>A</strong></a> |
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| <a href="#B"><strong>B</strong></a> |
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| <a href="#C"><strong>C</strong></a> |
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| <a href="#D"><strong>D</strong></a> |
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| <a href="#E"><strong>E</strong></a> |
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| <a href="#F"><strong>F</strong></a> |
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| <a href="#G"><strong>G</strong></a> |
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| <a href="#H"><strong>H</strong></a> |
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| <a href="#I"><strong>I</strong></a> |
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| <a href="#L"><strong>L</strong></a> |
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| <a href="#M"><strong>M</strong></a> |
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| <a href="#N"><strong>N</strong></a> |
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| <a href="#O"><strong>O</strong></a> |
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| <a href="#P"><strong>P</strong></a> |
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| <a href="#R"><strong>R</strong></a> |
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| <a href="#S"><strong>S</strong></a> |
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| <a href="#T"><strong>T</strong></a> |
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| <a href="#V"><strong>V</strong></a> |
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| <a href="#X"><strong>X</strong></a> |
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| <a href="#Z"><strong>Z</strong></a> |
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</div> |
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<h2 id="A">A</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.active_label">active_label (protac_degradation_predictor.config.Config attribute)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.add_module">add_module() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.apply">apply() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.apply_scalers">apply_scalers() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.apply_scaling">apply_scaling() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.apply_smote">apply_smote() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.avail_cell_lines">avail_cell_lines() (in module protac_degradation_predictor.data_utils)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.avail_e3_ligases">avail_e3_ligases() (in module protac_degradation_predictor.data_utils)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.avail_uniprots">avail_uniprots() (in module protac_degradation_predictor.data_utils)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="B">B</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.bfloat16">bfloat16() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.buffers">buffers() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="C">C</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.call_super_init">call_super_init (protac_degradation_predictor.pytorch_models.PROTAC_Predictor attribute)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.cell_embedding_size">cell_embedding_size (protac_degradation_predictor.config.Config attribute)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.children">children() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config">Config (class in protac_degradation_predictor.config)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.configure_optimizers">configure_optimizers() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.cpu">cpu() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.cuda">cuda() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="D">D</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.dmax_threshold">dmax_threshold (protac_degradation_predictor.config.Config attribute)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.double">double() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.dump_patches">dump_patches (protac_degradation_predictor.pytorch_models.PROTAC_Predictor attribute)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="E">E</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.e3_ligase2uniprot">e3_ligase2uniprot (protac_degradation_predictor.config.Config attribute)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.eval">eval() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.evaluate_model">evaluate_model() (in module protac_degradation_predictor.pytorch_models)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.extra_repr">extra_repr() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="F">F</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.fingerprint_size">fingerprint_size (protac_degradation_predictor.config.Config attribute)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.fit_scaling">fit_scaling() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.float">float() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.forward">forward() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.forward">(protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></li> |
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</ul></td> |
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</tr></table> |
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<h2 id="G">G</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.get_buffer">get_buffer() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.get_cell_emb_dim">get_cell_emb_dim() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.get_confidence_scores">get_confidence_scores() (in module protac_degradation_predictor.optuna_utils_xgboost)</a> |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.get_confidence_scores">(in module protac_degradation_predictor.pytorch_models)</a> |
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</li> |
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</ul></li> |
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<li><a href="source/protac_degradation_predictor.optuna.html#protac_degradation_predictor.optuna.utils.get_dataframe_stats">get_dataframe_stats() (in module protac_degradation_predictor.optuna.utils)</a> |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.get_dataframe_stats">(in module protac_degradation_predictor.optuna_utils)</a> |
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</li> |
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</ul></li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.get_datasets">get_datasets() (in module protac_degradation_predictor.protac_dataset)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.get_e3_ligase_split_indices">get_e3_ligase_split_indices() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.get_extra_state">get_extra_state() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.get_fingerprint">get_fingerprint() (in module protac_degradation_predictor.data_utils)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.optuna.html#protac_degradation_predictor.optuna.utils.get_majority_vote_metrics">get_majority_vote_metrics() (in module protac_degradation_predictor.optuna.utils)</a> |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.get_majority_vote_metrics">(in module protac_degradation_predictor.optuna_utils)</a> |
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</li> |
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</ul></li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.get_numpy_arrays">get_numpy_arrays() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.get_parameter">get_parameter() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_degradation_predictor.get_protac_active_proba">get_protac_active_proba() (in module protac_degradation_predictor.protac_degradation_predictor)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_degradation_predictor.get_protac_embedding">get_protac_embedding() (in module protac_degradation_predictor.protac_degradation_predictor)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.get_protein_emb_dim">get_protein_emb_dim() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.get_random_split_indices">get_random_split_indices() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.get_smiles2fp_and_avg_tanimoto">get_smiles2fp_and_avg_tanimoto() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.get_smiles_emb_dim">get_smiles_emb_dim() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.get_submodule">get_submodule() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.get_suggestion">get_suggestion() (in module protac_degradation_predictor.optuna_utils)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.get_tanimoto_split_indices">get_tanimoto_split_indices() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.get_target_split_indices">get_target_split_indices() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.half">half() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.hyperparameter_tuning_and_training">hyperparameter_tuning_and_training() (in module protac_degradation_predictor.optuna_utils)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.initialize_scalers">initialize_scalers() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.ipu">ipu() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.is_active">is_active() (in module protac_degradation_predictor.data_utils)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_degradation_predictor.is_protac_active">is_protac_active() (in module protac_degradation_predictor.protac_degradation_predictor)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.load_curated_dataset">load_curated_dataset() (in module protac_degradation_predictor.data_utils)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.load_model">load_model() (in module protac_degradation_predictor.pytorch_models)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.load_state_dict">load_state_dict() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="M">M</h2> |
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<li> |
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module |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor">protac_degradation_predictor</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.config">protac_degradation_predictor.config</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.data_utils">protac_degradation_predictor.data_utils</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.optuna.html#module-protac_degradation_predictor.optuna">protac_degradation_predictor.optuna</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.optuna.html#module-protac_degradation_predictor.optuna.utils">protac_degradation_predictor.optuna.utils</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.optuna_utils">protac_degradation_predictor.optuna_utils</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.optuna_utils_xgboost">protac_degradation_predictor.optuna_utils_xgboost</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.protac_dataset">protac_degradation_predictor.protac_dataset</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.protac_degradation_predictor">protac_degradation_predictor.protac_degradation_predictor</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.pytorch_models">protac_degradation_predictor.pytorch_models</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.sklearn_models">protac_degradation_predictor.sklearn_models</a> |
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</li> |
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</ul></li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.modules">modules() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.morgan_radius">morgan_radius (protac_degradation_predictor.config.Config attribute)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="N">N</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.named_buffers">named_buffers() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.named_children">named_children() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.named_modules">named_modules() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.named_parameters">named_parameters() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="O">O</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.on_load_checkpoint">on_load_checkpoint() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.on_save_checkpoint">on_save_checkpoint() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="P">P</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.parameters">parameters() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.pdc50_threshold">pdc50_threshold (protac_degradation_predictor.config.Config attribute)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.predict_step">predict_step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule">PROTAC_DataModule (class in protac_degradation_predictor.protac_dataset)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset">PROTAC_Dataset (class in protac_degradation_predictor.protac_dataset)</a> |
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</li> |
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<li> |
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protac_degradation_predictor |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor">module</a> |
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</li> |
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</ul></li> |
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<li> |
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protac_degradation_predictor.config |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.config">module</a> |
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</li> |
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</ul></li> |
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<li> |
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protac_degradation_predictor.data_utils |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.data_utils">module</a> |
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</ul></li> |
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<li> |
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protac_degradation_predictor.optuna |
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<ul> |
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<li><a href="source/protac_degradation_predictor.optuna.html#module-protac_degradation_predictor.optuna">module</a> |
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</li> |
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</ul></li> |
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<li> |
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protac_degradation_predictor.optuna.utils |
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<ul> |
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<li><a href="source/protac_degradation_predictor.optuna.html#module-protac_degradation_predictor.optuna.utils">module</a> |
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</li> |
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</ul></li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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protac_degradation_predictor.optuna_utils |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.optuna_utils">module</a> |
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</ul></li> |
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protac_degradation_predictor.optuna_utils_xgboost |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.optuna_utils_xgboost">module</a> |
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</li> |
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</ul></li> |
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<li> |
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protac_degradation_predictor.protac_dataset |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.protac_dataset">module</a> |
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</li> |
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</ul></li> |
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<li> |
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protac_degradation_predictor.protac_degradation_predictor |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.protac_degradation_predictor">module</a> |
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</li> |
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</ul></li> |
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<li> |
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protac_degradation_predictor.pytorch_models |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.pytorch_models">module</a> |
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</ul></li> |
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protac_degradation_predictor.sklearn_models |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.sklearn_models">module</a> |
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</li> |
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</ul></li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model">PROTAC_Model (class in protac_degradation_predictor.pytorch_models)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor">PROTAC_Predictor (class in protac_degradation_predictor.pytorch_models)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.protein_embedding_size">protein_embedding_size (protac_degradation_predictor.config.Config attribute)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.pytorch_model_objective">pytorch_model_objective() (in module protac_degradation_predictor.optuna_utils)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="R">R</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_backward_hook">register_backward_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_buffer">register_buffer() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_forward_hook">register_forward_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_forward_pre_hook">register_forward_pre_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_full_backward_hook">register_full_backward_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_full_backward_pre_hook">register_full_backward_pre_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_load_state_dict_post_hook">register_load_state_dict_post_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_module">register_module() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_parameter">register_parameter() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_state_dict_pre_hook">register_state_dict_pre_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.requires_grad_">requires_grad_() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></td> |
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</tr></table> |
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<h2 id="S">S</h2> |
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<table style="width: 100%" class="indextable genindextable"><tr> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.scale_tensor">scale_tensor() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.set_extra_state">set_extra_state() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.setup">setup() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.share_memory">share_memory() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.state_dict">state_dict() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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</li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.step">step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_gradient_boosting">suggest_gradient_boosting() (in module protac_degradation_predictor.sklearn_models)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_logistic_regression">suggest_logistic_regression() (in module protac_degradation_predictor.sklearn_models)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_random_forest">suggest_random_forest() (in module protac_degradation_predictor.sklearn_models)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_svc">suggest_svc() (in module protac_degradation_predictor.sklearn_models)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.T_destination">T_destination (protac_degradation_predictor.pytorch_models.PROTAC_Predictor attribute)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.test_dataloader">test_dataloader() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule method)</a> |
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<ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.test_dataloader">(protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.test_step">test_step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.to">to() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.to_empty">to_empty() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.train">train() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.train_and_evaluate_xgboost">train_and_evaluate_xgboost() (in module protac_degradation_predictor.optuna_utils_xgboost)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.train_dataloader">train_dataloader() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule method)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.train_dataloader">(protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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</li> |
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</ul></li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.train_model">train_model() (in module protac_degradation_predictor.pytorch_models)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.train_sklearn_model">train_sklearn_model() (in module protac_degradation_predictor.sklearn_models)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.training">training (protac_degradation_predictor.pytorch_models.PROTAC_Predictor attribute)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.training_step">training_step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.type">type() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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<h2 id="V">V</h2> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.val_dataloader">val_dataloader() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule method)</a> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.val_dataloader">(protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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</ul></li> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.validation_step">validation_step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a> |
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<h2 id="X">X</h2> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.xgboost_hyperparameter_tuning_and_training">xgboost_hyperparameter_tuning_and_training() (in module protac_degradation_predictor.optuna_utils_xgboost)</a> |
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</ul></td> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.xgboost_model_objective">xgboost_model_objective() (in module protac_degradation_predictor.optuna_utils_xgboost)</a> |
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</li> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.xpu">xpu() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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<h2 id="Z">Z</h2> |
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<td style="width: 33%; vertical-align: top;"><ul> |
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<li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.zero_grad">zero_grad() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a> |
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