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<section id="protac-degradation-predictor-documentation"> |
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<h1>PROTAC-Degradation-Predictor documentation<a class="headerlink" href="#protac-degradation-predictor-documentation" title="Link to this heading"></a></h1> |
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<p>Add your content using <code class="docutils literal notranslate"><span class="pre">reStructuredText</span></code> syntax. See the |
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<p class="caption" role="heading"><span class="caption-text">Contents:</span></p> |
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<ul> |
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<li class="toctree-l1"><a class="reference internal" href="source/modules.html">protac_degradation_predictor</a><ul> |
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<li class="toctree-l2"><a class="reference internal" href="source/protac_degradation_predictor.html">protac_degradation_predictor package</a><ul> |
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<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#subpackages">Subpackages</a><ul> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.optuna.html">protac_degradation_predictor.optuna package</a></li> |
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</ul> |
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</li> |
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<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#submodules">Submodules</a></li> |
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<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.config">protac_degradation_predictor.config module</a><ul> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config"><code class="docutils literal notranslate"><span class="pre">Config</span></code></a></li> |
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</ul> |
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</li> |
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<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.data_utils">protac_degradation_predictor.data_utils module</a><ul> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.avail_e3_ligases"><code class="docutils literal notranslate"><span class="pre">avail_e3_ligases()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.avail_cell_lines"><code class="docutils literal notranslate"><span class="pre">avail_cell_lines()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.avail_uniprots"><code class="docutils literal notranslate"><span class="pre">avail_uniprots()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.get_fingerprint"><code class="docutils literal notranslate"><span class="pre">get_fingerprint()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.is_active"><code class="docutils literal notranslate"><span class="pre">is_active()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.load_curated_dataset"><code class="docutils literal notranslate"><span class="pre">load_curated_dataset()</span></code></a></li> |
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</ul> |
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</li> |
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<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.optuna_utils">protac_degradation_predictor.optuna_utils module</a><ul> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.get_dataframe_stats"><code class="docutils literal notranslate"><span class="pre">get_dataframe_stats()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.get_majority_vote_metrics"><code class="docutils literal notranslate"><span class="pre">get_majority_vote_metrics()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.get_suggestion"><code class="docutils literal notranslate"><span class="pre">get_suggestion()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.pytorch_model_objective"><code class="docutils literal notranslate"><span class="pre">pytorch_model_objective()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.hyperparameter_tuning_and_training"><code class="docutils literal notranslate"><span class="pre">hyperparameter_tuning_and_training()</span></code></a></li> |
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</ul> |
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</li> |
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<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.optuna_utils_xgboost">protac_degradation_predictor.optuna_utils_xgboost module</a><ul> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.get_confidence_scores"><code class="docutils literal notranslate"><span class="pre">get_confidence_scores()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.train_and_evaluate_xgboost"><code class="docutils literal notranslate"><span class="pre">train_and_evaluate_xgboost()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.xgboost_model_objective"><code class="docutils literal notranslate"><span class="pre">xgboost_model_objective()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.xgboost_hyperparameter_tuning_and_training"><code class="docutils literal notranslate"><span class="pre">xgboost_hyperparameter_tuning_and_training()</span></code></a></li> |
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</ul> |
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</li> |
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<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.protac_dataset">protac_degradation_predictor.protac_dataset module</a><ul> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset"><code class="docutils literal notranslate"><span class="pre">PROTAC_Dataset</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.get_datasets"><code class="docutils literal notranslate"><span class="pre">get_datasets()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule"><code class="docutils literal notranslate"><span class="pre">PROTAC_DataModule</span></code></a></li> |
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</ul> |
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</li> |
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<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.protac_degradation_predictor">protac_degradation_predictor.protac_degradation_predictor module</a><ul> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_degradation_predictor.get_protac_active_proba"><code class="docutils literal notranslate"><span class="pre">get_protac_active_proba()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_degradation_predictor.is_protac_active"><code class="docutils literal notranslate"><span class="pre">is_protac_active()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_degradation_predictor.get_protac_embedding"><code class="docutils literal notranslate"><span class="pre">get_protac_embedding()</span></code></a></li> |
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</ul> |
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</li> |
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<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.pytorch_models">protac_degradation_predictor.pytorch_models module</a><ul> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor"><code class="docutils literal notranslate"><span class="pre">PROTAC_Predictor</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model"><code class="docutils literal notranslate"><span class="pre">PROTAC_Model</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.get_confidence_scores"><code class="docutils literal notranslate"><span class="pre">get_confidence_scores()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.train_model"><code class="docutils literal notranslate"><span class="pre">train_model()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.evaluate_model"><code class="docutils literal notranslate"><span class="pre">evaluate_model()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.load_model"><code class="docutils literal notranslate"><span class="pre">load_model()</span></code></a></li> |
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</ul> |
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</li> |
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<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.sklearn_models">protac_degradation_predictor.sklearn_models module</a><ul> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.train_sklearn_model"><code class="docutils literal notranslate"><span class="pre">train_sklearn_model()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_random_forest"><code class="docutils literal notranslate"><span class="pre">suggest_random_forest()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_logistic_regression"><code class="docutils literal notranslate"><span class="pre">suggest_logistic_regression()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_svc"><code class="docutils literal notranslate"><span class="pre">suggest_svc()</span></code></a></li> |
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<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_gradient_boosting"><code class="docutils literal notranslate"><span class="pre">suggest_gradient_boosting()</span></code></a></li> |
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</ul> |
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</li> |
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<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor">Module contents</a></li> |
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