immuneML.ml_methods package

Subpackages

• immuneML.ml_methods.classifiers package
  • Submodules
  • immuneML.ml_methods.classifiers.AtchleyKmerMILClassifier module
    • AtchleyKmerMILClassifier
      • AtchleyKmerMILClassifier.MAX_SEED_VALUE
      • AtchleyKmerMILClassifier.MIN_SEED_VALUE
      • AtchleyKmerMILClassifier.can_fit_with_example_weights()
      • AtchleyKmerMILClassifier.can_predict_proba()
      • AtchleyKmerMILClassifier.get_compatible_encoders()
      • AtchleyKmerMILClassifier.get_params()
      • AtchleyKmerMILClassifier.load()
      • AtchleyKmerMILClassifier.store()
  • immuneML.ml_methods.classifiers.BinaryFeatureClassifier module
    • BinaryFeatureClassifier
      • BinaryFeatureClassifier.can_fit_with_example_weights()
      • BinaryFeatureClassifier.can_predict_proba()
      • BinaryFeatureClassifier.get_compatible_encoders()
      • BinaryFeatureClassifier.get_params()
      • BinaryFeatureClassifier.load()
      • BinaryFeatureClassifier.store()
  • immuneML.ml_methods.classifiers.DeepRC module
    • DeepRC
      • DeepRC.can_fit_with_example_weights()
      • DeepRC.can_predict_proba()
      • DeepRC.check_is_fitted()
      • DeepRC.fit_by_cross_validation()
      • DeepRC.get_compatible_encoders()
      • DeepRC.get_package_info()
      • DeepRC.get_params()
      • DeepRC.load()
      • DeepRC.make_data_loader()
      • DeepRC.store()
  • immuneML.ml_methods.classifiers.GradientBoosting module
    • GradientBoosting
      • GradientBoosting.can_fit_with_example_weights()
      • GradientBoosting.can_predict_proba()
      • GradientBoosting.get_documentation()
      • GradientBoosting.get_params()
  • immuneML.ml_methods.classifiers.KNN module
    • KNN
      • KNN.can_fit_with_example_weights()
      • KNN.can_predict_proba()
      • KNN.get_compatible_encoders()
      • KNN.get_documentation()
      • KNN.get_params()
  • immuneML.ml_methods.classifiers.KerasSequenceCNN module
    • KerasSequenceCNN
      • KerasSequenceCNN.can_fit_with_example_weights()
      • KerasSequenceCNN.can_predict_proba()
      • KerasSequenceCNN.check_encoder_compatibility()
      • KerasSequenceCNN.get_compatible_encoders()
      • KerasSequenceCNN.get_params()
      • KerasSequenceCNN.load()
      • KerasSequenceCNN.store()
  • immuneML.ml_methods.classifiers.LogRegressionCustomPenalty module
    • LogRegressionCustomPenalty
      • LogRegressionCustomPenalty.can_fit_with_example_weights()
      • LogRegressionCustomPenalty.can_predict_proba()
      • LogRegressionCustomPenalty.get_compatible_encoders()
      • LogRegressionCustomPenalty.get_params()
      • LogRegressionCustomPenalty.load()
      • LogRegressionCustomPenalty.store()
  • immuneML.ml_methods.classifiers.LogisticRegression module
    • LogisticRegression
      • LogisticRegression.can_fit_with_example_weights()
      • LogisticRegression.can_predict_proba()
      • LogisticRegression.default_parameters
      • LogisticRegression.get_documentation()
      • LogisticRegression.get_params()
  • immuneML.ml_methods.classifiers.MLMethod module
    • MLMethod
      • MLMethod.DOCS_TITLE
      • MLMethod.can_fit_with_example_weights()
      • MLMethod.can_predict_proba()
      • MLMethod.check_encoder_compatibility()
      • MLMethod.fit()
      • MLMethod.fit_by_cross_validation()
      • MLMethod.get_classes()
      • MLMethod.get_compatible_encoders()
      • MLMethod.get_feature_names()
      • MLMethod.get_label_name()
      • MLMethod.get_package_info()
      • MLMethod.get_params()
      • MLMethod.get_positive_class()
      • MLMethod.load()
      • MLMethod.predict()
      • MLMethod.predict_proba()
      • MLMethod.store()
  • immuneML.ml_methods.classifiers.PrecomputedKNN module
    • PrecomputedKNN
      • PrecomputedKNN.can_fit_with_example_weights()
      • PrecomputedKNN.can_predict_proba()
      • PrecomputedKNN.get_compatible_encoders()
      • PrecomputedKNN.get_documentation()
      • PrecomputedKNN.get_params()
  • immuneML.ml_methods.classifiers.ProbabilisticBinaryClassifier module
    • ProbabilisticBinaryClassifier
      • ProbabilisticBinaryClassifier.SMALL_POSITIVE_NUMBER
      • ProbabilisticBinaryClassifier.can_fit_with_example_weights()
      • ProbabilisticBinaryClassifier.can_predict_proba()
      • ProbabilisticBinaryClassifier.get_compatible_encoders()
      • ProbabilisticBinaryClassifier.get_params()
      • ProbabilisticBinaryClassifier.load()
      • ProbabilisticBinaryClassifier.store()
  • immuneML.ml_methods.classifiers.RandomForestClassifier module
    • RandomForestClassifier
      • RandomForestClassifier.can_fit_with_example_weights()
      • RandomForestClassifier.can_predict_proba()
      • RandomForestClassifier.get_documentation()
      • RandomForestClassifier.get_params()
  • immuneML.ml_methods.classifiers.ReceptorCNN module
    • ReceptorCNN
      • ReceptorCNN.can_fit_with_example_weights()
      • ReceptorCNN.can_predict_proba()
      • ReceptorCNN.check_encoder_compatibility()
      • ReceptorCNN.get_compatible_encoders()
      • ReceptorCNN.get_params()
      • ReceptorCNN.load()
      • ReceptorCNN.set_background_probabilities()
      • ReceptorCNN.store()
  • immuneML.ml_methods.classifiers.SVC module
    • SVC
      • SVC.can_fit_with_example_weights()
      • SVC.can_predict_proba()
      • SVC.get_documentation()
      • SVC.get_params()
  • immuneML.ml_methods.classifiers.SVM module
    • SVM
      • SVM.can_fit_with_example_weights()
      • SVM.can_predict_proba()
      • SVM.get_documentation()
      • SVM.get_params()
  • immuneML.ml_methods.classifiers.SklearnMethod module
    • SklearnMethod
      • SklearnMethod.FIT
      • SklearnMethod.FIT_CV
      • SklearnMethod.apply_with_weights()
      • SklearnMethod.can_predict_proba()
      • SklearnMethod.check_is_fitted()
      • SklearnMethod.get_compatible_encoders()
      • SklearnMethod.get_package_info()
      • SklearnMethod.get_params()
      • SklearnMethod.get_usage_documentation()
      • SklearnMethod.load()
      • SklearnMethod.store()
  • immuneML.ml_methods.classifiers.TCRdistClassifier module
    • TCRdistClassifier
      • TCRdistClassifier.can_fit_with_example_weights()
      • TCRdistClassifier.can_predict_proba()
      • TCRdistClassifier.get_compatible_encoders()
      • TCRdistClassifier.get_params()
  • Module contents
• immuneML.ml_methods.clustering package
  • Submodules
  • immuneML.ml_methods.clustering.AgglomerativeClustering module
    • AgglomerativeClustering
      • AgglomerativeClustering.fit()
      • AgglomerativeClustering.fit_predict()
      • AgglomerativeClustering.predict()
      • AgglomerativeClustering.transform()
  • immuneML.ml_methods.clustering.ClusteringMethod module
    • ClusteringMethod
      • ClusteringMethod.DOCS_TITLE
      • ClusteringMethod.fit()
      • ClusteringMethod.fit_predict()
      • ClusteringMethod.predict()
      • ClusteringMethod.transform()
    • get_data_for_clustering()
  • immuneML.ml_methods.clustering.DBSCAN module
    • DBSCAN
      • DBSCAN.fit()
      • DBSCAN.fit_predict()
      • DBSCAN.predict()
      • DBSCAN.transform()
  • immuneML.ml_methods.clustering.HDBSCAN module
    • HDBSCAN
      • HDBSCAN.fit()
      • HDBSCAN.fit_predict()
      • HDBSCAN.predict()
      • HDBSCAN.transform()
  • immuneML.ml_methods.clustering.KMeans module
    • KMeans
      • KMeans.fit()
      • KMeans.fit_predict()
      • KMeans.predict()
      • KMeans.transform()
  • Module contents
• immuneML.ml_methods.dim_reduction package
  • Submodules
  • immuneML.ml_methods.dim_reduction.DimRedMethod module
    • DimRedMethod
      • DimRedMethod.DOCS_TITLE
      • DimRedMethod.fit()
      • DimRedMethod.fit_transform()
      • DimRedMethod.get_dimension_names()
      • DimRedMethod.get_title()
      • DimRedMethod.inverse_transform()
      • DimRedMethod.transform()
  • immuneML.ml_methods.dim_reduction.KernelPCA module
    • KernelPCA
      • KernelPCA.get_dimension_names()
  • immuneML.ml_methods.dim_reduction.PCA module
    • PCA
      • PCA.get_dimension_names()
  • immuneML.ml_methods.dim_reduction.TSNE module
    • TSNE
      • TSNE.get_dimension_names()
      • TSNE.transform()
  • immuneML.ml_methods.dim_reduction.UMAP module
    • UMAP
      • UMAP.get_dimension_names()
  • Module contents
• immuneML.ml_methods.generative_models package
  • Submodules
  • immuneML.ml_methods.generative_models.BackgroundSequences module
  • immuneML.ml_methods.generative_models.ExperimentalImport module
    • ExperimentalImport
      • ExperimentalImport.build_object()
      • ExperimentalImport.can_compute_p_gens()
      • ExperimentalImport.can_generate_from_skewed_gene_models()
      • ExperimentalImport.compute_p_gen()
      • ExperimentalImport.compute_p_gens()
      • ExperimentalImport.generate_from_skewed_gene_models()
      • ExperimentalImport.generate_sequences()
      • ExperimentalImport.is_same()
  • immuneML.ml_methods.generative_models.GenerativeModel module
    • GenerativeModel
      • GenerativeModel.DOCS_TITLE
      • GenerativeModel.OUTPUT_COLUMNS
      • GenerativeModel.can_compute_p_gens()
      • GenerativeModel.can_generate_from_skewed_gene_models()
      • GenerativeModel.compute_p_gen()
      • GenerativeModel.compute_p_gens()
      • GenerativeModel.fit()
      • GenerativeModel.generate_from_skewed_gene_models()
      • GenerativeModel.generate_sequences()
      • GenerativeModel.is_same()
      • GenerativeModel.load_model()
      • GenerativeModel.save_model()
      • GenerativeModel.set_locus()
  • immuneML.ml_methods.generative_models.InternalOlgaModel module
    • InternalOlgaModel
      • InternalOlgaModel.genomic_data
      • InternalOlgaModel.j_gene_mapping
      • InternalOlgaModel.olga_gen_model
      • InternalOlgaModel.sequence_gen_model
      • InternalOlgaModel.v_gene_mapping
  • immuneML.ml_methods.generative_models.KLEvaluator module
    • KL()
    • KLEvaluator
      • KLEvaluator.get_plot()
      • KLEvaluator.get_worst_simulated_sequences()
      • KLEvaluator.get_worst_true_sequences()
      • KLEvaluator.original_plot()
      • KLEvaluator.simulated_kl()
      • KLEvaluator.simulated_kl_weights()
      • KLEvaluator.simulated_plot()
      • KLEvaluator.true_kl()
      • KLEvaluator.true_kl_weights()
    • evaluate_similarities()
    • get_kl_weights()
  • immuneML.ml_methods.generative_models.MultinomialKmerModel module
    • EmpiricalLengthDistribution
      • EmpiricalLengthDistribution.log_prob()
      • EmpiricalLengthDistribution.sample()
    • KmerDistribution
      • KmerDistribution.log_prob()
      • KmerDistribution.sample()
    • KmerModel
      • KmerModel.log_prob()
      • KmerModel.sample()
    • MultinomialKmerModel
      • MultinomialKmerModel.log_prob()
      • MultinomialKmerModel.sample()
    • Poisson
      • Poisson.log_prob()
      • Poisson.mu
      • Poisson.sample()
    • SmoothedLengthDistribution
      • SmoothedLengthDistribution.log_prob()
      • SmoothedLengthDistribution.sample()
    • estimate_kmer_model()
    • estimate_length_distribution()
    • estimate_smoothed_length_distribution()
  • immuneML.ml_methods.generative_models.OLGA module
    • OLGA
      • OLGA.DEFAULT_MODEL_FOLDER_MAP
      • OLGA.MODEL_FILENAMES
      • OLGA.OUTPUT_COLUMNS
      • OLGA.build_object()
      • OLGA.can_compute_p_gens()
      • OLGA.can_generate_from_skewed_gene_models()
      • OLGA.compute_p_gen()
      • OLGA.compute_p_gens()
      • OLGA.default_model_name
      • OLGA.fit()
      • OLGA.generate_from_skewed_gene_models()
      • OLGA.generate_sequences()
      • OLGA.is_same()
      • OLGA.is_vdj
      • OLGA.load_internal_model()
      • OLGA.load_model()
      • OLGA.locus
      • OLGA.model_path
      • OLGA.region_type
      • OLGA.save_model()
  • immuneML.ml_methods.generative_models.PWM module
    • PWM
      • PWM.can_compute_p_gens()
      • PWM.can_generate_from_skewed_gene_models()
      • PWM.compute_p_gen()
      • PWM.compute_p_gens()
      • PWM.fit()
      • PWM.generate_from_skewed_gene_models()
      • PWM.generate_sequences()
      • PWM.is_same()
      • PWM.load_model()
      • PWM.save_model()
  • immuneML.ml_methods.generative_models.SequenceTransitionDistribution module
    • EncodedLookup
      • EncodedLookup.alphabet_size
      • EncodedLookup.encoding
      • EncodedLookup.raw()
    • SequenceTransitionDistribution
      • SequenceTransitionDistribution.end_probs
      • SequenceTransitionDistribution.from_probabilities()
      • SequenceTransitionDistribution.initial_distribution
      • SequenceTransitionDistribution.load()
      • SequenceTransitionDistribution.log_prob()
      • SequenceTransitionDistribution.sample()
      • SequenceTransitionDistribution.save()
      • SequenceTransitionDistribution.transition_matrix
    • estimate_transition_model()
  • immuneML.ml_methods.generative_models.SimpleLSTM module
    • SimpleLSTM
      • SimpleLSTM.can_compute_p_gens()
      • SimpleLSTM.can_generate_from_skewed_gene_models()
      • SimpleLSTM.compute_p_gen()
      • SimpleLSTM.compute_p_gens()
      • SimpleLSTM.fit()
      • SimpleLSTM.generate_from_skewed_gene_models()
      • SimpleLSTM.generate_sequences()
      • SimpleLSTM.is_same()
      • SimpleLSTM.load_model()
      • SimpleLSTM.make_new_model()
      • SimpleLSTM.save_model()
  • immuneML.ml_methods.generative_models.SimpleVAE module
    • SimpleVAE
      • SimpleVAE.can_compute_p_gens()
      • SimpleVAE.can_generate_from_skewed_gene_models()
      • SimpleVAE.compute_p_gen()
      • SimpleVAE.compute_p_gens()
      • SimpleVAE.encode_dataset()
      • SimpleVAE.fit()
      • SimpleVAE.generate_from_skewed_gene_models()
      • SimpleVAE.generate_sequences()
      • SimpleVAE.is_same()
      • SimpleVAE.load_model()
      • SimpleVAE.make_new_model()
      • SimpleVAE.save_model()
    • get_pytorch_seq_dataset_class()
  • immuneML.ml_methods.generative_models.SoNNia module
    • SoNNia
      • SoNNia.can_compute_p_gens()
      • SoNNia.can_generate_from_skewed_gene_models()
      • SoNNia.compute_p_gen()
      • SoNNia.compute_p_gens()
      • SoNNia.fit()
      • SoNNia.generate_from_skewed_gene_models()
      • SoNNia.generate_sequences()
      • SoNNia.is_same()
      • SoNNia.load_model()
      • SoNNia.save_model()
      • SoNNia.set_model_path()
  • Module contents
• immuneML.ml_methods.helper_methods package
  • Submodules
  • immuneML.ml_methods.helper_methods.FurthestNeighborClassifier module
    • FurthestNeighborClassifier
      • FurthestNeighborClassifier.fit()
      • FurthestNeighborClassifier.predict()
  • Module contents
• immuneML.ml_methods.pytorch_implementations package
  • Submodules
  • immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression module
    • PyTorchLogisticRegression
      • PyTorchLogisticRegression.forward()
  • immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN module
    • PyTorchReceptorCNN
      • PyTorchReceptorCNN.forward()
      • PyTorchReceptorCNN.get_max_information_gain()
      • PyTorchReceptorCNN.rescale_weights_for_IGM()
  • immuneML.ml_methods.pytorch_implementations.SimpleLSTMGenerator module
    • SimpleLSTMGenerator
      • SimpleLSTMGenerator.forward()
      • SimpleLSTMGenerator.init_zero_state()
  • immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator module
    • Decoder
      • Decoder.forward()
    • Encoder
      • Encoder.forward()
    • SimpleVAEGenerator
      • SimpleVAEGenerator.decode()
      • SimpleVAEGenerator.encode()
      • SimpleVAEGenerator.encoding_func()
      • SimpleVAEGenerator.forward()
    • UniformLinear
    • XavierLinear
    • vae_cdr3_loss()
  • Module contents
• immuneML.ml_methods.util package
  • Submodules
  • immuneML.ml_methods.util.Util module
    • Util
      • Util.binarize_label_classes()
      • Util.get_immuneML_version()
      • Util.get_train_val_indices()
      • Util.make_binary_class_mapping()
      • Util.make_class_mapping()
      • Util.map_to_new_class_values()
      • Util.map_to_old_class_values()
      • Util.setup_pytorch()
      • Util.subset_encoded_data()
  • immuneML.ml_methods.util.pytorch_util module
    • store_weights()
  • Module contents

Module contents