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
- immuneML.ml_methods.classifiers.DeepRC module
- immuneML.ml_methods.classifiers.KNN module
- immuneML.ml_methods.classifiers.KerasSequenceCNN module
- immuneML.ml_methods.classifiers.LogisticRegression module
- 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
- 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
- immuneML.ml_methods.classifiers.ReceptorCNN module
- immuneML.ml_methods.classifiers.SVC module
- immuneML.ml_methods.classifiers.SVM module
- 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
- Module contents
- immuneML.ml_methods.clustering package
- immuneML.ml_methods.dim_reduction package
- 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()
- immuneML.ml_methods.generative_models.InternalOlgaModel module
- immuneML.ml_methods.generative_models.KLEvaluator module
- immuneML.ml_methods.generative_models.MultinomialKmerModel module
- 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
- immuneML.ml_methods.generative_models.SequenceTransitionDistribution module
EncodedLookup
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.ITER_TO_REPORT
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
PyTorchSequenceDataset
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()
- immuneML.ml_methods.generative_models.SoNNia module
- Module contents
- immuneML.ml_methods.pytorch_implementations package
- Submodules
- immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression module
- immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN module
- immuneML.ml_methods.pytorch_implementations.SimpleLSTMGenerator module
- immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator module
- Module contents
- immuneML.ml_methods.util package