Index

A

AA_MASKED (PositionType attribute) AbstractDifferenceGradientEvaluator (class in seqgra.evaluator.gradientbased.abstractdifferencegradientevaluator) AbstractGradientEvaluator (class in seqgra.evaluator.gradientbased.abstractgradientevaluator) accuracy (Metrics attribute) add_element() (ExampleGenerator static method) add_module() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) add_spatially_constrained_elements() (ExampleGenerator static method) ALL_COMPARATOR_IDS (ComparatorID attribute) ALL_EVALUATOR_IDS (EvaluatorID attribute) ALL_LIBRARIES (LibraryType attribute) ALL_SEQUENCE_SPACES (SequenceSpaceType attribute) ALL_SETS (DataSet attribute) ALL_TASKS (TaskType attribute) AlphabetDistribution (class in seqgra.model.data.alphabetdistribution) AnnotatedExample (class in seqgra.schema) AnnotatedExampleSet (class in seqgra.schema) annotation (AnnotatedExample attribute) annotations (AnnotatedExampleSet attribute) (AnnotationSet attribute) AnnotationSet (class in seqgra.schema) apply() (Bottleneck method) (EBAvgPool2d method), [1] (EBConv2d method), [1] (EBLinear method), [1] (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method)

apply_rule() (ExampleGenerator static method) approx_equal() (SISResult method) Architecture (class in seqgra.model.model.architecture) architecture (ModelDefinition attribute) attach_alphabet_distribution() (XMLDataDefinitionWriter static method) attach_architecture_element() (XMLModelDefinitionWriter static method) attach_background_element() (XMLDataDefinitionWriter static method) attach_condition_element() (XMLDataDefinitionWriter static method) attach_conditions_element() (XMLDataDefinitionWriter static method) attach_data_generation_element() (XMLDataDefinitionWriter static method) attach_general_element() (XMLDataDefinitionWriter static method) (XMLModelDefinitionWriter static method) attach_hp_element() (XMLModelDefinitionWriter static method) attach_labels_element() (XMLModelDefinitionWriter static method) attach_loss_element() (XMLModelDefinitionWriter static method) attach_matrix_position_element() (XMLDataDefinitionWriter static method) attach_optimizer_element() (XMLModelDefinitionWriter static method) attach_rule_element() (XMLDataDefinitionWriter static method) attach_sc_element() (XMLDataDefinitionWriter static method) attach_se_element() (XMLDataDefinitionWriter static method) attach_ses_element() (XMLDataDefinitionWriter static method) attach_set_element() (XMLDataDefinitionWriter static method) attach_tp_element() (XMLModelDefinitionWriter static method)

B

Background (class in seqgra.model.data.background) BACKGROUND (PositionType attribute) BackgroundGenerator (class in seqgra.simulator.backgroundgenerator) backward() (EBAvgPool2d static method), [1] (EBConv2d static method), [1] (EBLinear static method), [1] BAYES_OPTIMAL_CLASSIFIER (LibraryType attribute) BayesOptimalDNAMultiClassClassificationLearner (class in seqgra.learner.bayes.bayeslearner) BayesOptimalDNAMultiLabelClassificationLearner (class in seqgra.learner.bayes.bayeslearner) BayesOptimalHelper (class in seqgra.learner.bayes.bayeshelper) BayesOptimalProteinMultiClassClassificationLearner (class in seqgra.learner.bayes.bayeslearner) BayesOptimalProteinMultiLabelClassificationLearner (class in seqgra.learner.bayes.bayeslearner) bfloat16() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method)

Blur (class in seqgra.evaluator.explainer.perturbation) Bottleneck (class in seqgra.evaluator.explainer.real_time.pytorch_fixes) Bottleneck.to() (in module seqgra.evaluator.explainer.real_time.pytorch_fixes), [1], [2], [3] BottleneckBlock() (in module seqgra.evaluator.explainer.real_time.pytorch_fixes) buffers() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method)

C

change_ds_size() (in module seqgra.seqgrae) check_annotations() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) check_grammar() (Simulator method) check_invalid_distances() (Simulator method) check_invalid_positions() (Simulator method) check_invalid_sequence_elements() (Simulator method) check_labels() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) check_missing_alphabet_distributions() (Simulator method) check_mutually_exclusive_probabilities() (Simulator method) check_overlapping_sequence_elements() (Simulator method) check_sequence() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAHelper static method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinHelper static method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) check_spacing_contraint_se_refs() (Simulator method) check_unused_conditions() (Simulator method) check_unused_sequence_elements() (Simulator method) children() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) Comparator (class in seqgra.comparator.comparator) ComparatorID (class in seqgra.constants) compare_models() (Comparator method) (CurveTableComparator method) (FIETableComparator method) (PRComparator method) (ROCComparator method) (TableComparator method)

Condition (class in seqgra.model.data.condition) CONFOUNDER (PositionType attribute) CONTRASTIVE_EXCITATION_BACKPROP (EvaluatorID attribute) ContrastiveExcitationBackpropEvaluator (class in seqgra.evaluator.gradientbased.contrastiveexcitationbackpropevaluator) ContrastiveExcitationBackpropExplainer (class in seqgra.evaluator.explainer.ebp.ebp) CONVENTIONAL_EVALUATORS (EvaluatorID attribute) convert_dense_to_one_hot_encoding() (DNAHelper static method) (ProteinHelper static method) convert_one_hot_to_dense_encoding() (DNAHelper static method) (ProteinHelper static method) CORE_FEATURE_IMPORTANCE_EVALUATORS (EvaluatorID attribute) count() (AnnotatedExampleSet method) (AnnotationSet method) (DataSessionInfo method) (ExampleSet method) (Metrics method) (ModelSessionInfo method) (ModelSize method) (ProbabilisticToken method) (SISResult method) cpu() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) create() (EmpiricalSimilarityScore static method) (GrammarPositionHeatmap static method) (KLDivergence static method) (MotifInfo static method) create_empirical_similarity_score_matrix() (Simulator method) create_grammar_heatmap() (Simulator method) create_model() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalHelper static method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasHelper static method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchHelper static method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) create_motif_info() (Simulator method) create_motif_kl_divergence_matrix() (Simulator method) create_parser() (in module seqgra.seqgra) (in module seqgra.seqgraa) (in module seqgra.seqgrae) (in module seqgra.seqgras) create_precision_recall_curve() (PRComparator method) (PREvaluator method) create_roc_curve() (ROCComparator method) (ROCEvaluator method) create_root_element() (XMLDataDefinitionWriter static method) (XMLModelDefinitionWriter static method) create_se_pwm_dict() (BayesOptimalHelper static method) create_single_precision_recall_curve() (PRComparator method) create_single_roc_curve() (ROCComparator method) criterion (Learner attribute) (MultiClassClassificationLearner attribute) (MultiLabelClassificationLearner attribute) (MultipleRegressionLearner attribute) (MultivariateRegressionLearner attribute) cuda() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) CURVE_TABLE (ComparatorID attribute) CurveTableComparator (class in seqgra.comparator.curvetablecomparator)

D

data_dir (Learner attribute) (MultiClassClassificationLearner attribute) (MultiLabelClassificationLearner attribute) (MultipleRegressionLearner attribute) (MultivariateRegressionLearner attribute) DataDefinition (class in seqgra.model.data.datadefinition) DataDefinitionParser (class in seqgra.parser.datadefinitionparser) DataDefinitionWriter (class in seqgra.writer.datadefinitionwriter) DataGeneration (class in seqgra.model.data.datageneration) DataGenerationExample (class in seqgra.model.data.datageneration) DataGenerationSet (class in seqgra.model.data.datageneration) DataSessionInfo (class in seqgra.schema) DataSet (class in seqgra.constants) dataset_generator() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) decode_x() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method)

decode_y() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) DECONV (EvaluatorID attribute) DeconvEvaluator (class in seqgra.evaluator.gradientbased.deconvevaluator) DeconvExplainer (class in seqgra.evaluator.explainer.backprop) DEEP_LIFT (EvaluatorID attribute) DeepLiftEvaluator (class in seqgra.evaluator.gradientbased.deepliftevaluator) DeepLIFTRescaleExplainer (class in seqgra.evaluator.explainer.deeplift) definition (Learner attribute) (MultiClassClassificationLearner attribute) (MultiLabelClassificationLearner attribute) (MultipleRegressionLearner attribute) (MultivariateRegressionLearner attribute) description (ModelDefinition attribute) detect_max_length() (GrammarPositionHeatmap static method) detect_task() (GrammarPositionHeatmap static method) DifferenceGradientEvaluator (class in seqgra.evaluator.gradientbased.differencegradientevaluator) dijkstra() (in module seqgra.evaluator.explainer.path) (NonlinearIntegratedGradientEvaluator static method) dirty_tensors (EBAvgPool2d attribute), [1] (EBConv2d attribute), [1] (EBLinear attribute), [1] DNA (SequenceSpaceType attribute) DNA_MASKED (PositionType attribute) DNAHelper (class in seqgra.learner.dnahelper) DNAMultiClassClassificationLearner (class in seqgra.learner.dna) DNAMultiLabelClassificationLearner (class in seqgra.learner.dna) double() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) dump_patches (Bottleneck attribute) (PixelShuffleBlock attribute) (ResNetEncoder attribute) (SaliencyModel attribute) (UNetUpsampler attribute)

E

EBAvgPool2d (class in seqgra.evaluator.explainer.ebp.functions) (class in seqgra.evaluator.gradientbased.ebphelper) EBConv2d (class in seqgra.evaluator.explainer.ebp.functions) (class in seqgra.evaluator.gradientbased.ebphelper) EBLinear (class in seqgra.evaluator.explainer.ebp.functions) (class in seqgra.evaluator.gradientbased.ebphelper) EmpiricalSimilarityScore (class in seqgra.simulator.motif.ess) encode_x() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) encode_y() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) eval() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) evaluate_model() (AbstractDifferenceGradientEvaluator method) (AbstractGradientEvaluator method) (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalHelper static method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (ContrastiveExcitationBackpropEvaluator method) (DeconvEvaluator method) (DeepLiftEvaluator method) (DifferenceGradientEvaluator method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (Evaluator method) (ExcitationBackpropEvaluator method) (FeatureImportanceEvaluator method) (FeedbackEvaluator method) (GradCamGradientEvaluator method) (GradientBasedEvaluator method) (GradientEvaluator method) (GradientxInputEvaluator method) (GuidedBackpropEvaluator method) (IntegratedGradientEvaluator method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasHelper static method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MetricsEvaluator method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (NonlinearIntegratedGradientEvaluator method) (PredictEvaluator method) (PREvaluator method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (ROCEvaluator method) (SaliencyEvaluator method) (SISEvaluator method) (SmoothGradEvaluator method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchHelper static method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method)

Evaluator (class in seqgra.evaluator.evaluator) EvaluatorID (class in seqgra.constants) Example (class in seqgra.schema) (class in seqgra.simulator.example) ExampleGenerator (class in seqgra.simulator.examplegenerator) ExampleSet (class in seqgra.schema) EXCITATION_BACKPROP (EvaluatorID attribute) ExcitationBackpropEvaluator (class in seqgra.evaluator.gradientbased.excitationbackpropevaluator) ExcitationBackpropExplainer (class in seqgra.evaluator.explainer.ebp.ebp) explain() (AbstractDifferenceGradientEvaluator method) (AbstractGradientEvaluator method) (ContrastiveExcitationBackpropEvaluator method) (ContrastiveExcitationBackpropExplainer method) (DeconvEvaluator method) (DeconvExplainer method) (DeepLiftEvaluator method) (DeepLIFTRescaleExplainer method) (DifferenceGradientEvaluator method) (ExcitationBackpropEvaluator method) (ExcitationBackpropExplainer method) (FeedbackEvaluator method) (FeedbackExplainer method) (GradCAMExplainer method) (GradCamGradientEvaluator method) (GradientBasedEvaluator method) (GradientEvaluator method) (GradientxInputEvaluator method) (GradxInputExplainer method) (GuidedBackpropEvaluator method) (GuidedBackpropExplainer method) (IntegratedGradientEvaluator method) (IntegrateGradExplainer method) (NonlinearIntegratedGradientEvaluator method) (NonlinearIntegrateGradExplainer method) (PatternLRPExplainer method) (PatternNetExplainer method) (PerturbExplainer method) (RealTimeSaliencyExplainer method) (SaliencyEvaluator method) (SaliencyExplainer method) (SmoothGradEvaluator method) (SmoothGradExplainer method) (VanillaDifferenceGradExplainer method) (VanillaGradExplainer method) extra_repr() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) extract_id() (in module seqgra.seqgrae)

F

FEATURE_IMPORTANCE_EVALUATOR_TABLE (ComparatorID attribute) FEATURE_IMPORTANCE_EVALUATORS (EvaluatorID attribute) FeatureImportanceEvaluator (class in seqgra.evaluator.evaluator) FEEDBACK (EvaluatorID attribute) FeedbackEvaluator (class in seqgra.evaluator.gradientbased.feedbackevaluator) FeedbackExplainer (class in seqgra.evaluator.explainer.feedback) FIETableComparator (class in seqgra.comparator.fietablecomparator) find_sis() (in module seqgra.evaluator.sis.sis) (SISEvaluator method) first_forward() (in module seqgra.evaluator.explainer.feedback) (in module seqgra.evaluator.gradientbased.feedbackevaluator) float() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method)

format_output_dir() (MiscHelper static method) forward() (Bottleneck method) (EBAvgPool2d static method), [1] (EBConv2d static method), [1] (EBLinear static method), [1] (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method)

G

generate() (KmerBasedSequenceElement method) (MatrixBasedSequenceElement method) (SequenceElement method) generate_background() (BackgroundGenerator static method) generate_example() (ExampleGenerator static method) generate_letters() (AlphabetDistribution method) get_all_grammar_ids() (in module seqgra.seqgras) get_all_model_ids() (in module seqgra.seqgras) get_annotations_file() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) get_architecture() (ModelDefinitionParser method) (XMLModelDefinitionParser method) get_background() (DataDefinitionParser method) (XMLDataDefinitionParser method) get_best_model_file_name() (TorchHelper static method) get_by_id() (Condition static method) (KmerBasedSequenceElement static method) (MatrixBasedSequenceElement static method) (SequenceElement static method) get_comparator() (IdResolver static method) get_conditions() (DataDefinitionParser method) (XMLDataDefinitionParser method) get_data_definition() (DataDefinitionParser method) (XMLDataDefinitionParser method) get_data_folder_name() (in module seqgra.seqgrae) get_data_generation() (DataDefinitionParser method) (XMLDataDefinitionParser method) get_data_session_info() (TableComparator method) get_description() (DataDefinitionParser method) (ModelDefinitionParser method) (XMLDataDefinitionParser method) (XMLModelDefinitionParser method) get_distance() (ExampleGenerator static method) get_evaluator() (IdResolver static method) get_examples_file() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) get_grammar_id() (DataDefinitionParser method) (in module seqgra.seqgrae) (XMLDataDefinitionParser method) get_implementation() (ModelDefinitionParser method) (XMLModelDefinitionParser method) get_input_encoding() (ModelDefinitionParser method) (XMLModelDefinitionParser method) get_keras_layer() (KerasHelper static method) get_label_set() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) get_labels() (Comparator method) (CurveTableComparator method) (FIETableComparator method) (ModelDefinitionParser method) (PRComparator method) (ROCComparator method) (TableComparator method) (XMLModelDefinitionParser method) get_last_epoch_completed() (TableComparator method) get_layer() (AbstractDifferenceGradientEvaluator method) (AbstractGradientEvaluator method) (ContrastiveExcitationBackpropEvaluator method) (DeconvEvaluator method) (DeepLiftEvaluator method) (DifferenceGradientEvaluator method) (ExcitationBackpropEvaluator method) (FeedbackEvaluator method) (GradCamGradientEvaluator method) (GradientBasedEvaluator method) (GradientEvaluator method) (GradientxInputEvaluator method) (GuidedBackpropEvaluator method) (in module seqgra.evaluator.explainer.ebp.ebp) (in module seqgra.evaluator.explainer.gradcam) (IntegratedGradientEvaluator method) (NonlinearIntegratedGradientEvaluator method) (SaliencyEvaluator method) (SmoothGradEvaluator method)

get_learner() (IdResolver static method) get_library() (ModelDefinitionParser method) (XMLModelDefinitionParser method) get_loss() (KerasHelper static method) (TorchHelper static method) get_loss_hyperparameters() (ModelDefinitionParser method) (XMLModelDefinitionParser method) get_max_length() (KmerBasedSequenceElement method) (MatrixBasedSequenceElement method) (SequenceElement method) get_metrics() (TableComparator method) (TorchHelper static method) get_model_definition() (ModelDefinitionParser method) (XMLModelDefinitionParser method) get_model_id() (in module seqgra.seqgrae) (ModelDefinitionParser method) (XMLModelDefinitionParser method) get_model_params() (TableComparator method) get_model_session_info() (TableComparator method) get_name() (DataDefinitionParser method) (ModelDefinitionParser method) (XMLDataDefinitionParser method) (XMLModelDefinitionParser method) get_num_params() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasHelper static method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchHelper static method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) get_optimizer() (KerasHelper static method) (TorchHelper static method) get_optimizer_hyperparameters() (ModelDefinitionParser method) (XMLModelDefinitionParser method) get_per_label_auc() (CurveTableComparator method) get_position() (ExampleGenerator static method) get_pr_auc() (TableComparator method) get_pretrained_saliency_fn() (in module seqgra.evaluator.explainer.real_time.saliency_eval) get_pwm_max_score() (BayesOptimalHelper static method) get_pwm_min_score() (BayesOptimalHelper static method) get_pwms_for_label() (BayesOptimalHelper static method) get_roc_auc() (TableComparator method) get_seed() (DataDefinitionParser method) (ModelDefinitionParser method) (XMLDataDefinitionParser method) (XMLModelDefinitionParser method) get_sequence_elements() (DataDefinitionParser method) (XMLDataDefinitionParser method) get_sequence_length() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) get_sequence_space() (DataDefinitionParser method) (ModelDefinitionParser method) (XMLDataDefinitionParser method) (XMLModelDefinitionParser method) get_set_size() (TableComparator method) get_task() (DataDefinitionParser method) (ModelDefinitionParser method) (XMLDataDefinitionParser method) (XMLModelDefinitionParser method) get_training_process_hyperparameters() (ModelDefinitionParser method) (XMLModelDefinitionParser method) get_transforms() (in module seqgra.evaluator.explainer.perturbation) get_valid_file() (MiscHelper static method) gpu_id (Learner attribute) (MultiClassClassificationLearner attribute) (MultiLabelClassificationLearner attribute) (MultipleRegressionLearner attribute) (MultivariateRegressionLearner attribute) GRAD_CAM (EvaluatorID attribute) GradCAMExplainer (class in seqgra.evaluator.explainer.gradcam) GradCamGradientEvaluator (class in seqgra.evaluator.gradientbased.gradcamgradientevaluator) GRADIENT (EvaluatorID attribute) GRADIENT_X_INPUT (EvaluatorID attribute) GradientBasedEvaluator (class in seqgra.evaluator.gradientbased.gradientbasedevaluator) GradientEvaluator (class in seqgra.evaluator.gradientbased.gradientevaluator) GradientxInputEvaluator (class in seqgra.evaluator.gradientbased.gradientxinputevaluator) GradxInputExplainer (class in seqgra.evaluator.explainer.backprop) GRAMMAR (PositionType attribute) GrammarPositionHeatmap (class in seqgra.simulator.heatmap.heatmap) GUIDED_BACKPROP (EvaluatorID attribute) GuidedBackpropEvaluator (class in seqgra.evaluator.gradientbased.guidedbackpropevaluator) GuidedBackpropExplainer (class in seqgra.evaluator.explainer.backprop)

H

half() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method)

I

id (ModelDefinition attribute) IdResolver (class in seqgra.idresolver) implementation (ModelDefinition attribute) index() (AnnotatedExampleSet method) (AnnotationSet method) (DataSessionInfo method) (ExampleSet method) (Metrics method) (ModelSessionInfo method) (ModelSize method) (ProbabilisticToken method) (SISResult method)

init_tf_memory_policy() (KerasHelper static method) INTEGRATED_GRADIENTS (EvaluatorID attribute) IntegratedGradientEvaluator (class in seqgra.evaluator.gradientbased.integratedgradientevaluator) IntegrateGradExplainer (class in seqgra.evaluator.explainer.backprop) is_traceable (EBAvgPool2d attribute), [1] (EBConv2d attribute), [1] (EBLinear attribute), [1] IterableMultiClassDataSet (class in seqgra.learner.torch.torchdataset) IterableMultiLabelDataSet (class in seqgra.learner.torch.torchdataset)

K

KerasDNAMultiClassClassificationLearner (class in seqgra.learner.tensorflow.keraslearner) KerasDNAMultiLabelClassificationLearner (class in seqgra.learner.tensorflow.keraslearner) KerasHelper (class in seqgra.learner.tensorflow.kerashelper)

KerasProteinMultiClassClassificationLearner (class in seqgra.learner.tensorflow.keraslearner) KerasProteinMultiLabelClassificationLearner (class in seqgra.learner.tensorflow.keraslearner) KLDivergence (class in seqgra.simulator.motif.kld) KmerBasedSequenceElement (class in seqgra.model.data.sequenceelement)

L

labels (ModelDefinition attribute) LastEpochCallback (class in seqgra.learner.tensorflow.kerascallback) Learner (class in seqgra.learner.learner) library (ModelDefinition attribute) (ModelSessionInfo attribute) library_version (ModelSessionInfo attribute) LibraryType (class in seqgra.constants) load_custom_weights() (KerasHelper static method) load_data() (in module seqgra.seqgraa) load_model() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasHelper static method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchHelper static method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method)

load_params() (in module seqgra.evaluator.explainer.patterns) load_patterns() (in module seqgra.evaluator.explainer.patterns) load_state_dict() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) loss (Metrics attribute) loss_hyperparameters (ModelDefinition attribute)

M

main() (in module seqgra.seqgra) (in module seqgra.seqgraa) (in module seqgra.seqgrae) (in module seqgra.seqgras) make_empty_boolean_mask() (in module seqgra.evaluator.sis.sis) make_empty_boolean_mask_broadcast_over_axis() (in module seqgra.evaluator.sis.sis) mark_dirty() (EBAvgPool2d method), [1] (EBConv2d method), [1] (EBLinear method), [1] mark_non_differentiable() (EBAvgPool2d method), [1] (EBConv2d method), [1] (EBLinear method), [1] mark_shared_storage() (EBAvgPool2d method), [1] (EBConv2d method), [1] (EBLinear method), [1] mask (SISResult attribute) mask_forward() (in module seqgra.evaluator.explainer.feedback) (in module seqgra.evaluator.gradientbased.feedbackevaluator) materialize_grads (EBAvgPool2d attribute), [1] (EBConv2d attribute), [1] (EBLinear attribute), [1] MatrixBasedSequenceElement (class in seqgra.model.data.sequenceelement) metadata (EBAvgPool2d attribute), [1] (EBConv2d attribute), [1] (EBLinear attribute), [1] Metrics (class in seqgra.schema) METRICS (EvaluatorID attribute) metrics (Learner attribute) (MultiClassClassificationLearner attribute) (MultiLabelClassificationLearner attribute) (MultipleRegressionLearner attribute) (MultivariateRegressionLearner attribute) MetricsEvaluator (class in seqgra.evaluator.metricsevaluator) minimialistic_restore() (SaliencyModel method) MiscHelper (class in seqgra.misc) model (Learner attribute) (MultiClassClassificationLearner attribute) (MultiLabelClassificationLearner attribute) (MultipleRegressionLearner attribute) (MultivariateRegressionLearner attribute) MODEL_AGNOSTIC_EVALUATORS (EvaluatorID attribute) ModelDefinition (class in seqgra.model.model.modeldefinition) ModelDefinitionParser (class in seqgra.parser.modeldefinitionparser) ModelDefinitionWriter (class in seqgra.writer.modeldefinitionwriter) ModelSessionInfo (class in seqgra.schema) ModelSize (class in seqgra.schema) module seqgra seqgra.comparator seqgra.comparator.comparator seqgra.comparator.curvetablecomparator seqgra.comparator.fietablecomparator seqgra.comparator.prcomparator seqgra.comparator.roccomparator seqgra.comparator.tablecomparator seqgra.constants seqgra.evaluator seqgra.evaluator.evaluator seqgra.evaluator.explainer.backprop seqgra.evaluator.explainer.deeplift seqgra.evaluator.explainer.ebp seqgra.evaluator.explainer.ebp.ebp seqgra.evaluator.explainer.ebp.functions seqgra.evaluator.explainer.feedback seqgra.evaluator.explainer.gradcam seqgra.evaluator.explainer.occlusion seqgra.evaluator.explainer.path seqgra.evaluator.explainer.patterns seqgra.evaluator.explainer.perturbation seqgra.evaluator.explainer.real_time seqgra.evaluator.explainer.real_time.pytorch_fixes seqgra.evaluator.explainer.real_time.resnet_encoder seqgra.evaluator.explainer.real_time.saliency_eval seqgra.evaluator.gradientbased seqgra.evaluator.gradientbased.abstractdifferencegradientevaluator seqgra.evaluator.gradientbased.abstractgradientevaluator seqgra.evaluator.gradientbased.contrastiveexcitationbackpropevaluator seqgra.evaluator.gradientbased.deconvevaluator seqgra.evaluator.gradientbased.deepliftevaluator seqgra.evaluator.gradientbased.differencegradientevaluator seqgra.evaluator.gradientbased.ebphelper seqgra.evaluator.gradientbased.excitationbackpropevaluator seqgra.evaluator.gradientbased.feedbackevaluator seqgra.evaluator.gradientbased.gradcamgradientevaluator seqgra.evaluator.gradientbased.gradientbasedevaluator seqgra.evaluator.gradientbased.gradientevaluator seqgra.evaluator.gradientbased.gradientxinputevaluator seqgra.evaluator.gradientbased.guidedbackpropevaluator seqgra.evaluator.gradientbased.integratedgradientevaluator seqgra.evaluator.gradientbased.nonlinearintegratedgradientevaluator seqgra.evaluator.gradientbased.saliencyevaluator seqgra.evaluator.gradientbased.smoothgradevaluator seqgra.evaluator.metricsevaluator seqgra.evaluator.predictevaluator seqgra.evaluator.prevaluator seqgra.evaluator.rocevaluator seqgra.evaluator.sis seqgra.evaluator.sis.sis seqgra.evaluator.sisevaluator seqgra.idresolver seqgra.learner seqgra.learner.bayes seqgra.learner.bayes.bayeshelper seqgra.learner.bayes.bayeslearner seqgra.learner.dna seqgra.learner.dnahelper seqgra.learner.learner seqgra.learner.protein seqgra.learner.proteinhelper seqgra.learner.tensorflow seqgra.learner.tensorflow.kerascallback seqgra.learner.tensorflow.kerashelper seqgra.learner.tensorflow.keraslearner seqgra.learner.torch seqgra.learner.torch.torchdataset seqgra.learner.torch.torchhelper seqgra.learner.torch.torchlearner seqgra.misc seqgra.model seqgra.model.data seqgra.model.data.alphabetdistribution seqgra.model.data.background seqgra.model.data.condition seqgra.model.data.datadefinition seqgra.model.data.datageneration seqgra.model.data.operation seqgra.model.data.rule seqgra.model.data.sequenceelement seqgra.model.data.spacingconstraint seqgra.model.model seqgra.model.model.architecture seqgra.model.model.modeldefinition seqgra.model.model.operation seqgra.parser seqgra.parser.datadefinitionparser seqgra.parser.modeldefinitionparser seqgra.parser.xmldatadefinitionparser seqgra.parser.xmlhelper seqgra.parser.xmlmodeldefinitionparser seqgra.schema seqgra.seqgra seqgra.seqgraa seqgra.seqgrae seqgra.seqgras seqgra.simulator seqgra.simulator.backgroundgenerator seqgra.simulator.example seqgra.simulator.examplegenerator seqgra.simulator.heatmap seqgra.simulator.heatmap.heatmap seqgra.simulator.motif seqgra.simulator.motif.ess seqgra.simulator.motif.kld seqgra.simulator.motif.motifinfo seqgra.simulator.simulator seqgra.writer seqgra.writer.datadefinitionwriter seqgra.writer.modeldefinitionwriter seqgra.writer.xmldatadefinitionwriter seqgra.writer.xmlmodeldefinitionwriter

modules() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) MotifInfo (class in seqgra.simulator.motif.motifinfo) MULTI_CLASS_CLASSIFICATION (TaskType attribute) MULTI_CLASS_CLASSIFICATION_LOSSES (KerasHelper attribute) (TorchHelper attribute) MULTI_LABEL_CLASSIFICATION (TaskType attribute) MULTI_LABEL_CLASSIFICATION_LOSSES (KerasHelper attribute) (TorchHelper attribute) MultiClassClassificationLearner (class in seqgra.learner.learner) MultiClassDataSet (class in seqgra.learner.torch.torchdataset) MultiLabelClassificationLearner (class in seqgra.learner.learner) MultiLabelDataSet (class in seqgra.learner.torch.torchdataset) MULTIPLE_REGRESSION (TaskType attribute) MULTIPLE_REGRESSION_LOSSES (KerasHelper attribute) (TorchHelper attribute) MultipleRegressionLearner (class in seqgra.learner.learner) MULTIVARIATE_REGRESSION (TaskType attribute) MULTIVARIATE_REGRESSION_LOSSES (KerasHelper attribute) (TorchHelper attribute) MultivariateRegressionLearner (class in seqgra.learner.learner)

N

name (ModelDefinition attribute) name() (EBAvgPool2d method), [1] (EBConv2d method), [1] (EBLinear method), [1] named_buffers() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) named_children() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) named_modules() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) named_parameters() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method)

needs_input_grad (EBAvgPool2d attribute), [1] (EBConv2d attribute), [1] (EBLinear attribute), [1] next_functions (EBAvgPool2d attribute), [1] (EBConv2d attribute), [1] (EBLinear attribute), [1] non_differentiable (EBAvgPool2d attribute), [1] (EBConv2d attribute), [1] (EBLinear attribute), [1] NONLINEAR_INTEGRATED_GRADIENTS (EvaluatorID attribute) NonlinearIntegratedGradientEvaluator (class in seqgra.evaluator.gradientbased.nonlinearintegratedgradientevaluator) NonlinearIntegrateGradExplainer (class in seqgra.evaluator.explainer.backprop) normalize_probabilities() (KmerBasedSequenceElement method) (MatrixBasedSequenceElement method) (SequenceElement method) normalize_pwm_score() (BayesOptimalHelper static method) num_non_trainable_params (ModelSize attribute) num_trainable_params (ModelSize attribute) numpy_version (DataSessionInfo attribute) (ModelSessionInfo attribute)

O

obtain_feature_attribution() (in module seqgra.seqgraa) occlusion() (in module seqgra.evaluator.explainer.occlusion) on_batch_begin() (LastEpochCallback method) on_batch_end() (LastEpochCallback method) on_epoch_begin() (LastEpochCallback method) on_epoch_end() (LastEpochCallback method) on_predict_batch_begin() (LastEpochCallback method) on_predict_batch_end() (LastEpochCallback method) on_predict_begin() (LastEpochCallback method) on_predict_end() (LastEpochCallback method) on_test_batch_begin() (LastEpochCallback method) on_test_batch_end() (LastEpochCallback method) on_test_begin() (LastEpochCallback method) on_test_end() (LastEpochCallback method) on_train_batch_begin() (LastEpochCallback method)

on_train_batch_end() (LastEpochCallback method) on_train_begin() (LastEpochCallback method) on_train_end() (LastEpochCallback method) Operation (class in seqgra.model.model.operation) optimizer (Learner attribute) (MultiClassClassificationLearner attribute) (MultiLabelClassificationLearner attribute) (MultipleRegressionLearner attribute) (MultivariateRegressionLearner attribute) optimizer_hyperparameters (ModelDefinition attribute) ordering_over_entire_backselect (SISResult attribute) output_dir (Learner attribute) (MultiClassClassificationLearner attribute) (MultiLabelClassificationLearner attribute) (MultipleRegressionLearner attribute) (MultivariateRegressionLearner attribute)

P

parameters() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) parse_annotations_data() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) parse_data_definition_file() (in module seqgra.seqgrae) parse_examples_data() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) parse_model_definition_file() (in module seqgra.seqgrae) PatternLRPExplainer (class in seqgra.evaluator.explainer.patterns) PatternNetExplainer (class in seqgra.evaluator.explainer.patterns) PerturbExplainer (class in seqgra.evaluator.explainer.perturbation) PixelShuffleBlock (class in seqgra.evaluator.explainer.real_time.pytorch_fixes) PixelShuffleBlock.to() (in module seqgra.evaluator.explainer.real_time.pytorch_fixes), [1], [2], [3] PositionType (class in seqgra.constants) PostprocessingOperation (class in seqgra.model.data.operation) ppm_to_pwm() (BayesOptimalHelper static method) PR (ComparatorID attribute) (EvaluatorID attribute) PRComparator (class in seqgra.comparator.prcomparator) PREDICT (EvaluatorID attribute)

predict() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalHelper static method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasHelper static method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchHelper static method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) PredictEvaluator (class in seqgra.evaluator.predictevaluator) prepare_model() (in module seqgra.seqgraa) prepare_path() (MiscHelper static method) PREvaluator (class in seqgra.evaluator.prevaluator) print_model_summary() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalHelper static method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasHelper static method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchHelper static method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) print_progress_bar() (MiscHelper static method) ProbabilisticToken (class in seqgra.schema) probability (ProbabilisticToken attribute) produce_masked_inputs() (in module seqgra.evaluator.sis.sis) PROTEIN (SequenceSpaceType attribute) ProteinHelper (class in seqgra.learner.proteinhelper) ProteinMultiClassClassificationLearner (class in seqgra.learner.protein) ProteinMultiLabelClassificationLearner (class in seqgra.learner.protein) python_version (DataSessionInfo attribute) (ModelSessionInfo attribute)

R

read_config_file() (MiscHelper static method) read_float_node() (XMLHelper static method) read_immediate_text_node() (XMLHelper static method) read_int_node() (XMLHelper static method) read_text_node() (XMLHelper static method) RealTimeSaliencyExplainer (class in seqgra.evaluator.explainer.real_time.saliency_eval) register_backward_hook() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) register_buffer() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) register_forward_hook() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) register_forward_pre_hook() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) register_full_backward_hook() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method)

register_hook() (EBAvgPool2d method), [1] (EBConv2d method), [1] (EBLinear method), [1] register_parameter() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) replace_first() (in module seqgra.evaluator.explainer.feedback) (in module seqgra.evaluator.gradientbased.feedbackevaluator) replace_mask() (in module seqgra.evaluator.explainer.feedback) (in module seqgra.evaluator.gradientbased.feedbackevaluator) requires_grad (EBAvgPool2d attribute), [1] (EBConv2d attribute), [1] (EBLinear attribute), [1] requires_grad_() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) resnet50encoder() (in module seqgra.evaluator.explainer.real_time.resnet_encoder) ResNetEncoder (class in seqgra.evaluator.explainer.real_time.resnet_encoder) ResNetEncoder.to() (in module seqgra.evaluator.explainer.real_time.resnet_encoder), [1], [2], [3] ROC (ComparatorID attribute) (EvaluatorID attribute) ROCComparator (class in seqgra.comparator.roccomparator) ROCEvaluator (class in seqgra.evaluator.rocevaluator) Rule (class in seqgra.model.data.rule) run_seqgra() (in module seqgra.seqgra) run_seqgra_attribution() (in module seqgra.seqgraa) run_seqgra_ensemble() (in module seqgra.seqgrae) run_seqgra_summary() (in module seqgra.seqgras)

S

SALIENCY (EvaluatorID attribute) SaliencyEvaluator (class in seqgra.evaluator.gradientbased.saliencyevaluator) SaliencyExplainer (class in seqgra.evaluator.explainer.backprop) SaliencyModel (class in seqgra.evaluator.explainer.real_time.pytorch_fixes) SaliencyModel.to() (in module seqgra.evaluator.explainer.real_time.pytorch_fixes), [1], [2], [3] sanitize_id() (MiscHelper static method) save_for_backward() (EBAvgPool2d method), [1] (EBConv2d method), [1] (EBLinear method), [1] save_model() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasHelper static method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchHelper static method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) saved_tensors (EBAvgPool2d attribute), [1] (EBConv2d attribute), [1] (EBLinear attribute), [1] saved_variables (EBAvgPool2d attribute), [1] (EBConv2d attribute), [1] (EBLinear attribute), [1] score_example() (BayesOptimalHelper static method) se_to_pwm() (BayesOptimalHelper static method) seed (ModelDefinition attribute) select_examples() (AbstractDifferenceGradientEvaluator method) (AbstractGradientEvaluator method) (ContrastiveExcitationBackpropEvaluator method) (DeconvEvaluator method) (DeepLiftEvaluator method) (DifferenceGradientEvaluator method) (Evaluator method) (ExcitationBackpropEvaluator method) (FeatureImportanceEvaluator method) (FeedbackEvaluator method) (GradCamGradientEvaluator method) (GradientBasedEvaluator method) (GradientEvaluator method) (GradientxInputEvaluator method) (GuidedBackpropEvaluator method) (IntegratedGradientEvaluator method) (MetricsEvaluator method) (NonlinearIntegratedGradientEvaluator method) (PredictEvaluator method) (PREvaluator method) (ROCEvaluator method) (SaliencyEvaluator method) (SISEvaluator method) (SmoothGradEvaluator method) select_n_examples() (AbstractDifferenceGradientEvaluator method) (AbstractGradientEvaluator method) (ContrastiveExcitationBackpropEvaluator method) (DeconvEvaluator method) (DeepLiftEvaluator method) (DifferenceGradientEvaluator method) (Evaluator method) (ExcitationBackpropEvaluator method) (FeatureImportanceEvaluator method) (FeedbackEvaluator method) (GradCamGradientEvaluator method) (GradientBasedEvaluator method) (GradientEvaluator method) (GradientxInputEvaluator method) (GuidedBackpropEvaluator method) (IntegratedGradientEvaluator method) (MetricsEvaluator method) (NonlinearIntegratedGradientEvaluator method) (PredictEvaluator method) (PREvaluator method) (ROCEvaluator method) (SaliencyEvaluator method) (SISEvaluator method) (SmoothGradEvaluator method) seqgra module seqgra.comparator module seqgra.comparator.comparator module seqgra.comparator.curvetablecomparator module seqgra.comparator.fietablecomparator module seqgra.comparator.prcomparator module seqgra.comparator.roccomparator module seqgra.comparator.tablecomparator module seqgra.constants module seqgra.evaluator module seqgra.evaluator.evaluator module seqgra.evaluator.explainer.backprop module seqgra.evaluator.explainer.deeplift module seqgra.evaluator.explainer.ebp module seqgra.evaluator.explainer.ebp.ebp module seqgra.evaluator.explainer.ebp.functions module seqgra.evaluator.explainer.feedback module seqgra.evaluator.explainer.gradcam module seqgra.evaluator.explainer.occlusion module seqgra.evaluator.explainer.path module seqgra.evaluator.explainer.patterns module seqgra.evaluator.explainer.perturbation module seqgra.evaluator.explainer.real_time module seqgra.evaluator.explainer.real_time.pytorch_fixes module seqgra.evaluator.explainer.real_time.resnet_encoder module seqgra.evaluator.explainer.real_time.saliency_eval module seqgra.evaluator.gradientbased module seqgra.evaluator.gradientbased.abstractdifferencegradientevaluator module seqgra.evaluator.gradientbased.abstractgradientevaluator module seqgra.evaluator.gradientbased.contrastiveexcitationbackpropevaluator module seqgra.evaluator.gradientbased.deconvevaluator module seqgra.evaluator.gradientbased.deepliftevaluator module seqgra.evaluator.gradientbased.differencegradientevaluator module seqgra.evaluator.gradientbased.ebphelper module seqgra.evaluator.gradientbased.excitationbackpropevaluator module seqgra.evaluator.gradientbased.feedbackevaluator module seqgra.evaluator.gradientbased.gradcamgradientevaluator module seqgra.evaluator.gradientbased.gradientbasedevaluator module seqgra.evaluator.gradientbased.gradientevaluator module seqgra.evaluator.gradientbased.gradientxinputevaluator module seqgra.evaluator.gradientbased.guidedbackpropevaluator module seqgra.evaluator.gradientbased.integratedgradientevaluator module seqgra.evaluator.gradientbased.nonlinearintegratedgradientevaluator module seqgra.evaluator.gradientbased.saliencyevaluator module seqgra.evaluator.gradientbased.smoothgradevaluator module seqgra.evaluator.metricsevaluator module seqgra.evaluator.predictevaluator module seqgra.evaluator.prevaluator module seqgra.evaluator.rocevaluator module seqgra.evaluator.sis module

seqgra.evaluator.sis.sis module seqgra.evaluator.sisevaluator module seqgra.idresolver module seqgra.learner module seqgra.learner.bayes module seqgra.learner.bayes.bayeshelper module seqgra.learner.bayes.bayeslearner module seqgra.learner.dna module seqgra.learner.dnahelper module seqgra.learner.learner module seqgra.learner.protein module seqgra.learner.proteinhelper module seqgra.learner.tensorflow module seqgra.learner.tensorflow.kerascallback module seqgra.learner.tensorflow.kerashelper module seqgra.learner.tensorflow.keraslearner module seqgra.learner.torch module seqgra.learner.torch.torchdataset module seqgra.learner.torch.torchhelper module seqgra.learner.torch.torchlearner module seqgra.misc module seqgra.model module seqgra.model.data module seqgra.model.data.alphabetdistribution module seqgra.model.data.background module seqgra.model.data.condition module seqgra.model.data.datadefinition module seqgra.model.data.datageneration module seqgra.model.data.operation module seqgra.model.data.rule module seqgra.model.data.sequenceelement module seqgra.model.data.spacingconstraint module seqgra.model.model module seqgra.model.model.architecture module seqgra.model.model.modeldefinition module seqgra.model.model.operation module seqgra.parser module seqgra.parser.datadefinitionparser module seqgra.parser.modeldefinitionparser module seqgra.parser.xmldatadefinitionparser module seqgra.parser.xmlhelper module seqgra.parser.xmlmodeldefinitionparser module seqgra.schema module seqgra.seqgra module seqgra.seqgraa module seqgra.seqgrae module seqgra.seqgras module seqgra.simulator module seqgra.simulator.backgroundgenerator module seqgra.simulator.example module seqgra.simulator.examplegenerator module seqgra.simulator.heatmap module seqgra.simulator.heatmap.heatmap module seqgra.simulator.motif module seqgra.simulator.motif.ess module seqgra.simulator.motif.kld module seqgra.simulator.motif.motifinfo module seqgra.simulator.simulator module seqgra.writer module seqgra.writer.datadefinitionwriter module seqgra.writer.modeldefinitionwriter module seqgra.writer.xmldatadefinitionwriter module seqgra.writer.xmlmodeldefinitionwriter module seqgra_version (DataSessionInfo attribute) (ModelSessionInfo attribute) sequence_path() (in module seqgra.evaluator.explainer.path) (NonlinearIntegratedGradientEvaluator static method) sequence_space (ModelDefinition attribute) SequenceElement (class in seqgra.model.data.sequenceelement) SequenceSpaceType (class in seqgra.constants) set_materialize_grads() (EBAvgPool2d method), [1] (EBConv2d method), [1] (EBLinear method), [1] set_model() (LastEpochCallback method) set_params() (LastEpochCallback method) set_seed() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalHelper static method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasHelper static method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchHelper static method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method) share_memory() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) shortest_path() (in module seqgra.evaluator.explainer.path) (NonlinearIntegratedGradientEvaluator static method) SimpleCNNBlock() (in module seqgra.evaluator.explainer.real_time.pytorch_fixes) SimpleUpsamplerSubpixel() (in module seqgra.evaluator.explainer.real_time.pytorch_fixes) simulate_data() (Simulator method) Simulator (class in seqgra.simulator.simulator) SIS (EvaluatorID attribute) sis (SISResult attribute) sis_collection() (in module seqgra.evaluator.sis.sis) SISEvaluator (class in seqgra.evaluator.sisevaluator) SISResult (class in seqgra.evaluator.sis.sis) SMOOTH_GRAD (EvaluatorID attribute) SmoothGradEvaluator (class in seqgra.evaluator.gradientbased.smoothgradevaluator) SmoothGradExplainer (class in seqgra.evaluator.explainer.backprop) SpacingConstraint (class in seqgra.model.data.spacingconstraint) state_dict() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) subsample_data_set() (in module seqgra.seqgrae) subsample_experimental_data() (in module seqgra.seqgrae)

T

T_destination (Bottleneck attribute) (PixelShuffleBlock attribute) (ResNetEncoder attribute) (SaliencyModel attribute) (UNetUpsampler attribute) TABLE (ComparatorID attribute) TableComparator (class in seqgra.comparator.tablecomparator) task (ModelDefinition attribute) TaskType (class in seqgra.constants) TENSORFLOW (LibraryType attribute) TEST (DataSet attribute) to() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) to_save (EBAvgPool2d attribute), [1] (EBConv2d attribute), [1] (EBLinear attribute), [1] token (ProbabilisticToken attribute) TORCH (LibraryType attribute) TorchDNAMultiClassClassificationLearner (class in seqgra.learner.torch.torchlearner) TorchDNAMultiLabelClassificationLearner (class in seqgra.learner.torch.torchlearner) TorchHelper (class in seqgra.learner.torch.torchhelper) TorchProteinMultiClassClassificationLearner (class in seqgra.learner.torch.torchlearner) TorchProteinMultiLabelClassificationLearner (class in seqgra.learner.torch.torchlearner) train() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method) train_model() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalHelper static method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (DNAMultiClassClassificationLearner method) (DNAMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasHelper static method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Learner method) (MultiClassClassificationLearner method) (MultiLabelClassificationLearner method) (MultipleRegressionLearner method) (MultivariateRegressionLearner method) (ProteinMultiClassClassificationLearner method) (ProteinMultiLabelClassificationLearner method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchHelper static method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method)

train_model_basic() (TorchHelper static method) training (Bottleneck attribute) TRAINING (DataSet attribute) training (PixelShuffleBlock attribute) (ResNetEncoder attribute) (SaliencyModel attribute) (UNetUpsampler attribute) training_process_hyperparameters (ModelDefinition attribute) tv_norm() (in module seqgra.evaluator.explainer.perturbation) type() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method)

U

UNetUpsampler (class in seqgra.evaluator.explainer.real_time.pytorch_fixes)

UNetUpsampler.to() (in module seqgra.evaluator.explainer.real_time.pytorch_fixes), [1], [2], [3]

V

validate() (XMLDataDefinitionParser method) (XMLModelDefinitionParser method) validate_data (Learner attribute) (MultiClassClassificationLearner attribute) (MultiLabelClassificationLearner attribute) (MultipleRegressionLearner attribute) (MultivariateRegressionLearner attribute)

VALIDATION (DataSet attribute) values_over_entire_backselect (SISResult attribute) VanillaDifferenceGradExplainer (class in seqgra.evaluator.explainer.backprop) VanillaGradExplainer (class in seqgra.evaluator.explainer.backprop)

W

write_analysis_script() (in module seqgra.seqgrae) write_data_definition_file() (in module seqgra.seqgrae) write_data_definition_files() (in module seqgra.seqgrae) write_data_definition_to_file() (DataDefinitionWriter static method) (XMLDataDefinitionWriter static method) write_model_definition_file() (in module seqgra.seqgrae) write_model_definition_files() (in module seqgra.seqgrae) write_model_definition_to_file() (ModelDefinitionWriter static method) (XMLModelDefinitionWriter static method) write_session_info() (BayesOptimalDNAMultiClassClassificationLearner method) (BayesOptimalDNAMultiLabelClassificationLearner method) (BayesOptimalHelper static method) (BayesOptimalProteinMultiClassClassificationLearner method) (BayesOptimalProteinMultiLabelClassificationLearner method) (KerasDNAMultiClassClassificationLearner method) (KerasDNAMultiLabelClassificationLearner method) (KerasHelper static method) (KerasProteinMultiClassClassificationLearner method) (KerasProteinMultiLabelClassificationLearner method) (Simulator method) (TorchDNAMultiClassClassificationLearner method) (TorchDNAMultiLabelClassificationLearner method) (TorchHelper static method) (TorchProteinMultiClassClassificationLearner method) (TorchProteinMultiLabelClassificationLearner method)

X

x (AnnotatedExample attribute) (AnnotatedExampleSet attribute) (Example attribute) (ExampleSet attribute) XMLDataDefinitionParser (class in seqgra.parser.xmldatadefinitionparser) XMLDataDefinitionWriter (class in seqgra.writer.xmldatadefinitionwriter) XMLHelper (class in seqgra.parser.xmlhelper)

XMLModelDefinitionParser (class in seqgra.parser.xmlmodeldefinitionparser) XMLModelDefinitionWriter (class in seqgra.writer.xmlmodeldefinitionwriter) xpu() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method)

Y

y (AnnotatedExample attribute) (AnnotatedExampleSet attribute) (AnnotationSet attribute) (Example attribute) (ExampleSet attribute)

Z

zero_grad() (Bottleneck method) (PixelShuffleBlock method) (ResNetEncoder method) (SaliencyModel method) (UNetUpsampler method)