Index

A

accum_opt() (in module amber.plots.plotsV1) add_layer() (ModelSpace method) add_state() (ModelSpace method) ALPHABET_TO_ARRAY (EncodedGenome attribute) (EncodedSequence property) Amber (class in amber.wrapper) amber.architect.buffer module amber.architect.commonOps module amber.architect.controller module amber.architect.controller.generalController module amber.architect.controller.multiioController module amber.architect.controller.operationController module amber.architect.controller.zeroShotController module amber.architect.manager module amber.architect.modelSpace module amber.architect.reward module amber.architect.store module amber.architect.trainEnv module amber.bootstrap module amber.bootstrap.analyze module amber.bootstrap.explore_lambda module amber.bootstrap.gold_standard module amber.bootstrap.grid_search module amber.bootstrap.mock_manager module amber.bootstrap.simple_conv1d_space module amber.getter module amber.modeler.architectureDecoder module amber.modeler.child module amber.modeler.dag module

amber.modeler.enasModeler module amber.modeler.kerasModeler module amber.objective module amber.objective.generalObjFunc module amber.objective.generalObjMath module amber.objective.graph module amber.objective.motif module amber.objective.motifUtils module amber.plots.heatmap2 module amber.plots.ontology module amber.plots.plot_all_stats module amber.plots.plotsV1 module amber.resources module amber.utils.data_parser module amber.utils.io module amber.utils.logging module amber.utils.motif module amber.utils.saliency module amber.utils.sampler module amber.utils.sequences module amber.utils.tensorflowMem module amber.wrapper module AmberSpecifications (class in amber.wrapper) annotate_probs_list() (in module amber.utils.io) approx_grad() (in module amber.utils.saliency) approx_grad_array() (in module amber.utils.saliency) approx_hessian() (in module amber.utils.saliency) approx_hessian_array() (in module amber.utils.saliency) AuxilaryAcc (class in amber.objective.generalObjFunc)

B

BaseController (class in amber.architect.controller) (class in amber.architect.controller.generalController) BaseNetworkManager (class in amber.architect.manager) basewise_bits() (in module amber.objective.motifUtils) batch_norm1d() (in module amber.architect.commonOps) BatchedBioIntervalSequence (class in amber.utils.sampler) BatchedBioIntervalSequenceGenerator (class in amber.utils.sampler) BatchedHDF5Generator (class in amber.utils.sampler) batchify() (in module amber.architect.commonOps) bias_var_decomp() (in module amber.objective.generalObjMath) BioIntervalGenerator (class in amber.utils.sampler)

BioIntervalSequence (class in amber.utils.sampler) BioIntervalSource (class in amber.utils.sampler) branch_to_layer (BranchedModelSpace property) BranchedModelSpace (class in amber.architect.modelSpace) Buffer (class in amber.architect.buffer) build() (ComputationNode method) build_actor() (in module amber.architect.controller.operationController) build_multi_gpu_sequential_model() (in module amber.modeler.kerasModeler) build_multi_gpu_sequential_model_from_string() (in module amber.modeler.kerasModeler) build_sequential_model() (in module amber.modeler.kerasModeler) build_sequential_model_from_string() (in module amber.modeler.kerasModeler)

C

clean() (ControllerTrainEnvironment method) close() (BatchedBioIntervalSequence method) (BatchedHDF5Generator method) (EncodedHDF5Genome method) close_handler() (DistributedGeneralManager method) combine_input_blocks() (in module amber.bootstrap.grid_search) compare_motif_diff_size() (in module amber.objective.motifUtils) compile() (DenseAddOutputChild method) (EnasAnnModel method) (EnasCnnModel method) ComputationNode (class in amber.modeler.dag) compute_entropy() (in module amber.architect.trainEnv)

connect_controller() (EnasAnnDAG method) controller (AmberSpecifications property) ControllerTrainEnvironment (class in amber.architect.trainEnv) convert_adjacency_to_knowledge() (GraphKnowledgeHessFunc method) convert_arc_to_onehot() (GeneralController static method), [1] convert_ppm_to_pwm() (in module amber.objective.motifUtils) convertlog2freq() (in module amber.utils.motif) coords_are_valid() (Genome method) (Sequence method) count_model_params() (in module amber.architect.commonOps) create_bias() (in module amber.architect.commonOps) create_conv_from_motif() (in module amber.objective.motifUtils) create_weight() (in module amber.architect.commonOps)

D

DAG (class in amber.modeler.dag) DAGModelBuilder (class in amber.modeler.enasModeler) DataToParse (class in amber.getter) decode() (MultiIOArchitecture method) (ResConvNetArchitecture method) delete_layer() (ModelSpace method) delete_state() (ModelSpace method)

DenseAddOutputChild (class in amber.modeler.child) discount_rewards() (Buffer method) DistributedGeneralManager (class in amber.architect.manager) draw_dnalogo_matplot() (in module amber.utils.motif) draw_dnalogo_Rscript() (in module amber.utils.motif) draw_logo() (in module amber.utils.motif) draw_path() (Scale method) dump_buffer() (MultiManagerBuffer method)

E

EnasAnnDAG (class in amber.modeler.dag) EnasAnnModel (class in amber.modeler.child) EnasAnnModelBuilder (class in amber.modeler.enasModeler) EnasCnnModel (class in amber.modeler.child) EnasCnnModelBuilder (class in amber.modeler.enasModeler) EnasConv1dDAG (class in amber.modeler.dag) EnasConv1DwDataDescrption (class in amber.modeler.dag) EnasTrainEnv (class in amber.architect.trainEnv) encode() (EncodedSequence method) (Encoding method) (ResConvNetArchitecture method)

EncodedGenome (class in amber.utils.sequences) EncodedHDF5Genome (class in amber.utils.sequences) EncodedSequence (class in amber.utils.sequences) Encoding (class in amber.utils.sequences) evaluate() (DenseAddOutputChild method) (EnasAnnModel method) (EnasCnnModel method) evaluate_ph() (EnasAnnModel method) evaluate_pipe() (EnasAnnModel method)

F

factorized_reduction_layer() (KerasResidualCnnBuilder static method) fasta_reader() (in module amber.utils.data_parser) fetch_seq() (in module amber.utils.data_parser) fetch_seq_pygr() (in module amber.utils.data_parser) finish_path() (Buffer method) (MultiManagerBuffer method) fit() (DenseAddOutputChild method) (EnasAnnModel method) (EnasCnnModel method)

fit_generator() (EnasAnnModel method) (EnasCnnModel method) fit_ph() (EnasAnnModel method) fit_pipe() (EnasAnnModel method) from_dict() (Amber method) (AmberSpecifications method) (ModelSpace static method)

G

GeneralChild (class in amber.modeler.child) GeneralController (class in amber.architect.controller) (class in amber.architect.controller.generalController) GeneralKnowledgeObjectiveFunction (class in amber.objective.generalObjFunc) GeneralManager (class in amber.architect.manager) Genome (class in amber.utils.sequences) get_action() (GeneralController method), [1] (OperationController method), [1] (ZeroShotController method), [1] get_advantage() (ReplayBuffer method) get_buffer() (in module amber.architect.buffer) get_config() (in module amber.bootstrap.analyze) get_controller() (in module amber.bootstrap.explore_lambda) (in module amber.getter) get_controller_history() (in module amber.architect.trainEnv) get_controller_states() (in module amber.architect.trainEnv) get_dag() (in module amber.modeler.dag) get_data() (Buffer method) (in module amber.bootstrap.simple_conv1d_space) (MultiManagerBuffer method) (ReplayBuffer method) get_data_from_fasta_sequence() (in module amber.utils.data_parser) get_data_from_simdata() (in module amber.utils.data_parser) get_default_mock_reward_fn() (in module amber.bootstrap.mock_manager) get_environment() (in module amber.bootstrap.explore_lambda) get_feed_dict() (GraphKnowledgeHessFunc method) get_generator_from_label_df() (in module amber.utils.data_parser) get_gold_standard() (in module amber.bootstrap.gold_standard) get_gold_standard_arc_seq() (in module amber.bootstrap.gold_standard) get_hess_op() (GraphKnowledgeHessFunc method) get_indexer() (in module amber.architect.controller.operationController) get_keras_train_ops() (in module amber.architect.commonOps) get_kl_divergence_n_entropy() (in module amber.architect.commonOps) get_knowledge_fn() (in module amber.getter) get_layer() (in module amber.modeler.dag) get_layer_shortname() (in module amber.architect.modelSpace) get_manager() (in module amber.getter) get_matched_model_weights() (MotifKLDivergence method) get_mock_manager() (in module amber.bootstrap.explore_lambda) get_mock_reward() (in module amber.bootstrap.mock_manager) get_mock_reward_fn() (in module amber.bootstrap.mock_manager)

get_model_and_io_nodes() (in module amber.getter) get_model_space() (in module amber.getter) get_model_space_generator() (in module amber.bootstrap.grid_search) get_modeler() (in module amber.getter) get_motif_dot_prod_for_label() (MotifSaliency method) get_motif_enrichment_for_label() (MotifSaliency method) get_obj_val() (GeneralKnowledgeObjectiveFunction method) get_optimizer() (in module amber.architect.controller.operationController) get_out_filters() (KerasResidualCnnBuilder static method) get_random_model_states() (ModelSpace method) get_rating() (in module amber.bootstrap.analyze) get_reward_fn() (in module amber.getter) get_rewards() (BaseNetworkManager method) (DistributedGeneralManager method) (GeneralManager method) (MockManager method) get_seq_chunks() (in module amber.objective.motifUtils) get_sequence_from_coords() (EncodedGenome method) (EncodedHDF5Genome method) (EncodedSequence method) (Genome method) (HDF5Genome method) (Sequence method) get_session() (in module amber.utils.tensorflowMem) get_session2() (in module amber.utils.tensorflowMem) get_space_size() (ModelSpace method) get_state_space() (in module amber.bootstrap.simple_conv1d_space) get_store_fn() (in module amber.architect.store) get_tf_layer() (in module amber.architect.commonOps) get_tf_loss() (in module amber.architect.commonOps) get_tf_metrics() (in module amber.architect.commonOps) get_train_env() (in module amber.getter) get_weights() (EnasAnnModel method) (EnasCnnModel method) (GeneralController method), [1] GraphHierarchyTree (class in amber.objective.graph) GraphHierarchyTreeAuxLoss (class in amber.objective.graph) GraphKnowledgeHessBias (class in amber.objective.graph) GraphKnowledgeHessFunc (class in amber.objective.graph) grid_search() (in module amber.bootstrap.grid_search) group_motif_by_factor() (in module amber.objective.motifUtils) gui_mapper() (in module amber.getter)

H

HDF5Genome (class in amber.utils.sequences) heatmap2() (in module amber.plots.heatmap2)

heatscatter() (in module amber.plots.plotsV1) heatscatter_sns() (in module amber.plots.plotsV1) hess_estimator() (GraphKnowledgeHessFunc method)

I

ID2arch() (in module amber.bootstrap.gold_standard)

InputBlockAuxLossDAG (class in amber.modeler.dag) InputBlockDAG (class in amber.modeler.dag)

K

KerasBranchModelBuilder (class in amber.modeler.kerasModeler) KerasModelBuilder (class in amber.modeler.kerasModeler) KerasMultiIOModelBuilder (class in amber.modeler.kerasModeler) KerasResidualCnnBuilder (class in amber.modeler.kerasModeler) KEY_ATTR_MAP (AmberSpecifications attribute) knowledge_encoder() (AuxilaryAcc method) (GeneralKnowledgeObjectiveFunction method) (GraphHierarchyTree method) (GraphKnowledgeHessFunc method) (MotifKLDivergence method) (MotifSaliency method)

KnowledgeReward (class in amber.architect.reward)

L

layer_to_branch (BranchedModelSpace property) load_binding_motif_pssm() (in module amber.utils.motif) load_data_dict() (in module amber.getter) load_weights() (EnasAnnModel method) (EnasCnnModel method) (GeneralController method), [1]

LossAucReward (class in amber.architect.reward) LossReward (class in amber.architect.reward) lstm() (in module amber.architect.commonOps) lt_abuffer (MultiManagerBuffer property) lt_adbuffer (MultiManagerBuffer property) lt_pbuffer (MultiManagerBuffer property)

M

main() (in module amber.bootstrap.analyze) (in module amber.bootstrap.explore_lambda) make_output_annot() (in module amber.objective.motifUtils) manager (AmberSpecifications property) matrix_to_seq() (in module amber.utils.data_parser) min() (LossAucReward method) MockManager (class in amber.bootstrap.mock_manager) MockReward() (in module amber.architect.reward) model_encoder() (AuxilaryAcc method) (GeneralKnowledgeObjectiveFunction method) (GraphHierarchyTree method) (GraphHierarchyTreeAuxLoss method) (GraphKnowledgeHessFunc method) (MotifKLDivergence method) (MotifSaliency method) ModelBuilder (class in amber.modeler.enasModeler) ModelSpace (class in amber.architect.modelSpace) module amber.architect.buffer amber.architect.commonOps amber.architect.controller amber.architect.controller.generalController amber.architect.controller.multiioController amber.architect.controller.operationController amber.architect.controller.zeroShotController amber.architect.manager amber.architect.modelSpace amber.architect.reward amber.architect.store amber.architect.trainEnv amber.bootstrap amber.bootstrap.analyze amber.bootstrap.explore_lambda amber.bootstrap.gold_standard amber.bootstrap.grid_search amber.bootstrap.mock_manager amber.bootstrap.simple_conv1d_space amber.getter amber.modeler.architectureDecoder amber.modeler.child amber.modeler.dag amber.modeler.enasModeler amber.modeler.kerasModeler amber.objective amber.objective.generalObjFunc amber.objective.generalObjMath amber.objective.graph amber.objective.motif amber.objective.motifUtils amber.plots.heatmap2 amber.plots.ontology amber.plots.plot_all_stats amber.plots.plotsV1 amber.resources amber.utils.data_parser amber.utils.io amber.utils.logging amber.utils.motif amber.utils.saliency amber.utils.sampler amber.utils.sequences amber.utils.tensorflowMem amber.wrapper

MotifKLDivergence (class in amber.objective.motif) MotifSaliency (class in amber.objective.motif) multi_distplot_sns() (in module amber.plots.plotsV1) MultiInputController (class in amber.architect.controller) (class in amber.architect.controller.multiioController) MultiIOArchitecture (class in amber.modeler.architectureDecoder) MultiIOController (class in amber.architect.controller) (class in amber.architect.controller.multiioController) MultiManagerBuffer (class in amber.architect.buffer) MultiManagerEnvironment (class in amber.architect.trainEnv) multinomial_KL_divergence() (in module amber.objective.generalObjMath)

N

numpy_shuffle_in_unison() (in module amber.architect.commonOps)

O

on_epoch_end() (BatchedBioIntervalSequence method) (BatchedBioIntervalSequenceGenerator method) one_hot_encoder() (in module amber.architect.controller.operationController)

Operation (in module amber.architect.modelSpace) OperationController (class in amber.architect.controller) (class in amber.architect.controller.operationController)

P

padding_is_valid() (BioIntervalSource method) ParallelMultiManagerEnvironment (class in amber.architect.trainEnv) parse_action_str() (in module amber.architect.buffer) (in module amber.architect.controller.operationController) parse_action_str_squeezed() (in module amber.architect.buffer) plot() (in module amber.bootstrap.analyze) (in module amber.bootstrap.explore_lambda) plot_action_weights() (in module amber.plots.plotsV1) plot_all_stats() (in module amber.plots.plot_all_stats) plot_controller_hidden_states() (in module amber.plots.plotsV1) plot_controller_performance() (in module amber.plots.plotsV1) plot_environment_entropy() (in module amber.plots.plotsV1) plot_hessian() (in module amber.plots.plotsV1)

plot_nx_dag() (in module amber.plots.ontology) plot_sequence_importance() (in module amber.plots.plotsV1) plot_stats() (in module amber.plots.plotsV1) plot_stats2() (in module amber.plots.plotsV1) plot_training_history() (in module amber.plots.plotsV1) plot_wiring_weights() (in module amber.plots.plotsV1) predict() (DenseAddOutputChild method) (EnasAnnModel method) (EnasCnnModel method) predict_ph() (EnasAnnModel method) predict_pipe() (EnasAnnModel method) print_gold_standard() (in module amber.bootstrap.analyze) print_state_space() (ModelSpace method) proximal_policy_optimization_loss() (in module amber.architect.commonOps)

R

rand_jitter() (in module amber.plots.plotsV1) read_action_weights() (in module amber.utils.io) read_action_weights_old() (in module amber.utils.io) read_file() (in module amber.utils.motif) read_history() (in module amber.utils.io) read_history_set() (in module amber.utils.io) read_label() (in module amber.utils.data_parser) remove_dup_motif() (in module amber.objective.motifUtils) remove_files() (BaseController method), [1] (GeneralController static method), [1] (OperationController method), [1] ReplayBuffer (class in amber.architect.buffer) res_layer() (KerasResidualCnnBuilder static method)

ResConvNetArchitecture (class in amber.modeler.architectureDecoder) reset() (ControllerTrainEnvironment method) reset_plot() (in module amber.plots.plotsV1) reset_short_term() (MultiManagerBuffer method) reset_style() (in module amber.plots.plotsV1) restore() (ControllerTrainEnvironment method) (ParallelMultiManagerEnvironment method) reverse_complement() (in module amber.utils.data_parser) Reward (class in amber.architect.reward) rewrite_train_hist() (in module amber.bootstrap.grid_search) run() (Amber method) (in module amber.bootstrap.explore_lambda) run_saliency() (MotifSaliency method)

S

save() (EnasAnnModel method) (EnasCnnModel method) save_action_weights() (in module amber.utils.io) save_pickle() (AmberSpecifications method) save_stats() (in module amber.utils.io) save_weights() (EnasAnnModel method) (EnasCnnModel method) (GeneralController method), [1] Scale (class in amber.utils.motif) scan_motif() (MotifSaliency method) Selector (class in amber.utils.sampler) seq_to_matrix() (in module amber.utils.data_parser) Sequence (class in amber.utils.sequences) set_controller() (EnasAnnDAG method) (EnasAnnModelBuilder method) (EnasCnnModelBuilder method) (EnasConv1dDAG method) set_controller_states() (in module amber.architect.trainEnv) set_left_pad() (BioIntervalSource method) set_pad() (BioIntervalSource method) set_right_pad() (BioIntervalSource method)

set_weights() (EnasAnnModel method) (EnasCnnModel method) (GeneralController method), [1] setup_logger() (in module amber.utils.logging) simdata_reader() (in module amber.utils.data_parser) sma() (in module amber.plots.plotsV1) SparseCategoricalReward (class in amber.architect.reward) stack_lstm() (in module amber.architect.commonOps) State (class in amber.architect.modelSpace) step() (ControllerTrainEnvironment method) store() (BaseController method), [1] (Buffer method) (GeneralController method), [1] (MultiManagerBuffer method) (OperationController method), [1] (ZeroShotController method), [1] store_general() (in module amber.architect.store) store_minimal() (in module amber.architect.store) store_with_hessian() (in module amber.architect.store) store_with_model_plot() (in module amber.architect.store) stratified_reward_mean() (MultiManagerBuffer method)

T

to_dict() (AmberSpecifications method) train() (BaseController method), [1] (ControllerTrainEnvironment method) (EnasTrainEnv method) (GeneralController method), [1] (MultiManagerEnvironment method) (OperationController method), [1] (ZeroShotController method), [1]

train_hist_csv_writter() (in module amber.bootstrap.grid_search) train_on_batch() (EnasAnnModel method) (EnasCnnModel method) train_simple_controller() (in module amber.bootstrap.explore_lambda) types (AmberSpecifications property)

U

unpack() (DataToParse method)

unpack_data() (in module amber.architect.commonOps)

V

violin_sns() (in module amber.plots.plotsV1)

W

write_pred_to_disk() (in module amber.architect.store)

Z

ZeroShotController (class in amber.architect.controller) (class in amber.architect.controller.zeroShotController)