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amber.architect
amber.modeler
amber.utils
amber.plots
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D
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H
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I
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M
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N
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O
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P
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T
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U
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Z
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)
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