Identifier Index

[ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ ]

A

aaHDFArchive (in dimer.data)	AELayer (in dimer.nnet.autoencoder)	assertAlmostZeroArray() (in NpyTester)
aAnchorDataset (in dimer.data)	AESpec (in dimer.nnet.config_spec)	assertDifferentArray() (in NpyTester)
ABCMeta	AEStack (in dimer.nnet.autoencoder)	assertEqualArray() (in NpyTester)
acquire() (in FileLock)	alloc_shared_weights_() (in dimer.nnet)	AssertionError
activation() (in Layer)	AnchorAnnotation (in dimer.data)	assertZeroArray() (in NpyTester)
activation() (in AELayer)	AnchorDataset (in dimer.data)	autoencoder (in dimer.nnet)
activation() (in ConvPoolLayer)	archive (in dimer)	AutoEncoder (in dimer.nnet.autoencoder)
activation() (in HiddenLayer)	archive_tests (in dimer)	autoencoder_tests (in dimer.nnet)
activation() (in LogisticReg)	archname() (in dimer.archive)
adjust_lr() (in dimer.nnet)	assertAlmostEqualArray() (in NpyTester)

B

base_test_classes (in dimer.nnet)	BEDMAP (in dimer.genome.bedops)	BedReader (in dimer.genome.bed)
basename() (in dimer.archive)	bedmap() (in dimer.genome.bedops)	BroadPeakReader (in dimer.genome.peak)
batches_from_data() (in DataSpec)	bedops (in dimer.genome)
bed (in dimer.genome)	bedops_tests (in dimer.genome)

C

CfgFactory (in dimer.nnet.config_spec)	config_spec (in dimer.nnet)	cost() (in AutoEncoder)
cnn_filters2raster_image() (in dimer.nnet.utils)	Configurable (in dimer.config)	cost() (in CnnModel)
CNNLayerTester (in dimer.nnet.base_test_classes)	ConvPoolLayer (in dimer.nnet.nccn)	cp_arch (in ModelSpec)
CnnModel (in dimer.nnet.nccn)	corrupt() (in AELayer)	cspec_tests (in dimer.nnet)
config (in dimer)	cost() (in AELayer)	csv (in Monitor)

D

DaeLearnMonitor (in dimer.nnet.monitor)	DataSpec (in dimer.nnet.config_spec)	DSPEC_MSG (in dimer.archive)
data (in dimer)	deprecated() (in dimer)	dump() (in AnchorDataset)
data_tests (in dimer)	dimer	dump() (in aaHDFArchive)
Dataset (in dimer.data)	dset_path() (in dimer.archive)

E

experiment (in dimer)

F

filelock (in dimer)	fit() (in dimer.ops)	fit_features() (in aAnchorDataset)
FileLock (in dimer.filelock)	fit_data() (in dimer.nnet)	ftype_frm (in Monitor)
FileLockException (in dimer.filelock)	fit_features() (in Dataset)	fzero (in Monitor)

G

genome (in dimer)	get_input() (in TestLRLayer)	get_output() (in TestAEStackModel)
get_flat_weights() (in Layer)	get_layer() (in TestAEl)	get_output() (in TestCnnModel)
get_gradient_f() (in TestAEModel)	get_layer() (in CNNLayerTester)	get_params() (in Layer)
get_gradient_f() (in TestAEStackModel)	get_layer() (in TestCPLayer)	get_params() (in Model)
get_input() (in TestAEModel)	get_layer() (in TestHLayer)	get_params() (in SpeedLayer)
get_input() (in TestAEStackModel)	get_layer() (in TestLRLayer)	get_speeds() (in SpeedLayer)
get_input() (in TestAEl)	get_model() (in TestAEModel)	get_speeds() (in CnnModel)
get_input() (in CNNLayerTester)	get_model() (in TestAEStackModel)	get_weights() (in Layer)
get_input() (in ModelTester)	get_model() (in ModelTester)	get_weights() (in Model)
get_input() (in TestCPLayer)	get_model() (in TestCnnModel)	getAttr() (in Configurable)
get_input() (in TestCnnModel)	get_ouput() (in ModelTester)
get_input() (in TestHLayer)	get_output() (in TestAEModel)

H

HiddenLayer (in dimer.nnet.nccn)

I

is_labeled (in Dataset)	is_min_down() (in Monitor)	iter_train() (in aAnchorDataset)
is_max_down() (in Monitor)	is_min_still() (in Monitor)	iter_valid() (in TrainDataset)
is_max_still() (in Monitor)	is_min_up() (in Monitor)	iter_valid() (in aAnchorDataset)
is_max_up() (in Monitor)	iter_train() (in TrainDataset)

J

join() (in dimer.archive)

L

labels (in AnchorDataset)	load_flat_weights() (in Layer)	log (in dimer.nnet.autoencoder)
labels (in Dataset)	load_object() (in dimer.archive)	log (in dimer.nnet.config_spec)
labels (in aAnchorDataset)	log (in dimer.archive)	log (in dimer.nnet)
Layer (in dimer.nnet)	log (in dimer.config)	log (in dimer.nnet.monitor)
LearnMonitor (in dimer.nnet.monitor)	log (in dimer.data)	log (in dimer.nnet.nccn)
load() (in Model)	log (in dimer)	LogisticReg (in dimer.nnet.nccn)

M

mean_sdX() (in AnchorDataset)	ModelSpec (in dimer.nnet.config_spec)	Monitor (in dimer.nnet.monitor)
measure_time() (in dimer)	ModelTester (in dimer.nnet.base_test_classes)	monitor_tests (in dimer.nnet)
Model (in dimer.nnet)	monitor (in dimer.nnet)	MtrainSpec (in dimer.nnet.config_spec)

N

NarrowPeakReader (in dimer.genome.peak)	next() (in BroadPeakReader)	normalize_features() (in Dataset)
nccn (in dimer.nnet)	next() (in NarrowPeakReader)	normalize_features() (in aAnchorDataset)
nccn_tests (in dimer.nnet)	nnet (in dimer)	NpyTester (in dimer.nnet.base_test_classes)
next() (in BedReader)	nnet_tests (in dimer.nnet)

O

ops (in dimer)	overlap_as_array() (in dimer.genome.bedops)

P

parseBED() (in dimer.genome)	peak (in dimer.genome)

R

reconstruction_cost() (in AELayer)	rnd_layer() (in CNNLayerTester)	rng (in dimer.nnet.base_test_classes)
RegrLearnMonitor (in dimer.nnet.monitor)	rnd_weights() (in CNNLayerTester)	rng (in dimer.nnet.cspec_tests)
rel_diff() (in Monitor)	rnd_weights() (in ModelTester)	rng (in dimer.nnet.nccn_tests)
release() (in FileLock)	rng (in dimer.data_tests)	rng (in dimer.nnet.nnet_tests)
report (in Monitor)	rng (in dimer.nnet.autoencoder_tests)

S

save() (in Model)	setUp() (in TestAEModel)	shT (in TheanoShare)
save_object() (in dimer.archive)	setUp() (in TestAEStackModel)	shT (in aAnchorDataset)
scale_data() (in dimer.nnet)	setUp() (in TestAEl)	shX (in TheanoShare)
scale_to_unit_interval() (in dimer.nnet.utils)	setUp() (in CNNLayerTester)	shX (in aAnchorDataset)
set_params() (in Layer)	setUp() (in ModelTester)	shY (in TheanoShare)
set_params() (in SpeedLayer)	setUp() (in TestMonitor)	shY (in aAnchorDataset)
set_speeds() (in SpeedLayer)	setUp() (in TestCPLayer)	spec_list (in dimer.nnet)
set_speeds() (in CnnModel)	setUp() (in TestCnnModel)	speed_update() (in SpeedLayer)
set_weights() (in Layer)	setUp() (in TestHLayer)	speed_update() (in TestAEl)
set_weights() (in Model)	setUp() (in TestLRLayer)	SpeedLayer (in dimer.nnet)
setAttr() (in Configurable)	setUp() (in TestLr)	split() (in dimer.archive)
setUp() (in TestAnchorDataset)	share() (in TheanoShare)	standardize() (in dimer.ops)
setUp() (in TestDataset)	share() (in aAnchorDataset)
setUp() (in TestBEDMAP)	shift_data() (in dimer.nnet)

T

Test (in dimer.nnet.cspec_tests)	test_init() (in TestHLayer)	TestAEl (in dimer.nnet.autoencoder_tests)
test_activation() (in TestAEStackModel)	test_init() (in TestLRLayer)	TestAEModel (in dimer.nnet.autoencoder_tests)
test_activation() (in TestAEl)	test_io() (in TestArchive)	TestAEStackModel (in dimer.nnet.autoencoder_tests)
test_activation() (in TestCPLayer)	test_io() (in TestAnchorDataset)	TestAnchorDataset (in dimer.data_tests)
test_activation() (in TestHLayer)	test_io() (in TestAEStackModel)	TestArchive (in dimer.archive_tests)
test_activation() (in TestLRLayer)	test_io() (in TestCnnModel)	TestBEDMAP (in dimer.genome.bedops_tests)
test_activation_vs_i() (in TestCnnModel)	test_labeled() (in TestDataset)	TestCnnModel (in dimer.nnet.nccn_tests)
test_activation_vs_w() (in TestCnnModel)	test_model_update() (in TestAEStackModel)	TestCPLayer (in dimer.nnet.nccn_tests)
test_aelinit() (in TestAEl)	test_normalize_feats() (in TestDataset)	TestDataset (in dimer.data_tests)
test_annotations() (in TestAnchorDataset)	test_norms() (in TestAEl)	testDataSpec() (in Test)
test_basename() (in TestArchive)	test_norms() (in TestCPLayer)	TestExp (in dimer.archive_tests)
test_batch_allocation() (in TestAnchorDataset)	test_norms() (in TestHLayer)	TestHLayer (in dimer.nnet.nccn_tests)
test_batch_iter (in TestAnchorDataset)	test_norms() (in TestLRLayer)	TestLr (in dimer.nnet.nnet_tests)
test_bedmap() (in TestBEDMAP)	test_reldiff() (in TestMonitor)	TestLRLayer (in dimer.nnet.nccn_tests)
test_corruption() (in TestAEl)	test_rlinit() (in TestLRLayer)	TestMonitor (in dimer.nnet.monitor_tests)
test_cost() (in TestAEStackModel)	test_scale() (in TestLr)	TheanoShare (in dimer.data)
test_cost() (in TestCnnModel)	test_seqmonotonicity() (in TestMonitor)	this_train_name() (in dimer.experiment)
test_fit() (in TestLr)	test_seqmonotonicity() (in TestLr)	tile_raster_images() (in dimer.nnet.utils)
test_fit_feats() (in TestDataset)	test_share() (in TestAnchorDataset)	top_cp_idx (in CnnModel)
test_hlinit() (in TestHLayer)	test_shift() (in TestLr)	track_names (in AnchorDataset)
test_iact() (in TestAEl)	test_topcpidx() (in TestCnnModel)	tracks (in AnchorDataset)
test_init() (in TestAEl)	test_trname() (in TestExp)	tracks (in aAnchorDataset)
test_init() (in TestCPLayer)	test_update() (in TestAEModel)	TrainAnchorDataset (in dimer.data)
test_init() (in TestCnnModel)	test_update() (in TestCnnModel)	TrainDataset (in dimer.data)

U

update_params() (in AEStack)	update_params() (in CnnModel)
update_params() (in AutoEncoder)	utils (in dimer.nnet)

V

verbose_compile() (in dimer.nnet)

W

weight_norm() (in Layer)	weight_update() (in SpeedLayer)	width (in AnchorDataset)
weight_norm() (in Model)	WeightMonitor (in dimer.nnet.monitor)	width (in aAnchorDataset)

Z

zero_input() (in CNNLayerTester)	zero_model() (in ModelTester)
zero_layer() (in CNNLayerTester)	zero_weights() (in CNNLayerTester)

_

__abstractmethods__ (in Configurable)	__next__() (in BedReader)	_abc_negative_cache_version (in Layer)
__abstractmethods__ (in Layer)	__next__() (in BroadPeakReader)	_abc_negative_cache_version (in Model)
__abstractmethods__ (in Model)	__next__() (in NarrowPeakReader)	_abc_registry (in Configurable)
__abstractmethods__ (in SpeedLayer)	__package__ (in dimer)	_abc_registry (in Layer)
__abstractmethods__ (in AELayer)	__package__ (in dimer.archive)	_abc_registry (in Model)
__abstractmethods__ (in ConvPoolLayer)	__package__ (in dimer.archive_tests)	_archive_dump() (in Monitor)
__abstractmethods__ (in HiddenLayer)	__package__ (in dimer.config)	_check_consistency() (in AESpec)
__abstractmethods__ (in LogisticReg)	__package__ (in dimer.data)	_check_consistency() (in CfgFactory)
__batches() (in TrainDataset)	__package__ (in dimer.data_tests)	_check_consistency() (in ModelSpec)
__batches() (in aAnchorDataset)	__package__ (in dimer.experiment)	_check_consistency() (in MtrainSpec)
__bootstrap__() (in dimer.genome.bed)	__package__ (in dimer.filelock)	_check_exist_f() (in dimer.nnet.config_spec)
__bootstrap__() (in dimer.genome.peak)	__package__ (in dimer.genome)	_check_get_pairs() (in dimer.nnet.config_spec)
__del__() (in FileLock)	__package__ (in dimer.genome.bed)	_check_get_singles() (in dimer.nnet.config_spec)
__delitem__() (in Model)	__package__ (in dimer.genome.bedops)	_config_check() (in Configurable)
__enter__() (in FileLock)	__package__ (in dimer.genome.bedops_tests)	_dump() (in Monitor)
__exit__() (in FileLock)	__package__ (in dimer.genome.peak)	_empty() (in Monitor)
__getitem__() (in Model)	__package__ (in dimer.nnet)	_from_archive() (in AnchorDataset)
__HDF_SUFFIX__ (in dimer.archive)	__package__ (in dimer.nnet.autoencoder)	_from_archive() (in TrainAnchorDataset)
__init__() (in Configurable)	__package__ (in dimer.nnet.autoencoder_tests)	_from_archive() (in aaHDFArchive)
__init__() (in AnchorAnnotation)	__package__ (in dimer.nnet.base_test_classes)	_from_archive() (in DataSpec)
__init__() (in AnchorDataset)	__package__ (in dimer.nnet.config_spec)	_from_fs() (in DaeLearnMonitor)
__init__() (in Dataset)	__package__ (in dimer.nnet.cspec_tests)	_from_fs() (in LearnMonitor)
__init__() (in TheanoShare)	__package__ (in dimer.nnet.monitor)	_from_fs() (in RegrLearnMonitor)
__init__() (in TrainAnchorDataset)	__package__ (in dimer.nnet.monitor_tests)	_from_model() (in WeightMonitor)
__init__() (in TrainDataset)	__package__ (in dimer.nnet.nccn)	_from_settings() (in CfgFactory)
__init__() (in aAnchorDataset)	__package__ (in dimer.nnet.nccn_tests)	_ftypes (in DaeLearnMonitor)
__init__() (in aaHDFArchive)	__package__ (in dimer.nnet.nnet_tests)	_ftypes (in LearnMonitor)
__init__() (in FileLock)	__package__ (in dimer.nnet.utils)	_ftypes (in RegrLearnMonitor)
__init__() (in BedReader)	__package__ (in dimer.ops)	_ftypes (in WeightMonitor)
__init__() (in BroadPeakReader)	__parse() (in dimer.archive)	_has_changed() (in Monitor)
__init__() (in NarrowPeakReader)	__setitem__() (in Model)	_open_cfg() (in dimer.nnet.config_spec)
__init__() (in Layer)	__sh_anon() (in TheanoShare)	_report_frm (in DaeLearnMonitor)
__init__() (in Model)	__sh_anon() (in aAnchorDataset)	_report_frm (in LearnMonitor)
__init__() (in SpeedLayer)	__spec_cls__() (in dimer.nnet)	_report_frm (in RegrLearnMonitor)
__init__() (in AELayer)	__SPEC_SEP__ (in dimer.archive)	_report_frm (in WeightMonitor)
__init__() (in AEStack)	__str__() (in Model)	_section (in AESpec)
__init__() (in AutoEncoder)	__str__() (in AELayer)	_section (in ModelSpec)
__init__() (in CnnModel)	__str__() (in ConvPoolLayer)	_section (in MtrainSpec)
__init__() (in ConvPoolLayer)	__str__() (in HiddenLayer)	_speed_update_f() (in SpeedLayer)
__init__() (in HiddenLayer)	__str__() (in LogisticReg)	_test_activation() (in CNNLayerTester)
__init__() (in LogisticReg)	__test__ (in dimer.genome.bed)	_test_init_() (in CNNLayerTester)
__iter__() (in BedReader)	__test__ (in dimer.genome.peak)	_test_io() (in ModelTester)
__iter__() (in BroadPeakReader)	_abc_cache (in Configurable)	_test_layer_update() (in TestAEStackModel)
__iter__() (in NarrowPeakReader)	_abc_cache (in Layer)	_test_norms_() (in CNNLayerTester)
__iter_batches() (in TrainDataset)	_abc_cache (in Model)	_test_s_cost_() (in ModelTester)
__iter_batches() (in aAnchorDataset)	_abc_invalidation_counter (in ABCMeta)	_types (in AESpec)
__len__() (in Model)	_abc_negative_cache (in Configurable)	_types (in ModelSpec)
__new__() (in BedReader)	_abc_negative_cache (in Layer)	_types (in MtrainSpec)
__new__() (in BroadPeakReader)	_abc_negative_cache (in Model)	_weight_update_f() (in SpeedLayer)
__new__() (in NarrowPeakReader)	_abc_negative_cache_version (in Configurable)	_weights_inrange() (in CNNLayerTester)