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User guide
Advanced user guide
BehaveNet data structure
Hyperparameter glossary
behavenet.data
behavenet.fitting
behavenet.models
behavenet.plotting
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Index
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B
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C
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D
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E
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F
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G
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I
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K
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M
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N
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__call__() (behavenet.data.transforms.BlockShuffle method)
(behavenet.data.transforms.ClipNormalize method)
(behavenet.data.transforms.Compose method)
(behavenet.data.transforms.MakeOneHot method)
(behavenet.data.transforms.MakeOneHot2D method)
(behavenet.data.transforms.MotionEnergy method)
(behavenet.data.transforms.SelectIdxs method)
(behavenet.data.transforms.Threshold method)
(behavenet.data.transforms.Transform method)
(behavenet.data.transforms.ZScore method)
A
AE (class in behavenet.models.aes)
AEMSP (class in behavenet.models.aes)
B
BaseModel (class in behavenet.models.base)
BaseModule (class in behavenet.models.base)
behavenet.data.data_generator
module
behavenet.data.preprocess
module
behavenet.data.transforms
module
behavenet.data.utils
module
behavenet.fitting.eval
module
behavenet.fitting.losses
module
behavenet.fitting.training
module
behavenet.fitting.utils
module
behavenet.models.ae_model_architecture_generator
module
behavenet.models.aes
module
behavenet.models.base
module
behavenet.models.decoders
module
behavenet.models.vaes
module
behavenet.plotting
module
behavenet.plotting.ae_utils
module
behavenet.plotting.arhmm_utils
module
behavenet.plotting.cond_ae_utils
module
behavenet.plotting.decoder_utils
module
BetaTCVAE (class in behavenet.models.vaes)
BlockShuffle (class in behavenet.data.transforms)
build_data_generator() (in module behavenet.data.utils)
build_hdf5() (in module behavenet.data.preprocess)
build_model() (behavenet.models.aes.AE method)
(behavenet.models.aes.AEMSP method)
(behavenet.models.aes.ConditionalAE method)
(behavenet.models.aes.ConvAEDecoder method)
(behavenet.models.aes.ConvAEEncoder method)
(behavenet.models.aes.LinearAEDecoder method)
(behavenet.models.aes.LinearAEEncoder method)
(behavenet.models.base.BaseModel method)
(behavenet.models.base.BaseModule method)
(behavenet.models.decoders.ConvDecoder method)
(behavenet.models.decoders.Decoder method)
(behavenet.models.decoders.LSTM method)
(behavenet.models.decoders.MLP method)
(behavenet.models.vaes.ConditionalVAE method)
(behavenet.models.vaes.MSPSVAE method)
(behavenet.models.vaes.PSVAE method)
C
calculate_output_dim() (in module behavenet.models.ae_model_architecture_generator)
check_same_training_split() (in module behavenet.data.utils)
ClipNormalize (class in behavenet.data.transforms)
Compose (class in behavenet.data.transforms)
compute_range() (in module behavenet.plotting.cond_ae_utils)
concat() (in module behavenet.plotting)
ConcatSessionsGenerator (class in behavenet.data.data_generator)
ConcatSessionsGeneratorMulti (class in behavenet.data.data_generator)
ConditionalAE (class in behavenet.models.aes)
ConditionalVAE (class in behavenet.models.vaes)
contains_session() (in module behavenet.fitting.utils)
ConvAEDecoder (class in behavenet.models.aes)
ConvAEEncoder (class in behavenet.models.aes)
ConvAEMSPSEncoder (class in behavenet.models.vaes)
ConvAEPSEncoder (class in behavenet.models.vaes)
ConvDecoder (class in behavenet.models.decoders)
create_metric_row() (behavenet.fitting.training.Logger method)
create_orthogonal_matrix() (behavenet.models.aes.AEMSP method)
create_tt_experiment() (in module behavenet.fitting.utils)
CustomDataParallel (class in behavenet.models.base)
D
Decoder (class in behavenet.models.decoders)
decomposed_kl() (in module behavenet.fitting.losses)
DiagLinear (class in behavenet.models.base)
dimension_wise_kl_to_std_normal() (in module behavenet.fitting.losses)
draw_archs() (in module behavenet.models.ae_model_architecture_generator)
E
EarlyStopping (class in behavenet.fitting.training)
estimate_model_footprint() (in module behavenet.models.ae_model_architecture_generator)
experiment_exists() (in module behavenet.fitting.utils)
export_hparams() (in module behavenet.fitting.utils)
export_latents() (behavenet.models.vaes.MSPSVAE method)
(in module behavenet.fitting.eval)
export_predictions() (in module behavenet.fitting.eval)
export_session_info_to_csv() (in module behavenet.fitting.utils)
export_states() (in module behavenet.fitting.eval)
export_train_plots() (in module behavenet.fitting.eval)
extra_repr() (behavenet.models.base.DiagLinear method)
F
find_session_dirs() (in module behavenet.fitting.utils)
fit() (in module behavenet.fitting.training)
fit_classifier() (in module behavenet.plotting.cond_ae_utils)
forward() (behavenet.models.aes.AE method)
(behavenet.models.aes.AEMSP method)
(behavenet.models.aes.ConditionalAE method)
(behavenet.models.aes.ConvAEDecoder method)
(behavenet.models.aes.ConvAEEncoder method)
(behavenet.models.aes.LinearAEDecoder method)
(behavenet.models.aes.LinearAEEncoder method)
(behavenet.models.base.BaseModel method)
(behavenet.models.base.BaseModule method)
(behavenet.models.base.DiagLinear method)
(behavenet.models.decoders.ConvDecoder method)
(behavenet.models.decoders.Decoder method)
(behavenet.models.decoders.LSTM method)
(behavenet.models.decoders.MLP method)
(behavenet.models.vaes.ConditionalVAE method)
(behavenet.models.vaes.ConvAEMSPSEncoder method)
(behavenet.models.vaes.ConvAEPSEncoder method)
(behavenet.models.vaes.MSPSVAE method)
(behavenet.models.vaes.PSVAE method)
(behavenet.models.vaes.VAE method)
freeze() (behavenet.models.base.BaseModule method)
G
gaussian_ll() (in module behavenet.fitting.losses)
gaussian_ll_to_mse() (in module behavenet.fitting.losses)
get_best_model_and_data() (in module behavenet.fitting.utils)
get_best_model_version() (in module behavenet.fitting.utils)
get_best_models() (in module behavenet.plotting.decoder_utils)
get_crop() (in module behavenet.plotting)
get_data_generator_inputs() (in module behavenet.data.utils)
get_decoding_conv_block() (in module behavenet.models.ae_model_architecture_generator)
get_discrete_chunks() (in module behavenet.plotting.arhmm_utils)
get_encoding_conv_block() (in module behavenet.models.ae_model_architecture_generator)
get_expt_dir() (in module behavenet.fitting.utils)
get_frames_from_idxs() (in module behavenet.data.preprocess)
get_handcrafted_dims() (in module behavenet.models.ae_model_architecture_generator)
get_input_range() (in module behavenet.plotting.cond_ae_utils)
get_inverse_transformed_latents() (behavenet.models.aes.AEMSP method)
(behavenet.models.vaes.MSPSVAE method)
(behavenet.models.vaes.PSVAE method)
get_lab_example() (in module behavenet.fitting.utils)
get_labels_2d_for_trial() (in module behavenet.plotting.cond_ae_utils)
get_latent_arrays_by_dtype() (in module behavenet.plotting.arhmm_utils)
get_loss() (behavenet.fitting.training.Logger method)
get_model_input() (in module behavenet.plotting.cond_ae_utils)
get_model_latents_states() (in module behavenet.plotting.arhmm_utils)
get_model_params() (in module behavenet.fitting.utils)
get_parameters() (behavenet.models.base.BaseModel method)
get_possible_arch() (in module behavenet.models.ae_model_architecture_generator)
get_predicted_labels() (behavenet.models.vaes.MSPSVAE method)
(behavenet.models.vaes.PSVAE method)
get_r2s_across_trials() (in module behavenet.plotting.decoder_utils)
get_r2s_by_trial() (in module behavenet.plotting.decoder_utils)
get_reconstruction() (in module behavenet.fitting.eval)
get_region_dir() (in module behavenet.fitting.utils)
get_region_list() (in module behavenet.data.utils)
get_session_dir() (in module behavenet.fitting.utils)
get_state_durations() (in module behavenet.plotting.arhmm_utils)
get_subdirs() (in module behavenet.fitting.utils)
get_test_metric() (in module behavenet.fitting.eval)
get_transformed_latents() (behavenet.models.aes.AEMSP method)
(behavenet.models.vaes.MSPSVAE method)
(behavenet.models.vaes.PSVAE method)
get_transforms_paths() (in module behavenet.data.utils)
I
index_code_mi() (in module behavenet.fitting.losses)
interpolate_1d() (in module behavenet.plotting.cond_ae_utils)
interpolate_2d() (in module behavenet.plotting.cond_ae_utils)
interpolate_point_path() (in module behavenet.plotting.cond_ae_utils)
K
kl_div_to_std_normal() (in module behavenet.fitting.losses)
L
LinearAEDecoder (class in behavenet.models.aes)
LinearAEEncoder (class in behavenet.models.aes)
load_default_arch() (in module behavenet.models.ae_model_architecture_generator)
load_handcrafted_arch() (in module behavenet.models.ae_model_architecture_generator)
load_handcrafted_arches() (in module behavenet.models.ae_model_architecture_generator)
load_labels_like_latents() (in module behavenet.data.utils)
load_latents() (in module behavenet.plotting)
load_metrics_csv_as_df() (in module behavenet.plotting)
load_pretrained_ae() (in module behavenet.models.aes)
load_raw_labels() (in module behavenet.data.preprocess)
Logger (class in behavenet.fitting.training)
loss() (behavenet.models.aes.AE method)
(behavenet.models.aes.AEMSP method)
(behavenet.models.aes.ConditionalAE method)
(behavenet.models.base.BaseModel method)
(behavenet.models.decoders.ConvDecoder method)
(behavenet.models.decoders.Decoder method)
(behavenet.models.vaes.BetaTCVAE method)
(behavenet.models.vaes.ConditionalVAE method)
(behavenet.models.vaes.MSPSVAE method)
(behavenet.models.vaes.PSVAE method)
(behavenet.models.vaes.VAE method)
LSTM (class in behavenet.models.decoders)
M
make_ae_reconstruction_movie_wrapper() (in module behavenet.plotting.ae_utils)
make_interpolated() (in module behavenet.plotting.cond_ae_utils)
make_interpolated_multipanel() (in module behavenet.plotting.cond_ae_utils)
make_latent_traversal_movie() (in module behavenet.plotting.cond_ae_utils)
make_neural_reconstruction_movie() (in module behavenet.plotting.decoder_utils)
make_neural_reconstruction_movie_wrapper() (in module behavenet.plotting.decoder_utils)
make_real_vs_sampled_movies() (in module behavenet.plotting.arhmm_utils)
make_reconstruction_movie() (in module behavenet.plotting.ae_utils)
make_session_swap_movie() (in module behavenet.plotting.cond_ae_utils)
make_syllable_movies() (in module behavenet.plotting.arhmm_utils)
make_syllable_movies_wrapper() (in module behavenet.plotting.arhmm_utils)
MakeOneHot (class in behavenet.data.transforms)
MakeOneHot2D (class in behavenet.data.transforms)
MLP (class in behavenet.models.decoders)
module
behavenet.data.data_generator
behavenet.data.preprocess
behavenet.data.transforms
behavenet.data.utils
behavenet.fitting.eval
behavenet.fitting.losses
behavenet.fitting.training
behavenet.fitting.utils
behavenet.models.ae_model_architecture_generator
behavenet.models.aes
behavenet.models.base
behavenet.models.decoders
behavenet.models.vaes
behavenet.plotting
behavenet.plotting.ae_utils
behavenet.plotting.arhmm_utils
behavenet.plotting.cond_ae_utils
behavenet.plotting.decoder_utils
MotionEnergy (class in behavenet.data.transforms)
mse() (in module behavenet.fitting.losses)
MSPSVAE (class in behavenet.models.vaes)
N
next_batch() (behavenet.data.data_generator.ConcatSessionsGenerator method)
(behavenet.data.data_generator.ConcatSessionsGeneratorMulti method)
O
on_val_check() (behavenet.fitting.training.EarlyStopping method)
P
plot_1d_frame_array() (in module behavenet.plotting.cond_ae_utils)
plot_2d_frame_array() (in module behavenet.plotting.cond_ae_utils)
plot_dynamics_matrices() (in module behavenet.plotting.arhmm_utils)
plot_hyperparameter_search_results() (in module behavenet.plotting.cond_ae_utils)
plot_label_reconstructions() (in module behavenet.plotting.cond_ae_utils)
plot_latent_traversals() (in module behavenet.plotting.cond_ae_utils)
plot_mspsvae_hyperparameter_search_results() (in module behavenet.plotting.cond_ae_utils)
plot_mspsvae_training_curves() (in module behavenet.plotting.cond_ae_utils)
plot_neural_reconstruction_traces() (in module behavenet.plotting.decoder_utils)
plot_neural_reconstruction_traces_wrapper() (in module behavenet.plotting.decoder_utils)
plot_obs_biases() (in module behavenet.plotting.arhmm_utils)
plot_obs_covariance_matrices() (in module behavenet.plotting.arhmm_utils)
plot_psvae_training_curves() (in module behavenet.plotting.cond_ae_utils)
plot_real_vs_sampled() (in module behavenet.plotting.arhmm_utils)
plot_state_transition_matrix() (in module behavenet.plotting.arhmm_utils)
plot_states_overlaid_with_latents() (in module behavenet.plotting.arhmm_utils)
PSVAE (class in behavenet.models.vaes)
R
read_session_info_from_csv() (in module behavenet.fitting.utils)
real_vs_sampled_wrapper() (in module behavenet.plotting.arhmm_utils)
reparameterize() (in module behavenet.models.vaes)
reset_iterators() (behavenet.data.data_generator.ConcatSessionsGenerator method)
reset_metrics() (behavenet.fitting.training.Logger method)
reset_parameters() (behavenet.models.base.DiagLinear method)
resize_labels() (in module behavenet.data.preprocess)
S
sample() (behavenet.models.aes.AEMSP method)
save() (behavenet.models.aes.AEMSP method)
(behavenet.models.base.BaseModel method)
save_movie() (in module behavenet.plotting)
SelectIdxs (class in behavenet.data.transforms)
SingleSessionDataset (class in behavenet.data.data_generator)
SingleSessionDatasetBatchedLoad (class in behavenet.data.data_generator)
split_trials() (in module behavenet.data.data_generator)
subspace_overlap() (in module behavenet.fitting.losses)
T
Threshold (class in behavenet.data.transforms)
total_correlation() (in module behavenet.fitting.losses)
Transform (class in behavenet.data.transforms)
triplet_loss() (in module behavenet.fitting.losses)
U
unfreeze() (behavenet.models.base.BaseModule method)
update_metrics() (behavenet.fitting.training.Logger method)
V
VAE (class in behavenet.models.vaes)
Z
ZScore (class in behavenet.data.transforms)
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