osl_dynamics.models.dive

DIVE (DyNeMo with Integrated Variability Estimation).

Classes

Config	Settings for DIVE.
Model	DIVE.

Module Contents

class osl_dynamics.models.dive.Config

Bases: osl_dynamics.models.mod_base.BaseModelConfig, osl_dynamics.models.inf_mod_base.VariationalInferenceModelConfig

Settings for DIVE.

Parameters:

• model_name (str) – Model name.

• n_modes (int) – Number of modes.

• n_channels (int) – Number of channels.

• sequence_length (int) – Length of sequence passed to the inference network and generative model.

• inference_rnn (str) – RNN to use, either 'gru' or 'lstm'.

• inference_n_layers (int) – Number of layers.

• inference_n_untis (int) – Number of units.

• inference_normalization (str) – Type of normalization to use. Either None, 'batch' or 'layer'.

• inference_activation (str) – Type of activation to use after normalization and before dropout. E.g. 'relu', 'elu', etc.

• inference_dropout (float) – Dropout rate.

• inference_regularizer (str) – Regularizer.

• model_rnn (str) – RNN to use, either 'gru' or 'lstm'.

• model_n_layers (int) – Number of layers.

• model_n_units (int) – Number of units.

• model_normalization (str) – Type of normalization to use. Either None, 'batch' or 'layer'.

• model_activation (str) – Type of activation to use after normalization and before dropout. E.g. 'relu', 'elu', etc.

• model_dropout (float) – Dropout rate.

• model_regularizer (str) – Regularizer.

• learn_alpha_temperature (bool) – Should we learn alpha_temperature?

• initial_alpha_temperature (float) – Initial value for alpha_temperature.

• learn_means (bool) – Should we make the mean vectors for each mode trainable?

• learn_covariances (bool) – Should we make the covariance matrix for each mode trainable?

• initial_means (np.ndarray) – Initialisation for mean vectors.

• initial_covariances (np.ndarray) – Initialisation for mode covariances.

• covariances_epsilon (float) – Error added to mode covariances for numerical stability.

• means_regularizer (tf.keras.regularizers.Regularizer) – Regularizer for group mean vectors.

• covariances_regularizer (tf.keras.regularizers.Regularizer) – Regularizer for group covariance matrices.

• do_kl_annealing (bool) – Should we use KL annealing during training?

• kl_annealing_curve (str) – Type of KL annealing curve. Either 'linear' or 'tanh'.

• kl_annealing_sharpness (float) – Parameter to control the shape of the annealing curve if kl_annealing_curve='tanh'.

• n_kl_annealing_epochs (int) – Number of epochs to perform KL annealing.

• init_method (str) – Initialization method to use. Defaults to ‘random_subset’.

• n_init (int) – Number of initializations. Defaults to 5.

• n_init_epochs (int) – Number of epochs for each initialization. Defaults to 2.

• init_take (float) – Fraction of dataset to use in the initialization. Defaults to 1.0.

• batch_size (int) – Mini-batch size.

• learning_rate (float) – Learning rate.

• lr_decay (float) – Decay for learning rate. Default is 0.1. We use lr = learning_rate * exp(-lr_decay * epoch).

• gradient_clip (float) – Value to clip gradients by. This is the clipnorm argument passed to the Keras optimizer. Cannot be used if multi_gpu=True.

• n_epochs (int) – Number of training epochs.

• optimizer (str or tf.keras.optimizers.Optimizer) – Optimizer to use. 'adam' is recommended.

• loss_calc (str) – How should we collapse the time dimension in the loss? Either 'mean' or 'sum'.

• multi_gpu (bool) – Should be use multiple GPUs for training?

• strategy (str) – Strategy for distributed learning.

• best_of (int) – Number of full training runs to perform. A single run includes its own initialization and fitting from scratch.

• n_sessions (int) – Number of sessions whose observation model parameters can vary.

• embeddings_dim (int) – Number of dimensions for the embedding vectors.

• spatial_embeddings_dim (int) – Number of dimensions for the spatial embeddings.

• unit_norm_embeddings (bool) – Should we normalize the embeddings to have unit norm?

• dev_n_layers (int) – Number of layers for the MLP for deviations.

• dev_n_units (int) – Number of units for the MLP for deviations.

• dev_normalization (str) – Type of normalization for the MLP for deviations.

• dev_activation (str) – Type of activation to use for the MLP for deviations.

• dev_dropout (float) – Dropout rate for the MLP for deviations.

• dev_regularizer (str) – Regularizer for the MLP for deviations.

• dev_regularizer_factor (float) – Regularizer factor for the MLP for deviations.

• initial_dev (dict) – Initialisation for dev posterior parameters.

• session_labels (List[SessionLabels]) – List of session labels.

model_name: str = 'DIVE'

inference_rnn: str = 'lstm'

inference_n_layers: int = 1

inference_n_units: int = None

inference_normalization: str = None

inference_activation: str = None

inference_dropout: float = 0.0

inference_regularizer: str = None

model_rnn: str = 'lstm'

model_n_layers: int = 1

model_n_units: int = None

model_normalization: str = None

model_activation: str = None

model_dropout: float = 0.0

model_regularizer: str = None

learn_means: bool = None

learn_covariances: bool = None

initial_means: numpy.ndarray = None

initial_covariances: numpy.ndarray = None

covariances_epsilon: float = None

means_regularizer: tensorflow.keras.regularizers.Regularizer = None

covariances_regularizer: tensorflow.keras.regularizers.Regularizer = None

n_sessions: int = None

embeddings_dim: int = None

spatial_embeddings_dim: int = None

unit_norm_embeddings: bool = False

dev_n_layers: int = 0

dev_n_units: int = None

dev_normalization: str = None

dev_activation: str = None

dev_dropout: float = 0.0

dev_regularizer: str = None

dev_regularizer_factor: float = 0.0

session_labels: List[osl_dynamics.data.SessionLabels] = None

init_method: str = 'random_subset'

n_init: int = 5

n_init_epochs: int = 2

init_take: float = 1.0

validate_rnn_parameters()

Return type:

None

validate_observation_model_parameters()

Return type:

None

validate_embedding_parameters()

Return type:

None

validate_session_labels()

Return type:

None

class osl_dynamics.models.dive.Model(config)

Bases: osl_dynamics.models.inf_mod_base.VariationalInferenceModelBase

DIVE.

Parameters:

config (osl_dynamics_models.dive.Config)

config_type

build_model()

Builds a keras model.

Return type:

None

get_group_means()

Get the group level mode means.

Returns:

means – Group means. Shape is (n_modes, n_channels).

Return type:

np.ndarray

get_group_covariances()

Get the group level mode covariances.

Returns:

covariances – Group covariances. Shape is (n_modes, n_channels, n_channels).

Return type:

np.ndarray

get_group_means_covariances()

Get the group level mode means and covariances.

This is a wrapper for get_group_means and get_group_covariances.

Returns:

• means (np.ndarray) – Group means. Shape is (n_modes, n_channels).

• covariances (np.ndarray) – Group covariances. Shape is (n_modes, n_channels, n_channels).

Return type:

Tuple[numpy.ndarray, numpy.ndarray]

get_group_observation_model_parameters()

Wrapper for get_group_means_covariances.

Return type:

Tuple[numpy.ndarray, numpy.ndarray]

get_embedding_weights()

Get the weights of the embedding layers.

Returns:

embedding_weights – Weights of the embedding layers.

Return type:

dict

get_session_embeddings()

Get the embedding vectors for sessions for each session label.

Returns:

embeddings – Embeddings for each session label.

Return type:

dict

get_summed_embeddings()

Get the summed embeddings.

Returns:

summed_embeddings – Summed embeddings. Shape is (n_sessions, embeddings_dim).

Return type:

np.ndarray

get_session_means_covariances()

Get the means and covariances for each session.

Returns:

• session_means (np.ndarray) – Mode means for each session. Shape is (n_sessions, n_modes, n_channels).

• session_covs (np.ndarray) – Mode covariances for each session. Shape is (n_sessions, n_modes, n_channels, n_channels).

Return type:

Tuple[numpy.ndarray, numpy.ndarray]

set_regularizers(training_dataset)

Set the means and covariances regularizer based on the training data.

A multivariate normal prior is applied to the mean vectors with mu=0, sigma=diag((range/2)**2) and an inverse Wishart prior is applied to the covariances matrices with nu=n_channels-1+0.1 and psi=diag(range).

Parameters:

training_dataset (tf.data.Dataset or osl_dynamics.data.Data) – Training dataset.

Return type:

None

set_dev_parameters_initializer(training_data)

Set the deviance parameters initializer based on training data.

Parameters:

training_data (osl_dynamics.data.Data or tf.data.Dataset) – The training data.

Return type:

None

set_embeddings_initializer(initial_embeddings)

Set the embeddings initializer.

Parameters:

initial_embeddings (dict) – Initial embeddings for each session label.

Return type:

None

set_group_means(group_means, update_initializer=True)

Set the group means of each mode.

Parameters:

• group_means (np.ndarray) – Group level mode means. Shape is (n_modes, n_channels).

• update_initializer (bool, optional) – Do we want to use the passed group means when we re-initialize the model?

Return type:

None

set_group_covariances(group_covariances, update_initializer=True)

Set the group covariances of each mode.

Parameters:

• group_covariances (np.ndarray) – Group level mode covariances. Shape is (n_modes, n_channels, n_channels).

• update_initializer (bool, optional) – Do we want to use the passed group covariances when we re-initialize the model?

Return type:

None

set_group_means_covariances(group_means, group_covariances, update_initializer=True)

This is a wrapper for set_group_means and set_group_covariances.

Parameters:

• group_means (numpy.ndarray)

• group_covariances (numpy.ndarray)

• update_initializer (bool)

Return type:

None

set_group_observation_model_parameters(group_observation_model_parameters, update_initializer=True)

Wrapper for set_group_means_covariances.

Parameters:

• group_observation_model_parameters (Tuple[numpy.ndarray, numpy.ndarray])

• update_initializer (bool)

Return type:

None

random_subject_initialization(**kwargs)

random subject initialisation not compatible with DIVE.

Return type:

None