braindecode.classifier.EEGClassifier#

class braindecode.classifier.EEGClassifier(*args, cropped=False, callbacks=None, iterator_train__shuffle=True, iterator_train__drop_last=True, aggregate_predictions=True, **kwargs)[source]#

Classifier that does not assume softmax activation. Calls loss function directly without applying log or anything.

Parameters

  • module (torch module (class or instance)) – A PyTorch Module. In general, the uninstantiated class should be passed, although instantiated modules will also work.

  • criterion (torch criterion (class, default=torch.nn.NLLLoss)) – Negative log likelihood loss. Note that the module should return probabilities, the log is applied during get_loss.

  • classes (None or list (default=None)) – If None, the classes_ attribute will be inferred from the y data passed to fit. If a non-empty list is passed, that list will be returned as classes_. If the initial skorch behavior should be restored, i.e. raising an AttributeError, pass an empty list.

  • optimizer (torch optim (class, default=torch.optim.SGD)) – The uninitialized optimizer (update rule) used to optimize the module

  • lr (float (default=0.01)) – Learning rate passed to the optimizer. You may use lr instead of using optimizer__lr, which would result in the same outcome.

  • max_epochs (int (default=10)) – The number of epochs to train for each fit call. Note that you may keyboard-interrupt training at any time.

  • batch_size (int (default=128)) – Mini-batch size. Use this instead of setting iterator_train__batch_size and iterator_test__batch_size, which would result in the same outcome. If batch_size is -1, a single batch with all the data will be used during training and validation.

  • iterator_train (torch DataLoader) – The default PyTorch DataLoader used for training data.

  • iterator_valid (torch DataLoader) – The default PyTorch DataLoader used for validation and test data, i.e. during inference.

  • dataset (torch Dataset (default=skorch.dataset.Dataset)) – The dataset is necessary for the incoming data to work with pytorch’s DataLoader. It has to implement the __len__ and __getitem__ methods. The provided dataset should be capable of dealing with a lot of data types out of the box, so only change this if your data is not supported. You should generally pass the uninitialized Dataset class and define additional arguments to X and y by prefixing them with dataset__. It is also possible to pass an initialzed Dataset, in which case no additional arguments may be passed.

  • train_split (None or callable (default=skorch.dataset.ValidSplit(5))) –

    If None, there is no train/validation split. Else, train_split should be a function or callable that is called with X and y data and should return the tuple dataset_train, dataset_valid. The validation data may be None.

    If callbacks=None, only use default callbacks, those returned by get_default_callbacks.

    If callbacks="disable", disable all callbacks, i.e. do not run any of the callbacks.

    If callbacks is a list of callbacks, use those callbacks in addition to the default callbacks. Each callback should be an instance of Callback.

    Callback names are inferred from the class name. Name conflicts are resolved by appending a count suffix starting with 1, e.g. EpochScoring_1. Alternatively, a tuple (name, callback) can be passed, where name should be unique. Callbacks may or may not be instantiated. The callback name can be used to set parameters on specific callbacks (e.g., for the callback with name 'print_log', use net.set_params(callbacks__print_log__keys_ignored=['epoch', 'train_loss'])).

  • predict_nonlinearity (callable, None, or 'auto' (default='auto')) –

    The nonlinearity to be applied to the prediction. When set to ‘auto’, infers the correct nonlinearity based on the criterion (softmax for CrossEntropyLoss and sigmoid for BCEWithLogitsLoss). If it cannot be inferred or if the parameter is None, just use the identity function. Don’t pass a lambda function if you want the net to be pickleable.

    In case a callable is passed, it should accept the output of the module (the first output if there is more than one), which is a PyTorch tensor, and return the transformed PyTorch tensor.

    This can be useful, e.g., when predict_proba() should return probabilities but a criterion is used that does not expect probabilities. In that case, the module can return whatever is required by the criterion and the predict_nonlinearity transforms this output into probabilities.

    The nonlinearity is applied only when calling predict() or predict_proba() but not anywhere else – notably, the loss is unaffected by this nonlinearity.

  • warm_start (bool (default=False)) – Whether each fit call should lead to a re-initialization of the module (cold start) or whether the module should be trained further (warm start).

  • verbose (int (default=1)) – This parameter controls how much print output is generated by the net and its callbacks. By setting this value to 0, e.g. the summary scores at the end of each epoch are no longer printed. This can be useful when running a hyperparameter search. The summary scores are always logged in the history attribute, regardless of the verbose setting.

  • device (str, torch.device (default='cpu')) – The compute device to be used. If set to ‘cuda’, data in torch tensors will be pushed to cuda tensors before being sent to the module. If set to None, then all compute devices will be left unmodified.

  • cropped (bool (default=False)) – Defines whether torch model passed to this class is cropped or not. Currently used for callbacks definition.

  • callbacks (None or list of strings or list of Callback instances (default=None)) – More callbacks, in addition to those returned by get_default_callbacks. Each callback should inherit from skorch.callbacks.Callback. If not None, callbacks can be a list of strings specifying sklearn scoring functions (for scoring functions names see: https://scikit-learn.org/stable/modules/model_evaluation.html#scoring-parameter) or a list of callbacks where the callback names are inferred from the class name. Name conflicts are resolved by appending a count suffix starting with 1, e.g. EpochScoring_1. Alternatively, a tuple (name, callback) can be passed, where name should be unique. Callbacks may or may not be instantiated. The callback name can be used to set parameters on specific callbacks (e.g., for the callback with name 'print_log', use net.set_params(callbacks__print_log__keys_ignored=['epoch', 'train_loss'])).

  • iterator_train__shuffle (bool (default=True)) – Defines whether train dataset will be shuffled. As skorch does not shuffle the train dataset by default this one overwrites this option.

  • aggregate_predictions (bool (default=True)) – Whether to average cropped predictions to obtain window predictions. Used only in the cropped mode.

prefixes_#

Contains the prefixes to special parameters. E.g., since there is the 'module' prefix, it is possible to set parameters like so: NeuralNet(..., optimizer__momentum=0.95).

Type

list of str

cuda_dependent_attributes_#

Contains a list of all attribute prefixes whose values depend on a CUDA device. If a NeuralNet trained with a CUDA-enabled device is unpickled on a machine without CUDA or with CUDA disabled, the listed attributes are mapped to CPU. Expand this list if you want to add other cuda-dependent attributes.

Type

list of str

initialized_#

Whether the NeuralNet was initialized.

Type

bool

module_#

The instantiated module.

Type

torch module (instance)

criterion_#

The instantiated criterion.

Type

torch criterion (instance)

callbacks_#

The complete (i.e. default and other), initialized callbacks, in a tuple with unique names.

Type

list of tuples

_modules#

List of names of all modules that are torch modules. This list is collected dynamically when the net is initialized. Typically, there is no reason for a user to modify this list.

Type

list of str

_criteria#

List of names of all criteria that are torch modules. This list is collected dynamically when the net is initialized. Typically, there is no reason for a user to modify this list.

Type

list of str

_optimizers#

List of names of all optimizers. This list is collected dynamically when the net is initialized. Typically, there is no reason for a user to modify this list.

Type

list of str

classes_#

A list of class labels known to the classifier.

Type

array, shape (n_classes, )

Methods

get_iterator(dataset, training=False, drop_index=True)[source]#

Get an iterator that allows to loop over the batches of the given data.

If self.iterator_train__batch_size and/or self.iterator_test__batch_size are not set, use self.batch_size instead.

Parameters

  • dataset (torch Dataset (default=skorch.dataset.Dataset)) – Usually, self.dataset, initialized with the corresponding data, is passed to get_iterator.

  • training (bool (default=False)) – Whether to use iterator_train or iterator_test.

Returns

An instantiated iterator that allows to loop over the mini-batches.

Return type

iterator

get_loss(y_pred, y_true, *args, **kwargs)[source]#

Return the loss for this batch by calling NeuralNet get_loss.

Parameters

  • y_pred (torch tensor) – Predicted target values

  • y_true (torch tensor) – True target values.

  • X (input data, compatible with skorch.dataset.Dataset) –

    By default, you should be able to pass:

    • numpy arrays

    • torch tensors

    • pandas DataFrame or Series

    • scipy sparse CSR matrices

    • a dictionary of the former three

    • a list/tuple of the former three

    • a Dataset

    If this doesn’t work with your data, you have to pass a Dataset that can deal with the data.

  • training (bool (default=False)) – Whether train mode should be used or not.

Returns

loss – The loss value.

Return type

float

on_batch_end(net, *batch, training=False, **kwargs)[source]#
predict(X)[source]#

Return class labels for samples in X.

Parameters

X (input data, compatible with skorch.dataset.Dataset) –

By default, you should be able to pass:

  • numpy arrays

  • torch tensors

  • pandas DataFrame or Series

  • scipy sparse CSR matrices

  • a dictionary of the former three

  • a list/tuple of the former three

  • a Dataset

If this doesn’t work with your data, you have to pass a Dataset that can deal with the data.

Returns

y_pred

Return type

numpy ndarray

predict_proba(X)[source]#

Return the output of the module’s forward method as a numpy array. In case of cropped decoding returns averaged values for each trial.

If the module’s forward method returns multiple outputs as a tuple, it is assumed that the first output contains the relevant information and the other values are ignored. If all values are relevant or module’s output for each crop is needed, consider using forward() instead.

Parameters

X (input data, compatible with skorch.dataset.Dataset) –

By default, you should be able to pass:

  • numpy arrays

  • torch tensors

  • pandas DataFrame or Series

  • scipy sparse CSR matrices

  • a dictionary of the former three

  • a list/tuple of the former three

  • a Dataset

If this doesn’t work with your data, you have to pass a Dataset that can deal with the data.

Returns

y_proba

Return type

numpy ndarray

predict_trials(X, return_targets=True)[source]#

Create trialwise predictions and optionally also return trialwise labels from cropped dataset.

Parameters
Returns

  • trial_predictions (np.ndarray) – 3-dimensional array (n_trials x n_classes x n_predictions), where the number of predictions depend on the chosen window size and the receptive field of the network.

  • trial_labels (np.ndarray) – 2-dimensional array (n_trials x n_targets) where the number of targets depends on the decoding paradigm and can be either a single value, multiple values, or a sequence.

predict_with_window_inds_and_ys(dataset)[source]#