braindecode 0.8__py3-none-any.whl → 1.0.0__py3-none-any.whl

braindecode/models/eegminer.py

@@ -0,0 +1,255 @@
+"""
+* Copyright (C) Cogitat, Ltd.
+* Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
+* Patent GB2609265 - Learnable filters for eeg classification
+* https://www.ipo.gov.uk/p-ipsum/Case/ApplicationNumber/GB2113420.0
+"""
+
+from functools import partial
+
+import torch
+from einops.layers.torch import Rearrange
+from torch import nn
+from torch.fft import fftfreq
+
+import braindecode.functional as F
+from braindecode.models.base import EEGModuleMixin
+from braindecode.modules import GeneralizedGaussianFilter
+
+_eeg_miner_methods = ["mag", "corr", "plv"]
+
+
+class EEGMiner(EEGModuleMixin, nn.Module):
+    """EEGMiner from Ludwig et al (2024) [eegminer]_.
+
+    .. figure:: https://content.cld.iop.org/journals/1741-2552/21/3/036010/revision2/jnead44d7f1_hr.jpg
+       :align: center
+       :alt: EEGMiner Architecture
+
+    EEGMiner is a neural network model for EEG signal classification using
+    learnable generalized Gaussian filters. The model leverages frequency domain
+    filtering and connectivity metrics or feature extraction, such as Phase Locking
+    Value (PLV) to extract meaningful features from EEG data, enabling effective
+    classification tasks.
+
+    The model has the following steps:
+
+    - **Generalized Gaussian** filters in the frequency domain to the input EEG signals.
+
+    - **Connectivity estimators** (corr, plv) or **Electrode-Wise Band Power** (mag), by default (plv).
+        - `'corr'`: Computes the correlation of the filtered signals.
+        - `'plv'`: Computes the phase locking value of the filtered signals.
+        - `'mag'`: Computes the magnitude of the filtered signals.
+
+    - **Feature Normalization**
+        - Apply batch normalization.
+
+    - **Final Layer**
+        - Feeds the batch-normalized features into a final linear layer for classification.
+
+    Depending on the selected method (`mag`, `corr`, or `plv`),
+    it computes the filtered signals' magnitude, correlation, or phase locking value.
+    These features are then normalized and passed through a batch normalization layer
+    before being fed into a final linear layer for classification.
+
+    The input to EEGMiner should be a three-dimensional tensor representing EEG signals:
+
+    ``(batch_size, n_channels, n_timesteps)``.
+
+    Notes
+    -----
+    EEGMiner incorporates learnable parameters for filter characteristics, allowing the
+    model to adaptively learn optimal frequency bands and phase delays for the classification task.
+    By default, using the PLV as a connectivity metric makes EEGMiner suitable for tasks requiring
+    the analysis of phase relationships between different EEG channels.
+
+    The model and the module have patent [eegminercode]_, and the code is CC BY-NC 4.0.
+
+    .. versionadded:: 0.9
+
+    Parameters
+    ----------
+    method : str, default="plv"
+        The method used for feature extraction. Options are:
+        - "mag": Electrode-Wise band power of the filtered signals.
+        - "corr": Correlation between filtered channels.
+        - "plv": Phase Locking Value connectivity metric.
+    filter_f_mean : list of float, default=[23.0, 23.0]
+        Mean frequencies for the generalized Gaussian filters.
+    filter_bandwidth : list of float, default=[44.0, 44.0]
+        Bandwidths for the generalized Gaussian filters.
+    filter_shape : list of float, default=[2.0, 2.0]
+        Shape parameters for the generalized Gaussian filters.
+    group_delay : tuple of float, default=(20.0, 20.0)
+        Group delay values for the filters in milliseconds.
+    clamp_f_mean : tuple of float, default=(1.0, 45.0)
+        Clamping range for the mean frequency parameters.
+
+    References
+    ----------
+    .. [eegminer] Ludwig, S., Bakas, S., Adamos, D. A., Laskaris, N., Panagakis,
+       Y., & Zafeiriou, S. (2024). EEGMiner: discovering interpretable features
+       of brain activity with learnable filters. Journal of Neural Engineering,
+       21(3), 036010.
+    .. [eegminercode] Ludwig, S., Bakas, S., Adamos, D. A., Laskaris, N., Panagakis,
+       Y., & Zafeiriou, S. (2024). EEGMiner: discovering interpretable features
+       of brain activity with learnable filters.
+       https://github.com/SMLudwig/EEGminer/.
+       Cogitat, Ltd. "Learnable filters for EEG classification."
+       Patent GB2609265.
+       https://www.ipo.gov.uk/p-ipsum/Case/ApplicationNumber/GB2113420.0
+    """
+
+    def __init__(
+        self,  # Signal related parameters
+        method: str = "plv",
+        n_chans=None,
+        n_outputs=None,
+        n_times=None,
+        chs_info=None,
+        input_window_seconds=None,
+        sfreq=None,
+        # model related
+        filter_f_mean=(23.0, 23.0),
+        filter_bandwidth=(44.0, 44.0),
+        filter_shape=(2.0, 2.0),
+        group_delay=(20.0, 20.0),
+        clamp_f_mean=(1.0, 45.0),
+    ):
+        super().__init__(
+            n_outputs=n_outputs,
+            n_chans=n_chans,
+            chs_info=chs_info,
+            n_times=n_times,
+            input_window_seconds=input_window_seconds,
+            sfreq=sfreq,
+        )
+        del n_outputs, n_chans, chs_info, n_times, input_window_seconds, sfreq
+
+        # Initialize filter parameters
+        self.filter_f_mean = filter_f_mean
+        self.filter_bandwidth = filter_bandwidth
+        self.filter_shape = filter_shape
+        self.n_filters = len(self.filter_f_mean)
+        self.group_delay = group_delay
+        self.clamp_f_mean = clamp_f_mean
+        self.method = method.lower()
+
+        if self.method not in _eeg_miner_methods:
+            raise ValueError(
+                f"The method {self.method} is not one of the valid options"
+                f" {_eeg_miner_methods}"
+            )
+
+        if self.method == "mag" or self.method == "corr":
+            inverse_fourier = True
+            in_channels = self.n_chans
+            out_channels = self.n_chans * self.n_filters
+        else:
+            inverse_fourier = False
+            in_channels = 1
+            out_channels = 1 * self.n_filters
+
+        # Generalized Gaussian Filter
+        self.filter = GeneralizedGaussianFilter(
+            in_channels=in_channels,
+            out_channels=out_channels,
+            sequence_length=self.n_times,
+            sample_rate=self.sfreq,
+            f_mean=self.filter_f_mean,
+            bandwidth=self.filter_bandwidth,
+            shape=self.filter_shape,
+            affine_group_delay=False,
+            inverse_fourier=inverse_fourier,
+            group_delay=self.group_delay,
+            clamp_f_mean=self.clamp_f_mean,
+        )
+
+        # Forward method
+        if self.method == "mag":
+            self.method_forward = self._apply_mag_forward
+            self.n_features = self.n_chans * self.n_filters
+            self.ensure_dim = nn.Identity()
+        elif self.method == "corr":
+            self.method_forward = partial(
+                self._apply_corr_forward,
+                n_chans=self.n_chans,
+                n_filters=self.n_filters,
+                n_times=self.n_times,
+            )
+            self.n_features = self.n_filters * self.n_chans * (self.n_chans - 1) // 2
+            self.ensure_dim = nn.Identity()
+        elif self.method == "plv":
+            self.method_forward = partial(self._apply_plv, n_chans=self.n_chans)
+            self.ensure_dim = Rearrange("... d -> ... 1 d")
+            self.n_features = (self.n_filters * self.n_chans * (self.n_chans - 1)) // 2
+
+        self.flatten_layer = nn.Flatten()
+        # Classifier
+        self.batch_layer = nn.BatchNorm1d(self.n_features, affine=False)
+        self.final_layer = nn.Linear(self.n_features, self.n_outputs)
+        nn.init.zeros_(self.final_layer.bias)
+
+    def forward(self, x):
+        """x: (batch, electrodes, time)"""
+        batch = x.shape[0]
+        x = self.ensure_dim(x)
+        # Apply Gaussian filters in frequency domain
+        # x -> (batch, electrodes * filters, time)
+        x = self.filter(x)
+
+        x = self.method_forward(x=x, batch=batch)
+        # Classifier
+        # Note that the order of dimensions before flattening the feature vector is important
+        # for attributing feature weights during interpretation.
+        x = x.reshape(batch, self.n_features)
+        x = self.batch_layer(x)
+        x = self.final_layer(x)
+
+        return x
+
+    @staticmethod
+    def _apply_mag_forward(x, batch=None):
+        # Signal magnitude
+        x = x * x
+        x = x.mean(dim=-1)
+        x = torch.sqrt(x)
+        return x
+
+    @staticmethod
+    def _apply_corr_forward(
+        x, batch, n_chans, n_filters, n_times, epilson: float = 1e-6
+    ):
+        x = x.reshape(batch, n_chans, n_filters, n_times).transpose(-3, -2)
+        x = (x - x.mean(dim=-1, keepdim=True)) / torch.sqrt(
+            x.var(dim=-1, keepdim=True) + epilson
+        )
+        x = torch.matmul(x, x.transpose(-2, -1)) / x.shape[-1]
+        # Original tensor shape: [batch, n_filters, chans, chans]
+        x = x.permute(0, 2, 3, 1)
+        # New tensor shape: [batch, chans, chans, n_filters]
+        # move filter channels to the end
+        x = x.abs()
+
+        # Get upper triu of symmetric connectivity matrix
+        triu = torch.triu_indices(n_chans, n_chans, 1)
+        x = x[:, triu[0], triu[1], :]
+
+        return x
+
+    @staticmethod
+    def _apply_plv(x, n_chans, batch=None):
+        # Compute PLV connectivity
+        # x -> (batch, electrodes, electrodes, filters)
+        x = x.transpose(-4, -3)  # swap electrodes and filters
+        # adjusting to compute the plv
+        x = F.plv_time(x, forward_fourier=False)
+        # batch, number of filters, connectivity matrix
+        # [batch, n_filters, chans, chans]
+        x = x.permute(0, 2, 3, 1)
+        # [batch, chans, chans, n_filters]
+
+        # Get upper triu of symmetric connectivity matrix
+        triu = torch.triu_indices(n_chans, n_chans, 1)
+        x = x[:, triu[0], triu[1], :]
+        return x