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

braindecode/models/ctnet.py

@@ -0,0 +1,450 @@
+"""
+CTNet: a convolutional transformer network for EEG-based motor imagery
+classification from Wei Zhao et al. (2024).
+"""
+
+# Authors: Wei Zhao <zhaowei701@163.com>
+#          Bruno Aristimunha <b.aristimunha@gmail.com> (braindecode adaptation)
+# License: MIT
+
+from __future__ import annotations
+
+import math
+
+import torch
+from einops.layers.torch import Rearrange
+from mne.utils import warn
+from torch import Tensor, nn
+
+from braindecode.models.base import EEGModuleMixin
+from braindecode.modules import (
+    FeedForwardBlock,
+    MultiHeadAttention,
+)
+
+
+class CTNet(EEGModuleMixin, nn.Module):
+    """CTNet from Zhao, W et al (2024) [ctnet]_.
+
+     A Convolutional Transformer Network for EEG-Based Motor Imagery Classification
+
+     .. figure:: https://raw.githubusercontent.com/snailpt/CTNet/main/architecture.png
+        :align: center
+        :alt: CTNet Architecture
+
+    CTNet is an end-to-end neural network architecture designed for classifying motor imagery (MI) tasks from EEG signals.
+    The model combines convolutional neural networks (CNNs) with a Transformer encoder to capture both local and global temporal dependencies in the EEG data.
+
+    The architecture consists of three main components:
+
+    1. **Convolutional Module**:
+        - Apply EEGNetV4 to perform some feature extraction, denoted here as
+        _PatchEmbeddingEEGNet module.
+
+    2. **Transformer Encoder Module**:
+        - Utilizes multi-head self-attention mechanisms as EEGConformer but
+        with residual blocks.
+
+    3. **Classifier Module**:
+        - Combines features from both the convolutional module
+        and the Transformer encoder.
+        - Flattens the combined features and applies dropout for regularization.
+        - Uses a fully connected layer to produce the final classification output.
+
+    Parameters
+    ----------
+    activation : nn.Module, default=nn.GELU
+        Activation function to use in the network.
+    heads : int, default=4
+        Number of attention heads in the Transformer encoder.
+    emb_size : int, default=40
+        Embedding size (dimensionality) for the Transformer encoder.
+    depth : int, default=6
+        Number of encoder layers in the Transformer.
+    n_filters_time : int, default=20
+        Number of temporal filters in the first convolutional layer.
+    kernel_size : int, default=64
+        Kernel size for the temporal convolutional layer.
+    depth_multiplier : int, default=2
+        Multiplier for the number of depth-wise convolutional filters.
+    pool_size_1 : int, default=8
+        Pooling size for the first average pooling layer.
+    pool_size_2 : int, default=8
+        Pooling size for the second average pooling layer.
+    drop_prob_cnn : float, default=0.3
+        Dropout probability after convolutional layers.
+    drop_prob_posi : float, default=0.1
+        Dropout probability for the positional encoding in the Transformer.
+    drop_prob_final : float, default=0.5
+        Dropout probability before the final classification layer.
+
+    Notes
+    -----
+    This implementation is adapted from the original CTNet source code
+    [ctnetcode]_ to comply with Braindecode's model standards.
+
+    References
+    ----------
+    .. [ctnet] Zhao, W., Jiang, X., Zhang, B., Xiao, S., & Weng, S. (2024).
+        CTNet: a convolutional transformer network for EEG-based motor imagery
+        classification. Scientific Reports, 14(1), 20237.
+    .. [ctnetcode] Zhao, W., Jiang, X., Zhang, B., Xiao, S., & Weng, S. (2024).
+        CTNet source code:
+        https://github.com/snailpt/CTNet
+    """
+
+    def __init__(
+        self,
+        # Base arguments
+        n_outputs=None,
+        n_chans=None,
+        sfreq=None,
+        chs_info=None,
+        n_times=None,
+        input_window_seconds=None,
+        # Model specific arguments
+        activation_patch: nn.Module = nn.ELU,
+        activation_transformer: nn.Module = nn.GELU,
+        drop_prob_cnn: float = 0.3,
+        drop_prob_posi: float = 0.1,
+        drop_prob_final: float = 0.5,
+        # other parameters
+        heads: int = 4,
+        emb_size: int = 40,
+        depth: int = 6,
+        n_filters_time: int = 20,
+        kernel_size: int = 64,
+        depth_multiplier: int = 2,
+        pool_size_1: int = 8,
+        pool_size_2: int = 8,
+    ):
+        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
+
+        self.emb_size = emb_size
+        self.activation_patch = activation_patch
+        self.activation_transformer = activation_transformer
+
+        self.n_filters_time = n_filters_time
+        self.drop_prob_cnn = drop_prob_cnn
+        self.pool_size_1 = pool_size_1
+        self.pool_size_2 = pool_size_2
+        self.depth_multiplier = depth_multiplier
+        self.kernel_size = kernel_size
+        self.drop_prob_posi = drop_prob_posi
+        self.drop_prob_final = drop_prob_final
+
+        # n_times - pool_size_1 / p
+        sequence_length = math.floor(
+            (
+                math.floor((self.n_times - self.pool_size_1) / self.pool_size_1 + 1)
+                - self.pool_size_2
+            )
+            / self.pool_size_2
+            + 1
+        )
+
+        # Layers
+        self.ensuredim = Rearrange("batch nchans time -> batch 1 nchans time")
+        self.flatten = nn.Flatten()
+
+        self.cnn = _PatchEmbeddingEEGNet(
+            n_filters_time=self.n_filters_time,
+            kernel_size=self.kernel_size,
+            depth_multiplier=self.depth_multiplier,
+            pool_size_1=self.pool_size_1,
+            pool_size_2=self.pool_size_2,
+            drop_prob=self.drop_prob_cnn,
+            n_chans=self.n_chans,
+            activation=self.activation_patch,
+        )
+
+        self.position = _PositionalEncoding(
+            emb_size=emb_size,
+            drop_prob=self.drop_prob_posi,
+            n_times=self.n_times,
+            pool_size=self.pool_size_1,
+        )
+
+        self.trans = _TransformerEncoder(
+            heads, depth, emb_size, activation=self.activation_transformer
+        )
+
+        self.flatten_drop_layer = nn.Sequential(
+            nn.Flatten(),
+            nn.Dropout(p=self.drop_prob_final),
+        )
+
+        self.final_layer = nn.Linear(
+            in_features=emb_size * sequence_length, out_features=self.n_outputs
+        )
+
+    def forward(self, x: Tensor) -> Tensor:
+        """
+        Forward pass of the CTNet model.
+
+        Parameters
+        ----------
+        x : Tensor
+            Input tensor of shape (batch_size, n_channels, n_times).
+
+        Returns
+        -------
+        Tensor
+            Output with shape (batch_size, n_outputs).
+        """
+        x = self.ensuredim(x)
+        cnn = self.cnn(x)
+        cnn = cnn * math.sqrt(self.emb_size)
+        cnn = self.position(cnn)
+        trans = self.trans(cnn)
+        features = cnn + trans
+        flatten_feature = self.flatten(features)
+        out = self.final_layer(flatten_feature)
+        return out
+
+
+class _PatchEmbeddingEEGNet(nn.Module):
+    def __init__(
+        self,
+        n_filters_time: int = 16,
+        kernel_size: int = 64,
+        depth_multiplier: int = 2,
+        pool_size_1: int = 8,
+        pool_size_2: int = 8,
+        drop_prob: float = 0.3,
+        n_chans: int = 22,
+        activation: nn.Module = nn.ELU,
+    ):
+        super().__init__()
+        n_filters_out = depth_multiplier * n_filters_time
+        self.eegnet_module = nn.Sequential(
+            # Temporal convolution
+            nn.Conv2d(
+                in_channels=1,
+                out_channels=n_filters_time,
+                kernel_size=(1, kernel_size),
+                stride=(1, 1),
+                padding="same",
+                bias=False,
+            ),
+            nn.BatchNorm2d(n_filters_time),
+            # Channel depth-wise convolution
+            nn.Conv2d(
+                in_channels=n_filters_time,
+                out_channels=n_filters_out,
+                kernel_size=(n_chans, 1),
+                stride=(1, 1),
+                groups=n_filters_time,
+                padding="valid",
+                bias=False,
+            ),
+            nn.BatchNorm2d(n_filters_out),
+            activation(),
+            # First average pooling
+            nn.AvgPool2d(kernel_size=(1, pool_size_1)),
+            nn.Dropout(drop_prob),
+            # Spatial convolution
+            nn.Conv2d(
+                in_channels=n_filters_out,
+                out_channels=n_filters_out,
+                kernel_size=(1, 16),
+                padding="same",
+                bias=False,
+            ),
+            nn.BatchNorm2d(n_filters_out),
+            activation(),
+            # Second average pooling
+            nn.AvgPool2d(kernel_size=(1, pool_size_2)),
+            nn.Dropout(drop_prob),
+        )
+
+        self.projection = nn.Sequential(
+            Rearrange("b e h w -> b (h w) e"),
+        )
+
+    def forward(self, x: Tensor) -> Tensor:
+        """
+        Forward pass of the Patch Embedding CNN.
+
+        Parameters
+        ----------
+        x : Tensor
+            Input tensor of shape (batch_size, 1, n_channels, n_times).
+
+        Returns
+        -------
+        Tensor
+            Embedded patches of shape (batch_size, num_patches, embedding_dim).
+        """
+        x = self.eegnet_module(x)
+        x = self.projection(x)
+        return x
+
+
+class _ResidualAdd(nn.Module):
+    def __init__(self, module: nn.Module, emb_size: int, drop_p: float):
+        super().__init__()
+        self.module = module
+        self.drop = nn.Dropout(drop_p)
+        self.layernorm = nn.LayerNorm(emb_size)
+
+    def forward(self, x: Tensor) -> Tensor:
+        """
+        Forward pass with residual connection.
+
+        Parameters
+        ----------
+        x : Tensor
+            Input tensor.
+        **kwargs : Any
+            Additional arguments.
+
+        Returns
+        -------
+        Tensor
+            Output tensor after applying residual connection.
+        """
+        res = self.module(x)
+        out = self.layernorm(self.drop(res) + x)
+        return out
+
+
+class _TransformerEncoderBlock(nn.Module):
+    def __init__(
+        self,
+        dim_feedforward: int,
+        num_heads: int = 4,
+        drop_prob: float = 0.5,
+        forward_expansion: int = 4,
+        forward_drop_p: float = 0.5,
+        activation: nn.Module = nn.GELU,
+    ):
+        super().__init__()
+        self.attention = _ResidualAdd(
+            nn.Sequential(
+                MultiHeadAttention(dim_feedforward, num_heads, drop_prob),
+            ),
+            dim_feedforward,
+            drop_prob,
+        )
+        self.feed_forward = _ResidualAdd(
+            nn.Sequential(
+                FeedForwardBlock(
+                    dim_feedforward,
+                    expansion=forward_expansion,
+                    drop_p=forward_drop_p,
+                    activation=activation,
+                ),
+            ),
+            dim_feedforward,
+            drop_prob,
+        )
+
+    def forward(self, x: Tensor) -> Tensor:
+        """
+        Forward pass of the transformer encoder block.
+
+        Parameters
+        ----------
+        x : Tensor
+            Input tensor.
+        **kwargs : Any
+            Additional arguments.
+
+        Returns
+        -------
+        Tensor
+            Output tensor after transformer encoder block.
+        """
+        x = self.attention(x)
+        x = self.feed_forward(x)
+        return x
+
+
+class _TransformerEncoder(nn.Module):
+    def __init__(
+        self,
+        nheads: int,
+        depth: int,
+        dim_feedforward: int,
+        activation: nn.Module = nn.GELU,
+    ):
+        super().__init__()
+        self.layers = nn.Sequential(
+            *[
+                _TransformerEncoderBlock(
+                    dim_feedforward=dim_feedforward,
+                    num_heads=nheads,
+                    activation=activation,
+                )
+                for _ in range(depth)
+            ]
+        )
+
+    def forward(self, x: Tensor) -> Tensor:
+        """
+        Forward pass of the transformer encoder.
+
+        Parameters
+        ----------
+        x : Tensor
+            Input tensor.
+
+        Returns
+        -------
+        Tensor
+            Output tensor after transformer encoder.
+        """
+        return self.layers(x)
+
+
+class _PositionalEncoding(nn.Module):
+    def __init__(
+        self,
+        n_times: int,
+        emb_size: int,
+        length: int = 100,
+        drop_prob: float = 0.1,
+        pool_size: int = 8,
+    ):
+        super().__init__()
+        self.pool_size = pool_size
+        self.n_times = n_times
+
+        if int(n_times / (pool_size * pool_size)) > length:
+            warn(
+                "the temporal dimensional is too long for this default length. "
+                "The length parameter will be automatically adjusted to "
+                "avoid inference issues."
+            )
+            length = int(n_times / (pool_size * pool_size))
+
+        self.dropout = nn.Dropout(drop_prob)
+        self.encoding = nn.Parameter(torch.randn(1, length, emb_size))
+
+    def forward(self, x: Tensor) -> Tensor:
+        """
+        Forward pass of the positional encoding.
+
+        Parameters
+        ----------
+        x : Tensor
+            Input tensor of shape (batch_size, sequence_length, embedding_dim).
+
+        Returns
+        -------
+        Tensor
+            Tensor with positional encoding added.
+        """
+        seq_length = x.size(1)
+        encoding = self.encoding[:, :seq_length, :]
+        x = x + encoding
+        return self.dropout(x)