braindecode 1.3.0.dev175955015__py3-none-any.whl → 1.3.0.dev176481332__py3-none-any.whl
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- braindecode/augmentation/base.py +1 -1
- braindecode/datasets/__init__.py +10 -2
- braindecode/datasets/base.py +115 -151
- braindecode/datasets/bcicomp.py +4 -4
- braindecode/datasets/bids.py +3 -3
- braindecode/datasets/experimental.py +2 -2
- braindecode/datasets/mne.py +3 -5
- braindecode/datasets/moabb.py +2 -2
- braindecode/datasets/nmt.py +2 -2
- braindecode/datasets/sleep_physio_challe_18.py +2 -2
- braindecode/datasets/sleep_physionet.py +2 -2
- braindecode/datasets/tuh.py +2 -2
- braindecode/datasets/xy.py +2 -2
- braindecode/datautil/serialization.py +7 -7
- braindecode/functional/functions.py +6 -2
- braindecode/functional/initialization.py +2 -3
- braindecode/models/__init__.py +2 -0
- braindecode/models/atcnet.py +26 -27
- braindecode/models/attentionbasenet.py +37 -32
- braindecode/models/attn_sleep.py +2 -0
- braindecode/models/base.py +2 -2
- braindecode/models/bendr.py +469 -0
- braindecode/models/biot.py +2 -0
- braindecode/models/contrawr.py +2 -0
- braindecode/models/ctnet.py +8 -3
- braindecode/models/deepsleepnet.py +28 -19
- braindecode/models/eegconformer.py +2 -2
- braindecode/models/eeginception_erp.py +31 -25
- braindecode/models/eegitnet.py +2 -0
- braindecode/models/eegminer.py +2 -0
- braindecode/models/eegnet.py +1 -1
- braindecode/models/eegtcnet.py +2 -0
- braindecode/models/fbcnet.py +2 -0
- braindecode/models/fblightconvnet.py +2 -0
- braindecode/models/fbmsnet.py +2 -0
- braindecode/models/ifnet.py +2 -0
- braindecode/models/labram.py +33 -26
- braindecode/models/msvtnet.py +2 -0
- braindecode/models/patchedtransformer.py +1 -1
- braindecode/models/signal_jepa.py +8 -0
- braindecode/models/sinc_shallow.py +12 -9
- braindecode/models/sstdpn.py +11 -11
- braindecode/models/summary.csv +1 -0
- braindecode/models/syncnet.py +2 -0
- braindecode/models/tcn.py +2 -0
- braindecode/models/usleep.py +26 -21
- braindecode/models/util.py +1 -0
- braindecode/modules/attention.py +10 -10
- braindecode/modules/blocks.py +3 -3
- braindecode/modules/filter.py +2 -3
- braindecode/modules/layers.py +18 -17
- braindecode/preprocessing/__init__.py +24 -0
- braindecode/preprocessing/eegprep_preprocess.py +1202 -0
- braindecode/preprocessing/preprocess.py +12 -12
- braindecode/preprocessing/util.py +166 -0
- braindecode/preprocessing/windowers.py +26 -20
- braindecode/samplers/base.py +8 -8
- braindecode/version.py +1 -1
- {braindecode-1.3.0.dev175955015.dist-info → braindecode-1.3.0.dev176481332.dist-info}/METADATA +4 -2
- braindecode-1.3.0.dev176481332.dist-info/RECORD +106 -0
- braindecode-1.3.0.dev175955015.dist-info/RECORD +0 -103
- {braindecode-1.3.0.dev175955015.dist-info → braindecode-1.3.0.dev176481332.dist-info}/WHEEL +0 -0
- {braindecode-1.3.0.dev175955015.dist-info → braindecode-1.3.0.dev176481332.dist-info}/licenses/LICENSE.txt +0 -0
- {braindecode-1.3.0.dev175955015.dist-info → braindecode-1.3.0.dev176481332.dist-info}/licenses/NOTICE.txt +0 -0
- {braindecode-1.3.0.dev175955015.dist-info → braindecode-1.3.0.dev176481332.dist-info}/top_level.txt +0 -0
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- :class:`_InceptionModule1` **(multi-scale temporal + spatial mixing)**
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- *Operations.*
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- `EEGInceptionERP.c1`: :class:`torch.nn.Conv2d` ``k=(64,1)``, stride ``(1,1)``, *same* pad on input reshaped to ``(B,1,128,8)`` → BN → activation → dropout.
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- `EEGInceptionERP.d1`: :class:`torch.nn.Conv2d` (depthwise) ``k=(1,8)``, *valid* pad over channels → BN → activation → dropout.
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- `EEGInceptionERP.c2`: :class:`torch.nn.Conv2d` ``k=(32,1)`` → BN → activation → dropout; then `EEGInceptionERP.d2` depthwise ``k=(1,8)`` → BN → activation → dropout.
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- `EEGInceptionERP.c3`: :class:`torch.nn.Conv2d` ``k=(16,1)`` → BN → activation → dropout; then `EEGInceptionERP.d3` depthwise ``k=(1,8)`` → BN → activation → dropout.
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- `EEGInceptionERP.n1`: :class:`torch.nn.Concat` over branch features.
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- `EEGInceptionERP.a1`: :class:`torch.nn.AvgPool2d` ``pool=(4,1)``, stride ``(4,1)`` for temporal downsampling.
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*Interpretability/robustness.* Depthwise `1 x n_chans` layers act as learnable montage-wide spatial filters per temporal scale; pooling stabilizes against jitter.
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- :class:`_InceptionModule2` **(refinement at coarser timebase)**
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- *Operations.*
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- `EEGInceptionERP.c4`: :class:`torch.nn.Conv2d` ``k=(16,1)`` → BN → activation → dropout.
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- `EEGInceptionERP.c5`: :class:`torch.nn.Conv2d` ``k=(8,1)`` → BN → activation → dropout.
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- `EEGInceptionERP.c6`: :class:`torch.nn.Conv2d` ``k=(4,1)`` → BN → activation → dropout.
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- `EEGInceptionERP.n2`: :class:`torch.nn.Concat` (merge C4-C6 outputs).
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- `EEGInceptionERP.a2`: :class:`torch.nn.AvgPool2d` ``pool=(2,1)``, stride ``(2,1)``.
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- `EEGInceptionERP.c7`: :class:`torch.nn.Conv2d` ``k=(8,1)`` → BN → activation → dropout; then `EEGInceptionERP.a3`: :class:`torch.nn.AvgPool2d` ``pool=(2,1)``.
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- `EEGInceptionERP.c8`: :class:`torch.nn.Conv2d` ``k=(4,1)`` → BN → activation → dropout; then `EEGInceptionERP.a4`: :class:`torch.nn.AvgPool2d` ``pool=(2,1)``.
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*Role.* Adds higher-level, shorter-window evidence while progressively compressing temporal dimension.
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- :class:`_OutputModule` **(aggregation + readout)**
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- *Operations.*
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- :class:`torch.nn.Flatten`
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- :class:`torch.nn.Linear` ``(features → 2)``
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.. rubric:: Convolutional Details
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- **Temporal (where time-domain patterns are learned).**
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First module uses 1D temporal kernels along the 128-sample axis: ``64``, ``32``, ``16``
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(≈500, 250, 125 ms at 128 Hz). After ``pool=(4,1)``, the second module applies ``16``,
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``8``, ``4`` (≈125, 62.5, 31.25 ms at the pooled rate). All strides are ``1`` in convs;
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temporal resolution changes only via average pooling.
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- **Spatial (how electrodes are processed).**
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Depthwise convs with ``k=(1,8)`` span all channels and are applied **per temporal branch**,
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yielding scale-specific channel projections (no cross-branch mixing until concatenation).
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There is no full 2D mixing kernel; spatial mixing is factorized and lightweight.
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- **Spectral (how frequency information is captured).**
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No explicit transform; multiple temporal kernels form a *learned filter bank* over
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ERP-relevant bands. Successive pooling acts as low-pass integration to emphasize sustained
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post-stimulus components.
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.. rubric:: Additional Mechanisms
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braindecode/models/eegitnet.py
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class EEGITNet(EEGModuleMixin, nn.Sequential):
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"""EEG-ITNet from Salami, et al (2022) [Salami2022]_
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:bdg-success:`Convolution` :bdg-secondary:`Recurrent`
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.. figure:: https://braindecode.org/dev/_static/model/eegitnet.jpg
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:align: center
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:alt: EEG-ITNet Architecture
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braindecode/models/eegminer.py
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class EEGMiner(EEGModuleMixin, nn.Module):
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"""EEGMiner from Ludwig et al (2024) [eegminer]_.
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:bdg-success:`Convolution` :bdg-warning:`Interpretability`
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.. figure:: https://content.cld.iop.org/journals/1741-2552/21/3/036010/revision2/jnead44d7f1_hr.jpg
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:align: center
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:alt: EEGMiner Architecture
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braindecode/models/eegnet.py
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- **Temporal.** The initial temporal convs serve as a *learned filter bank*:
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long 1-D kernels (implemented as 2-D with singleton spatial extent) emphasize oscillatory bands and transients.
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Because this stage is linear prior to BN/ELU, kernels can be analyzed as FIR filters to reveal each feature
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Because this stage is linear prior to BN/ELU, kernels can be analyzed as FIR filters to reveal each feature's spectrum [Lawhern2018]_.
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- **Spatial.** The depthwise spatial conv spans the full channel axis (kernel height = #electrodes; temporal size = 1).
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With ``groups = F1``, each temporal filter learns its own set of ``D`` spatial projections—akin to CSP, learned end-to-end and
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braindecode/models/eegtcnet.py
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class EEGTCNet(EEGModuleMixin, nn.Module):
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"""EEGTCNet model from Ingolfsson et al. (2020) [ingolfsson2020]_.
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:bdg-success:`Convolution` :bdg-secondary:`Recurrent`
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.. figure:: https://braindecode.org/dev/_static/model/eegtcnet.jpg
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:align: center
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:alt: EEGTCNet Architecture
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braindecode/models/fbcnet.py
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class FBCNet(EEGModuleMixin, nn.Module):
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"""FBCNet from Mane, R et al (2021) [fbcnet2021]_.
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:bdg-success:`Convolution` :bdg-primary:`Filterbank`
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.. figure:: https://raw.githubusercontent.com/ravikiran-mane/FBCNet/refs/heads/master/FBCNet-V2.png
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:align: center
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:alt: FBCNet Architecture
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class FBLightConvNet(EEGModuleMixin, nn.Module):
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"""LightConvNet from Ma, X et al (2023) [lightconvnet]_.
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:bdg-success:`Convolution` :bdg-primary:`Filterbank`
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.. figure:: https://raw.githubusercontent.com/Ma-Xinzhi/LightConvNet/refs/heads/main/network_architecture.png
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:align: center
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:alt: LightConvNet Neural Network
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class FBMSNet(EEGModuleMixin, nn.Module):
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"""FBMSNet from Liu et al (2022) [fbmsnet]_.
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:bdg-success:`Convolution` :bdg-primary:`Filterbank`
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.. figure:: https://raw.githubusercontent.com/Want2Vanish/FBMSNet/refs/heads/main/FBMSNet.png
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:align: center
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:alt: FBMSNet Architecture
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class IFNet(EEGModuleMixin, nn.Module):
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"""IFNetV2 from Wang J et al (2023) [ifnet]_.
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:bdg-success:`Convolution` :bdg-primary:`Filterbank`
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.. figure:: https://raw.githubusercontent.com/Jiaheng-Wang/IFNet/main/IFNet.png
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:align: center
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:alt: IFNetV2 Architecture
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Authors: Wei-Bang Jiang
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Bruno Aristimunha <b.aristimunha@gmail.com>
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Matthew Chen <matt.chen4260@gmail.com>
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"""
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class Labram(EEGModuleMixin, nn.Module):
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"""Labram from Jiang, W B et al (2024) [Jiang2024]_.
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:bdg-success:`Convolution` :bdg-danger:`Large Brain Model`
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.. figure:: https://arxiv.org/html/2405.18765v1/x1.png
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:align: center
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:alt: Labram Architecture.
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Large Brain Model for Learning Generic Representations with Tremendous
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EEG Data in BCI from [Jiang2024]_
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EEG Data in BCI from [Jiang2024]_.
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This is an **adaptation** of the code [Code2024]_ from the Labram model.
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BEiTv2 [BeiTv2]_.
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The models can be used in two modes:
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- Neural Tokenizer: Design to get an embedding layers (e.g. classification).
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- Neural Decoder: To extract the ampliture and phase outputs with a VQSNP.
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The braindecode's modification is to allow the model to be used in
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patch_size) as input with static segmentation of the input data.
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The models have the following sequence of steps
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The models have the following sequence of steps::
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- SegmentPatch: Segment the input data in patches;
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- TemporalConv: Apply a temporal convolution to the segmented data;
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- Residual adding cls, temporal and position embeddings (optional);
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- WindowsAttentionBlock: Apply a windows attention block to the data;
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- LayerNorm: Apply layer normalization to the data;
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- PatchEmbed: Apply a patch embedding to the input data;
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.. versionadded:: 0.9
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--------
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Load pre-trained weights::
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>>> import torch
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>>> model = Labram(n_times=1600, n_chans=64, n_outputs=4)
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>>> url = "https://huggingface.co/braindecode/Labram-Braindecode/blob/main/braindecode_labram_base.pt"
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>>> state = torch.hub.load_state_dict_from_url(url, progress=True)
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Parameters
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neural_tokenizer : bool (default=True)
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The model can be used in two modes: Neural Tokenizer or Neural Decoder.
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attn_head_dim : bool (default=None)
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during pre-training.
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braindecode/models/msvtnet.py
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class MSVTNet(EEGModuleMixin, nn.Module):
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"""MSVTNet model from Liu K et al (2024) from [msvt2024]_.
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:bdg-success:`Convolution` :bdg-secondary:`Recurrent` :bdg-info:`Small Attention`
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for EEG signal classification, as described in [msvt2024]_.
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r"""Patched Brain Transformer (PBT) model from Klein et al. (2025) [pbt]_.
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:bdg-danger:`Large Brain
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:bdg-danger:`Large Brain Model`
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This implementation was based in https://github.com/timonkl/PatchedBrainTransformer/
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"""Architecture introduced in signal-JEPA for self-supervised pre-training, Guetschel, P et al (2024) [1]_
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:bdg-success:`Convolution` :bdg-dark-line:`Channel` :bdg-danger:`Large Brain Model`
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This model is not meant for classification but for SSL pre-training.
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:bdg-success:`Convolution` :bdg-dark-line:`Channel` :bdg-danger:`Large Brain Model`
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:bdg-success:`Convolution` :bdg-dark-line:`Channel` :bdg-danger:`Large Brain Model`
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This architecture is one of the variants of :class:`SignalJEPA`
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that can be used for classification purposes.
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"""Pre-local downstream architecture introduced in signal-JEPA Guetschel, P et al (2024) [1]_.
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:bdg-success:`Convolution` :bdg-dark-line:`Channel` :bdg-danger:`Large Brain Model`
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This architecture is one of the variants of :class:`SignalJEPA`
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that can be used for classification purposes.
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"""Sinc-ShallowNet from Borra, D et al (2020) [borra2020]_.
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:bdg-success:`Convolution` :bdg-warning:`Interpretability`
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.. figure:: https://ars.els-cdn.com/content/image/1-s2.0-S0893608020302021-gr2_lrg.jpg
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:align: center
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:alt: SincShallowNet Architecture
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The Sinc-ShallowNet architecture has these fundamental blocks:
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significantly reducing the number of trainable parameters by only
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learning the lower and upper cutoff frequencies for each filter.
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each temporal feature map independently, further reducing
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parameters and enhancing interpretability.
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- *Dropout Layer*
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- *Flatten Layer*
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3. **Block 3: Classification**
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- *Fully Connected Layer*: Maps the feature vector to n_outputs.
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**Implementation Notes:**
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braindecode/models/sstdpn.py
CHANGED
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:alt: SSTDPN Architecture
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:width: 1000px
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The **Spatial
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The **Spatial-Spectral** and **Temporal - Dual Prototype Network** (SST-DPN)
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is an end-to-end 1D convolutional architecture designed for motor imagery (MI) EEG decoding,
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aiming to address challenges related to discriminative feature extraction and
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small-sample sizes [Han2025]_.
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SST-DPN consists of a feature extractor (_SSTEncoder, comprising Adaptive Spatial-Spectral
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Fusion and Multi-scale Variance Pooling) followed by Dual Prototype Learning classification [Han2025]_.
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1. **Adaptive Spatial
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multi-channel spatial
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(Spatial-Spectral Attention) to model relationships and highlight key spatial
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1. **Adaptive Spatial-Spectral Fusion (ASSF)**: Uses :class:`_DepthwiseTemporalConv1d` to generate a
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multi-channel spatial-spectral representation, followed by :class:`_SpatSpectralAttn`
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(Spatial-Spectral Attention) to model relationships and highlight key spatial-spectral
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channels [Han2025]_.
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2. **Multi-scale Variance Pooling (MVP)**: Applies :class:`_MultiScaleVarPooler` with variance pooling
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- `SSTDPN.encoder` **(Feature Extractor)**
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- *Operations.* Combines Adaptive Spatial
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- *Operations.* Combines Adaptive Spatial-Spectral Fusion and Multi-scale Variance Pooling
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via an internal :class:`_SSTEncoder`.
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- *Role.* Maps the raw MI-EEG trial :math:`X_i \in \mathbb{R}^{C \times T}` to the
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feature space :math:`z_i \in \mathbb{R}^d`.
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depth multiplier `n_spectral_filters_temporal` (equivalent to :math:`F_1` in the paper).
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- *Role.* Extracts multiple distinct spectral bands from each EEG channel independently.
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- `_SSTEncoder.spt_attn` **(Spatial
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- `_SSTEncoder.spt_attn` **(Spatial-Spectral Attention for Channel Gating)**
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- *Operations.* Internal :class:`_SpatSpectralAttn` module using Global Context Embedding
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via variance-based pooling, followed by adaptive channel normalization and gating.
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- *Role.* Reweights channels in the spatial
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- *Role.* Reweights channels in the spatial-spectral dimension to extract efficient and
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discriminative features by emphasizing task-relevant regions and frequency bands.
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- `_SSTEncoder.chan_conv` **(Pointwise Fusion across Channels)**
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- *Operations.* A 1D pointwise convolution with `n_fused_filters` output channels
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(equivalent to :math:`F_2` in the paper), followed by BatchNorm and the specified
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`activation` function (default: ELU).
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- *Role.* Fuses the weighted spatial
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- *Role.* Fuses the weighted spatial-spectral features across all electrodes to produce
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a fused representation :math:`X_{fused} \in \mathbb{R}^{F_2 \times T}`.
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- `_SSTEncoder.mvp` **(Multi-scale Variance Pooling for Temporal Extraction)**
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* **Spatial.**
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The initial convolution at the classes :class:`_DepthwiseTemporalConv1d` groups parameter :math:`h=1`,
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meaning :math:`F_1` temporal filters are shared across channels. The Spatial-Spectral Attention
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mechanism explicitly models the relationships among these channels in the spatial
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mechanism explicitly models the relationships among these channels in the spatial-spectral
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dimension, allowing for finer-grained spatial feature modeling compared to conventional
|
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GCNs according to the authors [Han2025]_.
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In other words, all electrode channels share :math:`F_1` temporal filters
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independently to produce the spatial
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independently to produce the spatial-spectral representation.
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* **Spectral.**
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Spectral information is implicitly extracted via the :math:`F_1` filters in :class:`_DepthwiseTemporalConv1d`.
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|
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.. rubric:: Additional Mechanisms
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- **Attention.** A lightweight Spatial-Spectral Attention mechanism models spatial
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- **Attention.** A lightweight Spatial-Spectral Attention mechanism models spatial-spectral relationships
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at the channel level, distinct from applying attention to deep feature dimensions,
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which is common in comparison methods like :class:`ATCNet`.
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- **Regularization.** Dual Prototype Learning acts as a regularization technique
|
braindecode/models/summary.csv
CHANGED
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@@ -39,3 +39,4 @@ FBLightConvNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times, sf
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IFNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times, sfreq",9860,"IFNet(n_chans=22, n_outputs=4, n_times=1000, sfreq=250)","Convolution,FilterBank"
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PBT,General,Classification,250,"n_chans, n_outputs, n_times",818948,"PBT(n_chans=22, n_outputs=4, n_times=1000, sfreq=250)","Large Brain Model"
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SSTDPN,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times",19502,"SSTDPN(n_chans=22, n_outputs=4, n_times=1000)","Convolution,Small Attention"
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BENDR,General,"Classification,Embedding",250,"n_chans, n_times, n_outputs",157141049,"BENDR(n_chans=22, n_outputs=4, n_times=1000)","Large Brain Model,Convolution"
|
braindecode/models/syncnet.py
CHANGED
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"""Synchronization Network (SyncNet) from Li, Y et al (2017) [Li2017]_.
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:bdg-warning:`Interpretability`
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.. figure:: https://braindecode.org/dev/_static/model/SyncNet.png
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|
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:alt: SyncNet Architecture
|
braindecode/models/tcn.py
CHANGED
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"""Braindecode TCN from Gemein, L et al (2020) [gemein2020]_.
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:bdg-success:`Convolution` :bdg-secondary:`Recurrent`
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.. figure:: https://ars.els-cdn.com/content/image/1-s2.0-S1053811920305073-gr3_lrg.jpg
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:align: center
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:alt: Braindecode TCN Architecture
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braindecode/models/usleep.py
CHANGED
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- **Nearest-neighbor upsample**, :class:`nn.Upsample` (x2)
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- **Convolution2d** (k=2), :class:`torch.nn.Conv2d`
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- ELU, :class:`torch.nn.ELU`
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- Batch Norm, :class:`torch.nn.BatchNorm2d`
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- **Concatenate** with the encoder skip at the same temporal scale, ``torch.cat``
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- **Convolution**, :class:`torch.nn.Conv2d`
|
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- ELU, :class:`torch.nn.ELU`
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- Batch Norm, :class:`torch.nn.BatchNorm2d`.
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**Output**: A multi-class, **high-frequency** per-sample representation aligned to the input rate (128 Hz).
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- **Segment Classifier incorporate into :class:`braindecode.models.USleep` (aggregation to fixed epochs)**
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- *Operations.*
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- **Mean-pool**, :class:`torch.nn.AvgPool2d` per class with kernel = epoch length *i* and stride *i*
|
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- **1x1 conv**, :class:`torch.nn.Conv2d`
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- ELU, :class:`torch.nn.ELU`
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- **1x1 conv**, :class:`torch.nn.Conv2d` with ``(T, K)`` (epochs x stages).
|
|
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**Role**: Learns a **non-linear** weighted combination over each 30-s window (unlike U-Time's linear combiner).
|
|
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|
|
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.. rubric:: Convolutional Details
|
|
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|
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- **Temporal (where time-domain patterns are learned).**
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|
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|
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All convolutions are **1-D along time**; depth (12 levels) plus pooling yields an extensive receptive field
|
|
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(reported sensitivity to ±6.75 min around each epoch; theoretical field ≈ 9.6 min at the deepest layer).
|
|
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The decoder restores sample-level resolution before epoch aggregation.
|
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- **Spatial (how channels are processed).**
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|
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|
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Convolutions mix across the *channel* dimension jointly with time (no separate spatial operator). The system
|
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is **montage-agnostic** (any reasonable EEG/EOG pair) and was trained across diverse cohorts/protocols,
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supporting robustness to channel placement and hardware differences.
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- **Spectral (how frequency content is captured).**
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|
104
|
+
No explicit Fourier/wavelet transform is used; the **stack of temporal convolutions** acts as a learned
|
|
105
|
+
filter bank whose effective bandwidth grows with depth. The high-frequency decoder output (128 Hz)
|
|
106
|
+
retains fine temporal detail for the segment classifier.
|
|
102
107
|
|
|
103
108
|
|
|
104
109
|
.. rubric:: Attention / Sequential Modules
|
braindecode/models/util.py
CHANGED
|
@@ -97,6 +97,7 @@ models_mandatory_parameters = [
|
|
|
97
97
|
("IFNet", ["n_chans", "n_outputs", "n_times", "sfreq"], dict(sfreq=200.0)),
|
|
98
98
|
("PBT", ["n_chans", "n_outputs", "n_times"], None),
|
|
99
99
|
("SSTDPN", ["n_chans", "n_outputs", "n_times", "sfreq"], None),
|
|
100
|
+
("BENDR", ["n_chans", "n_outputs", "n_times"], None),
|
|
100
101
|
]
|
|
101
102
|
|
|
102
103
|
################################################################
|