braindecode 1.2.0.dev180217551__tar.gz → 1.2.0.dev182051616__tar.gz

{braindecode-1.2.0.dev180217551/braindecode.egg-info → braindecode-1.2.0.dev182051616}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.2.0.dev180217551
+Version: 1.2.0.dev182051616
 Summary: Deep learning software to decode EEG, ECG or MEG signals
 Author-email: Robin Tibor Schirrmeister <robintibor@gmail.com>
 Maintainer-email: Alexandre Gramfort <agramfort@meta.com>, Bruno Aristimunha Pinto <b.aristimunha@gmail.com>, Robin Tibor Schirrmeister <robintibor@gmail.com>
@@ -49,6 +49,9 @@ Requires-Dist: mypy; extra == "tests"
 Provides-Extra: docs
 Requires-Dist: sphinx_gallery; extra == "docs"
 Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
+Requires-Dist: sphinx-autobuild; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
 Requires-Dist: pydata_sphinx_theme; extra == "docs"
 Requires-Dist: numpydoc; extra == "docs"
 Requires-Dist: memory_profiler; extra == "docs"
@@ -59,6 +62,7 @@ Requires-Dist: lightning; extra == "docs"
 Requires-Dist: seaborn; extra == "docs"
 Requires-Dist: pre-commit; extra == "docs"
 Requires-Dist: openneuro-py; extra == "docs"
+Requires-Dist: plotly; extra == "docs"
 Provides-Extra: all
 Requires-Dist: braindecode[docs,moabb,tests]; extra == "all"
 Dynamic: license-file

{braindecode-1.2.0.dev180217551 → braindecode-1.2.0.dev182051616}/braindecode/models/__init__.py

@@ -15,7 +15,7 @@ from .eeginception_erp import EEGInceptionERP
 from .eeginception_mi import EEGInceptionMI
 from .eegitnet import EEGITNet
 from .eegminer import EEGMiner
-from .eegnet import EEGNetv1, EEGNetv4
+from .eegnet import EEGNetv4
 from .eegnex import EEGNeX
 from .eegresnet import EEGResNet
 from .eegsimpleconv import EEGSimpleConv
@@ -65,7 +65,6 @@ __all__ = [
     "EEGInceptionMI",
     "EEGITNet",
     "EEGMiner",
-    "EEGNetv1",
     "EEGNetv4",
     "EEGNeX",
     "EEGResNet",

{braindecode-1.2.0.dev180217551 → braindecode-1.2.0.dev182051616}/braindecode/models/attentionbasenet.py

@@ -24,7 +24,7 @@ from braindecode.modules.attention import (
 
 
 class AttentionBaseNet(EEGModuleMixin, nn.Module):
-    """
+    """AttentionBaseNet from Wimpff M et al. (2023) [Martin2023]_.
 
     :bdg-success:`Convolution` :bdg-info:`Small Attention`
 
@@ -165,10 +165,11 @@ class AttentionBaseNet(EEGModuleMixin, nn.Module):
     Notes
     -----
     - Sequence length after each stage is computed internally; the final classifier expects
-    a flattened ``ch_dim x T₂`` vector.
+      a flattened ``ch_dim x T₂`` vector.
     - Attention operates on *channel* dimension by design; temporal gating exists only in
-    specific variants (CBAM/CAT).
-
+      specific variants (CBAM/CAT).
+    - The paper and original code with more details about the methodological
+      choices are available at the [Martin2023]_ and [MartinCode]_.
     .. versionadded:: 0.9
 
     Parameters

{braindecode-1.2.0.dev180217551 → braindecode-1.2.0.dev182051616}/braindecode/models/eegnex.py

@@ -129,7 +129,8 @@ class EEGNeX(EEGModuleMixin, nn.Module):
     -----
     - The braindecode implementation follows the paper's conv-only design with five blocks
       and reproduces the depthwise spatial step and dilated temporal stack. See the class
-      reference for exact kernel sizes, dilations, and pooling defaults.
+      reference for exact kernel sizes, dilations, and pooling defaults. You can check the
+      original implementation at [EEGNexCode]_.
 
     .. versionadded:: 1.1
 
@@ -159,12 +160,6 @@ class EEGNeX(EEGModuleMixin, nn.Module):
     avg_pool_block5 : tuple[int, int], optional
         Pooling size for block 5. Default is (1, 8).
 
-    Notes
-    -----
-    This implementation is not guaranteed to be correct, has not been checked
-    by original authors, only reimplemented from the paper description and
-    source code in tensorflow [EEGNexCode]_.
-
     References
     ----------
     .. [eegnex] Chen, X., Teng, X., Chen, H., Pan, Y., & Geyer, P. (2024).

{braindecode-1.2.0.dev180217551 → braindecode-1.2.0.dev182051616}/braindecode/models/summary.csv

@@ -1,41 +1,40 @@
-Model,Paradigm,Type,Freq(Hz),Hyperparameters,#Parameters,get_#Parameters
-ATCNet,General,Classification,250,"n_chans, n_outputs, n_times",113732,"ATCNet(n_chans=22, n_outputs=4, n_times=1000)"
-AttentionBaseNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times",3692,"AttentionBaseNet(n_chans=22, n_outputs=4, n_times=1000)"
-BDTCN,Normal/Abnormal,Classification,100,"n_chans, n_outputs, n_times",456502,"BDTCN(n_chans=21, n_outputs=2, n_times=6000, n_blocks=5, n_filters=55, kernel_size=16)"
-BIOT,"Sleep Staging, Epilepsy",Classification,200,"n_chans, n_outputs",3183879,"BIOT(n_chans=2,  n_outputs=5,  n_times=6000)"
-ContraWR,Sleep Staging,"Classification, Embedding",125,"n_chans, n_outputs, sfreq",1160165,"ContraWR(n_chans=2, n_outputs=5, n_times=3750, emb_size=256, sfreq=125)"
-CTNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times",26900,"CTNet(n_chans=22, n_outputs=4, n_times=1000, n_filters_time=8, kernel_size=16, heads=2, emb_size=16)"
-Deep4Net,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times",282879,"Deep4Net(n_chans=22, n_outputs=4, n_times=1000)"
-DeepSleepNet,Sleep Staging,Classification,256,"n_chans, n_outputs",24744837,"DeepSleepNet(n_chans=1, n_outputs=5, n_times=7680, sfreq=256)"
-EEGConformer,General,Classification,250,"n_chans, n_outputs, n_times",789572,"EEGConformer(n_chans=22, n_outputs=4, n_times=1000)."
-EEGInceptionERP,"ERP, SSVEP",Classification,128,"n_chans, n_outputs",14926,"EEGInceptionERP(n_chans=8, n_outputs=2, n_times=128, sfreq=128)"
-EEGInceptionMI,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times",558028,"EEGInceptionMI(n_chans=22, n_outputs=4, n_times=1000, n_convs=5, n_filters=12)"
-EEGITNet,Motor Imagery,Classification,125,"n_chans, n_outputs, n_times",5212,"EEGITNet(n_chans=22,  n_outputs=4,  n_times=500)"
-EEGNetv1,General,Classification,128,"n_chans, n_outputs, n_times",3052,"EEGNetv1(n_chans=22,  n_outputs=4,  n_times=512)"
-EEGNetv4,General,Classification,128,"n_chans, n_outputs, n_times",2484,"EEGNetv4(n_chans=22,  n_outputs=4,  n_times=512)"
-EEGNeX,Motor Imagery,Classification,125,"n_chans, n_outputs, n_times",55940,"EEGNeX(n_chans=22,  n_outputs=4,  n_times=500)"
-EEGMiner,Emotion Recognition,Classification,128,"n_chans, n_outputs, n_times, sfreq",7572,"EEGMiner(n_chans=62, n_outputs=2, n_times=2560, sfreq=128)"
-EEGResNet,General,Classification,250,"n_chans, n_outputs, n_times",247484,"EEGResNet(n_chans=22,  n_outputs=4,  n_times=1000)"
-EEGSimpleConv,Motor Imagery,Classification,80,"n_chans, n_outputs, sfreq",730404,"EEGSimpleConv(n_chans=22,  n_outputs=4,  n_times=320, sfreq=80)"
-EEGTCNet,Motor Imagery,Classification,250,"n_chans, n_outputs",4516,"EEGTCNet(n_chans=22,  n_outputs=4,  n_times=1000, kern_length=32)"
-Labram,General,"Classification, Embedding",200,"n_chans, n_outputs, n_times",5866180,"Labram(n_chans=22, n_outputs=4, n_times=1000, sfreq=250)"
-MSVTNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times",75494," MSVTNet(n_chans=22,  n_outputs=4,  n_times=1000)"
-SCCNet,Motor Imagery,Classification,125,"n_chans, n_outputs, n_times, sfreq",12070,"SCCNet(n_chans=22,  n_outputs=4,  n_times=1000, sfreq=125)"
-SignalJEPA,"Motor Imagery, ERP, SSVEP",Embedding,128,"n_times, chs_info",3456882,"SignalJEPA(n_times=512, chs_info=Lee2019_MI().get_data(subjects=[1])[1]['0']['1train'].info[""chs""][:62])"
-SignalJEPA_Contextual,"Motor Imagery, ERP, SSVEP",Classification,128,"n_outputs, n_times, chs_info",3459184,"SignalJEPA_Contextual(n_outputs=2, input_window_seconds=4.19, sfreq=128, chs_info=Lee2019_MI().get_data(subjects=[1])[1]['0']['1train'].info[""chs""][:62])"
-SignalJEPA_PostLocal,"Motor Imagery, ERP, SSVEP",Classification,128,"n_chans, n_outputs, n_times",16142,"SignalJEPA_PostLocal(n_chans=62, n_outputs=2, input_window_seconds=4.19, sfreq=128)"
-SignalJEPA_PreLocal,"Motor Imagery, ERP, SSVEP",Classification,128,"n_outputs, n_times, chs_info",16142,"SignalJEPA_PreLocal(n_chans=62, n_outputs=2, input_window_seconds=4.19, sfreq=128)"
-SincShallowNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times, sfreq",21892,"SincShallowNet(n_chans=22,  n_outputs=4,  n_times=1000, sfreq=250)"
-ShallowFBCSPNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times",46084,"ShallowFBCSPNet(n_chans=22,  n_outputs=4,  n_times=1000, sfreq=250)"
-SleepStagerBlanco2020,Sleep Staging,Classification,100,"n_chans, n_outputs, n_times",2845,"SleepStagerBlanco2020(n_chans=2, n_outputs=5, n_times=3000, sfreq=100)"
-SleepStagerChambon2018,Sleep Staging,Classification,128,"n_chans, n_outputs, n_times, sfreq",5835,"SleepStagerChambon2018(n_chans=2, n_outputs=5, n_times=3840, sfreq=128)"
-SleepStagerEldele2021,Sleep Staging,Classification,100,"n_chans, n_outputs, n_times, sfreq",719925,"SleepStagerEldele2021(n_chans=2, n_outputs=5, n_times=3000, sfreq=100)"
-SPARCNet,Epilepsy,Classification,200,"n_chans, n_outputs, n_times",1141921,"SPARCNet(n_chans=16, n_outputs=6, n_times=2000, sfreq=200)"
-SyncNet,"Emotion Recognition, Alcoholism",Classification,256,"n_chans, n_outputs, n_times",554,"SyncNet(n_chans=62, n_outputs=3, n_times=5120, sfreq=256)"
-TSceptionV1,Emotion Recognition,Classification,256,"n_chans, n_outputs, n_times, sfreq",2187206,"TSceptionV1(n_chans=62, n_outputs=3, n_times=5120, sfreq=256)"
-TIDNet,General,Classification,250,"n_chans, n_outputs, n_times",240404,"TIDNet(n_chans=22,  n_outputs=4,  n_times=1000)"
-USleep,Sleep Staging,Classification,128,"n_chans, n_outputs, n_times, sfreq",2482011,"USleep(n_chans=2, n_outputs=5, n_times=3000, sfreq=100)"
-FBCNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times, sfreq",11812,"FCNet(n_chans=22, n_outputs=4, n_times=1000, sfreq=250)"
-FBMSNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times, sfreq",16231,"FBMSNet(n_chans=22, n_outputs=4, n_times=1000, sfreq=250)"
-FBLightConvNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times, sfreq",6596,"FBLightConvNet(n_chans=22, n_outputs=4, n_times=1000, sfreq=250)"
-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)"
+Model,Paradigm,Type,Freq(Hz),Hyperparameters,#Parameters,get_#Parameters,Categorization
+ATCNet,General,Classification,250,"n_chans, n_outputs, n_times",113732,"ATCNet(n_chans=22, n_outputs=4, n_times=1000)","Convolution,Recurrent,Small Attention"
+AttentionBaseNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times",3692,"AttentionBaseNet(n_chans=22, n_outputs=4, n_times=1000)","Convolution,Small Attention"
+BDTCN,Normal Abnormal,Classification,100,"n_chans, n_outputs, n_times",456502,"BDTCN(n_chans=21, n_outputs=2, n_times=6000, n_blocks=5, n_filters=55, kernel_size=16)","Convolution,Recurrent"
+BIOT,"Sleep Staging, Epilepsy",Classification,200,"n_chans, n_outputs",3183879,"BIOT(n_chans=2,  n_outputs=5,  n_times=6000)","Large Language Model"
+ContraWR,Sleep Staging,"Classification, Embedding",125,"n_chans, n_outputs, sfreq",1160165,"ContraWR(n_chans=2, n_outputs=5, n_times=3750, emb_size=256, sfreq=125)",Convolution
+CTNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times",26900,"CTNet(n_chans=22, n_outputs=4, n_times=1000, n_filters_time=8, kernel_size=16, heads=2, emb_size=16)","Convolution,Small Attention"
+Deep4Net,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times",282879,"Deep4Net(n_chans=22, n_outputs=4, n_times=1000)","Convolution"
+DeepSleepNet,Sleep Staging,Classification,256,"n_chans, n_outputs",24744837,"DeepSleepNet(n_chans=1, n_outputs=5, n_times=7680, sfreq=256)","Convolution"
+EEGConformer,General,Classification,250,"n_chans, n_outputs, n_times",789572,"EEGConformer(n_chans=22, n_outputs=4, n_times=1000)","Convolution,Small Attention"
+EEGInceptionERP,"ERP, SSVEP",Classification,128,"n_chans, n_outputs",14926,"EEGInceptionERP(n_chans=8, n_outputs=2, n_times=128, sfreq=128)","Convolution"
+EEGInceptionMI,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times",558028,"EEGInceptionMI(n_chans=22, n_outputs=4, n_times=1000, n_convs=5, n_filters=12)","Convolution"
+EEGITNet,Motor Imagery,Classification,125,"n_chans, n_outputs, n_times",5212,"EEGITNet(n_chans=22,  n_outputs=4,  n_times=500)","Convolution,Recurrent"
+EEGNetv4,General,Classification,128,"n_chans, n_outputs, n_times",2484,"EEGNetv4(n_chans=22,  n_outputs=4,  n_times=512)","Convolution"
+EEGNeX,Motor Imagery,Classification,125,"n_chans, n_outputs, n_times",55940,"EEGNeX(n_chans=22,  n_outputs=4,  n_times=500)","Convolution"
+EEGMiner,Emotion Recognition,Classification,128,"n_chans, n_outputs, n_times, sfreq",7572,"EEGMiner(n_chans=62, n_outputs=2, n_times=2560, sfreq=128)","Convolution"
+EEGResNet,General,Classification,250,"n_chans, n_outputs, n_times",247484,"EEGResNet(n_chans=22,  n_outputs=4,  n_times=1000)","Interpretability"
+EEGSimpleConv,Motor Imagery,Classification,80,"n_chans, n_outputs, sfreq",730404,"EEGSimpleConv(n_chans=22,  n_outputs=4,  n_times=320, sfreq=80)","Convolution"
+EEGTCNet,Motor Imagery,Classification,250,"n_chans, n_outputs",4516,"EEGTCNet(n_chans=22,  n_outputs=4,  n_times=1000, kern_length=32)","Convolution,Recurrent"
+Labram,General,"Classification, Embedding",200,"n_chans, n_outputs, n_times",5866180,"Labram(n_chans=22, n_outputs=4, n_times=1000, sfreq=250)","Convolution,Large Language Model"
+MSVTNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times",75494," MSVTNet(n_chans=22,  n_outputs=4,  n_times=1000)","Convolution,Recurrent,Small Attention"
+SCCNet,Motor Imagery,Classification,125,"n_chans, n_outputs, n_times, sfreq",12070,"SCCNet(n_chans=22,  n_outputs=4,  n_times=1000, sfreq=125)","Convolution"
+SignalJEPA,"Motor Imagery, ERP, SSVEP",Embedding,128,"n_times, chs_info",3456882,"SignalJEPA(n_times=512, chs_info=Lee2019_MI().get_data(subjects=[1])[1]['0']['1train'].info[""chs""][:62])","Convolution,Channel,Large Language Model"
+SignalJEPA_Contextual,"Motor Imagery, ERP, SSVEP",Classification,128,"n_outputs, n_times, chs_info",3459184,"SignalJEPA_Contextual(n_outputs=2, input_window_seconds=4.19, sfreq=128, chs_info=Lee2019_MI().get_data(subjects=[1])[1]['0']['1train'].info[""chs""][:62])","Convolution,Channel,Large Language Model"
+SignalJEPA_PostLocal,"Motor Imagery, ERP, SSVEP",Classification,128,"n_chans, n_outputs, n_times",16142,"SignalJEPA_PostLocal(n_chans=62, n_outputs=2, input_window_seconds=4.19, sfreq=128)","Convolution,Channel,Large Language Model"
+SignalJEPA_PreLocal,"Motor Imagery, ERP, SSVEP",Classification,128,"n_outputs, n_times, chs_info",16142,"SignalJEPA_PreLocal(n_chans=62, n_outputs=2, input_window_seconds=4.19, sfreq=128)","Convolution,Channel,Large Language Model"
+SincShallowNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times, sfreq",21892,"SincShallowNet(n_chans=22,  n_outputs=4,  n_times=1000, sfreq=250)","Convolution,Interpretability"
+ShallowFBCSPNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times",46084,"ShallowFBCSPNet(n_chans=22,  n_outputs=4,  n_times=1000, sfreq=250)","Convolution"
+SleepStagerBlanco2020,Sleep Staging,Classification,100,"n_chans, n_outputs, n_times",2845,"SleepStagerBlanco2020(n_chans=2, n_outputs=5, n_times=3000, sfreq=100)","Convolution"
+SleepStagerChambon2018,Sleep Staging,Classification,128,"n_chans, n_outputs, n_times, sfreq",5835,"SleepStagerChambon2018(n_chans=2, n_outputs=5, n_times=3840, sfreq=128)","Convolution"
+SleepStagerEldele2021,Sleep Staging,Classification,100,"n_chans, n_outputs, n_times, sfreq",719925,"SleepStagerEldele2021(n_chans=2, n_outputs=5, n_times=3000, sfreq=100)","Convolution, Small Attention"
+SPARCNet,Epilepsy,Classification,200,"n_chans, n_outputs, n_times",1141921,"SPARCNet(n_chans=16, n_outputs=6, n_times=2000, sfreq=200)","Convolution"
+SyncNet,"Emotion Recognition, Alcoholism",Classification,256,"n_chans, n_outputs, n_times",554,"SyncNet(n_chans=62, n_outputs=3, n_times=5120, sfreq=256)","Interpretability"
+TSceptionV1,Emotion Recognition,Classification,256,"n_chans, n_outputs, n_times, sfreq",2187206,"TSceptionV1(n_chans=62, n_outputs=3, n_times=5120, sfreq=256)","Convolution"
+TIDNet,General,Classification,250,"n_chans, n_outputs, n_times",240404,"TIDNet(n_chans=22,  n_outputs=4,  n_times=1000)","Convolution"
+USleep,Sleep Staging,Classification,128,"n_chans, n_outputs, n_times, sfreq",2482011,"USleep(n_chans=2, n_outputs=5, n_times=3000, sfreq=100)","Convolution"
+FBCNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times, sfreq",11812,"FCNet(n_chans=22, n_outputs=4, n_times=1000, sfreq=250)","Convolution,FilterBank"
+FBMSNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times, sfreq",16231,"FBMSNet(n_chans=22, n_outputs=4, n_times=1000, sfreq=250)","Convolution,FilterBank"
+FBLightConvNet,Motor Imagery,Classification,250,"n_chans, n_outputs, n_times, sfreq",6596,"FBLightConvNet(n_chans=22, n_outputs=4, n_times=1000, sfreq=250)","Convolution,FilterBank"
+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"

{braindecode-1.2.0.dev180217551 → braindecode-1.2.0.dev182051616}/braindecode/models/util.py

@@ -55,7 +55,6 @@ models_mandatory_parameters = [
     ("EEGInceptionERP", ["n_chans", "n_outputs", "n_times", "sfreq"], None),
     ("EEGInceptionMI", ["n_chans", "n_outputs", "n_times", "sfreq"], None),
     ("EEGITNet", ["n_chans", "n_outputs", "n_times"], None),
-    ("EEGNetv1", ["n_chans", "n_outputs", "n_times"], None),
     ("EEGNetv4", ["n_chans", "n_outputs", "n_times"], None),
     ("EEGResNet", ["n_chans", "n_outputs", "n_times"], None),
     ("ShallowFBCSPNet", ["n_chans", "n_outputs", "n_times"], None),

braindecode-1.2.0.dev182051616/braindecode/version.py

@@ -0,0 +1 @@
+__version__ = "1.2.0.dev182051616"

{braindecode-1.2.0.dev180217551 → braindecode-1.2.0.dev182051616/braindecode.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: braindecode
-Version: 1.2.0.dev180217551
+Version: 1.2.0.dev182051616
 Summary: Deep learning software to decode EEG, ECG or MEG signals
 Author-email: Robin Tibor Schirrmeister <robintibor@gmail.com>
 Maintainer-email: Alexandre Gramfort <agramfort@meta.com>, Bruno Aristimunha Pinto <b.aristimunha@gmail.com>, Robin Tibor Schirrmeister <robintibor@gmail.com>
@@ -49,6 +49,9 @@ Requires-Dist: mypy; extra == "tests"
 Provides-Extra: docs
 Requires-Dist: sphinx_gallery; extra == "docs"
 Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
+Requires-Dist: sphinx-autobuild; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
 Requires-Dist: pydata_sphinx_theme; extra == "docs"
 Requires-Dist: numpydoc; extra == "docs"
 Requires-Dist: memory_profiler; extra == "docs"
@@ -59,6 +62,7 @@ Requires-Dist: lightning; extra == "docs"
 Requires-Dist: seaborn; extra == "docs"
 Requires-Dist: pre-commit; extra == "docs"
 Requires-Dist: openneuro-py; extra == "docs"
+Requires-Dist: plotly; extra == "docs"
 Provides-Extra: all
 Requires-Dist: braindecode[docs,moabb,tests]; extra == "all"
 Dynamic: license-file

{braindecode-1.2.0.dev180217551 → braindecode-1.2.0.dev182051616}/braindecode.egg-info/SOURCES.txt

@@ -110,11 +110,14 @@ docs/cite.rst
 docs/conf.py
 docs/help.rst
 docs/index.rst
-docs/models_summary.rst
 docs/sg_execution_times.rst
 docs/whats_new.rst
 docs/_templates/autosummary/class.rst
 docs/_templates/autosummary/function.rst
 docs/install/install.rst
 docs/install/install_pip.rst
-docs/install/install_source.rst
+docs/install/install_source.rst
+docs/models/models.rst
+docs/models/models_categorization.rst
+docs/models/models_table.rst
+docs/models/models_visualization.rst

{braindecode-1.2.0.dev180217551 → braindecode-1.2.0.dev182051616}/braindecode.egg-info/requires.txt

@@ -22,6 +22,9 @@ braindecode[docs,moabb,tests]
 [docs]
 sphinx_gallery
 sphinx_rtd_theme
+sphinx-autodoc-typehints
+sphinx-autobuild
+sphinxcontrib-bibtex
 pydata_sphinx_theme
 numpydoc
 memory_profiler
@@ -32,6 +35,7 @@ lightning
 seaborn
 pre-commit
 openneuro-py
+plotly
 
 [moabb]
 moabb>=1.2.0

{braindecode-1.2.0.dev180217551 → braindecode-1.2.0.dev182051616}/docs/api.rst

@@ -19,12 +19,12 @@ Model zoo availables in braindecode. The models are implemented as
 All the models have the convention of having the signal related parameters
 named the same way, following the braindecode's standards:
 
-+ ``n_outputs``: Number of labels or outputs of the model.
-+ ``n_chans``: Number of EEG channels.
-+ ``n_times``: Number of time points of the input window.
-+ ``input_window_seconds``: Length of the input window in seconds.
-+ ``sfreq``: Sampling frequency of the EEG recordings.
-+ ``chs_info``: Information about each individual EEG channel. Refer to :class:`mne.Info["chs"]`.
++ :fa:`shapes`\  ``n_outputs``: Number of labels or outputs of the model.
++ :fa:`wave-square`\  ``n_chans``: Number of EEG channels.
++ :fa:`clock`\  ``n_times``: Number of time points of the input window.
++ :fa:`wifi`\  ``sfreq``: Sampling frequency of the EEG recordings.
++ (:fa:`clock`\ / :fa:`wifi`\)  ``input_window_seconds``: Length of the input window in seconds.
++ :fa:`info-circle`\  ``chs_info``: Information about each individual EEG channel. Refer to :class:`mne.Info["chs"]`.
 
 All the models assume that the input data is a 3D tensor of shape
 ``(batch_size, n_chans, n_times)``, and some models also accept a 4D tensor of shape
@@ -65,7 +65,6 @@ provides a common interface for all EEG models and derivate variables names if n
     EEGInceptionMI
     EEGITNet
     EEGMiner
-    EEGNetv1
     EEGNetv4
     EEGNeX
     EEGResNet

{braindecode-1.2.0.dev180217551 → braindecode-1.2.0.dev182051616}/docs/conf.py

@@ -42,6 +42,10 @@ curdir = os.path.dirname(__file__)
 sys.path.append(os.path.abspath(os.path.join(curdir, "..", "braindecode")))
 sys.path.append(os.path.abspath(os.path.join(curdir, "sphinxext")))
 
+import sphinx_design
+
+print(f"--- Sphinx is using sphinx_design version: {sphinx_design.__version__} ---")
+
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
@@ -55,7 +59,9 @@ extensions = [
     "sphinx.ext.ifconfig",
     "sphinx.ext.intersphinx",
     "sphinx.ext.githubpages",
+    "sphinxcontrib.bibtex",
     "sphinx.ext.napoleon",
+    "sphinx_autodoc_typehints",
     "sphinx_gallery.gen_gallery",
     "sphinx.ext.linkcode",
     "sphinx_design",
@@ -166,15 +172,15 @@ templates_path = ["_templates"]
 # source_suffix = ['.rst', '.md']
 source_suffix = ".rst"
 
-rst_prolog = """
-.. role:: tag(bdg-success)
-"""
+
 # The master toctree document.
 master_doc = "index"
 
 # General information about the project.
 
-
+bibtex_bibfiles = ["references.bib"]
+bibtex_reference_style = "author_year"
+bibtex_default_style = "unsrt"
 # -- Project information -----------------------------------------------------
 
 project = "Braindecode"
@@ -356,7 +362,6 @@ html_context = {
 }
 
 html_sidebars = {
-    "models_summary": [],
     "cite": [],
     "help": [],
     "whats_new": [],
@@ -391,7 +396,7 @@ latex_documents = [
         master_doc,
         "Braindecode.tex",
         "Braindecode",
-        "Robin Tibor Schirrmeister",
+        "Bruno Aristimunha",
         "manual",
     ),
 ]
@@ -430,6 +435,16 @@ other_icons = (
     "cloud-download-alt",
     "wrench",
     "hourglass",
+    # Add your new icons here
+    "braille",
+    "repeat",
+    "lightbulb",
+    "layer-group",
+    "eye",
+    "circle-nodes",
+    "magnifying-glass-chart",
+    "share-nodes",
+    "clone",
 )
 icons = dict()
 for icon in brand_icons + fixed_icons + other_icons:
@@ -457,7 +472,7 @@ prolog += """
 prolog += """
 .. |ensp| unicode:: U+2002 .. EN SPACE
 """
-
+rst_prolog = prolog
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples

{braindecode-1.2.0.dev180217551 → braindecode-1.2.0.dev182051616}/docs/index.rst

@@ -42,7 +42,7 @@ Braindecode Homepage
    :hidden:
 
    Install <install/install>
-   Models <models_summary>
+   Models <models/models>
    Cite <cite>
    Tutorial and Examples <auto_examples/index>
    API <api>

braindecode-1.2.0.dev182051616/docs/models/models.rst

@@ -0,0 +1,76 @@
+:html_theme.sidebar_secondary.remove: true
+
+.. _models:
+
+The brain decode problem
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+All the models in this library tackle the following problem:
+given time-series signals :math:`X \in \mathbb{R}^{C \times T}` and labels
+:math:`y \in \mathcal{Y}`, :class:`braindecode` implements neural networks
+:math:`f` that **decode** brain activity, i.e., it applies a series of transformations
+layers (e.g. :class:`torch.nn.Conv2d`, :class:`torch.nn.Linear`, :class:`torch.nn.ELU`) to the data
+to allow us to filter and extract features that are relevant to what we are modeling, in other words:
+
+.. math::
+
+   f_{\theta} : X \to y,
+
+where :math:`C` (``n_chans``) is the number of channels/electrodes and :math:`T` (``n_times``) is the temporal window
+length/epoch size over the interval of interest.
+
+The definition of :math:`y` is broad; it may be anchored in a cognitive stimulus (e.g., BCI, ERP, SSVEP, cVEP),
+mental state (sleep stage), brain age, visual/audio/text/action inputs, or any target
+that can be quantized and modeled as a decoding task, see references :cite:label:`sleep2023,aristimunhaetal23,chevallier2024largest,levy2025brain,benchetrit2024brain,d2024decoding,engemann2022reusable,xu2024alljoined`.
+
+We aim to translate recorded brain activity into its originating stimulus, behavior,
+or mental state, :cite:t:`king2014characterizing,king2020`, again, :math:`f(X) \to y`.
+
+The neural networks model :math:`f` learns a representation that is useful for the encoded stimulus
+in the subject's brain over time series—also known as *reverse inference*.
+
+In supervised decoding, we usually learn the network parameters :math:`\theta` by minimizing
+the regularized the average loss over the training set :math:`\mathcal{D}_{\text{tr}}=\{(x_i,y_i)\}_{i=1}^{N_{\text{tr}}}`.
+
+.. math::
+
+   \begin{aligned}
+   \theta^{*}
+     &= \arg\min_{\theta}\, \hat{\mathcal{R}}(\theta) \\
+     &= \arg\min_{\theta}\, \frac{1}{N_{\text{tr}}}\sum_{i=1}^{N_{\text{tr}}}
+        \ell\!\left(f_{\theta}(x_i),\, y_i\right) \;+\; \lambda\,\Omega(\theta)\,,
+   \end{aligned}
+
+where :math:`\ell` is the task loss (e.g., cross-entropy :class:`torch.nn.CrossEntropyLoss`), :math:`\Omega` is an optional regularizer, and :math:`\lambda \ge 0` its weight (e.g. ``weight_decay`` parameter in :class:`torch.optim.Adam` is the example of regularization).
+
+Equivalently, the goal is to minimize the expected risk :math:`\mathcal{R}(\theta)=\mathbb{E}_{(x,y)\sim P_{\text{tr}}}
+[\ell(f_{\theta}(x),y)]`, for which the empirical average above is a finite-sample
+approximation.
+
+With this, in this model's sub-pages, we provide:
+
+    - 1) Our definition of the brain decoding problem (here);
+    - 2) :doc:`The categorization of the neural networks based on what is inside them <models_categorization>`;
+    - 3) :doc:`A table overview to understand what is inside the models  <models_table>`;
+    - 4) :doc:`A visualization of the common important information from the models <models_visualization>`.
+
+.. button-ref:: models_categorization
+   :ref-type: doc
+   :color: primary
+   :expand:
+
+   Next: Models categorization →
+
+
+.. rubric:: References
+.. bibliography::
+
+
+.. toctree::
+    :hidden:
+
+    models_categorization
+    models_table
+    models_visualization
+
+.. include:: /links.inc

braindecode-1.2.0.dev182051616/docs/models/models_categorization.rst

@@ -0,0 +1,174 @@
+:html_theme.sidebar_secondary.remove: true
+
+Models Categorization
+~~~~~~~~~~~~~~~~~~~~~
+
+Given the brain-decoding framework from the previous page, we define our neural networks,
+denoted :math:`f`, as a composition of sequential transformations:
+
+.. math::
+
+   f_{\mathrm{method}}
+   \;=\;
+   f_{\mathrm{convolution}} \circ \cdots \circ f_{\mathrm{MLP}}\,
+
+where each :math:`f_\ell` is a specific transformation (:math:`\ell` layer) in the network.
+Learning is the mapping :math:`f_{\mathrm{method}} : \mathcal{X} \to \mathcal{Y}` on the
+training data, with parameters :math:`\theta \in \Theta`.
+
+
+.. grid:: 1 2 3 3
+   :gutter: 3
+
+   .. grid-item-card:: |braille| Convolution Layers
+      :shadow: sm
+
+      :bdg-success:`Convolution`
+
+      .. figure:: ../_static/model_cat/convolution.png
+         :width: 90%
+         :align: center
+         :alt: Diagram of a convolutional layer
+         :class: no-scaled-link
+
+      Applies temporal and/or spatial convolutions to extract local features from brain signals.
+
+   .. grid-item-card:: |repeat| Recurrent Layers
+      :shadow: sm
+
+      :bdg-secondary:`Recurrent`
+
+      .. figure:: ../_static/model_cat/rnn.png
+         :class: no-scaled-link
+         :width: 90%
+         :align: center
+         :alt: Diagram of recurrent/TCN models
+
+      Models temporal dependencies via recurrent units or TCNs with dilations.
+
+   .. grid-item-card:: |magnifying-glass-chart| Small Attention
+      :shadow: sm
+
+      :bdg-info:`Small Attention`
+
+      .. figure:: ../_static/model_cat/attention.png
+         :class: no-scaled-link
+         :width: 90%
+         :align: center
+         :alt: Diagram of attention modules
+
+      Uses attention mechanisms for feature focusing. Can be trained effectively without self-supervised pre-training.
+
+   .. grid-item-card:: |layer-group| Filterbank Models
+      :shadow: sm
+
+      :bdg-primary:`Filterbank`
+
+      .. figure:: ../_static/model_cat/filterbank.png
+         :class: no-scaled-link
+         :width: 90%
+         :align: center
+         :alt: Diagram of filterbank models
+
+      Decomposes signals into multiple bands (learned or fixed) to capture frequency-specific information.
+
+   .. grid-item-card:: |eye| Interpretability-by-Design
+      :shadow: sm
+
+      :bdg-warning:`Interpretability`
+
+      .. figure:: ../_static/model_cat/interpre.png
+         :class: no-scaled-link
+         :width: 90%
+         :align: center
+         :alt: Diagram of interpretable architectures
+
+     Architectures with inherently interpretable layers allow direct neuroscientific validation of learned features.
+
+   .. grid-item-card:: |circle-nodes| Symmetric Positive-Definite
+      :shadow: sm
+
+      :bdg-dark:`SPD` :bdg-danger-line:`To be released soon!`
+
+      .. figure:: ../_static/model_cat/spd.png
+         :class: no-scaled-link
+         :width: 90%
+         :align: center
+         :alt: Diagram of SPD learning
+         :figclass: unavailable
+
+      Learns on covariance/connectivity as SPD matrices using BiMap/ReEig/LogEig layers.
+
+   .. grid-item-card:: |lightbulb| Large Transformer Models
+      :shadow: sm
+
+      :bdg-danger:`Large Language Model`
+
+      .. figure:: ../_static/model_cat/llm.png
+         :class: no-scaled-link
+         :width: 90%
+         :align: center
+         :alt: Diagram of transformer models
+
+     Large-scale transformer layers require self-supervised pre-training to work effectively.
+
+   .. grid-item-card:: |share-nodes| Graph Neural Network
+      :shadow: sm
+
+      :bdg-light:`Graph Neural Network`
+
+      .. figure:: ../_static/model_cat/gnn.png
+         :class: no-scaled-link
+         :width: 90%
+         :align: center
+         :alt: Diagram of GNN models
+         :figclass: unavailable
+
+      Treats channels/regions as nodes with learned/static edges to model connectivity.
+
+   .. grid-item-card:: |clone| Channel-Domain
+      :shadow: sm
+
+      :bdg-dark-line:`Channel`
+
+      .. figure:: ../_static/model_cat/channel.png
+         :class: no-scaled-link
+         :width: 90%
+         :align: center
+         :alt: Diagram of channel-domain methods
+
+      Usage montage information with spatial filtering / channel / hemisphere / brain region selection strategies.
+
+
+- Across most architectures, the earliest stages are convolutional (:bdg-success:`Convolution`), reflecting the brain time series's noisy, locally structured nature.
+  These layers apply temporal and/or spatial convolutions—often depthwise-separable as in EEGNet, per-channel or across channel groups to extract robust local features.
+  :class:`braindecode.models.EEGNetv4`, :class:`braindecode.models.ShallowFBCSPNet`, :class:`braindecode.models.EEGNeX`, and :class:`braindecode.models.EEGInceptionERP`
+- In the **recurrent** family (:bdg-secondary:`Recurrent`), many modern EEG models actually rely on *temporal convolutional networks* (TCNs) with dilations to grow the receptive field, rather than explicit recurrence (:cite:label:`bai2018tcn`),  :class:`braindecode.models.BDTCN`,
+- In contrast, several methods employ **small attention** modules (:bdg-info:`Small Attention`) to capture longer-range dependencies efficiently, e.g., :class:`braindecode.models.EEGConformer`, :class:`braindecode.models.CTNet`, :class:`braindecode.models.ATCNet`, :class:`braindecode.models.AttentionBaseNet` (:cite:label:`song2022eeg,zhao2024ctnet,altaheri2022atcnet`).
+- **Filterbank-style models** (:bdg-primary:`Filterbank`) explicitly decompose signals into multiple bands before (or while) learning, echoing the classic FBCSP pipeline; examples include :class:`braindecode.models.FBCNet` and :class:`braindecode.models.FBMSNet` (:cite:label:`mane2021fbcnet,liu2022fbmsnet`).
+- **Interpretability-by-design** (:bdg-warning:`Interpretability`) architectures expose physiologically meaningful primitives (e.g., band-pass/sinc filters, variance or connectivity features), enabling direct neuroscientific inspection; see :class:`braindecode.models.SincShallowNet` and :class:`braindecode.models.EEGMiner` (:cite:label:`borra2020interpretable,ludwig2024eegminer`).
+- **SPD / Riemannian** (:bdg-dark:`SPD`) methods operate on covariance (or connectivity) matrices as points on the SPD manifold, combining layers such as BiMap, ReEig, and LogEig; deep SPD networks and Riemannian classifiers motivate this family (:cite:label:`huang2017riemannian`). *(Coming soon in a dedicate repository.)*
+- **Large-model / Transformer** (:bdg-danger:`Large Language Model`) approaches pretrain attention-based encoders on diverse biosignals and fine-tune for EEG tasks; e.g., :class:`braindecode.models.BIOT` (:cite:label:`yang2023biot`). These typically need a heavily self-supervised pre-training before decoding.
+- **Graph neural networks** (:bdg-light:`Graph Neural Network`) treat channels/regions as nodes with learned (static or dynamic) edges to model functional connectivity explicitly; representative EEG-GNN, more common in the epileptic decoding (:cite:label:`klepl2024graph`).
+- **Channel-domain robustness** (:bdg-dark-line:`Channel`) techniques target variability in electrode layouts by learning montage-agnostic or channel-selective layers (e.g., dynamic spatial filtering, differentiable channel re-ordering); these strategies improve cross-setup generalization :class:`braindecode.models.SignalJEPA` (:cite:label:`guetschel2024sjepa,chen2024eegprogress`).
+
+
+We are continually expanding this collection and welcome contributions! If you have implemented a
+model relevant to EEG, ECoG, or MEG analysis, consider adding it to Braindecode.
+
+Submit a new model
+~~~~~~~~~~~~~~~~~~
+
+Want to contribute a new model to Braindecode? Great! You can propose a new model by opening an
+`issue <braindecode-issues_>`_ (please include a link to the relevant publication or description) or,
+even better, directly submit your implementation via a `pull request <braindecode-pulls_>`_.
+We appreciate your contributions to expanding the library!
+
+.. button-ref:: models_table
+   :ref-type: doc
+   :color: primary
+   :expand:
+
+   Next: Models Table
+
+.. include:: /links.inc