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github.com/AI4HealthUOL/ecg-fm-benchmarking
/ types & classes
Types & classes
227 in github.com/AI4HealthUOL/ecg-fm-benchmarking
⨍
Functions
823
◇
Types & classes
227
↓ 11 callers
Class
TimeSeriesDataset
timeseries dataset with partial crops.
code/clinical_ts/data/time_series_dataset.py:113
↓ 10 callers
Class
ConcatTimeSeriesDataset
ConcatDataset that handles id mapping correctly (to allow to aggregate predictions)
code/clinical_ts/data/time_series_dataset.py:95
↓ 7 callers
Class
ConvLayer
Create a sequence of convolutional (`ni` to `nf`), ReLU (if `use_activ`) and `norm_type` layers.
code/clinical_ts/models/xresnet1d.py:36
↓ 7 callers
Class
ConvLayer
Create a sequence of convolutional (`ni` to `nf`), ReLU (if `use_activ`) and `norm_type` layers.
code/clinical_ts/models/ecg_foundation_models/ecgfm_ked.py:103
↓ 7 callers
Class
InputShape
code/clinical_ts/models/fm_ecg.py:787
↓ 7 callers
Class
LearnableQueryAttentionPoolingHead
code/clinical_ts/utils/heads.py:72
↓ 7 callers
Class
LearnableQueryAttentionPoolingHeadConfig
code/clinical_ts/utils/heads.py:91
↓ 6 callers
Class
TransformerBlock
code/clinical_ts/models/ecg_foundation_models/st_mem/encoder/vit.py:114
↓ 5 callers
Class
ResNet
code/clinical_ts/models/ecg_foundation_models/merl/resnet1d.py:63
↓ 5 callers
Class
Swish
code/clinical_ts/models/ecg_foundation_models/ecg_founder.py:78
↓ 5 callers
Class
basic_conv1d
basic conv1d
code/clinical_ts/ts/basic_conv1d_modules/basic_conv1d.py:138
↓ 5 callers
Class
basic_conv1d
basic conv1d
code/clinical_ts/models/basic_conv1d.py:138
↓ 4 callers
Class
LambdaLayer
code/clinical_ts/ts/basic_conv1d_modules/basic_conv1d.py:43
↓ 4 callers
Class
LambdaLayer
code/clinical_ts/models/basic_conv1d.py:43
↓ 4 callers
Class
MyConv1dPadSame
extend nn.Conv1d to support SAME padding input: (n_sample, in_channels, n_length) output: (n_sample, out_channels, (n_length+stride-1)//
code/clinical_ts/models/ecg_foundation_models/ecg_founder.py:12
↓ 4 callers
Class
Resample
Resample on the fly
code/clinical_ts/data/time_series_dataset_transforms.py:179
↓ 4 callers
Class
ToTensor
Convert ndarrays in sample to Tensors.
code/clinical_ts/data/time_series_dataset_transforms.py:244
↓ 4 callers
Class
ViT
code/clinical_ts/models/ecg_foundation_models/merl/vit1d.py:145
↓ 3 callers
Class
DropPath
Drop paths (Stochastic Depth) per sample (when applied in main path of residual blocks).
code/clinical_ts/models/ecg_foundation_models/merl/vit1d.py:16
↓ 3 callers
Class
Flatten
Flatten `x` to a single dimension, often used at the end of a model. `full` for rank-1 tensor
code/clinical_ts/models/basic_conv1d.py:12
↓ 3 callers
Class
MLAE_ViT
code/clinical_ts/models/ecg_foundation_models/st_mem/encoder/mlae_vit.py:23
↓ 3 callers
Class
Normalize
Normalize using given stats.
code/clinical_ts/data/time_series_dataset_transforms.py:291
↓ 3 callers
Class
ST_MEM_ViT
code/clinical_ts/models/ecg_foundation_models/st_mem/encoder/st_mem_vit.py:24
↓ 3 callers
Class
TimeSeriesDatasetConfig
code/clinical_ts/data/time_series_dataset.py:443
↓ 3 callers
Class
ViT
code/clinical_ts/models/ecg_foundation_models/st_mem/encoder/vit.py:151
↓ 2 callers
Class
Block
code/clinical_ts/models/ecg_foundation_models/ecg_jepa/ecg_jepa.py:157
↓ 2 callers
Class
DropPath
Drop paths (Stochastic Depth) per sample (when applied in main path of residual blocks).
code/clinical_ts/models/ecg_foundation_models/st_mem/encoder/vit.py:22
↓ 2 callers
Class
Flatten
Flatten `x` to a single dimension, often used at the end of a model. `full` for rank-1 tensor
code/clinical_ts/ts/basic_conv1d_modules/basic_conv1d.py:12
↓ 2 callers
Class
KernelTuner
code/extensions/cauchy/tuner.py:135
↓ 2 callers
Class
MLAE
code/clinical_ts/models/ecg_foundation_models/st_mem/mlae.py:26
↓ 2 callers
Class
MTAE
code/clinical_ts/models/ecg_foundation_models/st_mem/mtae.py:46
↓ 2 callers
Class
Net1D
Input: X: (n_samples, n_channel, n_length) Y: (n_samples) Output: out: (n_samples) params:
code/clinical_ts/models/ecg_foundation_models/ecg_founder.py:280
↓ 2 callers
Class
PreNorm
code/clinical_ts/models/ecg_foundation_models/st_mem/encoder/vit.py:42
↓ 2 callers
Class
PreNorm
code/clinical_ts/models/ecg_foundation_models/merl/vit1d.py:36
↓ 2 callers
Class
S4Model
code/clinical_ts/ts/s4_modules/s4_model.py:10
↓ 2 callers
Class
ST_MEM
code/clinical_ts/models/ecg_foundation_models/st_mem/st_mem.py:47
↓ 2 callers
Class
SequenceToSampleLabelTransform
Transforms sequence-level to sample-level labels majority vote: pick the most frequent label as segment label (i.e. suitable for single-label clas
code/clinical_ts/data/time_series_dataset_transforms.py:433
↓ 2 callers
Class
Transform
Transforms data using a given function i.e. data_new = func(data) for input is True else label_new = func(label)
code/clinical_ts/data/time_series_dataset_transforms.py:395
↓ 2 callers
Class
ecg_jepa
code/clinical_ts/models/ecg_foundation_models/ecg_jepa/ecg_jepa.py:514
↓ 1 callers
Class
ActivationFunction
code/clinical_ts/models/ecg_foundation_models/hubert_ecg/hubert_ecg_classification.py:7
↓ 1 callers
Class
AdaptiveConcatPool1d
Layer that concats `AdaptiveAvgPool1d` and `AdaptiveMaxPool1d`.
code/clinical_ts/ts/basic_conv1d_modules/basic_conv1d.py:84
↓ 1 callers
Class
AdaptiveConcatPool1d
Layer that concats `AdaptiveAvgPool1d` and `AdaptiveMaxPool1d`.
code/clinical_ts/models/basic_conv1d.py:84
↓ 1 callers
Class
AdaptiveConcatPool1d
Layer that concats `AdaptiveAvgPool1d` and `AdaptiveMaxPool1d`.
code/clinical_ts/models/ecg_foundation_models/ecgfm_ked.py:57
↓ 1 callers
Class
AdaptiveConcatPoolRNN
code/clinical_ts/ts/head.py:101
↓ 1 callers
Class
Attention
code/clinical_ts/models/ecg_foundation_models/st_mem/encoder/vit.py:74
↓ 1 callers
Class
Attention
code/clinical_ts/models/ecg_foundation_models/merl/vit1d.py:68
↓ 1 callers
Class
Attention
code/clinical_ts/models/ecg_foundation_models/ecg_jepa/ecg_jepa.py:128
↓ 1 callers
Class
BasicBlock
Basic Block: conv1 -> convk -> conv1 params: in_channels: number of input channels out_channels: number of output c
code/clinical_ts/models/ecg_foundation_models/ecg_founder.py:82
↓ 1 callers
Class
BasicStage
Basic Stage: block_1 -> block_2 -> ... -> block_M
code/clinical_ts/models/ecg_foundation_models/ecg_founder.py:214
↓ 1 callers
Class
CPCWrapper
code/clinical_ts/models/fm_ecg.py:762
↓ 1 callers
Class
ChannelFilter
Select certain channels. axis: axis index of the channel axis
code/clinical_ts/data/time_series_dataset_transforms.py:377
↓ 1 callers
Class
Compose
composes several transformations into a single one (as provided by torchvision.transforms.Compose)
code/clinical_ts/data/time_series_dataset_transforms.py:63
↓ 1 callers
Class
DropoutNd
code/clinical_ts/ts/s4_modules/s4_utils.py:6
↓ 1 callers
Class
ECGFounderWrapper
Paper: https://arxiv.org/abs/2410.04133 Code: https://github.com/PKUDigitalHealth/ECGFounder Checkpoints: https://huggingface
code/clinical_ts/models/fm_ecg.py:32
↓ 1 callers
Class
ECGJEPAWrapper
Paper: https://arxiv.org/abs/2410.08559 Code: https://github.com/sehunfromdaegu/ECG_JEPA Checkpoints: https://drive.google.co
code/clinical_ts/models/fm_ecg.py:174
↓ 1 callers
Class
ECG_JEPA_Scratch
code/clinical_ts/models/fm_ecg.py:310
↓ 1 callers
Class
EcgFmKEDWrapper
Paper: https://doi.org/10.1016/j.xcrm.2024.101875 Code: https://github.com/control-spiderman/ECGFM-KED Checkpoints: https://z
code/clinical_ts/models/fm_ecg.py:631
↓ 1 callers
Class
Encoder_Block
code/clinical_ts/models/ecg_foundation_models/ecg_jepa/ecg_jepa.py:176
↓ 1 callers
Class
FMEEG1
code/clinical_ts/models/fm_eeg.py:6
↓ 1 callers
Class
FMEEG2
code/clinical_ts/models/fm_eeg.py:11
↓ 1 callers
Class
FMMovement1
code/clinical_ts/models/fm_movement.py:6
↓ 1 callers
Class
FMMovement2
code/clinical_ts/models/fm_movement.py:11
↓ 1 callers
Class
FeedForward
MLP Module with GELU activation fn + dropout.
code/clinical_ts/models/ecg_foundation_models/st_mem/encoder/vit.py:54
↓ 1 callers
Class
FeedForward
MLP Module with GELU activation fn + dropout.
code/clinical_ts/models/ecg_foundation_models/merl/vit1d.py:48
↓ 1 callers
Class
ForwardHook
Create a forward hook on module `m`
code/clinical_ts/utils/callbacks.py:10
↓ 1 callers
Class
HippoSSKernel
Wrapper around SSKernel that generates A, B, C, dt according to HiPPO arguments. The SSKernel is expected to support the interface forward()
code/clinical_ts/ts/s4_modules/s42.py:953
↓ 1 callers
Class
HippoSSKernel
Wrapper around SSKernel that generates A, B, C, dt according to HiPPO arguments. The SSKernel is expected to support the interface forward()
code/clinical_ts/models/s42.py:952
↓ 1 callers
Class
HuBERTECG
code/clinical_ts/models/ecg_foundation_models/hubert_ecg/hubert_ecg.py:21
↓ 1 callers
Class
HuBERTECGConfig
code/clinical_ts/models/ecg_foundation_models/hubert_ecg/hubert_ecg.py:12
↓ 1 callers
Class
HuBERTForECGClassification
code/clinical_ts/models/ecg_foundation_models/hubert_ecg/hubert_ecg_classification.py:26
↓ 1 callers
Class
HubertEcgWrapper
code/clinical_ts/models/fm_ecg.py:844
↓ 1 callers
Class
Inception1d
inception time architecture
code/clinical_ts/models/inception1d.py:72
↓ 1 callers
Class
InceptionBackbone
code/clinical_ts/models/inception1d.py:49
↓ 1 callers
Class
InceptionBlock1d
code/clinical_ts/models/inception1d.py:20
↓ 1 callers
Class
LRMonitorCallback
code/clinical_ts/utils/callbacks.py:70
↓ 1 callers
Class
LearnableQueryAttentionPool1d
V-JEPA (https://openreview.net/forum?id=WFYbBOEOtv) Learnable Query Attention Pooling
code/clinical_ts/utils/heads.py:33
↓ 1 callers
Class
MHSA1d
code/clinical_ts/models/xresnet1d.py:55
↓ 1 callers
Class
Main_Lite_ECG
code/main_lite_ecg.py:25
↓ 1 callers
Class
Main_Lite_EEG
code/main_lite_eeg.py:7
↓ 1 callers
Class
Main_Lite_Movement
code/main_lite_movement.py:7
↓ 1 callers
Class
MaskTransformer
code/clinical_ts/models/ecg_foundation_models/ecg_jepa/ecg_jepa.py:213
↓ 1 callers
Class
MaskTransformerPredictor
code/clinical_ts/models/ecg_foundation_models/ecg_jepa/ecg_jepa.py:412
↓ 1 callers
Class
MerlWrapper
Paper: https://arxiv.org/abs/2403.06659 Code: https://github.com/cheliu-computation/MERL-ICML2024 Checkpoints: https://drive.
code/clinical_ts/models/fm_ecg.py:480
↓ 1 callers
Class
Mlp
code/clinical_ts/models/ecg_foundation_models/ecg_jepa/ecg_jepa.py:109
↓ 1 callers
Class
MyMaxPool1dPadSame
extend nn.MaxPool1d to support SAME padding params: kernel_size: kernel size stride: the stride of the window. Default value
code/clinical_ts/models/ecg_foundation_models/ecg_founder.py:49
↓ 1 callers
Class
Predictor_Block
code/clinical_ts/models/ecg_foundation_models/ecg_jepa/ecg_jepa.py:194
↓ 1 callers
Class
RobustMLFlowLogger
Robust MLFLowLogger that does not crash if connection is down
code/pretrain.py:48
↓ 1 callers
Class
S4Model
code/clinical_ts/models/s4_model.py:7
↓ 1 callers
Class
SSKernelNPLR
Stores a representation of and computes the SSKernel function K_L(A^dt, B^dt, C) corresponding to a discretized state space, where A is Normal + Low R
code/clinical_ts/ts/s4_modules/s42.py:478
↓ 1 callers
Class
SSKernelNPLR
Stores a representation of and computes the SSKernel function K_L(A^dt, B^dt, C) corresponding to a discretized state space, where A is Normal + Low R
code/clinical_ts/models/s42.py:477
↓ 1 callers
Class
SequentialTimeSeriesEncoder
A sequence of TimeSeriesEncoders (somewhat similar to nn.Sequential) Note: this is the only module that gets instantiated directly in template_mod
code/clinical_ts/template_modules.py:644
↓ 1 callers
Class
ShapeConfig
code/clinical_ts/template_modules.py:193
↓ 1 callers
Class
Shortcut1d
code/clinical_ts/models/inception1d.py:36
↓ 1 callers
Class
SqueezeExcite1d
squeeze excite block as used for example in LSTM FCN
code/clinical_ts/ts/basic_conv1d_modules/basic_conv1d.py:94
↓ 1 callers
Class
SqueezeExcite1d
squeeze excite block as used for example in LSTM FCN
code/clinical_ts/models/basic_conv1d.py:94
↓ 1 callers
Class
StMemWrapper
Paper: https://arxiv.org/abs/2402.09450 Code: https://github.com/bakqui/ST-MEM Checkpoints: https://drive.google.com/file/d/1
code/clinical_ts/models/fm_ecg.py:337
↓ 1 callers
Class
StaticStats
code/clinical_ts/template_modules.py:220
↓ 1 callers
Class
TSData
code/clinical_ts/data/time_series_dataset.py:25
↓ 1 callers
Class
TransformerBlock
code/clinical_ts/models/ecg_foundation_models/merl/vit1d.py:108
↓ 1 callers
Class
Transpose
helper module: transpose operation that can be used like a nn.module
code/clinical_ts/ts/head.py:174
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