| --- |
| language: en |
| license: apache-2.0 |
| tags: |
| - sleep-staging |
| - eeg |
| - embeddings |
| - physioex |
| - tsinalis |
| pretty_name: Tsinalis-2016 Embeddings |
| size_categories: |
| - 10K<n<100K |
| --- |
| |
| # Tsinalis-2016 Embeddings |
|
|
| Pre-extracted per-epoch embeddings from **TsinalisCNN** (Tsinalis et al. 2016), |
| trained on Sleep-EDF via [PhysioEx](https://github.com/guidogagl/physioex). |
|
|
| Each subject directory contains: |
| - `embeddings.npy` — `(n_epochs, 500)` per-epoch embeddings (bfloat16) |
| - `labels.npy` — `(n_epochs,)` AASM sleep stage labels |
|
|
| **Note:** Tsinalis concatenates L=5 epochs before convolution. Embeddings are |
| extracted using centered windows (each epoch gets the feature vector from the |
| window centered on it). |
|
|
| ## Usage |
|
|
| ```python |
| from physioex.models import load_embeddings |
| path = load_embeddings("tsinalis-2016", "hmc", verbose=True) |
| ``` |
|
|
| ## Linear Probe Results (5-fold subject-wise CV) |
|
|
| | Dataset | Subjects | ACC | MF1 | κ | F1-W | F1-N1 | F1-N2 | F1-N3 | F1-REM | |
| |---|---|---|---|---|---|---|---|---|---| |
| | sleepedf | 153 | **0.8297** | **0.7563** | **0.7631** | 0.93 | 0.41 | 0.86 | 0.80 | 0.78 | |
| | mass_ss05 | 26 | 0.8157 | 0.7004 | 0.7297 | 0.72 | 0.26 | 0.87 | 0.82 | 0.83 | |
| | mass_ss02 | 19 | 0.8062 | 0.6925 | 0.7134 | 0.70 | 0.28 | 0.87 | 0.83 | 0.78 | |
| | mass_ss03 | 62 | 0.7950 | 0.7039 | 0.6923 | 0.77 | 0.33 | 0.87 | 0.76 | 0.80 | |
| | mass_ss04 | 40 | 0.7842 | 0.6791 | 0.6865 | 0.73 | 0.24 | 0.86 | 0.79 | 0.77 | |
| | mass_ss01 | 53 | 0.7473 | 0.6691 | 0.6388 | 0.83 | 0.36 | 0.83 | 0.61 | 0.72 | |
| | stages_GSDV | 232 | 0.7368 | 0.5371 | 0.5643 | 0.75 | 0.08 | 0.83 | 0.47 | 0.56 | |
| | dcsm | 255 | 0.7329 | 0.5575 | 0.5947 | 0.82 | 0.02 | 0.73 | 0.77 | 0.45 | |
| | shhs_visit2 | 2651 | 0.7301 | 0.5995 | 0.6097 | 0.80 | 0.11 | 0.77 | 0.71 | 0.60 | |
| | shhs_visit1 | 5793 | 0.7267 | 0.5957 | 0.6001 | 0.80 | 0.10 | 0.77 | 0.69 | 0.62 | |
| | stages_GSLH | 45 | 0.7178 | 0.5317 | 0.5367 | 0.79 | 0.13 | 0.80 | 0.57 | 0.37 | |
| | stages_MSMI | 63 | 0.7121 | 0.5953 | 0.5608 | 0.75 | 0.15 | 0.79 | 0.64 | 0.64 | |
| | stages_GSSW | 105 | 0.7096 | 0.5009 | 0.5234 | 0.72 | 0.07 | 0.81 | 0.36 | 0.54 | |
| | stages_GSSA | 26 | 0.6989 | 0.4432 | 0.4483 | 0.64 | 0.01 | 0.81 | 0.30 | 0.46 | |
| | stages_GSBB | 30 | 0.6912 | 0.5546 | 0.5269 | 0.81 | 0.16 | 0.77 | 0.59 | 0.45 | |
| | stages_MSQW | 153 | 0.6813 | 0.5477 | 0.5151 | 0.77 | 0.23 | 0.79 | 0.45 | 0.51 | |
| | stages_STLK | 158 | 0.6639 | 0.4954 | 0.4560 | 0.67 | 0.05 | 0.76 | 0.43 | 0.56 | |
| | hmc | 151 | 0.6634 | 0.6088 | 0.5473 | 0.72 | 0.25 | 0.70 | 0.74 | 0.63 | |
| | hpap | 247 | 0.6595 | 0.5774 | 0.5192 | 0.71 | 0.17 | 0.72 | 0.69 | 0.59 | |
| | mesa | 2056 | 0.5748 | 0.4225 | 0.3371 | 0.55 | 0.02 | 0.67 | 0.42 | 0.46 | |
| | stages_STNF | 460 | 0.5484 | 0.4682 | 0.3925 | 0.63 | 0.00 | 0.57 | 0.67 | 0.47 | |
| | stages_MSNF | 38 | 0.5108 | 0.2886 | 0.1714 | 0.45 | 0.02 | 0.65 | 0.26 | 0.06 | |
| | stages_MSTH | 31 | 0.4942 | 0.1529 | -0.0035 | 0.02 | 0.02 | 0.67 | 0.03 | 0.03 | |
| | stages_MSTR | 285 | 0.4938 | 0.2544 | 0.1110 | 0.30 | 0.01 | 0.64 | 0.25 | 0.08 | |
| | stages_BOGN | 85 | 0.4578 | 0.1892 | 0.0419 | 0.04 | 0.00 | 0.62 | 0.27 | 0.01 | |
|
|
| ## Model Details |
|
|
| - **Architecture**: TsinalisCNN (Tsinalis et al. 2016) — 2-layer CNN on concatenated 5-epoch signal |
| - **Training data**: Sleep-EDF (153 subjects, single EEG channel) |
| - **Pipeline**: `identity` (Sleep-EDF) / `raw` (other datasets, resample to 100 Hz) |
| - **Sequence length**: L=5 epochs |
| - **Embedding dim**: 500 |
|
|
| ## Datasets |
|
|
| | Dataset | Source | URL | |
| |---|---|---| |
| | Sleep-EDF | PhysioNet | https://physionet.org/content/sleep-edfx/1.0.0/ | |
| | HMC | PhysioNet | https://physionet.org/content/hmc-sleep-staging/1.1/ | |
| | DCSM | ERDA/KU | https://erda.ku.dk/public/archives/db553715ecbe1f3ac66c1dc569826eef/published-archive.html | |
| | SHHS | NSRR | https://sleepdata.org/datasets/shhs | |
| | MESA | NSRR | https://sleepdata.org/datasets/mesa | |
| | HomePAP | NSRR | https://sleepdata.org/datasets/homepap | |
| | STAGES | NSRR | https://sleepdata.org/datasets/stages | |
| | MASS | CEAMS | http://ceams-carsm.ca/mass/ | |
|
|
| ## Citations |
|
|
| ```bibtex |
| @article{gagliardi2025physioex, |
| author={Gagliardi, Guido and Alfeo, Luca and Cimino, Mario G C A and Valenza, Gaetano and De Vos, Maarten}, |
| title={PhysioEx, a new Python library for explainable sleep staging through deep learning}, |
| journal={Physiological Measurement}, |
| url={http://iopscience.iop.org/article/10.1088/1361-6579/adaf73}, |
| year={2025}, |
| } |
| |
| @article{tsinalis2016automatic, |
| title={Automatic Sleep Stage Scoring with Single-Channel EEG Using Convolutional Neural Networks}, |
| author={Tsinalis, Orestis and Matthews, Paul M and Guo, Yike and Zafeiriou, Stefanos}, |
| journal={arXiv:1610.01683}, |
| year={2016}, |
| } |
| ``` |
|
|
