--- a/README.md +++ b/README.md @@ -1,92 +1,85 @@ -# SleepEEGNet: Automated Sleep Stage Scoring with Sequence to Sequence Deep Learning Approach -In this study, we introduced a novel deep learning approach, called SleepEEGNet, for automated sleep stage scoring using a single-channel EEG. - -# Paper - Our paper can be downloaded from the [arxiv website](https://arxiv.org/pdf/1903.02108). - * The Model architecture -  - - * The CNN architecture - -  - -## Requirements -* Python 2.7 -* tensorflow/tensorflow-gpu -* numpy -* scipy -* matplotlib -* scikit-learn -* matplotlib -* imbalanced-learn(0.4.3) -* pandas -* mne -## Dataset and Data Preparation -We evaluated our model using [the Physionet Sleep-EDF datasets](https://physionet.org/physiobank/database/sleep-edfx/) published in 2013 and 2018. -We have used the source code provided by [github:akaraspt](https://github.com/akaraspt/deepsleepnet) to prepare the dataset. - -* To download SC subjects from the Sleep_EDF (2013) dataset, use the below script: - -``` -cd data_2013 -chmod +x download_physionet.sh -./download_physionet.sh -``` - -* To download SC subjects from the Sleep_EDF (2018) dataset, use the below script: -``` -cd data_2018 -chmod +x download_physionet.sh -./download_physionet.sh -``` - -Use below scripts to extract sleep stages from the specific EEG channels of the Sleep_EDF (2013) dataset: - -``` -python prepare_physionet.py --data_dir data_2013 --output_dir data_2013/eeg_fpz_cz --select_ch 'EEG Fpz-Cz' -python prepare_physionet.py --data_dir data_2013 --output_dir data_2013/eeg_pz_oz --select_ch 'EEG Pz-Oz' -``` - -## Train - -* Modify args settings in seq2seq_sleep_sleep-EDF.py for each dataset. - -* For example, run the below script to train SleepEEGNET model with the 20-fold cross-validation using Fpz-Cz channel of the Sleep_EDF (2013) dataset: -``` -python seq2seq_sleep_sleep-EDF.py --data_dir data_2013/eeg_fpz_cz --output_dir output_2013 --num_folds 20 -``` - -## Results -* Run the below script to present the achieved results by SleepEEGNet model for Fpz-Cz channel. -``` -python summary.py --data_dir output_2013/eeg_fpz_cz -``` - - - -## Visualization -* Run the below script to visualize attention maps of a sequence input (EEG epochs) for Fpz-Cz channel. -``` -python visualize.py --data_dir output_2013/eeg_fpz_cz -``` - - -## Citation - -If you find it useful, please cite our paper as follows: - -``` -@article{mousavi2019sleepEEGnet, - title={SleepEEGNet: Automated Sleep Stage Scoring with Sequence to Sequence Deep Learning Approach}, - author={Sajad Mousavi, Fatemeh Afghah and U. Rajendra Acharya}, - journal={arXiv preprint arXiv:1903.02108}, - year={2019} -} -``` - -## References - [github:akaraspt](https://github.com/akaraspt/deepsleepnet) - [deepschool.io](https://github.com/sachinruk/deepschool.io/blob/master/DL-Keras_Tensorflow) - -## Licence -For academtic and non-commercial usage +# SleepEEGNet: Automated Sleep Stage Scoring with Sequence to Sequence Deep Learning Approach +In this study, we introduced a novel deep learning approach, called SleepEEGNet, for automated sleep stage scoring using a single-channel EEG. + +# Paper + Our paper can be downloaded from the [arxiv website](https://arxiv.org/pdf/1903.02108). + + +## Requirements +* Python 2.7 +* tensorflow/tensorflow-gpu +* numpy +* scipy +* matplotlib +* scikit-learn +* matplotlib +* imbalanced-learn(0.4.3) +* pandas +* mne +## Dataset and Data Preparation +We evaluated our model using [the Physionet Sleep-EDF datasets](https://physionet.org/physiobank/database/sleep-edfx/) published in 2013 and 2018. +We have used the source code provided by [github:akaraspt](https://github.com/akaraspt/deepsleepnet) to prepare the dataset. + +* To download SC subjects from the Sleep_EDF (2013) dataset, use the below script: + +``` +cd data_2013 +chmod +x download_physionet.sh +./download_physionet.sh +``` + +* To download SC subjects from the Sleep_EDF (2018) dataset, use the below script: +``` +cd data_2018 +chmod +x download_physionet.sh +./download_physionet.sh +``` + +Use below scripts to extract sleep stages from the specific EEG channels of the Sleep_EDF (2013) dataset: + +``` +python prepare_physionet.py --data_dir data_2013 --output_dir data_2013/eeg_fpz_cz --select_ch 'EEG Fpz-Cz' +python prepare_physionet.py --data_dir data_2013 --output_dir data_2013/eeg_pz_oz --select_ch 'EEG Pz-Oz' +``` + +## Train + +* Modify args settings in seq2seq_sleep_sleep-EDF.py for each dataset. + +* For example, run the below script to train SleepEEGNET model with the 20-fold cross-validation using Fpz-Cz channel of the Sleep_EDF (2013) dataset: +``` +python seq2seq_sleep_sleep-EDF.py --data_dir data_2013/eeg_fpz_cz --output_dir output_2013 --num_folds 20 +``` + +## Results +* Run the below script to present the achieved results by SleepEEGNet model for Fpz-Cz channel. +``` +python summary.py --data_dir output_2013/eeg_fpz_cz +``` + +## Visualization +* Run the below script to visualize attention maps of a sequence input (EEG epochs) for Fpz-Cz channel. +``` +python visualize.py --data_dir output_2013/eeg_fpz_cz +``` + + +## Citation + +If you find it useful, please cite our paper as follows: + +``` +@article{mousavi2019sleepEEGnet, + title={SleepEEGNet: Automated Sleep Stage Scoring with Sequence to Sequence Deep Learning Approach}, + author={Sajad Mousavi, Fatemeh Afghah and U. Rajendra Acharya}, + journal={arXiv preprint arXiv:1903.02108}, + year={2019} +} +``` + +## References + [github:akaraspt](https://github.com/akaraspt/deepsleepnet) + [deepschool.io](https://github.com/sachinruk/deepschool.io/blob/master/DL-Keras_Tensorflow) + +## Licence +For academtic and non-commercial usage