--- a +++ b/ecg/README.md @@ -0,0 +1,81 @@ +##### This work and code is developed by the awesome team of Awni et al, StanfordML Group. I have just modified it to work with python3 and few other changes for my comfort of use. + +## Install + +Clone the repository + +``` +git clone git@github.com:manideep2510/ECG-acquisition-classification.git +``` + +**Python 3.5 or higher is required to run the code. To test the code the with the pretrained models, Python 3.5 is the only one it supports** + +Install the requirements (this may take a few minutes). + +For CPU only support run +``` +cd ecg +./setup.sh +``` + +To install with GPU support run +``` +env TF=gpu ./setup.sh +``` + +## Training + +In the repo root direcotry (`ecg`) make a new directory called `saved`. + +``` +mkdir saved +``` + +To train a model use the following command, replacing `path_to_config.json` +with an actual config: + +``` +python ecg/train.py path_to_config.json +``` + +Note that after each epoch the model is saved in +`ecg/saved/<experiment_id>/<timestamp>/<model_id>.hdf5`. + +For an actual example of how to run this code on a real dataset, you can follow +the instructions in the cinc17 [README](examples/cinc17/README.md). This will +walk through downloading the Physionet 2017 challenge dataset and training and +evaluating a model. + +## Testing + +After training the model for a few epochs, you can make predictions with. + +``` +python ecg/predict.py <dataset>.json <model>.hdf5 +``` + +replacing `<dataset>` with an actual path to the dataset and `<model>` with the +path to the model. + +## Citation and Reference + +This work is published in the following paper in *Nature Medicine* + +[Cardiologist-level arrhythmia detection and classification in ambulatory electrocardiograms using a deep neural network](https://www.nature.com/articles/s41591-018-0268-3) + +If you find this codebase useful for your research please cite: + +``` +@article{hannun2019cardiologist, + title={Cardiologist-level arrhythmia detection and classification in ambulatory electrocardiograms using a deep neural network}, + author={Hannun, Awni Y and Rajpurkar, Pranav and Haghpanahi, Masoumeh and Tison, Geoffrey H and Bourn, Codie and Turakhia, Mintu P and Ng, Andrew Y}, + journal={Nature Medicine}, + volume={25}, + number={1}, + pages={65}, + year={2019}, + publisher={Nature Publishing Group} +} +``` + +