File size: 2,333 Bytes
ff8e6c1 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 |
# Kardio-Net: A Deep Learning Model for Predicting Serum Potassium Levels from Apple Watch ECG in ESRD Patients
### I. Input preparation
1. Prerequisites
Ensure that all ECG files are saved in *.npy format with the following shapes:
- (5000, 12) for 12-lead ECGs
- (500 * 30 seconds, 1) for Apple Watch ECGs
Store these files in a single flat directory, and include a manifest CSV file in the same location to accompany
them.
2. Manifest File Format
The manifest CSV file should include a header.
Each row corresponds to one ECG file with the following columns:
- filename: Name of the .npy file (without the extension).
- label: serum potassium label.
### II. Inference
### For 12-Lead ECG
<!-- #region -->
1. use predict_potassium_12lead.py to get the potassium level prediction.
2. Edit data_path and manifest_path and run the predict_potassium.py script.
3. Upon completion, a file named "dataloader_0_predictions.csv" will be saved in the same directory. This file contains the inference results "preds" from the model.
4. Use generate_result.py to get the performance metric and figure.
<!-- #endregion -->
### For Single Lead ECG
### A. ECG preprocessing and segmentation
<!-- #region -->
1. Use preprocessing.py for denoise, normalize, and segment ECG into 5-second for input
2. Set the following paths in preprocessing.py:
- raw_directory = "path/to/raw_data_directory" #raw ecg folder for target task
- output_directory = "path/to/output_directory" #output folder for normalize ECG
- manifest_path = "/path/to/manifest.csv" # Manifest file path
- output_path = "path/to/output_path" # Output path for segmented ECGs
3. Execute predict.py.
4. If the ECG files were already normalize, can execute the segmentation function only.
<!-- #endregion -->
### B. potassium regression model
<!-- #region -->
1. use predict_potassium_1lead.py to get the potassium level prediction.
2. Edit data_path and manifest_path and run the predict_potassium.py script.
3. Upon completion, a file named "dataloader_0_predictions.csv" will be saved in the same directory. This file contains the inference results "preds" from the model.
4. Use generate_result.py to get the performance metric and figure.
<!-- #endregion -->
```python
```
|