initial commit

README.md

@@ -1,2 +1,38 @@
 # PF-TKRR
-Patient-Finetuned Seizure Detection using Tensor Kernel Ridge Regression
+## Intro
+
+This is the public repository for the paper: Efficient Patient-Finetuned Seizure Detection with Tensor Kernel Ridge Regression.
+
+## Required packages
+### Standard packages
+The required python packages can be found in [requirements.txt](requirements.txt).
+It is recommended to first create a conda environment to install the packages and required python version. This can be done with the [environment.yml](environment.yml) file, which also installs the conda packages. Note that the remaining packages still need to be installed with pip.
+
+### Additional packages
+
+For pre-processing the `seizure_data_processing` package is needed: https://github.com/sderooij/seizure_data_processing/releases/tag/v0.0.1
+
+In addition to that also the (self-created) `TensorLibrary` package is required, as it contains the CP-KRR model: https://github.com/sderooij/tensorlibrary/releases/tag/v0.0.1.
+
+
+## Usage
+Before running the scripts and notebooks please modify the `src/config.py` file.
+The order in which the scripts and notebooks need to be run is as follows:
+1. `find_tle_patients.ipynb`
+2. `feature_exstraction.py`
+3. `create_set.ipynb`
+4. `preprocess.py`
+5. `classification.py` (or run `classify.sh`)
+6. `fine_tune.py`
+7. `post_process.py`
+8. `visualize_results.py`
+9. `convergence.py`
+10. `convergence_auc_plot.ipynb`
+
+Explanation on their usage is (in principle) provided in the respective files. Note that there may be issues with import due to different (working) paths
+
+## Questions
+For any questions you can contact: [email protected]
+
+
+

classify.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+# This script runs the classification.py script and saves the output to a text file
+# Global variables
+FEATURES_DIR="/path/to/features/"
+FEATURE_FILE="${FEATURES_DIR}features_ordered.parquet"
+GROUP_FILE="${FEATURES_DIR}val_groups.parquet"
+OUTPUT_DIR="data/"
+CLASSIFIER="svm" # "svm" or "cpkrr"
+CV_TYPE="PS" # "PS" or "PI"
+GRID_SEARCH="full" # "full" or "random" or "none"
+
+# Set variables
+HYPERPARAM_FILE="data/hyper_parameters_${CLASSIFIER}.json"
+OUTPUT_FILE="${OUTPUT_DIR}results_${CLASSIFIER}_${CV_TYPE}.txt"
+MODEL_FOLDER="${FEATURES_DIR}models/${CV_TYPE}/"
+SAVE_FILE="${FEATURES_DIR}${CV_TYPE}/results_${CLASSIFIER}"
+
+source ~/miniconda3/etc/profile.d/conda.sh
+conda activate seizure_env
+start_time="$(date -u +%s)"
+python src/scripts/classification.py --cv_type ${CV_TYPE} --classifier ${CLASSIFIER} --hyper_param ${HYPERPARAM_FILE} --feat_file ${FEATURE_FILE} --group_file ${GROUP_FILE} --grid_search ${GRID_SEARCH} --save_file=${SAVE_FILE} --model_folder=${MODEL_FOLDER} >> ${OUTPUT_FILE} 
+end_time="$(date -u +%s)"
+
+elapsed="$(($end_time-$start_time))"
+echo "Total of $elapsed seconds elapsed for training"

data/TLE_patients.csv

@@ -0,0 +1,44 @@
+,file,side,patient,num_seizures
+0,train/02_tcp_le/000/00000077/s001_2003_03_18/00000077_s001.txt,left,77,0
+1,train/02_tcp_le/001/00000107/s001_2003_04_15/00000107_s001.txt,left,107,0
+3,train/02_tcp_le/002/00000244/s003_2004_01_08/00000244_s003.txt,right,244,0
+4,train/02_tcp_le/002/00000254/s001_2003_07_30/00000254_s001.txt,left,254,0
+5,train/02_tcp_le/002/00000281/s001_2003_06_21/00000281_s001.txt,right,281,1
+6,train/02_tcp_le/004/00000404/s002_2003_09_11/00000404_s002.txt,right,404,0
+7,train/02_tcp_le/004/00000427/s001_2003_09_15/00000427_s001.txt,left,427,0
+8,train/02_tcp_le/005/00000526/s002_2003_08_11/00000526_s002.txt,left,526,0
+9,train/02_tcp_le/005/00000529/s001_2003_04_28/00000529_s001.txt,left,529,4
+12,train/02_tcp_le/006/00000609/s001_2003_10_22/00000609_s001.txt,left,609,1
+13,train/02_tcp_le/007/00000705/s001_2003_11_26/00000705_s001.txt,left,705,0
+14,train/02_tcp_le/008/00000820/s003_2004_08_03/00000820_s003.txt,right,820,1
+15,train/02_tcp_le/008/00000827/s001_2003_06_05/00000827_s001.txt,left,827,0
+16,train/02_tcp_le/009/00000908/s001_2003_05_30/00000908_s001.txt,left,908,0
+17,train/02_tcp_le/009/00000922/s001_2003_06_17/00000922_s001.txt,left,922,0
+18,train/02_tcp_le/009/00000940/s001_2003_07_08/00000940_s001.txt,right,940,0
+19,train/02_tcp_le/010/00001006/s004_2003_05_05/00001006_s004.txt,left,1006,4
+20,train/02_tcp_le/010/00001026/s001_2003_05_05/00001026_s001.txt,left,1026,0
+21,train/02_tcp_le/010/00001081/s001_2004_03_16/00001081_s001.txt,left,1081,0
+22,train/02_tcp_le/011/00001169/s001_2004_04_21/00001169_s001.txt,right,1169,0
+23,train/02_tcp_le/012/00001267/s003_2004_09_14/00001267_s003.txt,left,1267,0
+24,train/02_tcp_le/013/00001317/s002_2004_05_25/00001317_s002.txt,left,1317,0
+25,train/02_tcp_le/013/00001349/s002_2004_09_21/00001349_s002.txt,right,1349,0
+26,train/02_tcp_le/015/00001543/s001_2004_07_14/00001543_s001.txt,left,1543,5
+28,train/02_tcp_le/016/00001605/s001_2004_01_09/00001605_s001.txt,right,1605,0
+29,train/02_tcp_le/016/00001698/s001_2004_02_13/00001698_s001.txt,right,1698,0
+30,train/02_tcp_le/017/00001795/s001_2004_08_05/00001795_s001.txt,left,1795,2
+31,train/02_tcp_le/018/00001843/s001_2004_07_29/00001843_s001.txt,left,1843,1
+32,train/02_tcp_le/018/00001891/s001_2004_09_08/00001891_s001.txt,right,1891,1
+34,train/02_tcp_le/020/00002021/s001_2004_10_06/00002021_s001.txt,left,2021,0
+35,train/02_tcp_le/020/00002051/s001_2004_02_26/00002051_s001.txt,right,2051,0
+40,train/02_tcp_le/028/00002806/s003_2004_12_28/00002806_s003.txt,right,2806,28
+41,train/02_tcp_le/030/00003005/s003_2010_01_19/00003005_s003.txt,right,3005,0
+44,train/02_tcp_le/031/00003101/s002_2006_07_13/00003101_s002.txt,left,3101,0
+74,train/02_tcp_le/065/00006514/s019_2010_05_17/00006514_s019.txt,left,6514,16
+78,train/02_tcp_le/068/00006811/s004_2010_07_30/00006811_s004.txt,left,6811,5
+81,dev/02_tcp_le/002/00000258/s001_2003_07_16/00000258_s001.txt,right,258,14
+83,dev/02_tcp_le/006/00000629/s001_2003_07_22/00000629_s001.txt,left,629,0
+84,dev/02_tcp_le/019/00001981/s001_2004_02_20/00001981_s001.txt,left,1981,2
+87,dev/02_tcp_le/019/00001984/s001_2004_02_17/00001984_s001.txt,left,1984,2
+88,dev/02_tcp_le/022/00002289/s001_2005_03_02/00002289_s001.txt,left,2289,0
+94,dev/02_tcp_le/054/00005479/s001_2008_11_14/00005479_s001.txt,left,5479,7
+96,dev/02_tcp_le/059/00005943/s001_2009_06_28/00005943_s001.txt,right,5943,11