seizure-prediction.ipynb

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    "# Prediction of seizures from EEG signals\n",
    "\n",
    "This [dataset](https://www.kaggle.com/c/seizure-prediction) contains EEG recordings from dogs with naturally occurring epilepsy using an ambulatory monitoring system. EEG was sampled from 16 electrodes at 400 Hz, and recorded voltages were referenced to the group average. These are long duration recordings, spanning multiple months up to a year and recording up to a hundred seizures in some dogs.\n",
    "The challenge is to distinguish between ten minute long data clips covering an hour prior to a seizure, and ten minute iEEG clips of interictal activity.\n",
    "\n",
    "The data is stored in a series of .mat files, each containing a data structure with fields as follows:\n",
    "\n",
    "* data: a matrix of EEG sample values arranged row x column as electrode x time.\n",
    "* data_length_sec: the time duration of each data row\n",
    "* sampling_frequency: the number of data samples representing 1 second of EEG data.\n",
    "* channels: a list of electrode names corresponding to the rows in the data field\n",
    "* sequence: the index of the data segment within the one hour series of clips. For example, preictal_segment_6.mat has a sequence number of 6, and represents the iEEG data from 50 to 60 minutes into the preictal data."
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   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "from tqdm.notebook import tqdm\n",
    "from scipy import stats\n",
    "import utils\n",
    "from feature_extraction import extractFeatures\n",
    "\n",
    "from sklearn.feature_selection import SelectKBest, f_classif\n",
    "from sklearn.model_selection import StratifiedKFold, RandomizedSearchCV\n",
    "from lightgbm import LGBMClassifier as lgb\n",
    "from sklearn.metrics import roc_auc_score\n",
    "from sklearn.pipeline import make_pipeline\n"
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   "source": [
    "## Light EDA"
   ]
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   "source": [
    "filedf = utils.indexFiles()\n",
    "\n",
    "filedf.drop('path', axis = 1).groupby(['subject', 'label']).count().plot(\n",
    "    kind    = 'barh', \n",
    "    figsize = (15, 5),\n",
    "    legend  = None,\n",
    "    title   = f'Class & balance per subject (Total no. samples: {filedf.shape[0]})');"
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   "source": [
    "### Plot one entire subject"
   ]
  },
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   "source": [
    "for subject, df in filedf.groupby('subject'):\n",
    "    utils.plotSubject(df)\n",
    "    break"
   ]
  },
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   "source": [
    "### No. channels\n",
    "Get number of channels present in each record:"
   ]
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    "metadf = []\n",
    "for idx, record in tqdm(filedf.iterrows(), total = filedf.shape[0]):\n",
    "    duration, Fs, _, _, signals = utils.parseFile(record['path']) \n",
    "    metadf.append((idx, duration, Fs, signals.shape[0], signals.shape[1]))\n",
    "\n",
    "metadf = pd.DataFrame(metadf, columns = ['idx', 'duration', 'frequency', 'channels', 'samples'])\n",
    "\n",
    "metadf.groupby('channels')['idx'].count()"
   ]
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   "source": [
    "Approximately 10% of the dataset consists of 15 channels. We need to find which are the missing channels:"
   ]
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    "# Get records with at least one channel missing\n",
    "missingChIdx = metadf['idx'][metadf['channels'] == 15]\n",
    "missingChdf = filedf.loc[missingChIdx]\n",
    "\n",
    "allChannels = range(1, 17) # All channels that should be present\n",
    "channelsMissing = []\n",
    "\n",
    "for idx, record in tqdm(missingChdf.iterrows(), total = missingChdf.shape[0]):\n",
    "    _, _, chNames, _, _ = utils.parseFile(record['path'])\n",
    "    \n",
    "    # Channel numbers that are present in the record\n",
    "    channelsPresent = [int(name.split('_')[-1].strip('c')) for name in chNames]\n",
    "    \n",
    "    # Channels missing in the record\n",
    "    channelsMissing.append(list(set(allChannels).difference(channelsPresent)))\n",
    "    \n",
    "print(np.unique(channelsMissing)[0])"
   ]
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   "source": [
    "Channel 4 is missing from 480 records (10% of the dataset). This channel will be removed from subsequent analysis.\n"
   ]
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   "source": [
    "## Feature Extraction\n",
    "\n",
    "EEG signals recorded with probes in symmetric locations on the left and right brain hemisphere will be averaged out. This effectively reduces the number of channels from 16 (15 without counting the missing channel) to 8.\n",
    "\n",
    "A discrete wavelet transformation will be performed, and a set of features will be extracted from each level and for each channel.\n",
    "The features to be extracted include:\n",
    "\n",
    "* Mean value\n",
    "* Absolute mean value\n",
    "* Standard deviation\n",
    "* Coefficient of variation \n",
    "* Skewness\n",
    "* Kurtosis\n",
    "* Absolute median value\n",
    "* Min value\n",
    "* Max value\n",
    "* RMS value\n",
    "* Curve length\n",
    "* Interquartile range\n",
    "* Mobility\n",
    "* Complexity\n",
    "\n",
    "For 8 channels and 8 wavelet levels, this amounts to approximately 900 features from roughly 4000 samples."
   ]
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   "source": [
    "# Extract features (requires approximately 30 mins)\n",
    "X, y = extractFeatures(filedf, waveletName = 'sym6', waveletLevels = 8)"
   ]
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   "source": [
    "## Modelling\n",
    "\n",
    "Nested 5-fold CV will be used with random search and automatic feature selection:"
   ]
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    "noFolds      = 5   # No folds for nested CV\n",
    "noSearchIter = 100 # Iterations for random search\n",
    "\n",
    "# Parameter grid for random search\n",
    "paramDistr = dict(\n",
    "    selectkbest__k                   = [50, 100, 200, 300, 500, X.shape[1]],\n",
    "    lgbmclassifier__reg_alpha        = stats.loguniform(10 ** -6, 10 ** 4),\n",
    "    lgbmclassifier__reg_lambda       = stats.loguniform(10 ** -6, 10 ** 4),\n",
    "    lgbmclassifier__n_estimators     = [20, 40, 80, 160, 320, 640, 1024],\n",
    "    lgbmclassifier__learning_rate    = [0.001, 0.002, 0.004, 0.008, 0.01, 0.02, 0.04, 0.08],\n",
    "    lgbmclassifier__max_depth        = np.arange(10, 35, 5),\n",
    "    lgbmclassifier__min_split_gain   = [0, 0.001,0.005,0.01],\n",
    "    lgbmclassifier__subsample        = [0.7, 0.9, 1.0],\n",
    "    lgbmclassifier__colsample_bytree = [0.1, 0.3, 0.5, 1.0],\n",
    "    lgbmclassifier__num_leaves       = [5, 10, 20, 40, 80]\n",
    ")\n",
    "\n",
    "# Outer k-fold CV\n",
    "splitter = StratifiedKFold(n_splits = noFolds, shuffle = True, random_state=1)\n",
    "\n",
    "# Pipeline\n",
    "model = make_pipeline(SelectKBest(f_classif), \n",
    "                      lgb(boosting_type = 'dart', random_state = 1, is_unbalance = True))\n",
    "\n",
    "# Random search object\n",
    "clf = RandomizedSearchCV(model, paramDistr, \n",
    "                         n_iter  = noSearchIter, # Fitting 4 folds for each of ->50<- candidates, totalling 200 fits: 5 mins\n",
    "                         scoring = 'roc_auc',\n",
    "                         cv      = StratifiedKFold(n_splits = noFolds - 1, \n",
    "                                                   shuffle = True, \n",
    "                                                   random_state=1),\n",
    "                         verbose = 0,\n",
    "                         n_jobs  = -1,\n",
    "                         random_state = 0)"
   ]
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   "source": [
    " Run nested CV:"
   ]
  },
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    "for foldId, (trainIdx, testIdx) in enumerate(splitter.split(X, y, filedf['subject'])):\n",
    "\n",
    "    # Split trainval and test set\n",
    "    Xl, yl = X[trainIdx, :], y[trainIdx]\n",
    "    Xt, yt = X[testIdx, :], y[testIdx]\n",
    "    \n",
    "    # Random search - will refit automatically\n",
    "    search = clf.fit(Xl, yl)\n",
    "    \n",
    "    # Get test set errors\n",
    "    yhat = clf.predict_proba(Xt)\n",
    "    testErr = roc_auc_score(yt, yhat[:, 1]).round(3)\n",
    "    \n",
    "    # Get best hyperparameter set performance\n",
    "    bestIdx   = search.best_index_\n",
    "    CVmeanErr = search.cv_results_['mean_test_score'][bestIdx].round(3)\n",
    "    CVstdErr  = search.cv_results_['std_test_score'][bestIdx].round(3)\n",
    "    \n",
    "    # Print results\n",
    "    print(f' Fold {foldId + 1} | CV AUROC: {CVmeanErr} +- {CVstdErr} | Test AUROC: {testErr}')"
   ]
  }
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