Volume 13 Supplement 2
A random forest model based classification scheme for neonatal amplitude-integrated EEG
© Chen et al.; licensee BioMed Central Ltd. 2014
Published: 11 December 2014
Modern medical advances have greatly increased the survival rate of infants, while they remain in the higher risk group for neurological problems later in life. For the infants with encephalopathy or seizures, identification of the extent of brain injury is clinically challenging. Continuous amplitude-integrated electroencephalography (aEEG) monitoring offers a possibility to directly monitor the brain functional state of the newborns over hours, and has seen an increasing application in neonatal intensive care units (NICUs).
This paper presents a novel combined feature set of aEEG and applies random forest (RF) method to classify aEEG tracings. To that end, a series of experiments were conducted on 282 aEEG tracing cases (209 normal and 73 abnormal ones). Basic features, statistic features and segmentation features were extracted from both the tracing as a whole and the segmented recordings, and then form a combined feature set. All the features were sent to a classifier afterwards. The significance of feature, the data segmentation, the optimization of RF parameters, and the problem of imbalanced datasets were examined through experiments. Experiments were also done to evaluate the performance of RF on aEEG signal classifying, compared with several other widely used classifiers including SVM-Linear, SVM-RBF, ANN, Decision Tree (DT), Logistic Regression(LR), ML, and LDA.
The combined feature set can better characterize aEEG signals, compared with basic features, statistic features and segmentation features respectively. With the combined feature set, the proposed RF-based aEEG classification system achieved a correct rate of 92.52% and a high F1-score of 95.26%. Among all of the seven classifiers examined in our work, the RF method got the highest correct rate, sensitivity, specificity, and F 1-score, which means that RF outperforms all of the other classifiers considered here. The results show that the proposed RF-based aEEG classification system with the combined feature set is efficient and helpful to better detect the brain disorders in newborns.
Over the past decades, modern medical advances have greatly increased the survival rate of term and preterm infants . Based on modern medical research, brain permanent damage can be minimized before it becomes irreversible . Amplitude-integrated electroencephalography is an important tool for the neurological assessment of critically ill newborns . Compared with imaging techniques such as Magnetic Resonance Imaging (MRI), aEEG is more suitable to continuously monitor the brain activity, which could record tracking changes and the maturation process of brain. Benefiting from the non-intrusive nature and high availability of aEEG, it is easy to be applied to portable bedside equipment.
The cerebral function monitor (CFM) was created in the 1960s by Douglas Maynard and first applied clinically by Pamela Prior . In 1970s and early 1980s, Ingmar Rosén and Nils Svenningsen introduced the CFM in the intensive monitoring of brain function in newborns . Later, Lena Hellström-Westas started to evaluate the method in the neonatal intensive care unit (NICU) .
AEEG signal is derived from a reduced EEG which can be captured by CFM. Unlike the standard EEG, whose setting up and interpreting are labor intensive, aEEG signals are recorded from limited channels with symmetric parietal electrodess . The aEEG processing scenario includes an asymmetric band pass filter with pass band of 2-15Hz, semi-logarithmic amplitude compression and time compression. The filtering will minimize artifacts from sweating, movements, muscle activity and electrical interference. The amplitude is semilogarithmic amplitude compression (linear display 0-10 µV ; logarithmic display 10-100 µV). Continuous aEEG monitoring offers a possibility to directly monitor the functional state of the brain over hours and days. Toet et al. gave a comparison between amplitude integrated electroencephalogram and standard electroencephalogram in neonates and pointed out CFM is a reliable tool for monitoring background patterns (especially normal and severely abnormal ones). Brain monitoring with aEEG is also reported to can better define brain injury and predict out-come than many other methods [3, 10].
To apply machine learning algorithms to aEEG interpretation task, the problem can be considered as a classification problem of signal. Different machine learning algorithms have been used for classification tasks. Among them, Random Forest (RF) and Support Vector Machines (SVMs) are two widely used algorithms. Some studies reported that RF performed better in classification tasks for complex data . In the previous work presented in the 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) , we explored a random forest model with combined features for aEEG classification. The experiment results showed that RF achieved better performance than other machine learning algorithms, indicating it is a promising algorithm for the automatic aEEG signal interpretation. This paper is an extension to our previous work, focusing on the optimizing the configuration of the classification scheme.
282 aEEG signals were acquired from Shanghai Children's Hospital of Fudan University, using the Olympic CFM 6000 (Olympic Medical Inc, Seattle, WA). Raw EEG signals were recorded through a pair of biparietal electrodes, and were then filtered, rectified, smoothed and selectively amplified to get aEEG. The positions of the recording electrodes were equivalent to the P3 and P4 electrode positions of the international 10-20 system. The aEEG samples with impedance greater than 10kΩ were discarded. The 282 cases include 209 normal cases and 73 abnormal ones, and the duration of each recording was 3 hours. All the aEEG tracings were interpreted to normal or abnormal ones by experienced clinicians independently.
Random forest model description
Random forest (RF) developed by Leo Breiman in 2001 has been proved to be a powerful approach with excellent performance in classification tasks . Introducing both bagging and random variable selection for tree building, RF utilizes an ensemble of classification trees, which are built on the bootstrap sample of the data. At each split, variable candidate set is randomly selected from the whole variable set. Randomness is injected by growing each tree on different random subsamples and determining splitter partly at random. Each tree is grown fully to obtain a low-bias. Both bagging and random variable selection assure the low correlation for individual trees. Through the averaging over a large ensemble of low-bias, high-variance but low correlation trees, the Algorithm 1 yields an ensemble forest .
In this paper, several algorithmic issues were examined, including parameter optimization and imbalanced dataset processing.
Algorithm 1 Algorithm of Random Forest
T : Training set ;
N tree : the number of trees to be built;
M try : the number of variables chosen for splitting at each node;
for each b = 1 : N tree do
Draw a bootstrap sample X b from the given training set T.
At each node of tree tr b , select M try variables randomly and determine the best split among these M try variables.
Construct an unpruned tree tr b using the above bootstrapped samples.
Classify by majority vote among the N trees.
In order to achieve desired performance, two important parameters need to be optimized in the RF algorithm. One is the number of input variables M try tried at each split, and the other is the number of trees to grow (N tree ) for each forest. M try considered at each split is a real parameter in the sense that its optimal value depends on the data. The default value (the square root of the number of input variables) is often a good choice for M try . Generally speaking, the number of trees N tree in the forest should increase with the number of candidate predictors M try , so that each predictor has enough opportunities to be selected. To get an appropriate value of N tree , we can try several increasing values and select the value when the prediction error stabilizes.
Imbalanced datasets processing
In our dataset, the number of abnormal data is much smaller than that of normal data. Most machine learning algorithms will perform poorly on the minority class because of the imbalance in the class distribution, and RF is no exception. As the cost of misclassifying of the minority abnormal class is much higher than the cost of other misclassifications, the imbalanced dataset problem is one of the important issues we need to consider to insure a satisfying result.
In this paper, we attempt to make the classifier more robust to the problem of class imbalance by using class weights. A heavier penalty is given when the RF misclassifies the minority class because the classifier tends to be biased towards the majority class . Each class is set a weight, with the minority class given a larger one. Class weights are applied in two places. The first one is in the tree building procedure, where class weights are used to weight the Gini criterion for split point finding. The second one lies in the prediction procedure to produce a "weighted majority vote" by each terminal node. In such a weighted RF model, the final prediction is determined by aggregating the weighted vote from each individual tree. As essential tuning parameters to achieve desired performance, the class weights can be selected through the out-of-bag estimate of the accuracy of RF model .
Three kinds of features were extracted to characterize the aEEG signals, including basic features, the histogram features from the signal as a whole, and the segment features got from segmented aEEG recordings.
Basic features were extracted from the initial 3-hour-length aEEG signal, including minimum amplitude, maximum amplitude, mean value of amplitude and percentage of the lower margin values under 5µV . For a 3-hour-length recording, we can get four features.
According to the clinical diagnosis criteria, the distribution of aEEG amplitude means a lot for interpretation of the signal . In this work, a histogram of amplitude was calculated to reveal the distribution of aEEG amplitudes.
For one 3-hour-length aEEG recording, 80 segments were observed. And for each segment, we can get four features: the upper boundary, the lower boundary, the mean value and ApEn. Thus for one 3-hour-length recording, we can get 320 features. Obviously it is time consuming if all these features are sent into a classifier. To speed up the classification processing, it's wise to reduce the dimension of the feature vector by ignoring those unimportant ones. According to our previous work , ApEn with higher or lower values may more likely indicate the abnormality of a signal. So the segment features were firstly sorted in an ascending order according to the values of ApEn, and then only those segments with high and low values of ApEn are selected. Through experiments, we picked up the segment features with the ten top and the five bottom values of ApEn, and thus we got a 60-dimensional feature vector for one 3-hour-length recording.
After the basic features, histogram features and segment features had been got respectively, they were integrated into one combined feature set with 119 features.
The weighted RF was applied to classify the 282 aEEG signals based on the feature sets got above. To evaluate the performance of RF on aEEG classification, other widely used classifiers were also tested on the same data sets and the identical feature sets. The compared classification methods include the support vector machine with RBF kernel (SVM-RBF), support vector machine with linear kernel (SVM-Linear) and artificial neural network (ANN). As a reference, we also considered the Maximum Likelihood (ML), Decision Tree using CART (DT), Logistic Regression (LR), Linear Discriminant Analysis (LDA) algorithm, four of the most popular traditional supervised classification methods.
Instead of using cross validation or estimating from a separate testing, an unbiased error can be estimated internally in random forest . Each tree is constructed under a different bootstrap sample. About one-third of the samples are left out of the bootstrap sampling and not used in the construction of the tree, so the left out samples can be put into the tree as test samples. At the end of the procedure, we took the number to be the class that got most of the votes every time. By calculating the proportion of misclassified samples over all cases, we can get the OOB error estimation, which has been proved to be an unbiased error estimation method for random forest .
Specificity, sensitivity and F 1-score were applied to evaluate the performance of the classifiers. The specificity is defined as the percentage of the number of true negatives over the sum of the number of true negatives and that of false positives. The sensitivity refers to the percentage of the number of true positives over the sum of the number of true positives and that of false negatives. The F 1-score can be interpreted as a harmonic compromise of precision and recall, which reaches its best value at 1 and worst score at 0 .
We conducted a series of experiments on 282-subject dataset to achieve an optimum configuration of the RF-based classifier. The experimental study can be divided into three parts. The first set of experiments examined the effects of parameters N tree , M try and evaluated the candidate feature sets. In the second set of experiments, we dealt with the problem of imbalanced datasets. And the third set of experiments compared the performance of RF-based classifier with those of other classifiers.
Parameters tuning and feature evaluation
As there are two relevant parameters to be optimized in RF algorithm, we have to try out one of the parameter with the other one supposed to be given.
Imbalanced datasets processing
To appraise the performance of the RF-based classifier, some widely used classifiers, including the SVM-RBF, SVM-Linear, ANN, DT, LR, ML, and LDA, were also applied to classify the identical data based on the identical feature sets. OOB method and 10-fold cross validation method were utilized to evaluate the prediction ability of RF and those of other classifiers respectively. Further more, we compared the performance of RF build on different feature sets. Based on previous analysis, we can select part of features with high significance to build our model for acceptable accuracy and efficiency.
Performance comparison for different classifiers.
Performance comparison for feature set under different sizes.
Selected feature set size(%)
In this paper, we proposed a RF-based method for aEEG classification and defined a combined feature set. Basic features, statistical features and segment features were extracted from the whole signal as well as from signal segmentations. The combined feature set consisting of the three kinds of features was then sent to the RF classifier. The significance of feature, the data segmentation, parameter optimization of RF algorithm, and the problem of imbalanced datasets were examined. Experiments were also conducted to evaluate the performance of RF on aEEG classification, compared with several other widely used classifiers. Results show that, outperforming other widely used classifiers examined here, random forest with the combined feature set is efficient and can help better detect the brain disorders in newborns.
All the aEEG data were provided by Shanghai Children's Hospital of Fudan University;
Publication of this article has been funded by the National Natural Science Foundation of China (Grant No. 81101119), Natural Science Foundation of China (Grant No. 61340036), the Open Project of Software/Hardware Co-design Engineering Research Center MoE, and National Key Basic Research Program (Grant No. 2011CB707104).
This article has been published as part of BioMedical Engineering OnLine Volume 13 Supplement 2, 2014: Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013): BioMedical Engineering OnLine. The full contents of the supplement are available online at http://www.biomedical-engineering-online.com/supplements/13/S2.
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