A comparison of different chemometrics approaches for the robust classification of electronic nose data

Accurate detection of certain chemical vapours is important, as these may be diagnostic for the presence of weapons, drugs of misuse or disease. In order to achieve this, chemical sensors could be deployed remotely. However, the readout from such sensors is a multivariate pattern, and this needs to be interpreted robustly using powerful supervised learning methods. Therefore, in this study, we compared the classification accuracy of four pattern recognition algorithms which include linear discriminant analysis (LDA), partial least squares-discriminant analysis (PLS-DA), random forests (RF) and support vector machines (SVM) which employed four different kernels. For this purpose, we have used electronic nose (e-nose) sensor data (Wedge et al., Sensors Actuators B Chem 143:365–372, 2009). In order to allow direct comparison between our four different algorithms, we employed two model validation procedures based on either 10-fold cross-validation or bootstrapping. The results show that LDA (91.56 % accuracy) and SVM with a polynomial kernel (91.66 % accuracy) were very effective at analysing these e-nose data. These two models gave superior prediction accuracy, sensitivity and specificity in comparison to the other techniques employed. With respect to the e-nose sensor data studied here, our findings recommend that SVM with a polynomial kernel should be favoured as a classification method over the other statistical models that we assessed. SVM with non-linear kernels have the advantage that they can be used for classifying non-linear as well as linear mapping from analytical data space to multi-group classifications and would thus be a suitable algorithm for the analysis of most e-nose sensor data.     

应用小波特征提取肺癌组织FTIR的支持向量机分类方法研究

提出了一种新的基于傅里叶变换红外光谱(Fourier Transform Infrared Spectroscopy, FTIR)的小波特征提取与支持向量机(SVM)分类方法以提高FTIR对早期肺癌的诊断准确率. 对肺正常组织、早期肺癌及进展期肺癌组织的FTIR, 利用连续小波(CW)多分辨率分析法提取9个特征量, 支持向量机把其分为正常组与非正常组(包括早期肺癌和进展期肺癌), 对正常组织、早期肺癌和进展期肺癌的识别, 多项式核函数和径向基函数的识别准确率最高. 多项式核函数对正常组织、早期肺癌和进展期肺癌的识别准确率分别为100%, 95%及100%; 径向基函数分别为100%, 95%和100%. 实验结果表明FTIR-CW-SVM模式分类方法对正常肺癌组织、早期肺癌及进展肺癌的识别具有较好的可行性.     

Operon prediction based on SVM

The operon is a specific functional organization of genes found in bacterial genomes. Most genes within operons share common features. The support vector machine (SVM) approach is here used to predict operons at the genomic level. Four features were chosen as SVM input vectors: the intergenic distances, the number of common pathways, the number of conserved gene pairs and the mutual information of phylogenetic profiles. The analysis reveals that these common properties are indeed characteristic of the genes within operons and are different from that of non-operonic genes. Jackknife testing indicates that these input feature vectors, employed with RBF kernel SVM, achieve high accuracy. To validate the method, Escherichia coli K12 and Bacillus subtilis were taken as benchmark genomes of known operon structure, and the prediction results in both show that the SVM can detect operon genes in target genomes efficiently and offers a satisfactory balance between sensitivity and specificity.     

Recognition for avian influenza virus proteins based on support vector machine and linear discriminant analysis

Total 200 properties related to structural characteristics were employed to represent structures of 400 HA coded proteins of influenza virus as training samples. Some recognition models for HA proteins of avian influenza virus (AIV) were developed using support vector machine (SVM) and linear discriminant analysis (LDA). The results obtained from LDA are as follows: the identification accuracy (Ria) for training samples is 99.8% and Ria by leave one out cross validation is 99.5%. Both Ria of 99.8% for training samples and Ria of 99.3% by leave one out cross validation are obtained using SVM model, respectively. External 200 HA proteins of influenza virus were used to validate the external predictive power of the resulting model. The external Ria for them is 95.5% by LDA and 96.5% by SVM, respectively, which shows that HA proteins of AIVs are preferably recognized by SVM and LDA, and the performances by SVM are superior to those by LDA.