Support Vector Machine Classification Technique Research Articles

Predictions of BuChE Inhibitors Using Support Vector Machine and Naive Bayesian Classification Techniques in Drug Discovery

Butyrylcholinesterase (BuChE, EC 3.1.1.8) is an important pharmacological target for Alzheimer's disease (AD) treatment. However, the currently available BuChE inhibitor screening assays are expensive, labor-intensive, and compound-dependent. It is necessary to develop robust in silico methods to predict the activities of BuChE inhibitors for the lead identification. In this investigation, support vector machine (SVM) models and naive Bayesian models were built to discriminate BuChE inhibitors (BuChEIs) from the noninhibitors. Each molecule was initially represented in 1870 structural descriptors (1235 from ADRIANA.Code, 334 from MOE, and 301 from Discovery studio). Correlation analysis and stepwise variable selection method were applied to figure out activity-related descriptors for prediction models. Additionally, structural fingerprint descriptors were added to improve the predictive ability of models, which were measured by cross-validation, a test set validation with 1001 compounds and an external test set validation with 317 diverse chemicals. The best two models gave Matthews correlation coefficient of 0.9551 and 0.9550 for the test set and 0.9132 and 0.9221 for the external test set. To demonstrate the practical applicability of the models in virtual screening, we screened an in-house data set with 3601 compounds, and 30 compounds were selected for further bioactivity assay. The assay results showed that 10 out of 30 compounds exerted significant BuChE inhibitory activities with IC50 values ranging from 0.32 to 22.22 μM, at which three new scaffolds as BuChE inhibitors were identified for the first time. To our best knowledge, this is the first report on BuChE inhibitors using machine learning approaches. The models generated from SVM and naive Bayesian approaches successfully predicted BuChE inhibitors. The study proved the feasibility of a new method for predicting bioactivities of ligands and discovering novel lead compounds.

A Development of The Road Surface Decision Algorithm Using SVM (Support Vector Machine) Clustering Methods

Road`s accidents caused by Ice, snow, Wet of roads surface conditions and weather conditions situations that are constantly occurring. That is, driver`s negligence and safe driving ability of individuals due to lack of awareness, and Road management main agent(the government and the public, etc.) due to road conditions, if there is insufficient information. So Related research needs is a trend that is required. In this study, gather Camera(Stereo camera)`s image data, and analysis polarization coefficients and wavelet transform. And unlike traditional single-dimensional classification algorithms as multi-dimensional analysis by using SVM classification techniques, develop an algorithm to determine road conditions. Four on the road conditions (dry, wet, snow, ice) recognition success rate for the detection and analysis of experiments.

Fluctuation enhanced sensing (FES) with a nanostructured, semiconducting metal oxide film for gas detection and classification

The feasibility of fluctuation-enhanced sensing (FES) for the detection and classification of different gases using a single chemiresistive microsensor has been investigated through experimental measurements and data analyses. A nanostructured semiconducting metal oxide film has been used as a chemiresistive sensor in the experiments. Similarity fingerprints have been introduced to be used with the FES signatures, and combining similarity fingerprints with slope fingerprints results in a considerable increase in the classification accuracy attained by both Linear Discriminant Analysis (LDA) and Support Vector Machine (SVM) classification techniques.

Comparative Prediction Performance with Support Vector Machine and Random Forest Classification Techniques

learning with classification can effectively be applied for many applications, especially those with complex measurements. Therefore classification technique can be used for prediction of diseases like cancer, liver disorders and heart disease etc which involve complex measurements. This is part of growing demand and much interesting towards predictive diagnosis. It has also been established that classification and learning methods can be used effectively to improve the accuracy of prediction of a diseases and its recurrence. In the present work machine learning techniques namely Support Vector Machine (SVM) and Random Forest (RF) are used to learn, classify and compare cancer, liver and heart disease data with varying kernels and kernel parameters. Results with Support Vector Machines and Random Forest are compared for different data sets. The results with different kernels are tuned with proper parameters selection. Results are better analyzed to establish better learning techniques for predictions.

Nationality and risk attitude: Testing differences and similarities of investors' behavior in selected financial markets

We first applied cluster analysis on selected stock market indexes (NASDAQ, DAX, Nikkei 225, FTSE 100, and Dow-Jones) for identifying four global fundamental patterns of stock markets behavior (to be named “market conditions”). On each of these patterns (attesting similar market conditions) we then applied Support Vector Machine (SVM) classification technique to test for the similarities and differences in the behavior of investors in the various stock markets. Our results show a good degree of separation of investors' behavior for the selected national stock markets (i.e., investors in different national financial markets react differently, facing the same market conditions, while the two US national markets (NASDAQ and Dow-Jones) behave the same). The results could be interpreted as a positive evidence for different investor behavior (and risk attitude) in different national stock markets. The presented approach could be used for further classification of financial indices behavior, and investment strategies associated with multinational investment portfolios.

Applying six classifiers to airborne hyperspectral imagery for detecting giant reed

This study evaluated and compared six image classifiers, including minimum distance (MD), Mahalanobis distance (MAHD), maximum likelihood (ML), spectral angle mapper (SAM), mixture tuned matched filtering (MTMF) and support vector machine (SVM), for detecting and mapping giant reed (Arundo donax L.), an invasive weed that presents a severe threat to agroecosystems throughout the southern US and northern Mexico. Airborne hyperspectral imagery was collected from a giant reed-infested site along the US-Mexican portion of the Rio Grande in 2009 and 2010. The imagery was transformed with minimum noise fraction (MFN) and the six classifiers were applied to the 30-band MNF imagery for each year. Accuracy assessment showed that SVM and ML generally performed better than the other four classifiers for overall classification and for distinguishing giant reed in both years. These results indicate that airborne hyperspectral imagery in conjunction with SVM and ML classification techniques is effective for detecting giant reed.

A novel semisupervised SVM for pixel classification of remote sensing imagery

This article introduces a semisupervised support vector machine classification technique that exploits both labeled and unlabeled points for addressing the problem of pixel classification of remote sensing images. The proposed technique is based on applying the margin maximization principle to both labeled and unlabeled patterns. Semisupervised SVM progressively searches a reliable discriminant hyperplane in the high dimensional space through iterative method exploiting both labeled and unlabeled samples. In particular, the dynamic thresholding and successive filtering of the unlabeled set are exploited to find a reliable separating hyperplane. The proposed technique is first demonstrated for six labeled datasets described in terms of feature vectors and then identifying different land cover regions in remote sensing imagery and compared with the standard SVM. Experimental results confirm that employing this learning scheme removes unnecessary points to a great extent from the unlabeled set and increases the accuracy level on the other hand. Comparison is made in terms of accuracy, ROC, AUC and F-measure for the labeled data and quantitative cluster validity indices as well as classified image quality for the image data.

Elastic SCAD as a novel penalization method for SVM classification tasks in high-dimensional data

BackgroundClassification and variable selection play an important role in knowledge discovery in high-dimensional data. Although Support Vector Machine (SVM) algorithms are among the most powerful classification and prediction methods with a wide range of scientific applications, the SVM does not include automatic feature selection and therefore a number of feature selection procedures have been developed. Regularisation approaches extend SVM to a feature selection method in a flexible way using penalty functions like LASSO, SCAD and Elastic Net.We propose a novel penalty function for SVM classification tasks, Elastic SCAD, a combination of SCAD and ridge penalties which overcomes the limitations of each penalty alone.Since SVM models are extremely sensitive to the choice of tuning parameters, we adopted an interval search algorithm, which in comparison to a fixed grid search finds rapidly and more precisely a global optimal solution.ResultsFeature selection methods with combined penalties (Elastic Net and Elastic SCAD SVMs) are more robust to a change of the model complexity than methods using single penalties. Our simulation study showed that Elastic SCAD SVM outperformed LASSO (L1) and SCAD SVMs. Moreover, Elastic SCAD SVM provided sparser classifiers in terms of median number of features selected than Elastic Net SVM and often better predicted than Elastic Net in terms of misclassification error.Finally, we applied the penalization methods described above on four publicly available breast cancer data sets. Elastic SCAD SVM was the only method providing robust classifiers in sparse and non-sparse situations.ConclusionsThe proposed Elastic SCAD SVM algorithm provides the advantages of the SCAD penalty and at the same time avoids sparsity limitations for non-sparse data. We were first to demonstrate that the integration of the interval search algorithm and penalized SVM classification techniques provides fast solutions on the optimization of tuning parameters.The penalized SVM classification algorithms as well as fixed grid and interval search for finding appropriate tuning parameters were implemented in our freely available R package 'penalizedSVM'.We conclude that the Elastic SCAD SVM is a flexible and robust tool for classification and feature selection tasks for high-dimensional data such as microarray data sets.

Evaluating high resolution SPOT 5 satellite imagery for crop identification

High resolution satellite imagery offers new opportunities for crop monitoring and assessment. A SPOT 5 image acquired in May 2006 with four spectral bands (green, red, near-infrared, and short-wave infrared) and 10-m pixel size covering intensively cropped areas in south Texas was evaluated for crop identification. Two images with pixel sizes of 20 m and 30 m were also generated from the original image to simulate coarser resolution satellite imagery. Two subset images covering a variety of crops with different growth stages were extracted from the satellite image and five supervised classification techniques, including minimum distance, Mahalanobis distance, maximum likelihood, spectral angle mapper (SAM), and support vector machine (SVM), were applied to the 10-m subset images and the two coarser resolution images to identify crop types. The effects of the short-wave infrared band and pixel size on classification results were also examined. Kappa analysis showed that maximum likelihood and SVM performed better than the other three classifiers, though there were no statistical differences between the two best classifiers. Accuracy assessment showed that the 10-m, four-band images based on maximum likelihood resulted in the best overall accuracy values of 91% and 87% for the two respective sites. The inclusion of the short-wave infrared band statistically significantly increased the overall accuracy from 82% to 91% for site 1 and from 75% to 87% for site 2. The increase in pixel size from 10 m to 20 m or 30 m did not significantly affect the classification accuracy for crop identification. These results indicate that SPOT 5 multispectral imagery in conjunction with maximum likelihood and SVM classification techniques can be used for identifying crop types and estimating crop areas.

Automated Detection of Cell Nuclei in Pap Smear Images Using Morphological Reconstruction and Clustering

In this paper, we present a fully automated method for cell nuclei detection in Pap smear images. The locations of the candidate nuclei centroids in the image are detected with morphological analysis and they are refined in a second step, which incorporates a priori knowledge about the circumference of each nucleus. The elimination of the undesirable artifacts is achieved in two steps: the application of a distance-dependent rule on the resulted centroids; and the application of classification algorithms. In our method, we have examined the performance of an unsupervised (fuzzy C-means) and a supervised (support vector machines) classification technique. In both classification techniques, the effect of the refinement step improves the performance of the clustering algorithm. The proposed method was evaluated using 38 cytological images of conventional Pap smears containing 5617 recognized squamous epithelial cells. The results are very promising, even in the case of images with high degree of cell overlapping.

Surface EMG pattern recognition for real-time control of a wrist exoskeleton

BackgroundSurface electromyography (sEMG) signals have been used in numerous studies for the classification of hand gestures and movements and successfully implemented in the position control of different prosthetic hands for amputees. sEMG could also potentially be used for controlling wearable devices which could assist persons with reduced muscle mass, such as those suffering from sarcopenia. While using sEMG for position control, estimation of the intended torque of the user could also provide sufficient information for an effective force control of the hand prosthesis or assistive device. This paper presents the use of pattern recognition to estimate the torque applied by a human wrist and its real-time implementation to control a novel two degree of freedom wrist exoskeleton prototype (WEP), which was specifically developed for this work.MethodsBoth sEMG data from four muscles of the forearm and wrist torque were collected from eight volunteers by using a custom-made testing rig. The features that were extracted from the sEMG signals included root mean square (rms) EMG amplitude, autoregressive (AR) model coefficients and waveform length. Support Vector Machines (SVM) was employed to extract classes of different force intensity from the sEMG signals. After assessing the off-line performance of the used classification technique, the WEP was used to validate in real-time the proposed classification scheme.ResultsThe data gathered from the volunteers were divided into two sets, one with nineteen classes and the second with thirteen classes. Each set of data was further divided into training and testing data. It was observed that the average testing accuracy in the case of nineteen classes was about 88% whereas the average accuracy in the case of thirteen classes reached about 96%. Classification and control algorithm implemented in the WEP was executed in less than 125 ms.ConclusionsThe results of this study showed that classification of EMG signals by separating different levels of torque is possible for wrist motion and the use of only four EMG channels is suitable. The study also showed that SVM classification technique is suitable for real-time classification of sEMG signals and can be effectively implemented for controlling an exoskeleton device for assisting the wrist.

Facial Expression Recognition from Global and a Combination of Local Features

In this paper, facial expressions are identified using contour information, along with the Gabor features extracted from highly expression-reflected facial features. We propose a novel technique to extract Gabor features from a selected region of interests. The computational complexity is reduced by a suitable selection of Gabor filters for the representation of transformed face images. Support Vector Machine classification technique is used to identify the expression that belongs to the face images.

Engine lubricating oil classification by SAE grade and source based on dielectric spectroscopy data

Dielectric spectroscopy (DS) is one of the most powerful and prevailing structural analysis techniques for dielectric materials. Engine lubricating oil is a typical dielectric material. But DS for qualitative or quantitative analysis of engine lubricating oil has received little attention. In this paper, DS in association with support vector machines (SVM) classification technique was employed to classify 20 samples of engine lubricating oils from Mobil, Shell and Esso by Society of Automotive Engineers (SAE) viscosity grade and source (manufacturer). Both distinguishing the multi-grade from the single-grade according to SAE grade and classification according to manufacturer were done perfectly, which proved that DS can provide useful compositional and structural information on engine lubricating oil. The work in this article has laid the foundation for further quantitative determination of properties of engine lubricating oil and will be a good start to application of DS to petroleum analysis and testing.

A Novel and Efficient Technique for Identification and Classification of GPCRs

G-protein coupled receptors (GPCRs) play a vital role in different biological processes, such as regulation of growth, death, and metabolism of cells. GPCRs are the focus of significant amount of current pharmaceutical research since they interact with more than 50% of prescription drugs. The dipeptide-based support vector machine (SVM) approach is the most accurate technique to identify and classify the GPCRs. However, this approach has two major disadvantages. First, the dimension of dipeptide-based feature vector is equal to 400. The large dimension makes the classification task computationally and memory wise inefficient. Second, it does not consider the biological properties of protein sequence for identification and classification of GPCRs. In this paper, we present a novel-feature-based SVM classification technique. The novel features are derived by applying wavelet-based time series analysis approach on protein sequences. The proposed feature space summarizes the variance information of seven important biological properties of amino acids in a protein sequence. In addition, the dimension of the feature vector for proposed technique is equal to 35. Experiments were performed on GPCRs protein sequences available at GPCRs Database. Our approach achieves an accuracy of 99.9%, 98.06%, 97.78%, and 94.08% for GPCR superfamily, families, subfamilies, and subsubfamilies (amine group), respectively, when evaluated using fivefold cross-validation. Further, an accuracy of 99.8%, 97.26%, and 97.84% was obtained when evaluated on unseen or recall datasets of GPCR superfamily, families, and subfamilies, respectively. Comparison with dipeptide-based SVM technique shows the effectiveness of our approach.

CARSVM: A class association rule-based classification framework and its application to gene expression data

In this study, we aim at building a classification framework, namely the CARSVM model, which integrates association rule mining and support vector machine (SVM). The goal is to benefit from advantages of both, the discriminative knowledge represented by class association rules and the classification power of the SVM algorithm, to construct an efficient and accurate classifier model that improves the interpretability problem of SVM as a traditional machine learning technique and overcomes the efficiency issues of associative classification algorithms. In our proposed framework: instead of using the original training set, a set of rule-based feature vectors, which are generated based on the discriminative ability of class association rules over the training samples, are presented to the learning component of the SVM algorithm. We show that rule-based feature vectors present a high-qualified source of discrimination knowledge that can impact substantially the prediction power of SVM and associative classification techniques. They provide users with more conveniences in terms of understandability and interpretability as well. We have used four datasets from UCI ML repository to evaluate the performance of the developed system in comparison with five well-known existing classification methods. Because of the importance and popularity of gene expression analysis as real world application of the classification model, we present an extension of CARSVM combined with feature selection to be applied to gene expression data. Then, we describe how this combination will provide biologists with an efficient and understandable classifier model. The reported test results and their biological interpretation demonstrate the applicability, efficiency and effectiveness of the proposed model. From the results, it can be concluded that a considerable increase in classification accuracy can be obtained when the rule-based feature vectors are integrated in the learning process of the SVM algorithm. In the context of applicability, according to the results obtained from gene expression analysis, we can conclude that the CARSVM system can be utilized in a variety of real world applications with some adjustments.

New Predictive Models for Blood–Brain Barrier Permeability of Drug-like Molecules

The goals of the present study were to apply a generalized regression model and support vector machine (SVM) models with Shape Signatures descriptors, to the domain of blood-brain barrier (BBB) modeling. The Shape Signatures method is a novel computational tool that was used to generate molecular descriptors utilized with the SVM classification technique with various BBB datasets. For comparison purposes we have created a generalized linear regression model with eight MOE descriptors and these same descriptors were also used to create SVM models. The generalized regression model was tested on 100 molecules not in the model and resulted in a correlation r2 = 0.65. SVM models with MOE descriptors were superior to regression models, while Shape Signatures SVM models were comparable or better than those with MOE descriptors. The best 2D shape signature models had 10-fold cross validation prediction accuracy between 80-83% and leave-20%-out testing prediction accuracy between 80-82% as well as correctly predicting 84% of BBB+ compounds (n = 95) in an external database of drugs. Our data indicate that Shape Signatures descriptors can be used with SVM and these models may have utility for predicting blood-brain barrier permeation in drug discovery.

Optimization of biaryl piperidine and 4-amino-2-biarylurea MCH1 receptor antagonists using QSAR modeling, classification techniques and virtual screening

This paper presents the results of an optimization study on biaryl piperidine and 4-amino-2-biarylurea MCH1 receptor antagonists, which was accomplished by using quantitative-structure activity relationships (QSARs), classification and virtual screening techniques. First, a linear QSAR model was developed using Multiple Linear Regression (MLR) Analysis, while the Elimination Selection-Stepwise Regression (ES-SWR) method was adopted for selecting the most suitable input variables. The predictive activity of the model was evaluated using an external validation set and the Y-randomization technique. Based on the selected descriptors, the Support Vector Machines (SVM) classification technique was utilized to classify data into two categories: "actives" or "non-actives". Several attempts were made to optimize the scaffold of most potent compounds by inducing various structural modifications. Potential derivatives with improved activities were identified, as they were classified "actives" by the SVM classifier. Their activities were estimated using the produced MLR model. A detailed analysis on the model applicability domain defined the compounds, whose estimations can be accepted with confidence.