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Results for “Support Vector Machine”

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PubMed2003

Protein function classification via support vector machine approach.

Support vector machine (SVM) is introduced as a method for the classification of proteins into functionally distinguished classes. Studies are conducted on a number of protein classes including RNA-binding proteins; protein homodimers, proteins responsible for drug absorption, proteins involved in drug distribution and excretion, and drug metabolizing enzymes. Testing accuracy for the classification of these protein classes is found to be in the range of 84-96%. This suggests the usefulness of SVM in the classification of protein functional classes and its potential application in protein function prediction.

Amino Acid Sequence↗

PubMedDate not supplied

An accurate QSPR study of O-H bond dissociation energy in substituted phenols based on support vector machines.

The support vector machine (SVM), as a novel type of learning machine, was used to develop a Quantitative Structure-Property Relationship (QSPR) model of the O-H bond dissociation energy (BDE) of 78 substituted phenols. The six descriptors calculated solely from the molecular structures of compounds selected by forward stepwise regression were used as inputs for the SVM model. The root-mean-square (rms) errors in BDE predictions for the training, test, and overall data sets were 3.808, 3.320, and 3.713 BDE units (kJ mol(-1)), respectively. The results obtained by Gaussian-kernel SVM were much better than those obtained by multiple linear regression, radial basis function neural networks, linear-kernel SVM, and other QSPR approaches.

Journal Article↗

PubMedDate not supplied

Study of the quantitative structure-mobility relationship of carboxylic acids in capillary electrophoresis based on support vector machines.

The support vector machines (SVM), as a novel type of learning machine, were used to develop a quantitative structure-mobility relationship (QSMR) model of 58 aliphatic and aromatic carboxylic acids based on molecular descriptors calculated from the structure alone. Multiple linear regression (MLR) and radial basis function neural networks (RBFNNs) were also utilized to construct the linear and the nonlinear model to compare with the results obtained by SVM. The root-mean-square errors in absolute mobility predictions for the whole data set given by MLR, RBFNNs, and SVM were 1.530, 1.373, and 0.888 mobility units (10(-5) cm(2) S(-1) V(-1)), respectively, which indicated that the prediction result agrees well with the experimental values of these compounds and also revealed the superiority of SVM over MLR and RBFNNs models for the prediction of the absolute mobility of carboxylic acids. Moreover, the models we proposed could also provide some insight into what structural features are related to the absolute mobility of aliphatic and aromatic carboxylic acids.

Journal Article↗

PubMed2005

[Study on application of Fourier transformation near-infrared spectroscopy analysis with support vector machine (SVM)].

Support Vector Machine (SVM) is a method for the research on identifying two types of problem. It is the latest branch in the statistics study theories, and the identification model has a strict mathematics foundation. In this paper, the basic principle and method of SVM are not only introduced, but also applied to chemometrics. One hundred and three rhubarb samples were used as experimental materials. The identification models were established with near-infrared spectroscopy and SVM training method with the intention of identifying whether the rhubarb samples are true or false. The thirty-three samples in training set were identified by the identifying models with the accurate rate of 100%, while seventy estimate samples had an accurate rate of 96.77%. The research result provided the method of identifying the traditional Chinese medicine rhubarb quickly. So, it shows the feasibility of establishing the models with near-infrared spectroscopy and SVM method to identify biological samples. This paper introduced the theme of SVM training method in order to beget the attention of the research members who deal with chemometrics.

Algorithms↗

PubMed2004

Wavelet support vector machine.

An admissible support vector (SV) kernel (the wavelet kernel), by which we can construct a wavelet support vector machine (SVM), is presented. The wavelet kernel is a kind of multidimensional wavelet function that can approximate arbitrary nonlinear functions. The existence of wavelet kernels is proven by results of theoretic analysis. Computer simulations show the feasibility and validity of wavelet support vector machines (WSVMs) in regression and pattern recognition.

Journal Article↗

PubMed2004

Hidden space support vector machines.

Hidden space support vector machines (HSSVMs) are presented in this paper. The input patterns are mapped into a high-dimensional hidden space by a set of hidden nonlinear functions and then the structural risk is introduced into the hidden space to construct HSSVMs. Moreover, the conditions for the nonlinear kernel function in HSSVMs are more relaxed, and even differentiability is not required. Compared with support vector machines (SVMs), HSSVMs can adopt more kinds of kernel functions because the positive definite property of the kernel function is not a necessary condition. The performance of HSSVMs for pattern recognition and regression estimation is also analyzed. Experiments on artificial and real-world domains confirm the feasibility and the validity of our algorithms.

Algorithms↗

PubMed2005

Perceptual adaptive insensitivity for support vector machine image coding.

Support vector machine (SVM) learning has been recently proposed for image compression in the frequency domain using a constant epsilon-insensitivity zone by Robinson and Kecman. However, according to the statistical properties of natural images and the properties of human perception, a constant insensitivity makes sense in the spatial domain but it is certainly not a good option in a frequency domain. In fact, in their approach, they made a fixed low-pass assumption as the number of discrete cosine transform (DCT) coefficients to be used in the training was limited. This paper extends the work of Robinson and Kecman by proposing the use of adaptive insensitivity SVMs [2] for image coding using an appropriate distortion criterion [3], [4] based on a simple visual cortex model. Training the SVM by using an accurate perception model avoids any a priori assumption and improves the rate-distortion performance of the original approach.

Algorithms↗

PubMed2005

Analysis of alcoholism data using support vector machines.

A supervised learning method, support vector machine, was used to analyze the microsatellite marker dataset of the Collaborative Study on the Genetics of Alcoholism Problem 1 for the Genetic Analysis Workshop 14. Twelve binary-valued phenotype variables were chosen for analyses using the markers from all autosomal chromosomes. Using various polynomial kernel functions of the support vector machine and randomly divided genome regions, we were able to observe the association of some marker sets with the chosen phenotypes and thus reduce the size of the dataset. The successful classifications established with the chosen support vector machine kernel function had high levels of correctness for each prediction, e.g., 96% in the fourfold cross-validations. However, owing to the limited sample data, we were not able to test the predictions of the classifiers in the new sample data.

Alcoholism↗

PubMedDate not supplied

Substructure-based support vector machine classifiers for prediction of adverse effects in diverse classes of drugs.

Unforeseen adverse effects exhibited by drugs contribute heavily to late-phase failure and even withdrawal of marketed drugs. Torsade de pointes (TdP) is one such important adverse effect, which causes cardiac arrhythmia and, in some cases, sudden death, making it crucial for potential drugs to be screened for torsadogenicity. The need to tap the power of computational approaches for the prediction of adverse effects such as TdP is increasingly becoming evident. The availability of screening data including those in organized databases greatly facilitates exploration of newer computational approaches. In this paper, we report the development of a prediction method based on a support machine vector algorithm. The method uses a combination of descriptors, encoding both the type of toxicophore as well as the position of the toxicophore in the drug molecule, thus considering both the pharmacophore and the three-dimensional shape information of the molecule. For delineating toxicophores, a novel pattern-recognition method that utilizes substructures within a molecule has been developed. The results obtained using the hybrid approach have been compared with those available in the literature for the same data set. An improvement in prediction accuracy is clearly seen, with the accuracy reaching up to 97% in predicting compounds that can cause TdP and 90% for predicting compounds that do not cause TdP. The generic nature of the method has been demonstrated with four data sets available for carcinogenicity, where prediction accuracies were significantly higher, with a best receiver operating characteristics (ROC) value of 0.81 as against a best ROC value of 0.7 reported in the literature for the same data set. Thus, the method holds promise for wide applicability in toxicity prediction.

Algorithms↗

PubMed2006

Rule generation for protein secondary structure prediction with support vector machines and decision tree.

Support vector machines (SVMs) have shown strong generalization ability in a number of application areas, including protein structure prediction. However, the poor comprehensibility hinders the success of the SVM for protein structure prediction. The explanation of how a decision made is important for accepting the machine learning technology, especially for applications such as bioinformatics. The reasonable interpretation is not only useful to guide the "wet experiments," but also the extracted rules are helpful to integrate computational intelligence with symbolic AI systems for advanced deduction. On the other hand, a decision tree has good comprehensibility. In this paper, a novel approach to rule generation for protein secondary structure prediction by integrating merits of both the SVM and decision tree is presented. This approach combines the SVM with decision tree into a new algorithm called SVM_ DT, which proceeds in three steps. This algorithm first trains an SVM. Then, a new training set is generated through careful selection from the output of the SVM. Finally, the obtained training set is used to train a decision tree learning system and to extract the corresponding rule sets. The results of the experiments of protein secondary structure prediction on RS126 data set show that the comprehensibility of SVM_DT is much better than that of the SVM. Moreover, the generalization ability of SVM_DT is better than that of C4.5 decision trees and is similar to that of the SVM. Hence, SVM_DT can be used not only for prediction, but also for guiding biological experiments.

Algorithms↗

PubMed2003

Asymptotic behaviors of support vector machines with Gaussian kernel.

Support vector machines (SVMs) with the gaussian (RBF) kernel have been popular for practical use. Model selection in this class of SVMs involves two hyperparameters: the penalty parameter C and the kernel width sigma. This letter analyzes the behavior of the SVM classifier when these hyperparameters take very small or very large values. Our results help in understanding the hyperparameter space that leads to an efficient heuristic method of searching for hyperparameter values with small generalization errors. The analysis also indicates that if complete model selection using the gaussian kernel has been conducted, there is no need to consider linear SVM.

Models, Theoretical↗

PubMedDate not supplied

Quantitative prediction of logk of peptides in high-performance liquid chromatography based on molecular descriptors by using the heuristic method and support vector machine.

A new method support vector machine (SVM) and the heuristic method (HM) were used to develop the nonlinear and linear models between the capacity factor (logk) and seven molecular descriptors of 75 peptides for the first time. The molecular descriptors representing the structural features of the compounds only included the constitutional and topological descriptors, which can be obtained easily without optimizing the structure of the molecule. The seven molecular descriptors selected by the heuristic method in CODESSA were used as inputs for SVM. The results obtained by SVM were compared with those obtained by the heuristic method. The prediction result of the SVM model is better than that of heuristic method. For the test set, a predictive correlation coefficient R = 0.9801 and root-mean-square error of 0.1523 were obtained. The prediction results are in very good agreement with the experimental values. But the linear model of the heuristic method is easier to understand and ready to use for a chemist. This paper provided a new and effective method for predicting the chromatography retention of peptides and some insight into the structural features which are related to the capacity factor of peptides.

Artificial Intelligence↗

PubMedDate not supplied

QSAR and classification study of 1,4-dihydropyridine calcium channel antagonists based on least squares support vector machines.

The least squares support vector machine (LSSVM), as a novel machine learning algorithm, was used to develop quantitative and classification models as a potential screening mechanism for a novel series of 1,4-dihydropyridine calcium channel antagonists for the first time. Each compound was represented by calculated structural descriptors that encode constitutional, topological, geometrical, electrostatic, quantum-chemical features. The heuristic method was then used to search the descriptor space and select the descriptors responsible for activity. Quantitative modeling results in a nonlinear, seven-descriptor model based on LSSVM with mean-square errors 0.2593, a predicted correlation coefficient (R(2)) 0.8696, and a cross-validated correlation coefficient (R(cv)(2)) 0.8167. The best classification results are found using LSSVM: the percentage (%) of correct prediction based on leave one out cross-validation was 91.1%. This paper provides a new and effective method for drug design and screening.

Algorithms↗

PubMed2005

SMO-based pruning methods for sparse least squares support vector machines.

Solutions of least squares support vector machines (LS-SVMs) are typically nonsparse. The sparseness is imposed by subsequently omitting data that introduce the smallest training errors and retraining the remaining data. Iterative retraining requires more intensive computations than training a single nonsparse LS-SVM. In this paper, we propose a new pruning algorithm for sparse LS-SVMs: the sequential minimal optimization (SMO) method is introduced into pruning process; in addition, instead of determining the pruning points by errors, we omit the data points that will introduce minimum changes to a dual objective function. This new criterion is computationally efficient. The effectiveness of the proposed method in terms of computational cost and classification accuracy is demonstrated by numerical experiments.

Algorithms↗

PubMed2003

Support vector machine applications in bioinformatics.

The support vector machine (SVM) approach represents a data-driven method for solving classification tasks. It has been shown to produce lower prediction error compared to classifiers based on other methods like artificial neural networks, especially when large numbers of features are considered for sample description. In this review, the theory and main principles of the SVM approach are outlined, and successful applications in traditional areas of bioinformatics research are described. Current developments in techniques related to the SVM approach are reviewed which might become relevant for future functional genomics and chemogenomics projects. In a comparative study, we developed neural network and SVM models to identify small organic molecules that potentially modulate the function of G-protein coupled receptors. The SVM system was able to correctly classify approximately 90% of the compounds in a cross-validation study yielding a Matthews correlation coefficient of 0.78. This classifier can be used for fast filtering of compound libraries in virtual screening applications.

Algorithms↗

PubMedDate not supplied

Classification of in vivo autofluorescence spectra using support vector machines.

An algorithm based on support vector machines (SVM), the most recent advance in pattern recognition, is presented for use in classifying light-induced autofluorescence collected from cancerous and normal tissues. The in vivo autofluorescence spectra used for development and evaluation of SVM diagnostic algorithms were measured from 85 nasopharyngeal carcinoma (NPC) lesions and 131 normal tissue sites from 59 subjects during routine nasal endoscopy. Leave-one-out cross-validation was used to evaluate the performance of the algorithms. An overall diagnostic accuracy of 96%, a sensitivity of 94%, and a specificity of 97% for discriminating nasopharyngeal carcinomas from normal tissues were achieved using a linear SVM algorithm. A diagnostic accuracy of 98%, a sensitivity of 95%, and a specificity of 99% for detecting NPC were achieved with a nonlinear SVM algorithm. In a comparison with previously developed algorithms using the same dataset and the principal component analysis (PCA) technique, the SVM algorithms produced better diagnostic accuracy in all instances. In addition, we investigated a method combining PCA and SVM techniques for reducing the complexity of the SVM algorithms.

Algorithms↗

PubMed2005

Accurate quantitative structure-property relationship model to predict the solubility of C60 in various solvents based on a novel approach using a least-squares support vector machine.

A least-squares support vector machine (LSSVM) was used for the first time as a novel machine-learning technique for the prediction of the solubility of C60 in a large number of diverse solvents using calculated molecular descriptors from the molecular structure alone and on the basis of the software CODESSA as inputs. The heuristic method of CODESSA was used to select the correlated descriptors and build the linear model. Both the linear and the nonlinear models can give very satisfactory prediction results: the square of the correlation coefficient R(2) was 0.892 and 0.903, and the root-mean-square error was 0.126 and 0.116, respectively, for the whole data set. The prediction result of the LSSVM model is better than that obtained by the heuristic method and the reference, which proved LSSVM was a useful tool in the prediction of the solubility of C60. In addition, this paper provided a new and effective method for predicting the solubility of C60 from its structures and gave some insight into the structural features related to the solubility of C60 in different solvents.

Electrochemistry↗

PubMed2006

Associative memory design using support vector machines.

The relation existing between support vector machines (SVMs) and recurrent associative memories is investigated. The design of associative memories based on the generalized brain-state-in-a-box (GBSB) neural model is formulated as a set of independent classification tasks which can be efficiently solved by standard software packages for SVM learning. Some properties of the networks designed in this way are evidenced, like the fact that surprisingly they follow a generalized Hebb's law. The performance of the SVM approach is compared to existing methods with nonsymmetric connections, by some design examples.

Algorithms↗