Variable and feature selection have become the focus of much research in areas of application for which datasets with tens or hundreds of thousands of variables are available. These areas include text processing of internet documents, gene expression array analysis, and combinatorial chemistry. The objective of variable selection is three-fold: improving the prediction performance of the predictors, providing faster and more cost-effective predictors, and providing a better understanding of the underlying process that generated the data. The contributions of this special issue cover a wide range of aspects of such problems: providing a better definition of the objective function, feature construction, feature ranking, multivariate feature selection, efficient search methods, and feature validity assessment methods.

/pdf/an-introduction-to-variable-and-feature-selection-22eu49r0zd.pdf

An introduction to variable and feature selection

Solid tumours contain regions at very low oxygen concentrations (hypoxia), often surrounding areas of necrosis. The cells in these hypoxic regions are resistant to both radiotherapy and chemotherapy. However, the existence of hypoxia and necrosis also provides an opportunity for tumour-selective therapy, including prodrugs activated by hypoxia, hypoxia-specific gene therapy, targeting the hypoxia-inducible factor 1 transcription factor, and recombinant anaerobic bacteria. These strategies could turn what is now an impediment into a significant advantage for cancer therapy.

Exploiting tumour hypoxia in cancer treatment.

Instead of minimizing the observed training error, Support Vector Regression (SVR) attempts to minimize the generalization error bound so as to achieve generalized performance. The idea of SVR is based on the computation of a linear regression function in a high dimensional feature space where the input data are mapped via a nonlinear function. SVR has been applied in various fields - time series and financial (noisy and risky) prediction, approximation of complex engineering analyses, convex quadratic programming and choices of loss functions, etc. In this paper, an attempt has been made to review the existing theory, methods, recent developments and scopes of SVR.

Support Vector Regression

Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature.

/pdf/computational-methods-in-drug-discovery-3sww6kbvd5.pdf

Computational Methods in Drug Discovery

8. Subset Selection in Regression (Monographs on Statistics and Applied Probability, no. 40). By A. J. Miller. ISBN 0 412 35380 6. Chapman and Hall, London, 1990. 240 pp. £25.00.

Subset Selection in Regression

We describe a methodology for performing variable ranking and selection using support vector machines (SVMs). The method constructs a series of sparse linear SVMs to generate linear models that can generalize well, and uses a subset of nonzero weighted variables found by the linear models to produce a final nonlinear model. The method exploits the fact that a linear SVM (no kernels) with l1-norm regularization inherently performs variable selection as a side-effect of minimizing capacity of the SVM model. The distribution of the linear model weights provides a mechanism for ranking and interpreting the effects of variables. Starplots are used to visualize the magnitude and variance of the weights for each variable. We illustrate the effectiveness of the methodology on synthetic data, benchmark problems, and challenging regression problems in drug design. This method can dramatically reduce the number of variables and outperforms SVMs trained using all attributes and using the attributes selected according to correlation coefficients. The visualization of the resulting models is useful for understanding the role of underlying variables.

/pdf/dimensionality-reduction-via-sparse-support-vector-machines-2l49i4ilez.pdf

Dimensionality reduction via sparse support vector machines

Quantitative Structure-Retention Relationship (QSRR) models are developed for the prediction of protein retention times in anion-exchange chromatography systems. Topological, subdivided surface are...

/pdf/prediction-of-protein-retention-times-in-anion-exchange-nl7bpv3z31.pdf

Prediction of protein retention times in anion-exchange chromatography systems using support vector regression.

It has been recognized that drug-induced QT prolongation is related to blockage of the human ether-a-go-go-related gene (hERG) ion channel. Therefore, it is prudent to evaluate the hERG binding of active compounds in early stages of drug discovery. In silico approaches provide an economic and quick method to screen for potential hERG liability. A diverse set of 90 compounds with hERG IC(50) inhibition data was collected from literature references. Fragment-based QSAR descriptors and three different statistical methods, support vector regression, partial least squares, and random forests, were employed to construct QSAR models for hERG binding affinity. Important fragment descriptors relevant to hERG binding affinity were identified through an efficient feature selection method based on sparse linear support vector regression. The support vector regression predictive model built upon selected fragment descriptors outperforms the other two statistical methods in this study, resulting in an r(2) of 0.912 and 0.848 for the training and testing data sets, respectively. The support vector regression model was applied to predict hERG binding affinities of 20 in-house compounds belonging to three different series. The model predicted the relative binding affinity well for two out of three compound series. The hierarchical clustering and dendrogram results show that the compound series with the best prediction has much higher structural similarity and more neighbors of training compounds than the other two compound series, demonstrating the predictive scope of the model. The combination of a QSAR model and postprocessing analysis, such as clustering and visualization, provides a way to assess the confidence level of QSAR prediction results on the basis of similarity to the training set.

Development and evaluation of an in silico model for hERG binding.

https://faculty.missouri.edu/~gatesk/gatespapers/JASMS2003.pdf

A mass spectrometry study of tirapazamine and its metabolites: Insights into the mechanism of metabolic transformations and the characterization of reaction intermediates

This study examines the effect of different salt types on protein retention and selectivity in anion exchange systems. Particularly, linear retention data for various proteins were obtained on two structurally different anion exchange stationary-phase materials in the presence of three salts with different counterions. The data indicated that the effects are, for the most part, nonspecific, although various specific effects could also be observed. Quantitative structure retention relationship (QSRR) models based on support vector machine feature selection and regression models were developed using the experimental chromatographic data in conjunction with various molecular descriptors computed from protein crystal structure geometries. Star plots for each descriptor used in the final model were generated to aid in interpretation. The resulting QSRR models were predictive, with cross-validated r2 values of 0.9445, 0.9676, and 0.8897 for Source 15Q and 0.9561, 0.9876, and 0.9760 for Q Sepharose resins in the presence of three different salts. The predictive power of these models was validated using a set of test proteins that were not used in the generation of these models. Interpretation of the models revealed that particular trends for proteins and salts could be captured using QSRR techniques.

Minghu Song

Papers

Dimensionality reduction via sparse support vector machines

Prediction of protein retention times in anion-exchange chromatography systems using support vector regression.

Development and evaluation of an in silico model for hERG binding.

A mass spectrometry study of tirapazamine and its metabolites: Insights into the mechanism of metabolic transformations and the characterization of reaction intermediates

Prediction of the effect of mobile-phase salt type on protein retention and selectivity in anion exchange systems.