Support Vector Machines in R

Being among the most popular and efficient classification and regression methods currently available, implementations of support vector machines exist in almost every popular programming language. Currently four R packages contain SVM related software. The purpose of this paper is to present and compare these implementations.

A CASE STUDY ON SUPPORT VECTOR MACHINES VERSUS ARTIFICIAL NEURAL NETWORKS

The capability of artificial neural networks for pattern recognition of real world problems is well known. In recent years, the support vector machine has been advocated for its structure risk minimization leading to tolerance margins of decision boundaries. Structures and performances of these pattern classifiers depend on the feature dimension and training data size. The objective of this research is to compare these pattern recognition systems based on a case study. The particular case considered is on classification of hypertensive and normotensive right ventricle (RV) shapes obtained from Magnetic Resonance Image (MRI) sequences. In this case, the feature dimension is reasonable, but the available training data set is small, however, the decision surface is highly nonlinear.For diagnosis of congenital heart defects, especially those associated with pressure and volume overload problems, a reliable pattern classifier for determining right ventricle function is needed. RV¡¦s global and regional surface to volume ratios are assessed from an individual¡¦s MRI heart images. These are used as features for pattern classifiers. We considered first two linear classification methods: the Fisher linear discriminant and the linear classifier trained by the Ho-Kayshap algorithm. When the data are not linearly separable, artificial neural networks with back-propagation training and radial basis function networks were then considered, providing nonlinear decision surfaces. Thirdly, a support vector machine was trained which gives tolerance margins on both sides of the decision surface. We have found in this case study that the back-propagation training of an artificial neural network depends heavily on the selection of initial weights, even though randomized. The support vector machine where radial basis function kernels are used is easily trained and provides decision tolerance margins, in spite of only small margins

Neural networks and support vector machines based bio-activity classification

Classification of various compounds into their respective biological activity classes is important in drug discovery applications from an early phase virtual compound filtering and screening point of view. In this work two types of neural networks, multi layer perceptron (MLP) and radial basis functions (RBF), and support vector machines (SVM) were employed for the classification of three types of biologically active enzyme inhibitors. Both of the networks were trained with back propagation learning method with chemical compounds whose active inhibition properties were previously known. A group of topological indices, selected with the help of principle component analysis (PCA) were used as descriptors. The results of all the three classification methods show that the performance of both the neural networks is better than the SVM

Feature Optimization for Atomistic Machine Learning Yields A Data-Driven Construction of the Periodic Table of the Elements

Machine-learning of atomic-scale properties amounts to extracting correlations between structure, composition and the quantity that one wants to predict. Representing the input structure in a way that best reflects such correlations makes it possible to improve the accuracy of the model for a given amount of reference data. When using a description of the structures that is transparent and well-principled, optimizing the representation might reveal insights into the chemistry of the data set. Here we show how one can generalize the SOAP kernel to introduce a distance-dependent weight that accounts for the multi-scale nature of the interactions, and a description of correlations between chemical species. We show that this improves substantially the performance of ML models of molecular and materials stability, while making it easier to work with complex, multi-component systems and to extend SOAP to coarse-grained intermolecular potentials. The element correlations that give the best performing model show striking similarities with the conventional periodic table of the elements, providing an inspiring example of how machine learning can rediscover, and generalize, intuitive concepts that constitute the foundations of chemistry.Comment: 9 pages, 4 figure