Protein sequences classification based on weighting scheme

We present a new technique to recognize remote protein homologies that rely on combining probabilistic modeling and supervised learning in high-dimensional feature spaces. The main novelty of our technique is the method of constructing feature vectors using Hidden Markov Model and the combination of this representation with a classifier capable of learning in very sparse high-dimensional spaces. Each feature vector records the sensitivity of each protein domain to a previously learned set of sub-sequences (strings). Unlike other previous methods, our method takes in consideration the conserved and non-conserved regions. The system subsequently utilizes Support Vector Machines (SVM) classifiers to learn the boundaries between structural protein classes. Experiments show that this method, which we call the String Weighting Scheme-SVM (SWS-SVM) method, significantly improves on previous methods for the classification of protein domains based on remote homologies. Our method is then compared to five existing homology detection methods

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.

kernlab - An S4 Package for Kernel Methods in R

kernlab is an extensible package for kernel-based machine learning methods in R. It takes advantage of R's new S4 ob ject model and provides a framework for creating and using kernel-based algorithms. The package contains dot product primitives (kernels), implementations of support vector machines and the relevance vector machine, Gaussian processes, a ranking algorithm, kernel PCA, kernel CCA, and a spectral clustering algorithm. Moreover it provides a general purpose quadratic programming solver, and an incomplete Cholesky decomposition method.

Enhanced Industrial Machinery Condition Monitoring Methodology based on Novelty Detection and Multi-Modal Analysis

This paper presents a condition-based monitoring methodology based on novelty detection applied to industrial machinery. The proposed approach includes both, the classical classification of multiple a priori known scenarios, and the innovative detection capability of new operating modes not previously available. The development of condition-based monitoring methodologies considering the isolation capabilities of unexpected scenarios represents, nowadays, a trending topic able to answer the demanding requirements of the future industrial processes monitoring systems. First, the method is based on the temporal segmentation of the available physical magnitudes, and the estimation of a set of time-based statistical features. Then, a double feature reduction stage based on Principal Component Analysis and Linear Discriminant Analysis is applied in order to optimize the classification and novelty detection performances. The posterior combination of a Feed-forward Neural Network and One-Class Support Vector Machine allows the proper interpretation of known and unknown operating conditions. The effectiveness of this novel condition monitoring scheme has been verified by experimental results obtained from an automotive industry machine.Postprint (published version