Support vector machine for functional data classification

In many applications, input data are sampled functions taking their values in infinite dimensional spaces rather than standard vectors. This fact has complex consequences on data analysis algorithms that motivate modifications of them. In fact most of the traditional data analysis tools for regression, classification and clustering have been adapted to functional inputs under the general name of functional Data Analysis (FDA). In this paper, we investigate the use of Support Vector Machines (SVMs) for functional data analysis and we focus on the problem of curves discrimination. SVMs are large margin classifier tools based on implicit non linear mappings of the considered data into high dimensional spaces thanks to kernels. We show how to define simple kernels that take into account the unctional nature of the data and lead to consistent classification. Experiments conducted on real world data emphasize the benefit of taking into account some functional aspects of the problems.Comment: 13 page

Functional classification of G-Protein coupled receptors, based on their specific ligand coupling patterns

Functional identification of G-Protein Coupled Receptors (GPCRs) is one of the current focus areas of pharmaceutical research. Although thousands of GPCR sequences are known, many of them re- main as orphan sequences (the activating ligand is unknown). Therefore, classification methods for automated characterization of orphan GPCRs are imperative. In this study, for predicting Level 2 subfamilies of Amine GPCRs, a novel method for obtaining fixed-length feature vectors, based on the existence of activating ligand specific patterns, has been developed and utilized for a Support Vector Machine (SVM)-based classification. Exploiting the fact that there is a non-promiscuous relationship between the specific binding of GPCRs into their ligands and their functional classification, our method classifies Level 2 subfamilies of Amine GPCRs with a high predictive accuracy of 97.02% in a ten-fold cross validation test. The presented machine learning approach, bridges the gulf between the excess amount of GPCR sequence data and their poor functional characterization

Searching for Imaging Biomarkers of Psychotic Dysconnectivity

Background: Progress in precision psychiatry is predicated on identifying reliable individual-level diagnostic biomarkers. For psychosis, measures of structural and functional connectivity could be promising biomarkers given consistent reports of dysconnectivity across psychotic disorders using magnetic resonance imaging. Methods: We leveraged data from four independent cohorts of patients with psychosis and control subjects with observations from approximately 800 individuals. We used group-level analyses and two supervised machine learning algorithms (support vector machines and ridge regression) to test within-, between-, and across-sample classification performance of white matter and resting-state connectivity metrics. Results: Although we replicated group-level differences in brain connectivity, individual-level classification was suboptimal. Classification performance within samples was variable across folds (highest area under the curve [AUC] range = 0.30) and across datasets (average support vector machine AUC range = 0.50; average ridge regression AUC range = 0.18). Classification performance between samples was similarly variable or resulted in AUC values of approximately 0.65, indicating a lack of model generalizability. Furthermore, collapsing across samples (resting-state functional magnetic resonance imaging, N = 888; diffusion tensor imaging, N = 860) did not improve model performance (maximal AUC = 0.67). Ridge regression models generally outperformed support vector machine models, although classification performance was still suboptimal in terms of clinical relevance. Adjusting for demographic covariates did not greatly affect results. Conclusions: Connectivity measures were not suitable as diagnostic biomarkers for psychosis as assessed in this study. Our results do not negate that other approaches may be more successful, although it is clear that a systematic approach to individual-level classification with large independent validation samples is necessary to properly vet neuroimaging features as diagnostic biomarkers

Multivariate pattern classification of pediatric Tourette syndrome using functional connectivity MRI

Tourette syndrome (TS) is a developmental neuropsychiatric disorder characterized by motor and vocal tics. Individuals with TS would benefit greatly from advances in prediction of symptom timecourse and treatment effectiveness. As a first step, we applied a multivariate method - support vector machine (SVM) classification - to test whether patterns in brain network activity, measured with resting state functional connectivity (RSFC) MRI, could predict diagnostic group membership for individuals. RSFC data from 42 children with TS (8-15 yrs) and 42 unaffected controls (age, IQ, in-scanner movement matched) were included. While univariate tests identified no significant group differences, SVM classified group membership with ~70% accuracy (p < .001). We also report a novel adaptation of SVM binary classification that, in addition to an overall accuracy rate for the SVM, provides a confidence measure for the accurate classification of each individual. Our results support the contention that multivariate methods can better capture the complexity of some brain disorders, and hold promise for predicting prognosis and treatment outcome for individuals with TS

On the combination of kernels for support vector classifiers

The problem of combining different sources of information arises in several situations, for instance, the classification of data with asymmetric similarity matrices or the construction of an optimal classifier from a collection of kernels. Often, each source of information can be expressed as a kernel (similarity) matrix and, therefore, a collection of kernels is available. In this paper we propose a new class of methods in order to produce, for classification purposes, an unique and optimal kernel. Then, the constructed kernel is used to train a Support Vector Machine (SVM). The key ideas within the kernel construction are two: the quantification, relative to the classification labels, of the difference of information among the kernels; and the extension of the concept of linear combination of kernels to the concept of functional (matrix) combination of kernels. The proposed methods have been successfully evaluated and compared with other powerful classifiers and kernel combination techniques on a variety of artificial and real classification problems

ON THE COMBINATION OF KERNELS FOR SUPPORT VECTOR CLASSIFIERS

The problem of combining different sources of information arises in several situations, for instance, the classification of data with asymmetric similarity matrices or the construction of an optimal classifier from a collection of kernels. Often, each source of information can be expressed as a kernel (similarity) matrix and, therefore, a collection of kernels is available. In this paper we propose a new class of methods in order to produce, for classification purposes, an unique and optimal kernel. Then, the constructed kernel is used to train a Support Vector Machine (SVM). The key ideas within the kernel construction are two: the quantification, relative to the classification labels, of the difference of information among the kernels; and the extension of the concept of linear combination of kernels to the concept of functional (matrix) combination of kernels. The proposed methods have been successfully evaluated and compared with other powerful classifiers and kernel combination techniques on a variety of artificial and real classification problems.

Learning the kernel with hyperkernels

This paper addresses the problem of choosing a kernel suitable for estimation with a support vector machine, hence further automating machine learning. This goal is achieved by defining a reproducing kernel Hilbert space on the space of kernels itself. Such a formulation leads to a statistical estimation problem similar to the problem of minimizing a regularized risk functional. We state the equivalent representer theorem for the choice of kernels and present a semidefinite programming formulation of the resulting optimization problem. Several recipes for constructing hyperkernels are provided, as well as the details of common machine learning problems. Experimental results for classification, regression and novelty detection on UCI data show the feasibility of our approach

SVM Classifier – a comprehensive java interface for support vector machine classification of microarray data

MOTIVATION: Graphical user interface (GUI) software promotes novelty by allowing users to extend the functionality. SVM Classifier is a cross-platform graphical application that handles very large datasets well. The purpose of this study is to create a GUI application that allows SVM users to perform SVM training, classification and prediction. RESULTS: The GUI provides user-friendly access to state-of-the-art SVM methods embodied in the LIBSVM implementation of Support Vector Machine. We implemented the java interface using standard swing libraries. We used a sample data from a breast cancer study for testing classification accuracy. We achieved 100% accuracy in classification among the BRCA1–BRCA2 samples with RBF kernel of SVM. CONCLUSION: We have developed a java GUI application that allows SVM users to perform SVM training, classification and prediction. We have demonstrated that support vector machines can accurately classify genes into functional categories based upon expression data from DNA microarray hybridization experiments. Among the different kernel functions that we examined, the SVM that uses a radial basis kernel function provides the best performance. The SVM Classifier is available at

Support vector machine classification of arterial volumeâ weighted arterial spin tagging images

IntroductionIn recent years, machineâ learning techniques have gained growing popularity in medical image analysis. Temporal brainâ state classification is one of the major applications of machineâ learning techniques in functional magnetic resonance imaging (fMRI) brain data. This article explores the use of support vector machine (SVM) classification technique with motorâ visual activation paradigm to perform brainâ state classification into activation and rest with an emphasis on different acquisition techniques.MethodsImages were acquired using a recently developed variant of traditional pseudocontinuous arterial spin labeling technique called arterial volumeâ weighted arterial spin tagging (AVAST). The classification scheme is also performed on images acquired using blood oxygenationâ level dependent (BOLD) and traditional perfusionâ weighted arterial spin labeling (ASL) techniques for comparison.ResultsThe AVAST technique outperforms traditional pseudocontinuous ASL, achieving classification accuracy comparable to that of BOLD contrast images.ConclusionThis study demonstrates that AVAST has superior signalâ toâ noise ratio and improved temporal resolution as compared with traditional perfusionâ weighted ASL and reduced sensitivity to scanner drift as compared with BOLD. Owing to these characteristics, AVAST lends itself as an ideal choice for dynamic fMRI and realâ time neurofeedback experiments with sustained activation periods.In this article, we test the performance of our recently introduced method for dynamic arterial blood volume imaging (AVAST) in the context of functional MRI data classification. AVAST is compared with blood oxygenationâ level dependent (BOLD) and arterial spin labeling (ASL) perfusion data collected during a simple motor task using a support vector machine algorithm to classify the brain state. Findings suggest that the AVAST technique has similar performance as BOLD imaging, while preserving the statistical benefits of ASL techniques.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135476/1/brb3549_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135476/2/brb3549.pd