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Journal ArticleDOI

LIBSVM: A library for support vector machines

TL;DR: Issues such as solving SVM optimization problems theoretical convergence multiclass classification probability estimates and parameter selection are discussed in detail.
Abstract: LIBSVM is a library for Support Vector Machines (SVMs). We have been actively developing this package since the year 2000. The goal is to help users to easily apply SVM to their applications. LIBSVM has gained wide popularity in machine learning and many other areas. In this article, we present all implementation details of LIBSVM. Issues such as solving SVM optimization problems theoretical convergence multiclass classification probability estimates and parameter selection are discussed in detail.

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Citations
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Proceedings ArticleDOI
20 Jun 2009
TL;DR: An uncertainty measure is proposed that generalizes margin-based uncertainty to the multi-class case and is easy to compute, so that active learning can handle a large number of classes and large data sizes efficiently.
Abstract: One of the principal bottlenecks in applying learning techniques to classification problems is the large amount of labeled training data required. Especially for images and video, providing training data is very expensive in terms of human time and effort. In this paper we propose an active learning approach to tackle the problem. Instead of passively accepting random training examples, the active learning algorithm iteratively selects unlabeled examples for the user to label, so that human effort is focused on labeling the most “useful” examples. Our method relies on the idea of uncertainty sampling, in which the algorithm selects unlabeled examples that it finds hardest to classify. Specifically, we propose an uncertainty measure that generalizes margin-based uncertainty to the multi-class case and is easy to compute, so that active learning can handle a large number of classes and large data sizes efficiently. We demonstrate results for letter and digit recognition on datasets from the UCI repository, object recognition results on the Caltech-101 dataset, and scene categorization results on a dataset of 13 natural scene categories. The proposed method gives large reductions in the number of training examples required over random selection to achieve similar classification accuracy, with little computational overhead.

578 citations


Cites methods from "LIBSVM: A library for support vecto..."

  • ...We use the toolbox LIBSVM [3] that implements the methods described above for classification and probability estimation in the multiclass problem....

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Journal ArticleDOI
Marcel Dettling1
TL;DR: When bagging is used as a module in boosting, the resulting classifier consistently improves the predictive performance and the probability estimates of both bagging and boosting on real and simulated gene expression data.
Abstract: Motivation: Microarray experiments are expected to contribute significantly to the progress in cancer treatment by enabling a precise and early diagnosis. They create a need for class prediction tools, which can deal with a large number of highly correlated input variables, perform feature selection and provide class probability estimates that serve as a quantification of the predictive uncertainty. A very promising solution is to combine the two ensemble schemes bagging and boosting to a novel algorithm called BagBoosting. Results: When bagging is used as a module in boosting, the resulting classifier consistently improves the predictive performance and the probability estimates of both bagging and boosting on real and simulated gene expression data. This quasi-guaranteed improvement can be obtained by simply making a bigger computing effort. The advantageous predictive potential is also confirmed by comparing BagBoosting to several established class prediction tools for microarray data. Availability: Software for the modified boosting algorithms, for benchmark studies and for the simulation of microarray data are available as an R package under GNU public license at http://stat.ethz.ch/~dettling/bagboost.html

577 citations

Journal ArticleDOI
TL;DR: The purpose of this paper is to present and compare these implementations of support vector machines, among the most popular and efficient classification and regression methods currently available.
Abstract: 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. (authors' abstract)

576 citations

Journal ArticleDOI
TL;DR: This study constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated prediction tools, and returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools.
Abstract: Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of various genetic diseases. Computational tools for the prediction of the effects of mutations on protein function are very important for analysis of single nucleotide variants and their prioritization for experimental characterization. Many computational tools are already widely employed for this purpose. Unfortunately, their comparison and further improvement is hindered by large overlaps between the training datasets and benchmark datasets, which lead to biased and overly optimistic reported performances. In this study, we have constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated tools. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance, and at the same time returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. A user-friendly web interface enables easy access to all eight prediction tools, the consensus classifier PredictSNP and annotations from the Protein Mutant Database and the UniProt database. The web server and the datasets are freely available to the academic community at http://loschmidt.chemi.muni.cz/predictsnp.

571 citations


Additional excerpts

  • ...LibSVM) [50]....

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Journal ArticleDOI
TL;DR: A predictor, called ‘iRSpot-PseDNC’, was developed for identifying the recombination hotspots and coldspots and the overall success rate achieved was >82% in identifying recombination spots in Saccharomyces cerevisiae, indicating the new predictor is promising or at least may become a complementary tool to the existing methods in this area.
Abstract: Meiotic recombination is an important biological process. As a main driving force of evolution, recombination provides natural new combinations of genetic variations. Rather than randomly occurring across a genome, meiotic recombination takes place in some genomic regions (the so-called 'hotspots') with higher frequencies, and in the other regions (the so-called 'coldspots') with lower frequencies. Therefore, the information of the hotspots and coldspots would provide useful insights for in-depth studying of the mechanism of recombination and the genome evolution process as well. So far, the recombination regions have been mainly determined by experiments, which are both expensive and time-consuming. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the recombination regions. In this study, a predictor, called 'iRSpot-PseDNC', was developed for identifying the recombination hotspots and coldspots. In the new predictor, the samples of DNA sequences are formulated by a novel feature vector, the so-called 'pseudo dinucleotide composition' (PseDNC), into which six local DNA structural properties, i.e. three angular parameters (twist, tilt and roll) and three translational parameters (shift, slide and rise), are incorporated. It was observed by the rigorous jackknife test that the overall success rate achieved by iRSpot-PseDNC was >82% in identifying recombination spots in Saccharomyces cerevisiae, indicating the new predictor is promising or at least may become a complementary tool to the existing methods in this area. Although the benchmark data set used to train and test the current method was from S. cerevisiae, the basic approaches can also be extended to deal with all the other genomes. Particularly, it has not escaped our notice that the PseDNC approach can be also used to study many other DNA-related problems. As a user-friendly web-server, iRSpot-PseDNC is freely accessible at http://lin.uestc.edu.cn/server/iRSpot-PseDNC.

568 citations


Cites methods from "LIBSVM: A library for support vecto..."

  • ...The parameters used: 1⁄4 3 and w 1⁄4 0:05 for Equation 9; C 1⁄4 32 and 1⁄4 0:5 for the LIBSVM operation engine (47)....

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References
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Journal ArticleDOI
TL;DR: High generalization ability of support-vector networks utilizing polynomial input transformations is demonstrated and the performance of the support- vector network is compared to various classical learning algorithms that all took part in a benchmark study of Optical Character Recognition.
Abstract: The support-vector network is a new learning machine for two-group classification problems. The machine conceptually implements the following idea: input vectors are non-linearly mapped to a very high-dimension feature space. In this feature space a linear decision surface is constructed. Special properties of the decision surface ensures high generalization ability of the learning machine. The idea behind the support-vector network was previously implemented for the restricted case where the training data can be separated without errors. We here extend this result to non-separable training data. High generalization ability of support-vector networks utilizing polynomial input transformations is demonstrated. We also compare the performance of the support-vector network to various classical learning algorithms that all took part in a benchmark study of Optical Character Recognition.

37,861 citations


"LIBSVM: A library for support vecto..." refers background in this paper

  • ...{1,-1}, C-SVC [Boser et al. 1992; Cortes and Vapnik 1995] solves 4LIBSVM Tools: http://www.csie.ntu.edu.tw/~cjlin/libsvmtools. the following primal optimization problem: l t min 1 w T w +C .i (1) w,b,. 2 i=1 subject to yi(w T f(xi) +b) =1 -.i, .i =0,i =1,...,l, where f(xi)maps xi into a…...

    [...]

01 Jan 1998
TL;DR: Presenting a method for determining the necessary and sufficient conditions for consistency of learning process, the author covers function estimates from small data pools, applying these estimations to real-life problems, and much more.
Abstract: A comprehensive look at learning and generalization theory. The statistical theory of learning and generalization concerns the problem of choosing desired functions on the basis of empirical data. Highly applicable to a variety of computer science and robotics fields, this book offers lucid coverage of the theory as a whole. Presenting a method for determining the necessary and sufficient conditions for consistency of learning process, the author covers function estimates from small data pools, applying these estimations to real-life problems, and much more.

26,531 citations


"LIBSVM: A library for support vecto..." refers background in this paper

  • ...Under given parameters C > 0and E> 0, the standard form of support vector regression [Vapnik 1998] is ll tt 1 T min w w + C .i + C .i * w,b,.,. * 2 i=1 i=1 subject to w T f(xi) + b- zi = E + .i, zi - w T f(xi) - b = E + .i * , * .i,.i = 0,i = 1,...,l....

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  • ...It can be clearly seen that C-SVC and one-class SVM are already in the form of problem (11)....

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  • ..., l, in two classes, and a vector y ∈ Rl such that yi ∈ {1,−1}, C-SVC (Cortes and Vapnik, 1995; Vapnik, 1998) solves the following primal problem:...

    [...]

  • ...Then, according to the SVM formulation, svm train one calls a corresponding subroutine such as solve c svc for C-SVC and solve nu svc for ....

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  • ...Note that b of C-SVC and E-SVR plays the same role as -. in one-class SVM, so we de.ne ....

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Proceedings ArticleDOI
01 Jul 1992
TL;DR: A training algorithm that maximizes the margin between the training patterns and the decision boundary is presented, applicable to a wide variety of the classification functions, including Perceptrons, polynomials, and Radial Basis Functions.
Abstract: A training algorithm that maximizes the margin between the training patterns and the decision boundary is presented. The technique is applicable to a wide variety of the classification functions, including Perceptrons, polynomials, and Radial Basis Functions. The effective number of parameters is adjusted automatically to match the complexity of the problem. The solution is expressed as a linear combination of supporting patterns. These are the subset of training patterns that are closest to the decision boundary. Bounds on the generalization performance based on the leave-one-out method and the VC-dimension are given. Experimental results on optical character recognition problems demonstrate the good generalization obtained when compared with other learning algorithms.

11,211 citations


"LIBSVM: A library for support vecto..." refers background in this paper

  • ...It can be clearly seen that C-SVC and one-class SVM are already in the form of problem (11)....

    [...]

  • ...Then, according to the SVM formulation, svm train one calls a corresponding subroutine such as solve c svc for C-SVC and solve nu svc for ....

    [...]

  • ...Note that b of C-SVC and E-SVR plays the same role as -. in one-class SVM, so we de.ne ....

    [...]

  • ...In Section 2, we describe SVM formulations sup­ported in LIBSVM: C-Support Vector Classi.cation (C-SVC), ....

    [...]

  • ...{1,-1}, C-SVC [Boser et al. 1992; Cortes and Vapnik 1995] solves 4LIBSVM Tools: http://www.csie.ntu.edu.tw/~cjlin/libsvmtools. the following primal optimization problem: l t min 1 w T w +C .i (1) w,b,. 2 i=1 subject to yi(w T f(xi) +b) =1 -.i, .i =0,i =1,...,l, where f(xi)maps xi into a higher-dimensional space and C > 0 is the regularization parameter....

    [...]

01 Jan 2008
TL;DR: A simple procedure is proposed, which usually gives reasonable results and is suitable for beginners who are not familiar with SVM.
Abstract: Support vector machine (SVM) is a popular technique for classication. However, beginners who are not familiar with SVM often get unsatisfactory results since they miss some easy but signicant steps. In this guide, we propose a simple procedure, which usually gives reasonable results.

7,069 citations


"LIBSVM: A library for support vecto..." refers methods in this paper

  • ...A Simple Example of Running LIBSVM While detailed instructions of using LIBSVM are available in the README file of the package and the practical guide by Hsu et al. [2003], here we give a simple example....

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  • ...For instructions of using LIBSVM, see the README file included in the package, the LIBSVM FAQ,3 and the practical guide by Hsu et al. [2003]. LIBSVM supports the following learning tasks....

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Journal ArticleDOI
TL;DR: Decomposition implementations for two "all-together" multiclass SVM methods are given and it is shown that for large problems methods by considering all data at once in general need fewer support vectors.
Abstract: Support vector machines (SVMs) were originally designed for binary classification. How to effectively extend it for multiclass classification is still an ongoing research issue. Several methods have been proposed where typically we construct a multiclass classifier by combining several binary classifiers. Some authors also proposed methods that consider all classes at once. As it is computationally more expensive to solve multiclass problems, comparisons of these methods using large-scale problems have not been seriously conducted. Especially for methods solving multiclass SVM in one step, a much larger optimization problem is required so up to now experiments are limited to small data sets. In this paper we give decomposition implementations for two such "all-together" methods. We then compare their performance with three methods based on binary classifications: "one-against-all," "one-against-one," and directed acyclic graph SVM (DAGSVM). Our experiments indicate that the "one-against-one" and DAG methods are more suitable for practical use than the other methods. Results also show that for large problems methods by considering all data at once in general need fewer support vectors.

6,562 citations