Results 11  20
of
255
Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites
, 2000
"... Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS). Results: The task of finding TIS can be modeled as a classification pro ..."
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Cited by 104 (13 self)
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Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS). Results: The task of finding TIS can be modeled as a classification problem. We demonstrate the applicability of support vector machines (SVMs) for this task, and show how to incorporate prior biological knowledge by engineering an appropriate kernel function. With the described techniques the recognition performance can be improved by 26% over leading existing approaches. We provide evidence that existing related methods (e.g. ESTScan) could profit from advanced TIS recognition.
Incremental Online Learning in High Dimensions
 Neural Computation
, 2005
"... Locally weighted projection regression (LWPR) is a new algorithm for incremental nonlinear function approximation in high dimensional spaces with redundant and irrelevant input dimensions. At its core, it employs nonparametric regression with locally linear models. In order to stay computationally e ..."
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Cited by 104 (15 self)
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Locally weighted projection regression (LWPR) is a new algorithm for incremental nonlinear function approximation in high dimensional spaces with redundant and irrelevant input dimensions. At its core, it employs nonparametric regression with locally linear models. In order to stay computationally e#cient and numerically robust, each local model performs the regression analysis with a small number of univariate regressions in selected directions in input space in the spirit of partial least squares regression. We discuss when and how local learning techniques can successfully work in high dimensional spaces and review the various techniques for local dimensionality reduction before finally deriving the LWPR algorithm. The properties of LWPR are that it i) learns rapidly with second order learning methods based on incremental training, ii) uses statistically sound stochastic leaveoneout cross validation for learning without the need to memorize training data, iii) adjusts its weighting kernels based only on local information in order to minimize the danger of negative interference of incremental learning, iv) has a computational complexity that is linear in the number of inputs, and v) can deal with a large number of  possibly redundant  inputs, as shown in various empirical evaluations with up to 90 dimensional data sets. For a probabilistic interpretation, predictive variance and confidence intervals are derived. To our knowledge, LWPR is the first truly incremental spatially localized learning method that can successfully and e#ciently operate in very high dimensional spaces.
Support Vector Machines: Hype or Hallelujah?
 SIGKDD Explorations
, 2003
"... Support Vector Machines (SVMs) and related kernel methods have become increasingly popular tools for data mining tasks such as classification, regression, and novelty detection. The goal of this tutorial is to provide an intuitive explanation of SVMs from a geometric perspective. The classification ..."
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Cited by 81 (0 self)
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Support Vector Machines (SVMs) and related kernel methods have become increasingly popular tools for data mining tasks such as classification, regression, and novelty detection. The goal of this tutorial is to provide an intuitive explanation of SVMs from a geometric perspective. The classification problem is used to investigate the basic concepts behind SVMs and to examine their strengths and weaknesses from a data mining perspective. While this overview is not comprehensive, it does provide resources for those interested in further exploring SVMs.
Incremental algorithms for hierarchical classification
 Journal of Machine Learning Research
, 2004
"... We study the problem of classifying data in a given taxonomy when classifications associated with multiple and/or partial paths are allowed. We introduce a new algorithm that incrementally learns a linearthreshold classifier for each node of the taxonomy. A hierarchical classification is obtained b ..."
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Cited by 80 (8 self)
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We study the problem of classifying data in a given taxonomy when classifications associated with multiple and/or partial paths are allowed. We introduce a new algorithm that incrementally learns a linearthreshold classifier for each node of the taxonomy. A hierarchical classification is obtained by evaluating the trained node classifiers in a topdown fashion. To evaluate classifiers in our multipath framework, we define a new hierarchical loss function, the Hloss, capturing the intuition that whenever a classification mistake is made on a node of the taxonomy, then no loss should be charged for any additional mistake occurring in the subtree of that node. Making no assumptions on the mechanism generating the data instances, and assuming a linear noise model for the labels, we bound the Hloss of our online algorithm in terms of the Hloss of a reference classifier knowing the true parameters of the labelgenerating process. We show that, in expectation, the excess cumulative Hloss grows at most logarithmically in the length of the data sequence. Furthermore, our analysis reveals the precise dependence of the rate of convergence on the eigenstructure of the data each node observes. Our theoretical results are complemented by a number of experiments on texual corpora. In these experiments we show that, after only one epoch of training, our algorithm performs much better than Perceptronbased hierarchical classifiers, and reasonably close to a hierarchical support vector machine.
Learning the Kernel with Hyperkernels
, 2003
"... 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 es ..."
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Cited by 79 (2 self)
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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 very much akin to the problem of minimizing a regularized risk functional.
Dimensionality Reduction via Sparse Support Vector Machines
 Journal of Machine Learning Research
, 2003
"... 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 prod ..."
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Cited by 67 (13 self)
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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 # 1 norm regularization inherently performs variable selection as a sidee#ect of minimizing capacity of the SVM model. The distribution of the linear model weights provides a mechanism for ranking and interpreting the e#ects of variables.
Ranking with large margin principle: Two approaches
 In Proceedings of Advances in Neural Information Processing Systems
, 2002
"... We discuss the problem of ranking instances with the use of a “large margin ” principle. We introduce two main approaches: the first is the “fixed margin ” policy in which the margin of the closest neighboring classes is being maximized — which turns out to be a direct generalization of SVM to ranki ..."
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Cited by 65 (0 self)
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We discuss the problem of ranking instances with the use of a “large margin ” principle. We introduce two main approaches: the first is the “fixed margin ” policy in which the margin of the closest neighboring classes is being maximized — which turns out to be a direct generalization of SVM to ranking learning. The second approach allows for different margins where the sum of margins is maximized. This approach is shown to reduce toSVM when the number of classes. Both approaches are optimal in size of where is the total number of training examples. Experiments performed on visual classification and “collaborative filtering ” show that both approaches outperform existing ordinal regression algorithms applied for ranking and multiclass SVM applied to general multiclass classification. 1
Duality and Geometry in SVM Classifiers
 In Proc. 17th International Conf. on Machine Learning
, 2000
"... We develop an intuitive geometric interpretation of the standard support vector machine (SVM) for classification of both linearly separable and inseparable data and provide a rigorous derivation of the concepts behind the geometry. For the separable case finding the maximum margin between the ..."
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Cited by 59 (4 self)
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We develop an intuitive geometric interpretation of the standard support vector machine (SVM) for classification of both linearly separable and inseparable data and provide a rigorous derivation of the concepts behind the geometry. For the separable case finding the maximum margin between the two sets is equivalent to finding the closest points in the smallest convex sets that contain each class (the convex hulls). We now extend this argument to the inseparable case by using a reduced convex hull reduced away from outliers. We prove that solving the reduced convex hull formulation is exactly equivalent to solving the standard inseparable SVM for appropriate choices of parameters. Some additional advantages of the new formulation are that the e#ect of the choice of parameters becomes geometrically clear and that the formulation may be solved by fast nearest point algorithms. By changing norms these arguments hold for both the standard 2norm and 1norm SVM. 1. Int...
Feature space interpretation of svms with indefinite kernels
 IEEE Trans Pattern Anal Mach Intell
, 2005
"... Abstract—Kernel methods are becoming increasingly popular for various kinds of machine learning tasks, the most famous being the support vector machine (SVM) for classification. The SVM is well understood when using conditionally positive definite (cpd) kernel functions. However, in practice, noncp ..."
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Cited by 57 (2 self)
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Abstract—Kernel methods are becoming increasingly popular for various kinds of machine learning tasks, the most famous being the support vector machine (SVM) for classification. The SVM is well understood when using conditionally positive definite (cpd) kernel functions. However, in practice, noncpd kernels arise and demand application in SVMs. The procedure of “plugging ” these indefinite kernels in SVMs often yields good empirical classification results. However, they are hard to interpret due to missing geometrical and theoretical understanding. In this paper, we provide a step toward the comprehension of SVM classifiers in these situations. We give a geometric interpretation of SVMs with indefinite kernel functions. We show that such SVMs are optimal hyperplane classifiers not by margin maximization, but by minimization of distances between convex hulls in pseudoEuclidean spaces. By this, we obtain a sound framework and motivation for indefinite SVMs. This interpretation is the basis for further theoretical analysis, e.g., investigating uniqueness, and for the derivation of practical guidelines like characterizing the suitability of indefinite SVMs. Index Terms—Support vector machine, indefinite kernel, pseudoEuclidean space, separation of convex hulls, pattern recognition. æ 1
Generalized Kernel Approach to Dissimilaritybased Classification
 JOURNAL OF MACHINE LEARNING RESEARCH
, 2001
"... Usually, objects to be classified are represented by features. In this paper, we discuss an alternative object representation based on dissimilarity values. If such distances separate the classes well, the nearest neighbor method offers a good solution. However, dissimilarities used in practice are ..."
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Cited by 53 (2 self)
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Usually, objects to be classified are represented by features. In this paper, we discuss an alternative object representation based on dissimilarity values. If such distances separate the classes well, the nearest neighbor method offers a good solution. However, dissimilarities used in practice are usually far from ideal and the performance of the nearest neighbor rule suffers from its sensitivity to noisy examples. We show that other, more global classification techniques are preferable to the nearest neighbor rule, in such cases. For classification purposes, two different ways of using generalized dissimilarity kernels are considered. In the first one, distances are isometrically embedded in a pseudoEuclidean space and the classification task is performed there. In the second approach, classifiers are built directly on distance kernels. Both approaches are described theoretically and then compared using experiments with different dissimilarity measures and datasets including degraded data simulating the problem of missing values.