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97
Support Vector Machine Classification and Validation of Cancer Tissue Samples Using Microarray Expression Data
, 2000
"... Motivation: DNA microarray experiments generating thousands of gene expression measurements, are being used to gather information from tissue and cell samples regarding gene expression differences that will be useful in diagnosing disease. We have developed a new method to analyse this kind of data ..."
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Cited by 566 (1 self)
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Motivation: DNA microarray experiments generating thousands of gene expression measurements, are being used to gather information from tissue and cell samples regarding gene expression differences that will be useful in diagnosing disease. We have developed a new method to analyse this kind of data using support vector machines (SVMs). This analysis consists of both classification of the tissue samples, and an exploration of the data for mislabeled or questionable tissue results. Results: We demonstrate the method in detail on samples consisting of ovarian cancer tissues, normal ovarian tissues, and other normal tissues. The dataset consists of expression experiment results for 97 802 cDNAs for each tissue. As a result of computational analysis, a tissue sample is discovered and confirmed to be wrongly labeled. Upon correction of this mistake and the removal of an outlier, perfect classification of tissues is achieved, but not with high confidence. We identify and analyse a subset of genes from the ovarian dataset whose expression is highly differentiated between the types of tissues. To show robustness of the SVM method, two previously published datasets from other types of tissues or cells are analysed. The results are comparable to those previously obtained. We show that other machine learning methods also perform comparably to the SVM on many of those datasets. Availability: The SVM software is available at http:// www. cs.columbia.edu/#bgrundy/svm. Contact: booch@cse.ucsc.edu
Ultraconservative Online Algorithms for Multiclass Problems
 Journal of Machine Learning Research
, 2001
"... In this paper we study online classification algorithms for multiclass problems in the mistake bound model. The hypotheses we use maintain one prototype vector per class. Given an input instance, a multiclass hypothesis computes a similarityscore between each prototype and the input instance and th ..."
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Cited by 313 (21 self)
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In this paper we study online classification algorithms for multiclass problems in the mistake bound model. The hypotheses we use maintain one prototype vector per class. Given an input instance, a multiclass hypothesis computes a similarityscore between each prototype and the input instance and then sets the predicted label to be the index of the prototype achieving the highest similarity. To design and analyze the learning algorithms in this paper we introduce the notion of ultraconservativeness. Ultraconservative algorithms are algorithms that update only the prototypes attaining similarityscores which are higher than the score of the correct label's prototype. We start by describing a family of additive ultraconservative algorithms where each algorithm in the family updates its prototypes by finding a feasible solution for a set of linear constraints that depend on the instantaneous similarityscores. We then discuss a specific online algorithm that seeks a set of prototypes which have a small norm. The resulting algorithm, which we term MIRA (for Margin Infused Relaxed Algorithm) is ultraconservative as well. We derive mistake bounds for all the algorithms and provide further analysis of MIRA using a generalized notion of the margin for multiclass problems.
On the Generalization Ability of Online Learning Algorithms
 IEEE Transactions on Information Theory
, 2001
"... In this paper we show that online algorithms for classification and regression can be naturally used to obtain hypotheses with good datadependent tail bounds on their risk. Our results are proven without requiring complicated concentrationofmeasure arguments and they hold for arbitrary onlin ..."
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Cited by 184 (8 self)
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In this paper we show that online algorithms for classification and regression can be naturally used to obtain hypotheses with good datadependent tail bounds on their risk. Our results are proven without requiring complicated concentrationofmeasure arguments and they hold for arbitrary online learning algorithms. Furthermore, when applied to concrete online algorithms, our results yield tail bounds that in many cases are comparable or better than the best known bounds.
Relative Loss Bounds for Online Density Estimation with the Exponential Family of Distributions
 MACHINE LEARNING
, 2000
"... We consider online density estimation with a parameterized density from the exponential family. The online algorithm receives one example at a time and maintains a parameter that is essentially an average of the past examples. After receiving an example the algorithm incurs a loss, which is the n ..."
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Cited by 152 (14 self)
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We consider online density estimation with a parameterized density from the exponential family. The online algorithm receives one example at a time and maintains a parameter that is essentially an average of the past examples. After receiving an example the algorithm incurs a loss, which is the negative loglikelihood of the example with respect to the past parameter of the algorithm. An oline algorithm can choose the best parameter based on all the examples. We prove bounds on the additional total loss of the online algorithm over the total loss of the best oline parameter. These relative loss bounds hold for an arbitrary sequence of examples. The goal is to design algorithms with the best possible relative loss bounds. We use a Bregman divergence to derive and analyze each algorithm. These divergences are relative entropies between two exponential distributions. We also use our methods to prove relative loss bounds for linear regression.
A New Approximate Maximal Margin Classification Algorithm
 JOURNAL OF MACHINE LEARNING RESEARCH
, 2001
"... A new incremental learning algorithm is described which approximates the maximal margin hyperplane w.r.t. norm p 2 for a set of linearly separable data. Our algorithm, called alma p (Approximate Large Margin algorithm w.r.t. norm p), takes O (p 1) 2 2 corrections to separate the data wi ..."
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Cited by 102 (5 self)
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A new incremental learning algorithm is described which approximates the maximal margin hyperplane w.r.t. norm p 2 for a set of linearly separable data. Our algorithm, called alma p (Approximate Large Margin algorithm w.r.t. norm p), takes O (p 1) 2 2 corrections to separate the data with pnorm margin larger than (1 ) , where is the (normalized) pnorm margin of the data. alma p avoids quadratic (or higherorder) programming methods. It is very easy to implement and is as fast as online algorithms, such as Rosenblatt's Perceptron algorithm. We performed extensive experiments on both realworld and artificial datasets. We compared alma 2 (i.e., alma p with p = 2) to standard Support vector Machines (SVM) and to two incremental algorithms: the Perceptron algorithm and Li and Long's ROMMA. The accuracy levels achieved by alma 2 are superior to those achieved by the Perceptron algorithm and ROMMA, but slightly inferior to SVM's. On the other hand, alma 2 is quite faster and easier to implement than standard SVM training algorithms. When learning sparse target vectors, alma p with p > 2 largely outperforms Perceptronlike algorithms, such as alma 2 .
Adaptive and SelfConfident OnLine Learning Algorithms
, 2000
"... We study online learning in the linear regression framework. Most of the performance bounds for online algorithms in this framework assume a constant learning rate. To achieve these bounds the learning rate must be optimized based on a posteriori information. This information depends on the wh ..."
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Cited by 99 (8 self)
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We study online learning in the linear regression framework. Most of the performance bounds for online algorithms in this framework assume a constant learning rate. To achieve these bounds the learning rate must be optimized based on a posteriori information. This information depends on the whole sequence of examples and thus it is not available to any strictly online algorithm. We introduce new techniques for adaptively tuning the learning rate as the data sequence is progressively revealed. Our techniques allow us to prove essentially the same bounds as if we knew the optimal learning rate in advance. Moreover, such techniques apply to a wide class of online algorithms, including pnorm algorithms for generalized linear regression and Weighted Majority for linear regression with absolute loss. Our adaptive tunings are radically dierent from previous techniques, such as the socalled doubling trick. Whereas the doubling trick restarts the online algorithm several ti...
Relative Loss Bounds for Multidimensional Regression Problems
 MACHINE LEARNING
, 2001
"... We study online generalized linear regression with multidimensional outputs, i.e., neural networks with multiple output nodes but no hidden nodes. We allow at the final layer transfer functions such as the softmax function that need to consider the linear activations to all the output neurons. The ..."
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Cited by 90 (15 self)
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We study online generalized linear regression with multidimensional outputs, i.e., neural networks with multiple output nodes but no hidden nodes. We allow at the final layer transfer functions such as the softmax function that need to consider the linear activations to all the output neurons. The weight vectors used to produce the linear activations are represented indirectly by maintaining separate parameter vectors. We get the weight vector by applying a particular parameterization function to the parameter vector. Updating the parameter vectors upon seeing new examples is done additively, as in the usual gradient descent update. However, by using a nonlinear parameterization function between the parameter vectors and the weight vectors, we can make the resulting update of the weight vector quite different from a true gradient descent update. To analyse such updates, we define a notion of a matching loss function and apply it both to the transfer function and to the parameterization function. The loss function that matches the transfer function is used to measure the goodness of the predictions of the algorithm. The loss function that matches the parameterization function can be used both as a measure of divergence between models in motivating the update rule of the algorithm and as a measure of progress in analyzing its relative performance compared to an arbitrary fixed model. As a result, we have a unified treatment that generalizes earlier results for the gradient descent and exponentiated gradient algorithms to multidimensional outputs, including multiclass logistic regression.
A secondorder perceptron algorithm
, 2005
"... Kernelbased linearthreshold algorithms, such as support vector machines and Perceptronlike algorithms, are among the best available techniques for solving pattern classification problems. In this paper, we describe an extension of the classical Perceptron algorithm, called secondorder Perceptr ..."
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Cited by 82 (22 self)
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Kernelbased linearthreshold algorithms, such as support vector machines and Perceptronlike algorithms, are among the best available techniques for solving pattern classification problems. In this paper, we describe an extension of the classical Perceptron algorithm, called secondorder Perceptron, and analyze its performance within the mistake bound model of online learning. The bound achieved by our algorithm depends on the sensitivity to secondorder data information and is the best known mistake bound for (efficient) kernelbased linearthreshold classifiers to date. This mistake bound, which strictly generalizes the wellknown Perceptron bound, is expressed in terms of the eigenvalues of the empirical data correlation matrix and depends on a parameter controlling the sensitivity of the algorithm to the distribution of these eigenvalues. Since the optimal setting of this parameter is not known a priori, we also analyze two variants of the secondorder Perceptron algorithm: one that adaptively sets the value of the parameter in terms of the number of mistakes made so far, and one that is parameterless, based on pseudoinverses.
Tracking the Best Linear Predictor
 Journal of Machine Learning Research
, 2001
"... In most online learning research the total online loss of the algorithm is compared to the total loss of the best offline predictor u from a comparison class of predictors. We call such bounds static bounds. The interesting feature of these bounds is that they hold for an arbitrary sequence of ex ..."
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Cited by 75 (13 self)
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In most online learning research the total online loss of the algorithm is compared to the total loss of the best offline predictor u from a comparison class of predictors. We call such bounds static bounds. The interesting feature of these bounds is that they hold for an arbitrary sequence of examples. Recently some work has been done where the predictor u t at each trial t is allowed to change with time, and the total online loss of the algorithm is compared to the sum of the losses of u t at each trial plus the total "cost" for shifting to successive predictors. This is to model situations in which the examples change over time, and different predictors from the comparison class are best for different segments of the sequence of examples. We call such bounds shifting bounds. They hold for arbitrary sequences of examples and arbitrary sequences of predictors. Naturally shifting bounds are much harder to prove. The only known bounds are for the case when the comparison class consists of a sequences of experts or boolean disjunctions. In this paper we develop the methodology for lifting known static bounds to the shifting case. In particular we obtain bounds when the comparison class consists of linear neurons (linear combinations of experts). Our essential technique is to project the hypothesis of the static algorithm at the end of each trial into a suitably chosen convex region. This keeps the hypothesis of the algorithm wellbehaved and the static bounds can be converted to shifting bounds.
Covering Number Bounds of Certain Regularized Linear Function Classes
 Journal of Machine Learning Research
, 2002
"... Recently, sample complexity bounds have been derived for problems involving linear functions such as neural networks and support vector machines. In many of these theoretical studies, the concept of covering numbers played an important role. It is thus useful to study covering numbers for linear ..."
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Cited by 61 (3 self)
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Recently, sample complexity bounds have been derived for problems involving linear functions such as neural networks and support vector machines. In many of these theoretical studies, the concept of covering numbers played an important role. It is thus useful to study covering numbers for linear function classes. In this paper, we investigate two closely related methods to derive upper bounds on these covering numbers. The first method, already employed in some earlier studies, relies on the socalled Maurey's lemma; the second method uses techniques from the mistake bound framework in online learning. We compare results from these two methods, as well as their consequences in some learning formulations.