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224
Statistical Comparisons of Classifiers over Multiple Data Sets
, 2006
"... While methods for comparing two learning algorithms on a single data set have been scrutinized for quite some time already, the issue of statistical tests for comparisons of more algorithms on multiple data sets, which is even more essential to typical machine learning studies, has been all but igno ..."
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Cited by 744 (0 self)
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While methods for comparing two learning algorithms on a single data set have been scrutinized for quite some time already, the issue of statistical tests for comparisons of more algorithms on multiple data sets, which is even more essential to typical machine learning studies, has been all but ignored. This article reviews the current practice and then theoretically and empirically examines several suitable tests. Based on that, we recommend a set of simple, yet safe and robust non-parametric tests for statistical comparisons of classifiers: the Wilcoxon signed ranks test for comparison of two classifiers and the Friedman test with the corresponding post-hoc tests for comparison of more classifiers over multiple data sets. Results of the latter can also be neatly presented with the newly introduced CD (critical difference) diagrams.
Robust Classification for Imprecise Environments
, 1989
"... In real-world environments it is usually difficult to specify target operating conditions precisely. This uncertainty makes building robust classification systems problematic. We present a method for the comparison of classifier performance that is robust to imprecise class distributions and misclas ..."
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Cited by 341 (15 self)
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In real-world environments it is usually difficult to specify target operating conditions precisely. This uncertainty makes building robust classification systems problematic. We present a method for the comparison of classifier performance that is robust to imprecise class distributions and misclassification costs. The ROC convex hull method combines techniques from ROC analysis, decision analysis and computational geometry, and adapts them to the particulars of analyzing learned classifiers. The method is efficient and incremental, minimizes the management of classifier performance data, and allows for clear visual comparisons and sensitivity analyses. We then show that it is possible to build a hybrid classifier that will perform at least as well as the best available classifier for any target conditions. This robust performance extends across a wide variety of comparison frameworks, including the optimization of metrics such as accuracy, expected cost, lift, precision, recall, and ...
Combining pairwise sequence similarity and support vector machines for remote protein homology detection
- Proc. 6th Ann. Int. Conf. Computational Molecular Biology
, 2002
"... One key element in understanding the molecular machinery of the cell is to understand the structure and function of each protein encoded in the genome. A very successful means of inferring the structure or function of a previously unannotated protein is via sequence similarity with one or more prote ..."
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Cited by 205 (20 self)
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One key element in understanding the molecular machinery of the cell is to understand the structure and function of each protein encoded in the genome. A very successful means of inferring the structure or function of a previously unannotated protein is via sequence similarity with one or more proteins whose structure or function is already known. Toward this end, we propose a means of representing proteins using pairwise sequence similarity scores. This representation, combined with a discriminative classi � cation algorithm known as the support vector machine (SVM), provides a powerful means of detecting subtle structural and evolutionary relationships among proteins. The algorithm, called SVM-pairwise, when tested on its ability to recognize previously unseen families from the SCOP database, yields signi � cantly better performance than SVM-Fisher, pro � le HMMs, and PSI-BLAST. Key words: pairwise sequence comparison, homology, detection, support vector machines. 1.
Mismatch string kernels for discriminative protein classification
- Bioinformatics
, 2004
"... Motivation: Classification of proteins sequences into functional and structural families based on sequence homology is a central problem in computational biology. Discriminative supervised machine learning approaches provide good performance, but simplicity and computational efficiency of training a ..."
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Cited by 193 (9 self)
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Motivation: Classification of proteins sequences into functional and structural families based on sequence homology is a central problem in computational biology. Discriminative supervised machine learning approaches provide good performance, but simplicity and computational efficiency of training and prediction are also important concerns. Results: We introduce a class of string kernels, called mismatch kernels, for use with support vector machines (SVMs) in a discriminative approach to the problem of protein classification and remote homology detection. These kernels measure sequence similarity based on shared occurrences of fixed-length patterns in the data, allowing for mutations between patterns.Thus, the kernels provide a biologically wellmotivated way to compare protein sequences without relying on family-based generative models such as hidden Markov models. We compute the kernels efficiently using a mismatch tree data structure, allowing us to calculate the contributions of all patterns occurring in the data in one pass while traversing the tree. When used with an SVM, the kernels enable fast prediction on test sequences. We report experiments on two benchmark SCOP datasets, where we show that the mismatch kernel used with an SVM classifier performs competitively with state-of-the-art methods for homology detection, particularly when very few training examples are available. Examination of the highest-weighted patterns learned by the SVM classifier recovers biologically important motifs in protein families and superfamilies. Availability: SVM software is publicly available at
W.S.: Mismatch string kernels for SVM protein classification
- In: Proc. of NIPS. (2003
"... We introduce a class of string kernels, called mismatch kernels, for use with support vector machines (SVMs) in a discriminative approach to the protein classification problem. These kernels measure sequence similarity based on shared occurrences of k-length subsequences, counted with up to m mismat ..."
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Cited by 155 (18 self)
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We introduce a class of string kernels, called mismatch kernels, for use with support vector machines (SVMs) in a discriminative approach to the protein classification problem. These kernels measure sequence similarity based on shared occurrences of k-length subsequences, counted with up to m mismatches, and do not rely on any generative model for the positive training sequences. We compute the kernels efficiently using a mismatch tree data structure and report experiments on a benchmark SCOP dataset, where we show that the mismatch kernel used with an SVM classifier performs as well as the Fisher kernel, the most successful method for remote homology detection, while achieving considerable computational savings. 1
Towards parameter-free data mining
- In: Proc. 10th ACM SIGKDD Intn’l Conf. Knowledge Discovery and Data Mining
, 2004
"... Most data mining algorithms require the setting of many input parameters. Two main dangers of working with parameter-laden algorithms are the following. First, incorrect settings may cause an algorithm to fail in finding the true patterns. Second, a perhaps more insidious problem is that the algorit ..."
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Cited by 145 (19 self)
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Most data mining algorithms require the setting of many input parameters. Two main dangers of working with parameter-laden algorithms are the following. First, incorrect settings may cause an algorithm to fail in finding the true patterns. Second, a perhaps more insidious problem is that the algorithm may report spurious patterns that do not really exist, or greatly overestimate the significance of the reported patterns. This is especially likely when the user fails to understand the role of parameters in the data mining process. Data mining algorithms should have as few parameters as possible, ideally none. A parameter-free algorithm would limit our ability to impose our prejudices, expectations, and presumptions on the problem at hand, and would let the data itself speak to us. In this work, we show that recent results in bioinformatics and computational theory hold great promise for a parameter-free datamining paradigm. The results are motivated by observations in Kolmogorov complexity theory. However, as a practical matter, they can be implemented using any off-the-shelf compression algorithm with the addition of just a dozen or so lines of code. We will show that this approach is competitive or superior to the stateof-the-art approaches in anomaly/interestingness detection, classification, and clustering with empirical tests on time series/DNA/text/video datasets.
Querying and Mining of Time Series Data: Experimental Comparison of Representations and Distance Measures
"... The last decade has witnessed a tremendous growths of interests in applications that deal with querying and mining of time series data. Numerous representation methods for dimensionality reduction and similarity measures geared towards time series have been introduced. Each individual work introduci ..."
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Cited by 141 (24 self)
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The last decade has witnessed a tremendous growths of interests in applications that deal with querying and mining of time series data. Numerous representation methods for dimensionality reduction and similarity measures geared towards time series have been introduced. Each individual work introducing a particular method has made specific claims and, aside from the occasional theoretical justifications, provided quantitative experimental observations. However, for the most part, the comparative aspects of these experiments were too narrowly focused on demonstrating the benefits of the proposed methods over some of the previously introduced ones. In order to provide a comprehensive validation, we conducted an extensive set of time series experiments re-implementing 8 different representation methods and 9 similarity measures and their variants, and testing their effectiveness on 38 time series data sets from a wide variety of application domains. In this paper, we give an overview of these different techniques and present our comparative experimental findings regarding their effectiveness. Our experiments have provided both a unified validation of some of the existing achievements, and in some cases, suggested that certain claims in the literature may be unduly optimistic. 1.
Neural networks for classification: a survey
- and Cybernetics - Part C: Applications and Reviews
, 2000
"... Abstract—Classification is one of the most active research and application areas of neural networks. The literature is vast and growing. This paper summarizes the some of the most important developments in neural network classification research. Specifically, the issues of posterior probability esti ..."
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Cited by 138 (0 self)
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Abstract—Classification is one of the most active research and application areas of neural networks. The literature is vast and growing. This paper summarizes the some of the most important developments in neural network classification research. Specifically, the issues of posterior probability estimation, the link between neural and conventional classifiers, learning and generalization tradeoff in classification, the feature variable selection, as well as the effect of misclassification costs are examined. Our purpose is to provide a synthesis of the published research in this area and stimulate further research interests and efforts in the identified topics. Index Terms—Bayesian classifier, classification, ensemble methods, feature variable selection, learning and generalization, misclassification costs, neural networks. I.
MultiBoosting: A Technique for Combining Boosting and Wagging
- MACHINE LEARNING
, 2000
"... MultiBoosting is an extension to the highly successful AdaBoost technique for forming decision committees. MultiBoosting can be viewed as combining AdaBoost with wagging. It is able to harness both AdaBoost's high bias and variance reduction with wagging's superior variance reduction. Usin ..."
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Cited by 133 (24 self)
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MultiBoosting is an extension to the highly successful AdaBoost technique for forming decision committees. MultiBoosting can be viewed as combining AdaBoost with wagging. It is able to harness both AdaBoost's high bias and variance reduction with wagging's superior variance reduction. Using C4.5 as the base learning algorithm, Multi-boosting is demonstrated to produce decision committees with lower error than either AdaBoost or wagging significantly more often than the reverse over a large representative cross-section of UCI data sets. It offers the further advantage over AdaBoost of suiting parallel execution.
Multiple Comparisons in Induction Algorithms
- MACHINE LEARNING
, 1998
"... A single mechanism is responsible for three pathologies of induction algorithms: attribute selection errors, overfitting, and oversearching. In each pathology, induction algorithms compare multiple items based on scores from an evaluation function and select the item with the maximum score. We ..."
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Cited by 94 (10 self)
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A single mechanism is responsible for three pathologies of induction algorithms: attribute selection errors, overfitting, and oversearching. In each pathology, induction algorithms compare multiple items based on scores from an evaluation function and select the item with the maximum score. We call this a ( ). We analyze the statistical properties of and show how failure to adjust for these properties leads to the pathologies. We also discuss approaches that can control pathological behavior, including Bonferroni adjustment, randomization testing, and cross-validation.
