Validation of Soft Classification Models using Partial Class Memberships: An Extended Concept of Sensitivity & Co. applied to the Grading of Astrocytoma Tissues

We use partial class memberships in soft classification to model uncertain labelling and mixtures of classes. Partial class memberships are not restricted to predictions, but may also occur in reference labels (ground truth, gold standard diagnosis) for training and validation data. Classifier performance is usually expressed as fractions of the confusion matrix, such as sensitivity, specificity, negative and positive predictive values. We extend this concept to soft classification and discuss the bias and variance properties of the extended performance measures. Ambiguity in reference labels translates to differences between best-case, expected and worst-case performance. We show a second set of measures comparing expected and ideal performance which is closely related to regression performance, namely the root mean squared error RMSE and the mean absolute error MAE. All calculations apply to classical crisp classification as well as to soft classification (partial class memberships and/or one-class classifiers). The proposed performance measures allow to test classifiers with actual borderline cases. In addition, hardening of e.g. posterior probabilities into class labels is not necessary, avoiding the corresponding information loss and increase in variance. We implement the proposed performance measures in the R package "softclassval", which is available from CRAN and at http://softclassval.r-forge.r-project.org. Our reasoning as well as the importance of partial memberships for chemometric classification is illustrated by a real-word application: astrocytoma brain tumor tissue grading (80 patients, 37000 spectra) for finding surgical excision borders. As borderline cases are the actual target of the analytical technique, samples which are diagnosed to be borderline cases must be included in the validation.Comment: The manuscript is accepted for publication in Chemometrics and Intelligent Laboratory Systems. Supplementary figures and tables are at the end of the pd

On Machine-Learned Classification of Variable Stars with Sparse and Noisy Time-Series Data

With the coming data deluge from synoptic surveys, there is a growing need for frameworks that can quickly and automatically produce calibrated classification probabilities for newly-observed variables based on a small number of time-series measurements. In this paper, we introduce a methodology for variable-star classification, drawing from modern machine-learning techniques. We describe how to homogenize the information gleaned from light curves by selection and computation of real-numbered metrics ("feature"), detail methods to robustly estimate periodic light-curve features, introduce tree-ensemble methods for accurate variable star classification, and show how to rigorously evaluate the classification results using cross validation. On a 25-class data set of 1542 well-studied variable stars, we achieve a 22.8% overall classification error using the random forest classifier; this represents a 24% improvement over the best previous classifier on these data. This methodology is effective for identifying samples of specific science classes: for pulsational variables used in Milky Way tomography we obtain a discovery efficiency of 98.2% and for eclipsing systems we find an efficiency of 99.1%, both at 95% purity. We show that the random forest (RF) classifier is superior to other machine-learned methods in terms of accuracy, speed, and relative immunity to features with no useful class information; the RF classifier can also be used to estimate the importance of each feature in classification. Additionally, we present the first astronomical use of hierarchical classification methods to incorporate a known class taxonomy in the classifier, which further reduces the catastrophic error rate to 7.8%. Excluding low-amplitude sources, our overall error rate improves to 14%, with a catastrophic error rate of 3.5%.Comment: 23 pages, 9 figure

A Winnow-Based Approach to Context-Sensitive Spelling Correction

A large class of machine-learning problems in natural language require the characterization of linguistic context. Two characteristic properties of such problems are that their feature space is of very high dimensionality, and their target concepts refer to only a small subset of the features in the space. Under such conditions, multiplicative weight-update algorithms such as Winnow have been shown to have exceptionally good theoretical properties. We present an algorithm combining variants of Winnow and weighted-majority voting, and apply it to a problem in the aforementioned class: context-sensitive spelling correction. This is the task of fixing spelling errors that happen to result in valid words, such as substituting "to" for "too", "casual" for "causal", etc. We evaluate our algorithm, WinSpell, by comparing it against BaySpell, a statistics-based method representing the state of the art for this task. We find: (1) When run with a full (unpruned) set of features, WinSpell achieves accuracies significantly higher than BaySpell was able to achieve in either the pruned or unpruned condition; (2) When compared with other systems in the literature, WinSpell exhibits the highest performance; (3) The primary reason that WinSpell outperforms BaySpell is that WinSpell learns a better linear separator; (4) When run on a test set drawn from a different corpus than the training set was drawn from, WinSpell is better able than BaySpell to adapt, using a strategy we will present that combines supervised learning on the training set with unsupervised learning on the (noisy) test set.Comment: To appear in Machine Learning, Special Issue on Natural Language Learning, 1999. 25 page