A study of hierarchical and flat classification of proteins

Automatic classification of proteins using machine learning is an important problem that has received significant attention in the literature. One feature of this problem is that expert-defined hierarchies of protein classes exist and can potentially be exploited to improve classification performance. In this article we investigate empirically whether this is the case for two such hierarchies. We compare multi-class classification techniques that exploit the information in those class hierarchies and those that do not, using logistic regression, decision trees, bagged decision trees, and support vector machines as the underlying base learners. In particular, we compare hierarchical and flat variants of ensembles of nested dichotomies. The latter have been shown to deliver strong classification performance in multi-class settings. We present experimental results for synthetic, fold recognition, enzyme classification, and remote homology detection data. Our results show that exploiting the class hierarchy improves performance on the synthetic data, but not in the case of the protein classification problems. Based on this we recommend that strong flat multi-class methods be used as a baseline to establish the benefit of exploiting class hierarchies in this area

Machine Learning in Automated Text Categorization

The automated categorization (or classification) of texts into predefined categories has witnessed a booming interest in the last ten years, due to the increased availability of documents in digital form and the ensuing need to organize them. In the research community the dominant approach to this problem is based on machine learning techniques: a general inductive process automatically builds a classifier by learning, from a set of preclassified documents, the characteristics of the categories. The advantages of this approach over the knowledge engineering approach (consisting in the manual definition of a classifier by domain experts) are a very good effectiveness, considerable savings in terms of expert manpower, and straightforward portability to different domains. This survey discusses the main approaches to text categorization that fall within the machine learning paradigm. We will discuss in detail issues pertaining to three different problems, namely document representation, classifier construction, and classifier evaluation.Comment: Accepted for publication on ACM Computing Survey

Robust Classification for Imprecise Environments

In real-world environments it usually is difficult to specify target operating conditions precisely, for example, target misclassification costs. This uncertainty makes building robust classification systems problematic. We 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. In some cases, the performance of the hybrid actually can surpass that of the best known classifier. 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 workforce utilization. The hybrid also is efficient to build, to store, and to update. The hybrid is based on a method for the comparison of classifier performance that is robust to imprecise class distributions and misclassification costs. The ROC convex hull (ROCCH) 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. Finally, we point to empirical evidence that a robust hybrid classifier indeed is needed for many real-world problems.Comment: 24 pages, 12 figures. To be published in Machine Learning Journal. For related papers, see http://www.hpl.hp.com/personal/Tom_Fawcett/ROCCH

Relatedness Measures to Aid the Transfer of Building Blocks among Multiple Tasks

Multitask Learning is a learning paradigm that deals with multiple different tasks in parallel and transfers knowledge among them. XOF, a Learning Classifier System using tree-based programs to encode building blocks (meta-features), constructs and collects features with rich discriminative information for classification tasks in an observed list. This paper seeks to facilitate the automation of feature transferring in between tasks by utilising the observed list. We hypothesise that the best discriminative features of a classification task carry its characteristics. Therefore, the relatedness between any two tasks can be estimated by comparing their most appropriate patterns. We propose a multiple-XOF system, called mXOF, that can dynamically adapt feature transfer among XOFs. This system utilises the observed list to estimate the task relatedness. This method enables the automation of transferring features. In terms of knowledge discovery, the resemblance estimation provides insightful relations among multiple data. We experimented mXOF on various scenarios, e.g. representative Hierarchical Boolean problems, classification of distinct classes in the UCI Zoo dataset, and unrelated tasks, to validate its abilities of automatic knowledge-transfer and estimating task relatedness. Results show that mXOF can estimate the relatedness reasonably between multiple tasks to aid the learning performance with the dynamic feature transferring.Comment: accepted by The Genetic and Evolutionary Computation Conference (GECCO 2020

A survey of cost-sensitive decision tree induction algorithms

The past decade has seen a significant interest on the problem of inducing decision trees that take account of costs of misclassification and costs of acquiring the features used for decision making. This survey identifies over 50 algorithms including approaches that are direct adaptations of accuracy based methods, use genetic algorithms, use anytime methods and utilize boosting and bagging. The survey brings together these different studies and novel approaches to cost-sensitive decision tree learning, provides a useful taxonomy, a historical timeline of how the field has developed and should provide a useful reference point for future research in this field

Ensemble Learning for Free with Evolutionary Algorithms ?

Evolutionary Learning proceeds by evolving a population of classifiers, from which it generally returns (with some notable exceptions) the single best-of-run classifier as final result. In the meanwhile, Ensemble Learning, one of the most efficient approaches in supervised Machine Learning for the last decade, proceeds by building a population of diverse classifiers. Ensemble Learning with Evolutionary Computation thus receives increasing attention. The Evolutionary Ensemble Learning (EEL) approach presented in this paper features two contributions. First, a new fitness function, inspired by co-evolution and enforcing the classifier diversity, is presented. Further, a new selection criterion based on the classification margin is proposed. This criterion is used to extract the classifier ensemble from the final population only (Off-line) or incrementally along evolution (On-line). Experiments on a set of benchmark problems show that Off-line outperforms single-hypothesis evolutionary learning and state-of-art Boosting and generates smaller classifier ensembles