Instance-based concept learning from multiclass DNA microarray data

BACKGROUND: Various statistical and machine learning methods have been successfully applied to the classification of DNA microarray data. Simple instance-based classifiers such as nearest neighbor (NN) approaches perform remarkably well in comparison to more complex models, and are currently experiencing a renaissance in the analysis of data sets from biology and biotechnology. While binary classification of microarray data has been extensively investigated, studies involving multiclass data are rare. The question remains open whether there exists a significant difference in performance between NN approaches and more complex multiclass methods. Comparative studies in this field commonly assess different models based on their classification accuracy only; however, this approach lacks the rigor needed to draw reliable conclusions and is inadequate for testing the null hypothesis of equal performance. Comparing novel classification models to existing approaches requires focusing on the significance of differences in performance. RESULTS: We investigated the performance of instance-based classifiers, including a NN classifier able to assign a degree of class membership to each sample. This model alleviates a major problem of conventional instance-based learners, namely the lack of confidence values for predictions. The model translates the distances to the nearest neighbors into 'confidence scores'; the higher the confidence score, the closer is the considered instance to a pre-defined class. We applied the models to three real gene expression data sets and compared them with state-of-the-art methods for classifying microarray data of multiple classes, assessing performance using a statistical significance test that took into account the data resampling strategy. Simple NN classifiers performed as well as, or significantly better than, their more intricate competitors. CONCLUSION: Given its highly intuitive underlying principles – simplicity, ease-of-use, and robustness – the k-NN classifier complemented by a suitable distance-weighting regime constitutes an excellent alternative to more complex models for multiclass microarray data sets. Instance-based classifiers using weighted distances are not limited to microarray data sets, but are likely to perform competitively in classifications of high-dimensional biological data sets such as those generated by high-throughput mass spectrometry

Supervised Classification: Quite a Brief Overview

The original problem of supervised classification considers the task of automatically assigning objects to their respective classes on the basis of numerical measurements derived from these objects. Classifiers are the tools that implement the actual functional mapping from these measurements---also called features or inputs---to the so-called class label---or output. The fields of pattern recognition and machine learning study ways of constructing such classifiers. The main idea behind supervised methods is that of learning from examples: given a number of example input-output relations, to what extent can the general mapping be learned that takes any new and unseen feature vector to its correct class? This chapter provides a basic introduction to the underlying ideas of how to come to a supervised classification problem. In addition, it provides an overview of some specific classification techniques, delves into the issues of object representation and classifier evaluation, and (very) briefly covers some variations on the basic supervised classification task that may also be of interest to the practitioner

A Comparative Analysis of Ensemble Classifiers: Case Studies in Genomics

The combination of multiple classifiers using ensemble methods is increasingly important for making progress in a variety of difficult prediction problems. We present a comparative analysis of several ensemble methods through two case studies in genomics, namely the prediction of genetic interactions and protein functions, to demonstrate their efficacy on real-world datasets and draw useful conclusions about their behavior. These methods include simple aggregation, meta-learning, cluster-based meta-learning, and ensemble selection using heterogeneous classifiers trained on resampled data to improve the diversity of their predictions. We present a detailed analysis of these methods across 4 genomics datasets and find the best of these methods offer statistically significant improvements over the state of the art in their respective domains. In addition, we establish a novel connection between ensemble selection and meta-learning, demonstrating how both of these disparate methods establish a balance between ensemble diversity and performance.Comment: 10 pages, 3 figures, 8 tables, to appear in Proceedings of the 2013 International Conference on Data Minin

A Conditional Random Field for Multiple-Instance Learning

We present MI-CRF, a conditional random field (CRF) model for multiple instance learning (MIL). MI-CRF models bags as nodes in a CRF with instances as their states. It combines discriminative unary instance classifiers and pairwise dissimilarity measures. We show that both forces improve the classification performance. Unlike other approaches, MI-CRF considers all bags jointly during training as well as during testing. This makes it possible to classify test bags in an imputation setup. The parameters of MI-CRF are learned using constraint generation. Furthermore, we show that MI-CRF can incorporate previous MIL algorithms to improve on their results. MI-CRF obtains competitive results on five standard MIL datasets. 1