Abstract-Data stream mining has been receiving increasing attention due to its presence in a wide range of applications such as sensor networks, banking, and telecommunication. One of the most important challenges in learning from data streams is reacting to concept drift, i.e., unforeseen changes of the stream's underlying data distribution. Several classification algorithms that cope with concept drift have been put forward, however, most of them specialize in one type of change. In this paper, we propose a new data stream classifier, called the Accuracy Updated Ensemble (AUE2), which aims at reacting equally well to different types of drift. AUE2 combines accuracy-based weighting mechanisms known from block-based ensembles with the incremental nature of Hoeffding Trees. The proposed algorithm was experimentally compared with 11 state-of-the-art stream methods, including single classifiers, block-based and online ensembles, and hybrid approaches in different drift scenarios. Out of all the compared algorithms, AUE2 provided best average classification accuracy while proving to be less memory consuming than other ensemble approaches. Experimental results show that AUE2 can be considered suitable for scenarios involving many types of drift as well as static environments.

Every day, huge volumes of sensory, transactional, and web data are continuously generated as streams, which need to be analyzed online as they arrive. Streaming data can be considered as one of the main sources of what is called big data. While predictive modeling for data streams and big data have received a lot of attention over the last decade, many research approaches are typically designed for well-behaved controlled problem settings, overlooking important challenges imposed by real-world applications. This article presents a discussion on eight open challenges for data stream mining. Our goal is to identify gaps between current research and meaningful applications, highlight open problems, and define new application-relevant research directions for data stream mining. The identified challenges cover the full cycle of knowledge discovery and involve such problems as: protecting data privacy, dealing with legacy systems, handling incomplete and delayed information, analysis of complex data, and evaluation of stream mining algorithms. The resulting analysis is illustrated by practical applications and provides general suggestions concerning lines of future research in data stream mining.

Abstract. In this paper we study the problem of constructing accurate block-based ensemble classifiers from time evolving data streams. AWE is the best-known representative of these ensembles. We propose a new algorithm called Accuracy Updated Ensemble (AUE), which extends AWE by using online component classifiers and updating them according to the current distribution. Additional modifications of weighting functions solve problems with undesired classifier excluding seen in AWE. Experiments with several evolving data sets show that, while still requiring constant processing time and memory, AUE is more accurate than AWE.

No abstract

Modern data-driven systems often require classifiers capable of dealing with streaming imbalanced data and concept changes. The assessment of learning algorithms in such scenarios is still a challenge, as existing online evaluation measures focus on efficiency, but are susceptible to class ratio changes over time. In case of static data, the area under the receiver operating characteristics curve, or simply AUC, is a popular measure for evaluating classifiers both on balanced and imbalanced class distributions. However, the characteristics of AUC calculated on time-changing data streams have not been studied. This paper analyzes the properties of our recent proposal, an incremental algorithm that uses a sorted tree structure with a sliding window to compute AUC with forgetting. The resulting evaluation measure, called prequential AUC, is studied in terms of: visualization over time, processing speed, differences compared to AUC calculated on blocks of examples, and consistency with AUC calculated traditionally. Simulation results show that the proposed measure is statistically consistent with AUC computed traditionally on streams without drift and comparably fast to existing evaluation procedures. Finally, experiments on real-world and synthetic data showcase characteristic properties of prequential AUC compared to classification accuracy, G-mean, Kappa, Kappa M, and recall when used to evaluate classifiers on imbalanced streams with various difficulty factors.

A bright spot in the SARS‐CoV‐2 (CoV‐2) coronavirus pandemic has been the immediate mobilization of the biomedical community, working to develop treatments and vaccines for COVID‐19. Rational drug design against emerging threats depends on well‐established methodology, mainly utilizing X‐ray crystallography, to provide accurate structure models of the macromolecular drug targets and of their complexes with candidates for drug development. In the current crisis, the structural biological community has responded by presenting structure models of CoV‐2 proteins and depositing them in the Protein Data Bank (PDB), usually without time embargo and before publication. Since the structures from the first‐line research are produced in an accelerated mode, there is an elevated chance of mistakes and errors, with the ultimate risk of hindering, rather than speeding up, drug development. In the present work, we have used model‐validation metrics and examined the electron density maps for the deposited models of CoV‐2 proteins and a sample of related proteins available in the PDB as of April 1, 2020. We present these results with the aim of helping the biomedical community establish a better‐validated pool of data. The proteins are divided into groups according to their structure and function. In most cases, no major corrections were necessary. However, in several cases significant revisions in the functionally sensitive area of protein–inhibitor complexes or for bound ions justified correction, re‐refinement, and eventually reversioning in the PDB. The re‐refined coordinate files and a tool for facilitating model comparisons are available at https://covid-19.bioreproducibility.org. Database Validated models of CoV‐2 proteins are available in a dedicated, publicly accessible web service https://covid-19.bioreproducibility.org

No abstract

Supplementary data are available at Bioinformatics online.