A report on the results of the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools.

Motivated by the need for unification of the field of data mining and the growing demand for formalized representation of outcomes of research, we address the task of constructing an ontology of data mining. The proposed ontology, named OntoDM, is based on a recent proposal of a general framework for data mining, and includes definitions of basic data mining entities, such as datatype and dataset, data mining task, data mining algorithm and components thereof (e.g., distance function), etc. It also allows for the definition of more complex entities, e.g., constraints in constraint-based data mining, sets of such constraints (inductive queries) and data mining scenarios (sequences of inductive queries). Unlike most existing approaches to constructing ontologies of data mining, OntoDM is a deep/heavy-weight ontology and follows best practices in ontology engineering, such as not allowing multiple inheritance of classes, using a predefined set of relations and using a top level ontology.

Multi-label classification (MLC) tasks are encountered more and more frequently in machine learning applications. While MLC methods exist for the classical batch setting, only a few methods are available for streaming setting. In this paper, we propose a new methodology for MLC via multi-target regression in a streaming setting. Moreover, we develop a streaming multi-target regressor iSOUP-Tree that uses this approach. We experimentally compare two variants of the iSOUP-Tree method (building regression and model trees), as well as ensembles of iSOUP-Trees with state-of-the-art tree and ensemble methods for MLC on data streams. We evaluate these methods on a variety of measures of predictive performance (appropriate for the MLC task). The ensembles of iSOUP-Trees perform significantly better on some of these measures, especially the ones based on label ranking, and are not significantly worse than the competitors on any of the remaining measures. We identify the thresholding problem for the task of MLC on data streams as a key issue that needs to be addressed in order to obtain even better results in terms of predictive performance.