Abstract We present a knowledge representation framework on the basis of the Event Calculus that allows an agent to recognize complex activities from low‐level observations received by multiple sensors, reason about the life cycle of such activities, and take action to support their successful completion. Activities are multivalue fluents that change according to events that occur in the environment. The parameters of an activity consist of a unique label, a set of participants involved in the performing of the activity, and a unique goal associated with the activity revealing the activity's desired outcome. Our contribution is the identification of an activity life cycle describing how activities can be started, interrupted, suspended, resumed, or completed over time, as well as how these can be represented. The framework also specifies activity goals, their associated life cycle, and their relation with the activity life cycle. We provide the complete implementation of the framework, which includes an activity generator that automatically creates synthetic sensor data in the form of event streams that represent the everyday lifestyle of a type 1 diabetic patient. Moreover, we test the framework by generating very large activity streams that we use to evaluate the performance of the recognition capability and study its relative merits.

OBJECTIVE: In the context of "network medicine", gene prioritization methods represent one of the main tools to discover candidate disease genes by exploiting the large amount of data covering different types of functional relationships between genes. Several works proposed to integrate multiple sources of data to improve disease gene prioritization, but to our knowledge no systematic studies focused on the quantitative evaluation of the impact of network integration on gene prioritization. In this paper, we aim at providing an extensive analysis of gene-disease associations not limited to genetic disorders, and a systematic comparison of different network integration methods for gene prioritization. MATERIALS AND METHODS: We collected nine different functional networks representing different functional relationships between genes, and we combined them through both unweighted and weighted network integration methods. We then prioritized genes with respect to each of the considered 708 medical subject headings (MeSH) diseases by applying classical guilt-by-association, random walk and random walk with restart algorithms, and the recently proposed kernelized score functions. RESULTS: The results obtained with classical random walk algorithms and the best single network achieved an average area under the curve (AUC) across the 708 MeSH diseases of about 0.82, while kernelized score functions and network integration boosted the average AUC to about 0.89. Weighted integration, by exploiting the different "informativeness" embedded in different functional networks, outperforms unweighted integration at 0.01 significance level, according to the Wilcoxon signed rank sum test. For each MeSH disease we provide the top-ranked unannotated candidate genes, available for further bio-medical investigation. CONCLUSIONS: Network integration is necessary to boost the performances of gene prioritization methods. Moreover the methods based on kernelized score functions can further enhance disease gene ranking results, by adopting both local and global learning strategies, able to exploit the overall topology of the network.

SUMMARY: We present GOssTo, the Gene Ontology semantic similarity Tool, a user-friendly software system for calculating semantic similarities between gene products according to the Gene Ontology. GOssTo is bundled with six semantic similarity measures, including both term- and graph-based measures, and has extension capabilities to allow the user to add new similarities. Importantly, for any measure, GOssTo can also calculate the Random Walk Contribution that has been shown to greatly improve the accuracy of similarity measures. GOssTo is very fast, easy to use, and it allows the calculation of similarities on a genomic scale in a few minutes on a regular desktop machine. CONTACT: [email protected] AVAILABILITY: GOssTo is available both as a stand-alone application running on GNU/Linux, Windows and MacOS from www.paccanarolab.org/gossto and as a web application from www.paccanarolab.org/gosstoweb. The stand-alone application features a simple and concise command line interface for easy integration into high-throughput data processing pipelines.

Multilabel classification is a relatively recent subfield of machine learning. Unlike to the classical approach, where instances are labeled with only one category, in multilabel classification, an arbitrary number of categories is chosen to label an

In this article, we propose a measure to assess scientific impact that discounts self‐citations and does not require any prior knowledge of their distribution among publications. This index can be applied to both researchers and journals. In particular, we show that it fills the gap of the h‐index and similar measures that do not take into account the effect of self‐citations for authors or journals impact evaluation. We provide 2 real‐world examples: First, we evaluate the research impact of the most productive scholars in computer science (according to DBLP Computer Science Bibliography, Universität Trier, Trier, Germany); then we revisit the impact of the journals ranked in the Computer Science Applications section of the SCImago Journal & Country Rank ranking service (Consejo Superior de Investigaciones Científicas, University of Granada, Extremadura, Madrid, Spain). We observe how self‐citations, in many cases, affect the rankings obtained according to different measures (including h‐index and ch‐index), and show how the proposed measure mitigates this effect.