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Mall R.,QCRI Qatar Computing Research Institute | Cerulo L.,University of Sannio | Cerulo L.,Institute of Genetic Research Gaetano Salvatore | Bensmail H.,QCRI Qatar Computing Research Institute | And 3 more authors.
BMC Systems Biology | Year: 2017

Background: Biological networks contribute effectively to unveil the complex structure of molecular interactions and to discover driver genes especially in cancer context. It can happen that due to gene mutations, as for example when cancer progresses, the gene expression network undergoes some amount of localized re-wiring. The ability to detect statistical relevant changes in the interaction patterns induced by the progression of the disease can lead to the discovery of novel relevant signatures. Several procedures have been recently proposed to detect sub-network differences in pairwise labeled weighted networks. Methods: In this paper, we propose an improvement over the state-of-the-art based on the Generalized Hamming Distance adopted for evaluating the topological difference between two networks and estimating its statistical significance. The proposed procedure exploits a more effective model selection criteria to generate p-values for statistical significance and is more efficient in terms of computational time and prediction accuracy than literature methods. Moreover, the structure of the proposed algorithm allows for a faster parallelized implementation. Results: In the case of dense random geometric networks the proposed approach is 10-15x faster and achieves 5-10% higher AUC, Precision/Recall, and Kappa value than the state-of-the-art. We also report the application of the method to dissect the difference between the regulatory networks of IDH-mutant versus IDH-wild-type glioma cancer. In such a case our method is able to identify some recently reported master regulators as well as novel important candidates. Conclusions: We show that our network differencing procedure can effectively and efficiently detect statistical significant network re-wirings in different conditions. When applied to detect the main differences between the networks of IDH-mutant and IDH-wild-type glioma tumors, it correctly selects sub-networks centered on important key regulators of these two different subtypes. In addition, its application highlights several novel candidates that cannot be detected by standard single network-based approaches. © 2017 The Author(s).

Cerulo L.,University of Sannio | Cerulo L.,Institute of Genetic Research Gaetano Salvatore | Di Penta M.,University of Sannio | Bacchelli A.,Technical University of Delft | And 3 more authors.
Science of Computer Programming | Year: 2015

Developers' communication, as contained in emails, issue trackers, and forums, is a precious source of information to support the development process. For example, it can be used to capture knowledge about development practice or about a software project itself. Thus, extracting the content of developers' communication can be useful to support several software engineering tasks, such as program comprehension, source code analysis, and software analytics. However, automating the extraction process is challenging, due to the unstructured nature of free text, which mixes different coding languages (e.g., source code, stack dumps, and log traces) with natural language parts. We conduct an extensive evaluation of Irish (InfoRmation ISlands Hmm), an approach we proposed to extract islands of coded information from free text at token granularity, with respect to the state of art approaches based on island parsing or island parsing combined with machine learners. The evaluation considers a wide set of natural language documents (e.g., textbooks, forum discussions, and development emails) taken from different contexts and encompassing different coding languages. Results indicate an F-measure of Irish between 74% and 99%; this is in line with existing approaches which, differently from Irish, require specific expertise for the definition of regular expressions or grammars. © 2015 Elsevier B.V. All rights reserved.

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