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See detailComputational analysis of molecular network perturbations in complex diseases
Glaab, Enrico UL

Presentation (2019, November 01)

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See detailA Computational-Hermeneutic Approach for Conceptual Explicitation
Fuenmayor, David; Benzmüller, Christoph UL

in Nepomuceno, A.; Magnani, L.; Salguero, F. (Eds.) et al Model-Based Reasoning in Science and Technology -- Inferential Models for Logic, Language, Cognition and Computation (2019)

We present a computer-supported approach for the logical analysis and conceptual explicitation of argumentative discourse. Computational hermeneutics harnesses recent progresses in automated reasoning for ... [more ▼]

We present a computer-supported approach for the logical analysis and conceptual explicitation of argumentative discourse. Computational hermeneutics harnesses recent progresses in automated reasoning for higher-order logics and aims at formalizing natural-language argumentative discourse using flexible combinations of expressive non-classical logics. In doing so, it allows us to render explicit the tacit conceptualizations implicit in argumentative discursive practices. Our approach operates on networks of structured arguments and is iterative and two-layered. At one layer we search for logically correct formalizations for each of the individual arguments. At the next layer we select among those correct formalizations the ones which honor the argument’s dialectic role, i.e. attacking or supporting other arguments as intended. We operate at these two layers in parallel and continuously rate sentences’ formalizations by using, primarily, inferential adequacy criteria. An interpretive, logical theory will thus gradually evolve. This theory is composed of meaning postulates serving as explications for concepts playing a role in the analyzed arguments. Such a recursive, iterative approach to interpretation does justice to the inherent circularity of understanding: the whole is understood compositionally on the basis of its parts, while each part is understood only in the context of the whole (hermeneutic circle). We summarily discuss previous work on exemplary applications of human-in-the-loop computational hermeneutics in metaphysical discourse. We also discuss some of the main challenges involved in fully-automating our approach. By sketching some design ideas and reviewing relevant technologies, we argue for the technological feasibility of a highly-automated computational hermeneutics. [less ▲]

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See detailHarnessing Higher-Order (Meta-)Logic to Represent and Reason with Complex Ethical Theories
Fuenmayor, David; Benzmüller, Christoph UL

in Nayak, A.; Sharma, A. (Eds.) PRICAI 2019: Trends in Artificial Intelligence (2019, August 23)

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See detailClosing the gap between formats for storing layout information in systems biology.
Hoksza, David UL; Gawron, Piotr UL; Ostaszewski, Marek UL et al

in Briefings in bioinformatics (2019)

The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no ... [more ▼]

The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology. [less ▲]

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See detailMINERVA API and plugins: opening molecular network analysis and visualization to the community.
Hoksza, David UL; Gawron, Piotr UL; Ostaszewski, Marek UL et al

in Bioinformatics (Oxford, England) (2019)

SUMMARY: The complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and ... [more ▼]

SUMMARY: The complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and management of molecular networks. Here, we introduce an extension to MINERVA architecture that greatly facilitates the access and use of the stored molecular network data. It allows to incorporate such data in analytical pipelines via a programmatic access interface, and to extend the platform's visual exploration and analytics functionality via plugin architecture. This is possible for any molecular network hosted by the MINERVA platform encoded in well-recognized systems biology formats. To showcase the possibilities of the plugin architecture, we have developed several plugins extending the MINERVA core functionalities. In the article, we demonstrate the plugins for interactive tree traversal of molecular networks, for enrichment analysis and for mapping and visualization of known disease variants or known adverse drug reactions to molecules in the network. AVAILABILITY AND IMPLEMENTATION: Plugins developed and maintained by the MINERVA team are available under the AGPL v3 license at https://git-r3lab.uni.lu/minerva/plugins/. The MINERVA API and plugin documentation is available at https://minerva-web.lcsb.uni.lu. [less ▲]

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