Traditional canonical signaling pathways help to understand overall signaling processes inside the cell. Large scale phosphoproteomic data provide insight into alterations among different proteins under different expe...
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Traditional canonical signaling pathways help to understand overall signaling processes inside the cell. Large scale phosphoproteomic data provide insight into alterations among different proteins under different experimental settings. Our goal is to combine the traditional signaling networks with complex phosphoproteomic time-series data in order to unravel cell specific signaling networks. On the application side, we apply and improve a caspo time series method conceived to integrate time series phosphoproteomic data into protein signaling networks. We use a large-scale real case study from the HPN-DREAM Breast Cancer challenge. We infer a family of Boolean models from multiple perturbation time series data of four breast cancer cell lines given a prior protein signaling network. The obtained results are comparable to the top performing teams of the HPN-DREAM challenge. We also discovered that the similar models are clustered together in the solutions space. On the computational side, we improved the method to discover diverse solutions and improve the computational time.
In this paper, we present a new knowledge representation and reasoning tool to handle uncertainty, inconsistencies, and preferences by combining the ideas of LPMLN and logic programming with ordered disjunction (LPOD)...
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There has been an increasing interest in recent years towards the development of efficient solvers for Answer Set programming (ASP) and towards the application of ASP to solve increasing more challenging problems. In ...
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The aim of this paper is to briey introduce some of our experiences with agent oriented programming, in particular combined with logic programming paradigm, in the context of software engineering, and with a focus on ...
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We describe a transformation from the legally descriptive language PROLEG to a bipolar argumentation framework (BAF). PROLEG is a language consisting of general rules and exceptions and employs the negation-as-failure...
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Rule-based systems are important in application domains such as artificial intelligence and business rule engines. When translated into an implementation, simple expressions in rules may map to a large body of code th...
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A formal graph system (FGS) is a logic programming system that directly manipulates graphs by dealing with term graph patterns instead of terms of first-order predicate logic. In this paper, based on FGS, we introduce...
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With the recent prevalence of darkweb/deepweb (D2web) sites specializing in the trade of exploit kits and malware, malicious actors have easy-access to a wide-range of tools that can empower their offensive capability...
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Unlike object-oriented programming approaches in which a solution is clearly represented by objects, classes, inheritance and polymorphism, the logic programming approach is focus on the inference that applies the rul...
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The paper describes an application of logic programming to story understanding. Substantial work in this direction has been done by Erik Mueller, who focused on texts about stereotypical activities (or scripts), in pa...
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