scholarly journals System Z FO : Default reasoning with system Z-like ranking functions for unary first-order conditional knowledge bases

2017 ◽  
Vol 90 ◽  
pp. 120-143
Author(s):  
Christoph Beierle ◽  
Tobias Falke ◽  
Steven Kutsch ◽  
Gabriele Kern-Isberner
Nature Cancer ◽  
2021 ◽  
Author(s):  
Brendan Reardon ◽  
Nathanael D. Moore ◽  
Nicholas S. Moore ◽  
Eric Kofman ◽  
Saud H. AlDubayan ◽  
...  

AbstractTumor molecular profiling of single gene-variant (‘first-order’) genomic alterations informs potential therapeutic approaches. Interactions between such first-order events and global molecular features (for example, mutational signatures) are increasingly associated with clinical outcomes, but these ‘second-order’ alterations are not yet accounted for in clinical interpretation algorithms and knowledge bases. We introduce the Molecular Oncology Almanac (MOAlmanac), a paired clinical interpretation algorithm and knowledge base to enable integrative interpretation of multimodal genomic data for point-of-care decision making and translational-hypothesis generation. We benchmarked MOAlmanac to a first-order interpretation method across multiple retrospective cohorts and observed an increased number of clinical hypotheses from evaluation of molecular features and profile-to-cell line matchmaking. When applied to a prospective precision oncology trial cohort, MOAlmanac nominated a median of two therapies per patient and identified therapeutic strategies administered in 47% of patients. Overall, we present an open-source computational method for integrative clinical interpretation of individualized molecular profiles.


Author(s):  
Stephan Schulz ◽  
Geoff Sutcliffe ◽  
Josef Urban ◽  
Adam Pease
Keyword(s):  

2020 ◽  
Vol 21 (1) ◽  
pp. 51-79
Author(s):  
STATHIS DELIVORIAS ◽  
MICHEL LECLÈRE ◽  
MARIE-LAURE MUGNIER ◽  
FEDERICO ULLIANA

AbstractExistential rules are a positive fragment of first-order logic that generalizes function-free Horn rules by allowing existentially quantified variables in rule heads. This family of languages has recently attracted significant interest in the context of ontology-mediated query answering. Forward chaining, also known as the chase, is a fundamental tool for computing universal models of knowledge bases, which consist of existential rules and facts. Several chase variants have been defined, which differ on the way they handle redundancies. A set of existential rules is bounded if it ensures the existence of a bound on the depth of the chase, independently from any set of facts. Deciding if a set of rules is bounded is an undecidable problem for all chase variants. Nevertheless, when computing universal models, knowing that a set of rules is bounded for some chase variant does not help much in practice if the bound remains unknown or even very large. Hence, we investigate the decidability of the k-boundedness problem, which asks whether the depth of the chase for a given set of rules is bounded by an integer k. We identify a general property which, when satisfied by a chase variant, leads to the decidability of k-boundedness. We then show that the main chase variants satisfy this property, namely the oblivious, semi-oblivious (aka Skolem), and restricted chase, as well as their breadth-first versions.


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