František Simančík

The Incredible ELK

Abstractℰℒ

On Recombination-Induced Multiple and Simultaneous Coalescent Events

\mathcal {E} \mathcal {L}

Concurrent classification of EL ontologies

is a simple tractable Description Logic that features conjunctions and existential restrictions. Due to its favorable computational properties and relevance to existing ontologies, ℰℒ

Consequence-based reasoning beyond horn ontologies

\mathcal {E} \mathcal {L}

ELK Reasoner: Architecture and Evaluation.

has become the language of choice for terminological reasoning in biomedical applications, and has formed the basis of the OWL EL profile of the Web ontology language OWL. This paper describes ELK—a high performance reasoner for OWL EL ontologies—and details various aspects from theory to implementation that make ELK one of the most competitive reasoning systems for ℰℒ

Practical reasoning with nominals in the EL family of description logics

\mathcal {E} \mathcal {L}

Unchain My EL Reasoner

ontologies available today.

Elimination of Complex RIAs without Automata.

Coalescent theory deals with the dynamics of how sampled genetic material has spread through a population from a single ancestor over many generations and is ubiquitous in contemporary molecular population genetics. Inherent in most applications is a continuous-time approximation that is derived under the assumption that sample size is small relative to the actual population size. In effect, this precludes multiple and simultaneous coalescent events that take place in the history of large samples. If sequences do not recombine, the number of sequences ancestral to a large sample is reduced sufficiently after relatively few generations such that use of the continuous-time approximation is justified. However, in tracing the history of large chromosomal segments, a large recombination rate per generation will consistently maintain a large number of ancestors. This can create a major disparity between discrete-time and continuous-time models and we analyze its importance, illustrated with model parameters typical of the human genome. The presence of gene conversion exacerbates the disparity and could seriously undermine applications of coalescent theory to complete genomes. However, we show that multiple and simultaneous coalescent events influence global quantities, such as total number of ancestors, but have negligible effect on local quantities, such as linkage disequilibrium. Reassuringly, most applications of the coalescent model with recombination (including association mapping) focus on local quantities.