Efficient Solving of Time-dependent Answer Set Programs

Answer set programs with time predicates are useful to model systems whose properties depend on time, like for example gene regulatory networks. A state of such a system at time point t then corresponds to the literals of an answer set that are grounded with time constant t. An important task when modelling time-dependent systems is to find steady states from which the system\u27s behaviour does not change anymore. This task is complicated by the fact that it is typically not known in advance at what time steps these steady states occur. A brute force approach of estimating a time upper bound tmax and grounding and solving the program w.r.t. that upper bound leads to a suboptimal solving time when the estimate is too low or too high. In this paper we propose a more efficient algorithm for solving Markovian programs, which are time-dependent programs for which the next state depends only on the previous state. Instead of solving these Markovian programs for a long time interval {0,...,tmax}, we successively find answer sets of parts of the grounded program. Our approach guarantees the discovery of all steady states and cycles while avoiding unnecessary extra work

HyQue: evaluating hypotheses using Semantic Web technologies

<p>Abstract</p> <p>Background</p> <p>Key to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integrating large amounts of diverse information to compose and evaluate a hypothesis. Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks.</p> <p>Results</p> <p>We present HyQue, a Semantic Web tool for querying scientific knowledge bases with the purpose of evaluating user submitted hypotheses. HyQue features a knowledge model to accommodate diverse hypotheses structured as events and represented using Semantic Web languages (RDF/OWL). Hypothesis validity is evaluated against experimental and literature-sourced evidence through a combination of SPARQL queries and evaluation rules. Inference over OWL ontologies (for type specifications, subclass assertions and parthood relations) and retrieval of facts stored as Bio2RDF linked data provide support for a given hypothesis. We evaluate hypotheses of varying levels of detail about the genetic network controlling galactose metabolism in <it>Saccharomyces cerevisiae</it> to demonstrate the feasibility of deploying such semantic computing tools over a growing body of structured knowledge in Bio2RDF.</p> <p>Conclusions</p> <p>HyQue is a query-based hypothesis evaluation system that can currently evaluate hypotheses about the galactose metabolism in <it>S. cerevisiae</it>. Hypotheses as well as the supporting or refuting data are represented in RDF and directly linked to one another allowing scientists to browse from data to hypothesis and <it>vice versa.</it> HyQue hypotheses and data are available at <url>http://semanticscience.org/projects/hyque</url>.</p