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OBJECTIVES
To quantify semantic inconsistency in UMLS concepts from the perspective of their hierarchical relations and to show through examples how semantically-inconsistent concepts can help reveal erroneous synonymy relations.
METHODS
Inconsistency is defined in reference to concepts from the UMLS Metathesaurus. Consistency is evaluated by comparing… (More)

For some computational problems (e.g., product configuration, planning, diagnosis, query answering, phylogeny reconstruction) computing a set of similar/diverse solutions may be desirable for better decision-making. With this motivation, we have studied several decision/optimization versions of this problem in the context of Answer Set Programming (ASP),… (More)

We study finding similar or diverse solutions of a given computational problem, in answer set programming, and introduce offline methods and online methods to compute them using answer set solvers. We analyze the computational complexity of some problems that are related to finding similar or diverse solutions , and show the applicability and effectiveness… (More)

We present new methods to efficiently answer complex queries over biomedical ontologies and databases considering the relevant parts of these knowledge resources, and to generate shortest explanations to justify these answers. Both algorithms rely on the high-level representation and efficient solvers of Answer Set Programming. We apply these algorithms to… (More)

- Mehmet Çelik, Halit Erdoğan, Fırat Tahaoğlu, Tansel Uras, Esra Erdem
- 2009

We study two declarative programming languages namely Answer Set Programming (ASP) and Constraint Programming (CP) on four grid puzzles: Akari, Kakuro, Nurikabe, and Heyawake. We represent these problems in both formalisms in a systematic way and compute their solutions using ASP system Clasp and CP system Comet. We compare the ASP approach with the CP… (More)

For some problems with many solutions, like planning and phylogeny reconstruction, one way to compute more desirable solutions is to assign weights to solutions, and then pick the ones whose weights are over (resp. below) a threshold. This paper studies computing weighted solutions to such problems in Answer Set Programming. We investigate two sorts of… (More)

We introduce a new method to find semantic inconsistencies (i.e., concepts with erroneous synonymity) in the Unified Medical Language System (UMLS). The idea is to identify the inconsistencies by comparing the semantic groups of hierarchically-related concepts using Answer Set Programming. With this method, we identified several inconsistent concepts in… (More)

We describe a software system, called BIOQUERY-ASP, that finds answers and generates explanations to complex biomedical queries over the avail

Recent advances in health and life sciences have led to generation of a large amount of data. To facilitate access to its desired parts, such a big mass of data has been represented in structured forms, like biomedical ontologies. On the other hand, representing ontologies in a formal language, constructing them independently from each other and storing… (More)

- Halit Erdoğan, Mehmet Serkan Apaydın
- 2010

—Nuclear Magnetic Resonance (NMR 1) spectroscopy is an important experimental technique that allows one to study protein structure in solution. An important challenge in NMR protein structure determination is the assignment of NMR peaks to corresponding nuclei. In structure-based assignment (SBA), the aim is to perform the assignments with the help of a… (More)