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Esra Erdem

Publications and source records attributed to Esra Erdem.

27 records · Page 2Linked to original sources

Generating Explanations for Biomedical Queries

We introduce novel mathematical models and algorithms to generate (shortest or k different) explanations for biomedical queries, using answer set programming. We implement these algorithms and integrate them in BIOQUERY-ASP. We illustrate the usefulness of these methods with some complex biomedical queries related to drug discovery, over the biomedical knowledge resources PHARMGKB, DRUGBANK, BIOGRID, CTD, SIDER, DISEASE ONTOLOGY and ORPHADATA. To appear in Theory and Practice of Logic Programming (TPLP).

cs.AI↗

Levels of Integration between Low-Level Reasoning and Task Planning

We provide a systematic analysis of levels of integration between discrete high-level reasoning and continuous low-level reasoning to address hybrid planning problems in robotics. We identify four distinct strategies for such an integration: (i) low-level checks are done for all possible cases in advance and then this information is used during plan generation, (ii) low-level checks are done exactly when they are needed during the search for a plan, (iii) first all plans are computed and then infeasible ones are filtered, and (iv) by means of replanning, after finding a plan, low-level checks identify whether it is infeasible or not; if it is infeasible, a new plan is computed considering the results of previous low- level checks. We perform experiments on hybrid planning problems in robotic manipulation and legged locomotion domains considering these four methods of integration, as well as some of their combinations. We analyze the usefulness of levels of integration in these domains, both from the point of view of computational efficiency (in time and space) and from the point of view of plan quality relative to its feasibility. We discuss advantages and disadvantages of each strategy in the light of experimental results and provide some guidelines on choosing proper strategies for a given domain.

cs.RO↗

Integration of 3D Object Recognition and Planning for Robotic Manipulation: A Preliminary Report

We investigate different approaches to integrating object recognition and planning in a tabletop manipulation domain with the set of objects used in the 2012 RoboCup@Work competition. Results of our preliminary experiments show that, with some approaches, close integration of perception and planning improves the quality of plans, as well as the computation times of feasible plans.

cs.AI↗

ReAct! An Interactive Tool for Hybrid Planning in Robotics

We present ReAct!, an interactive tool for high-level reasoning for cognitive robotic applications. ReAct! enables robotic researchers to describe robots' actions and change in dynamic domains, without having to know about the syntactic and semantic details of the underlying formalism in advance, and solve planning problems using state-of-the-art automated reasoners, without having to learn about their input/output language or usage. In particular, ReAct! can be used to represent sophisticated dynamic domains that feature concurrency, indirect effects of actions, and state/transition constraints. It allows for embedding externally defined calculations (e.g., checking for collision-free continuous trajectories) into representations of hybrid domains that require a tight integration of (discrete) high-level reasoning with (continuous) geometric reasoning. ReAct! also enables users to solve planning problems that involve complex goals. Such variety of utilities are useful for robotic researchers to work on interesting and challenging domains, ranging from service robotics to cognitive factories. ReAct! provides sample formalizations of some action domains (e.g., multi-agent path planning, Tower of Hanoi), as well as dynamic simulations of plans computed by a state-of-the-art automated reasoner (e.g., a SAT solver or an ASP solver).

cs.AI↗

Finding Similar/Diverse Solutions in Answer Set Programming

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 studied several decision/optimization versions of this problem in the context of Answer Set Programming (ASP), analyzed their computational complexity, and introduced offline/online methods to compute similar/diverse solutions of such computational problems with respect to a given distance function. All these methods rely on the idea of computing solutions to a problem by means of finding the answer sets for an ASP program that describes the problem. The offline methods compute all solutions in advance using the ASP formulation of the problem with an ASP solver, like Clasp, and then identify similar/diverse solutions using clustering methods. The online methods compute similar/diverse solutions following one of the three approaches: by reformulating the ASP representation of the problem to compute similar/diverse solutions at once using an ASP solver; by computing similar/diverse solutions iteratively (one after other) using an ASP solver; by modifying the search algorithm of an ASP solver to compute similar/diverse solutions incrementally. We modified Clasp to implement the last online method and called it Clasp-NK. In the first two online methods, the given distance function is represented in ASP; in the last one it is implemented in C++. We showed the applicability and the effectiveness of these methods on reconstruction of similar/diverse phylogenies for Indo-European languages, and on several planning problems in Blocks World. We observed that in terms of computational efficiency the last online method outperforms the others; also it allows us to compute similar/diverse solutions when the distance function cannot be represented in ASP.

cs.AI↗

Querying Biomedical Ontologies in Natural Language using Answer Set

In this work, we develop an intelligent user interface that allows users to enter biomedical queries in a natural language, and that presents the answers (possibly with explanations if requested) in a natural language. We develop a rule layer over biomedical ontologies and databases, and use automated reasoners to answer queries considering relevant parts of the rule layer.

cs.AI↗

Temporal Phylogenetic Networks and Logic Programming

The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities are in contact, and also that a contact is only possible when the languages are spoken at the same time. We show how computational methods of answer set programming and constraint logic programming can be used to generate plausible conjectures about contacts between prehistoric linguistic communities, and illustrate our approach by applying it to the evolutionary history of Indo-European languages. To appear in Theory and Practice of Logic Programming (TPLP).

cs.LO↗

Tight Logic Programs

This note is about the relationship between two theories of negation as failure -- one based on program completion, the other based on stable models, or answer sets. Francois Fages showed that if a logic program satisfies a certain syntactic condition, which is now called ``tightness,'' then its stable models can be characterized as the models of its completion. We extend the definition of tightness and Fages' theorem to programs with nested expressions in the bodies of rules, and study tight logic programs containing the definition of the transitive closure of a predicate.

cs.AI↗

Fages' Theorem and Answer Set Programming

We generalize a theorem by Francois Fages that describes the relationship between the completion semantics and the answer set semantics for logic programs with negation as failure. The study of this relationship is important in connection with the emergence of answer set programming. Whenever the two semantics are equivalent, answer sets can be computed by a satisfiability solver, and the use of answer set solvers such as smodels and dlv is unnecessary. A logic programming representation of the blocks world due to Ilkka Niemelae is discussed as an example.

cs.AI↗