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114
Efficient Haplotype Inference with Answer Set Programming
"... Identifying maternal and paternal inheritance is essential to be able to find the set of genes responsible for a particular disease. However, due to technological limitations, we have access to genotype data (genetic makeup of an individual), and determining haplotypes (genetic makeup of the parents ..."
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Identifying maternal and paternal inheritance is essential to be able to find the set of genes responsible for a particular disease. However, due to technological limitations, we have access to genotype data (genetic makeup of an individual), and determining haplotypes (genetic makeup of the parents) experimentally is a costly and time consuming procedure. With these biological motivations, we study a computational problem, called Haplotype Inference by Pure Parsimony (HIPP), that asks for the minimal number of haplotypes that form a given set of genotypes. HIPP has been studied using integer linear programming, branch and bound algorithms, SATbased algorithms, or pseudoboolean optimization methods. We introduce a new approach to solving HIPP, using Answer Set Programming (ASP). According to our experiments with a large number of problem instances (some automatically generated and some real), our ASPbased approach solves the most number of problems compared with other approaches. Due to the expressivity of the knowledge representation language of ASP, our approach allows us to solve variations of HIPP, e.g., with additional domain specific information, such as patterns/parts of haplotypes observed for some gene family, or with some missing genotype information. In this sense, the ASPbased approach is more general than the existing approaches to haplotype inference.
Solution Enumeration for Projected Boolean Search Problems
"... Abstract. Many realworld problems require the enumeration of all solutions of combinatorial search problems, even though this is often infeasible in practice. However, not always all parts of a solution are needed. We are thus interested in projecting solutions to a restricted vocabulary. Yet, the ..."
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Abstract. Many realworld problems require the enumeration of all solutions of combinatorial search problems, even though this is often infeasible in practice. However, not always all parts of a solution are needed. We are thus interested in projecting solutions to a restricted vocabulary. Yet, the adaption of Boolean constraint solving algorithms turns out to be nonobvious provided one wants a repetitionfree enumeration in polynomial space. We address this problem and propose a new algorithm computing projective solutions. Although we have implemented our approach in the context of Answer Set Programming, it is readily applicable to any solver based on modern Boolean constraint technology. 1
Finding similar or diverse solutions in answer set programming
 IN: PROC. OF ICLP
, 2009
"... 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 diver ..."
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Cited by 7 (5 self)
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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 of our methods in phylogeny reconstruction.
On the Implementation of Weight Constraint Rules in ConflictDriven ASP Solvers
"... Abstract. We present the first comprehensive approach to integrating cardinality and weight rules into conflictdriven ASP solving. We begin with a uniform, constraintbased characterization of answer sets in terms of nogoods. This provides the semantic underpinnings of our approach in fixing all ne ..."
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Cited by 7 (4 self)
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Abstract. We present the first comprehensive approach to integrating cardinality and weight rules into conflictdriven ASP solving. We begin with a uniform, constraintbased characterization of answer sets in terms of nogoods. This provides the semantic underpinnings of our approach in fixing all necessary inferences that must be supported by an appropriate implementation. We then provide key algorithms detailing the salient features needed for implementing weight constraint rules. This involves a sophisticated unfounded set checker as well as an extended propagation algorithm along with the underlying data structures. We implemented our techniques within the ASP solver clasp and demonstrate their effectiveness by an experimental evaluation. 1
Decomposition of Distributed Nonmonotonic MultiContext Systems ∗
"... MultiContext Systems (MCS) are formalisms that enable the interlinkage of single knowledge bases, called contexts, via bridge rules. Recently, the evaluation of heterogeneous, nonmonotonic MCS was considered in DaoTran et al. (2010), where a fully distributed algorithm was described. In this paper ..."
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Cited by 6 (4 self)
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MultiContext Systems (MCS) are formalisms that enable the interlinkage of single knowledge bases, called contexts, via bridge rules. Recently, the evaluation of heterogeneous, nonmonotonic MCS was considered in DaoTran et al. (2010), where a fully distributed algorithm was described. In this paper, we continue this line of work and present a decomposition technique for MCS which analyzes the topology of an MCS. It applies pruning techniques to get economically small representations of context dependencies. Orthogonal to this, we characterize minimal interfaces for information exchange between contexts, such that data transmissions can be minimized. We then present a novel evaluation algorithm that operates on a query plan which is compiled with topology pruning and interface minimization. The effectiveness of the optimization techniques is demonstrated by a prototype implementation, which uses an offtheshelf SAT solver and shows encouraging experimental results.
Advanced Preprocessing for Answer Set Solving
"... Abstract. We introduce the first substantial approach to preprocessing in the context of answer set solving. The idea is to simplify a logic program while identifying equivalences among its relevant constituents. These equivalences are then used for building a compact representation of the program ( ..."
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Abstract. We introduce the first substantial approach to preprocessing in the context of answer set solving. The idea is to simplify a logic program while identifying equivalences among its relevant constituents. These equivalences are then used for building a compact representation of the program (in terms of Boolean constraints). We implemented our approach as well as a SATbased technique to reduce Boolean constraints. This allows us to empirically analyze both preprocessing types and to demonstrate their computational impact. 1
Representing Biological Processes in Modular Action Language ALM
 Proceedings of AAAI 2011 Spring Symposium on Common Sense Reasoning
, 2011
"... This paper presents the formalization of a biological process, cell division, in modular action language ALM. We show how the features of ALM—modularity, separation between an uninterpreted theory and its interpretation—lead to a simple and elegant solution that can be used in answering questions fr ..."
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This paper presents the formalization of a biological process, cell division, in modular action language ALM. We show how the features of ALM—modularity, separation between an uninterpreted theory and its interpretation—lead to a simple and elegant solution that can be used in answering questions from biology textbooks.
A case study of expressively constrainable level design automation tools for a puzzle game
 In Proceedings of the Conference on Foundations of Digital Games
, 2012
"... Some problems in procedural content generation for games involve hard constraints (e.g. that a generated puzzle is necessarily solvable). Common techniques for generator design lack a way to specify crisp (yes/no) constraints on what counts as a valid content artifact and guarantee these constraints ..."
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Cited by 5 (4 self)
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Some problems in procedural content generation for games involve hard constraints (e.g. that a generated puzzle is necessarily solvable). Common techniques for generator design lack a way to specify crisp (yes/no) constraints on what counts as a valid content artifact and guarantee these constraints are satisfied in the generator’s output. In this paper we present two independent implementations of three diverse level design automation tools for the popular online educational game Refraction. All of the systems guarantee key properties of their output. Applying a constraintfocused generator design perspective in depth, we found that even emergent aesthetic style properties were straightforward to directly control. Our results with Refraction provide further concrete evidence for the claim that the expressive power of constraints and the ease with which they can be incorporated into suitably designed generative processes makes them a powerful tool for producing reliablycontrollable generators for game content.
Extended ASP Tableaux and Rule Redundancy in Normal Logic Programs
 Proceedings of International Conference on Logic Programming, 2007
, 1951
"... Abstract. We introduce an extended tableau calculus for answer set programming (ASP). The proof system is based on the ASP tableaux defined in [Gebser&Schaub, ICLP 2006], with an added extension rule. We investigate the power of Extended ASP Tableaux both theoretically and empirically. We study the ..."
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Cited by 4 (1 self)
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Abstract. We introduce an extended tableau calculus for answer set programming (ASP). The proof system is based on the ASP tableaux defined in [Gebser&Schaub, ICLP 2006], with an added extension rule. We investigate the power of Extended ASP Tableaux both theoretically and empirically. We study the relationship of Extended ASP Tableaux with the Extended Resolution proof system defined by Tseitin for clause sets, and separate Extended ASP Tableaux from ASP Tableaux by giving a polynomial length proof of a family of normal logic programs {Πn} for which ASP Tableaux has exponential length minimal proofs with respect to n. Additionally, Extended ASP Tableaux imply interesting insight into the effect of program simplification on the length of proofs in ASP. Closely related to Extended ASP Tableaux, we empirically investigate the effect of redundant rules on the efficiency of ASP solving. 1
Computing Loops with at Most One External Support Rule for Disjunctive Logic Programs
"... Abstract. We extend to disjunctive logic programs our previous work on computing loop formulas of loops with at most one external support. We show that for these logic programs, loop formulas of loops with no external support can be computed in polynomial time, and if the given program has no constr ..."
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Cited by 4 (1 self)
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Abstract. We extend to disjunctive logic programs our previous work on computing loop formulas of loops with at most one external support. We show that for these logic programs, loop formulas of loops with no external support can be computed in polynomial time, and if the given program has no constraints, an iterative procedure based on these formulas, the program completion, and unit propagation computes the least fixed point of a simplification operator used by DLV. We also relate loops with no external supports to the unfounded sets and the wellfounded semantics of disjunctive logic programs by Wang and Zhou. However, the problem of computing loop formulas of loops with at most one external support rule is NPhard for disjunctive logic programs. We thus propose a polynomial algorithm for computing some of these loop formulas, and show experimentally that this polynomial approximation algorithm can be effective in practice. 1