HAPLO-ASP: Haplotype Inference Using Answer Set Programming

Erdem, Esra; Erdem, Ozan; Ture, Ferhan

doi:10.1007/978-3-642-04238-6_60

Cited by 18 publications

(9 citation statements)

References 12 publications

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“…A recent contribution to the HIPP problem is the HAPLO-ASP solver (Erdem and Türe 2008), based on Answer Set Programming (ASP). ASP is a declarative programming paradigm that provides a high-level language to represent combinatorial search problems, and efficient solvers to compute solutions for them.…”

Section: Answer Set Programming Model: Haplo-aspmentioning

confidence: 99%

Haplotype inference with pseudo-Boolean optimization

et al. 2009

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The fast development of sequencing techniques in the recent past has required an urgent development of efficient and accurate haplotype inference tools. Besides being a crucial issue in genetics, haplotype inference is also a challenging computational problem. Among others, pure parsimony is a viable modeling approach to solve the problem of haplotype inference and also an interesting NP-hard problem in itself. Recently, the introduction of SAT-based methods, including pseudo-Boolean optimization (PBO) methods, has produced very efficient solvers. This paper provides a detailed description of RPoly, a PBO approach for the haplotype inference by pure parsimony (HIPP) problem. Moreover, an extensive evaluation of existent HIPP solvers, on a comprehensive set of instances, confirms that RPoly is currently the most efficient and robust HIPP approach.

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Section: Answer Set Programming Model: Haplo-aspmentioning

confidence: 99%

Haplotype inference with pseudo-Boolean optimization

et al. 2009

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“…Similar and often much more refined techniques can be found in the literature, however, frequently in different research areas, like (deductive) databases, traditional logic programming, automated planning, etc. As a proof-of-concept, we have implemented both techniques in the prototypical grounder pyngo 8 [29] and conducted some preliminary experiments. First and foremost, it is worth mentioning that both techniques are useless for common benchmarks because most of them have been designed by experts in ASP.…”

Section: Non-ground Pre-processingmentioning

confidence: 99%

“…ASP allows for solving all search problems in NP (and NP NP ) in a uniform way, offering more succinct problem representations than propositional logic [3]. Meanwhile, ASP has been used in many application areas, among them, product configuration [4], decision support for NASA shuttle controllers [5], composition of Renaissance music [6], synthesis of multiprocessor systems [7], reasoning tools in systems biology [8,9], team-building [10], and many more. 1 The success story of ASP has its roots in the early availability of ASP solvers, beginning with the smodels system [11], followed by dlv [12], SAT-based ASP solvers, like assat [13] and cmodels [14], and the conflict-driven ASP solver clasp, demonstrating the performance and versatility of ASP solvers by winning first places at international competitions like ASP'09, PB'09, and SAT'09.…”

Section: Introductionmentioning

confidence: 99%

Challenges in Answer Set Solving

Gebser

Kaminski

Kaufmann

et al. 2011

Lecture Notes in Computer Science

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Michael Gelfond's application of Answer Set Programming (ASP) in the context of NASA's space shuttle has opened the door of the ivory tower. His project has not only given our community self-confidence and served us as a reference for grant agencies and neighboring fields, but ultimately it helped freeing the penguins making them exclaim "Yes, we can [fly] !". The community has taken up this wonderful assist to establish ASP as a prime tool for declarative problem solving in the area of Knowledge Representation and Reasoning. Despite this success, however, ASP has not yet attracted broad attention outside this area. This paper aims at identifying some current challenges that our field has to overcome in the mid-run to ultimately become a full-fledged technology in Informatics. Affiliated with the

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“…More recent work addressed using local search algorithms for improving lower bounds in SAT-based approaches for the HIPP problem [13]. Another sucessful approch used answer set programming (ASP) [4]. Similarly to SHIPs, this ASP-based approach uses a SAT solver as a search engine.…”

Section: Figure 3 Boolean Variables Used In Shipsmentioning

confidence: 99%