2011
DOI: 10.1609/icaps.v21i1.13485
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The Minimal Seed Set Problem

Abstract: This paper defines and studies a new, interesting, and challenging benchmark problem that originates in systems biology. The minimal seed-set problem is defined as follows: given a description of the metabolic reactions of an organism, characterize the minimal set of nutrients with which it could synthesize all nutrients it is capable of synthesizing. Current methods used in systems biology yield only approximate solutions. And although it is natural to cast it as a planning problem, current optimal planners a… Show more

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Cited by 8 publications
(10 citation statements)
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“…We also tried the algorithm on the minimal seed-set problem. It solves all instances, in marginally less time (2/3 on average) than that reported by Gefen and Brafman (2011) for their domain-specific algorithm.…”
Section: Results and Conclusionmentioning
confidence: 75%
See 1 more Smart Citation
“…We also tried the algorithm on the minimal seed-set problem. It solves all instances, in marginally less time (2/3 on average) than that reported by Gefen and Brafman (2011) for their domain-specific algorithm.…”
Section: Results and Conclusionmentioning
confidence: 75%
“…Delete-free problems of interest in their own right are also starting to appear. An example originating in systems biology is the minimal seed-set problem (Gefen and Brafman 2011), which challenges both classical optimisation methods and optimal planners. Moreover, recent work on translating NP problems into an NP fragment of classical planning opens the possibility that optimal delete-free planning could directly be used to solve a wide range of NP-hard problems (Porco, Machado, and Bonet 2011).…”
Section: Introductionmentioning
confidence: 99%
“…All models also use some of the preprocessing methods presented in (Imai and Fukunaga 2015). These methods are 1) finding fact landmarks (Gefen and Brafman 2011) and adding them to the goal conditions; 2) doing action relevance analysis and removing non-relevant actions; and 3) dominated action elimination. The implementation of these methods was part of the base HSP* package.…”
Section: Resultsmentioning
confidence: 99%
“…That is because there exist delete-free planning tasks that are of interest for the planning community. Examples are the minimal seed-set problem (Gefen and Brafman 2011), and the problem of determining join orders in relational database query plan generation (Robinson, McIlraith, and Toman 2014).…”
Section: Introductionmentioning
confidence: 99%
“…Thus, any method that effectively solves delete-free planning problems has immediate use in standard planning. Finally, a number of interesting, naturally delete-free planning problems (Gefen and Brafman 2011;Gallo et al 1993) cannot be solved by standard planning techniques.…”
Section: Introductionmentioning
confidence: 99%