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Maximizing output and recognizing autocatalysis in chemical reaction networks is npcomplete
 Journal of Systems Chemistry 2012
"... Background: A classical problem in metabolic design is to maximize the production of desired compound in a given chemical reaction network by appropriately directing the mass flow through the network. Computationally, this problem is addressed as a linear optimization problem over the “flux cone”. T ..."
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Background: A classical problem in metabolic design is to maximize the production of desired compound in a given chemical reaction network by appropriately directing the mass flow through the network. Computationally, this problem is addressed as a linear optimization problem over the “flux cone”. The prior construction of the flux cone is computationally expensive and no polynomialtime algorithms are known. Results: Here we show that the output maximization problem in chemical reaction networks is NPcomplete. This statement remains true even if all reactions are monomolecular or bimolecular and if only a single molecular species is used as influx. As a corollary we show, furthermore, that the detection of autocatalytic species, i.e., types that can only be produced from the influx material when they are present in the initial reaction mixture, is an NPcomplete computational problem. Conclusions: Hardness results on combinatorial problems and optimization problems are important to guide the development of computational tools for the analysis of metabolic networks in particular and chemical reaction networks in general. Our results indicate that efficient heuristics and approximate algorithms need to be employed for the analysis of large chemical networks since even conceptually simple flow problems are provably intractable.
Linear Connectivity Problems in Directed Hypergraphs
"... We introduce a notion of hyperconnection (formally denoted Lhyperpath) between nodes in a directed hypergraph and relate this notion to existing notions of hyperpaths in directed hypergraphs. We show that some interesting questions in problem domains such as secret transfer protocols and routing in ..."
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We introduce a notion of hyperconnection (formally denoted Lhyperpath) between nodes in a directed hypergraph and relate this notion to existing notions of hyperpaths in directed hypergraphs. We show that some interesting questions in problem domains such as secret transfer protocols and routing in packet filtered networks are basically questions about the existence of Lhyperpaths in directed hypergraphs. We study the computational complexity of problems related to Lhyperpaths and the Lcyclomatic number of directed hypergraphs (the minimum number of hyperedges that need to be deleted to make a directed hypergraph free of Lhypercycles). We prove that the Lhyperpath existence problem, the Lcyclomatic number problem, the minimum Lcyclomatic set problem, and the minimal Lcyclomatic, Πp, and DP, respectively. set problem are each complete for the complexity class NP, Σ p 2 1
A.: OneQL: An Ontologybased Architecture to Efficiently Query
 Resources on the Semantic Web. In: The 5th International Workshop on Scalable Semantic Web Knowledge Base Systems at ISWC. (2009
"... Abstract. The widespread explosion of Web accessible resources has led to new problems on the traditional tasks of query evaluation and efficient data access. With this is mind, we have developed the ontologybased OneQL system which provides optimization and query evaluation techniques to scale up ..."
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Abstract. The widespread explosion of Web accessible resources has led to new problems on the traditional tasks of query evaluation and efficient data access. With this is mind, we have developed the ontologybased OneQL system which provides optimization and query evaluation techniques to scale up to large RDF/RDFS documents and complex queries, i.e., queries of any shape and with a large number of triple patterns. Efficiency of OneQL relies on the following components: – Query optimization and evaluation techniques that focus on cost models to estimate the execution time of a plan, and on searching the space of plans of any shape, i.e., bushy plans can be generated according to their estimated cost. – Bhyper: A directed hypergraphbased representation of RDF documents to directly access triples that share the same subject and property values, or the same property and object values. We report on the quality of the developed strategies, and have observed that implementing RDF documents with Bhyper and producing low estimated cost bushy plans, can speed up the evaluation time by up to four orders of magnitude. 1
A Survey on Hypergraph Products
"... Abstract. A surprising diversity of different products of hypergraphs have been discussed in the literature. Most of the hypergraph products can be viewed as generalizations of one of the four standard graph products. The most widely studied variant, the socalled square product, does not have this ..."
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Abstract. A surprising diversity of different products of hypergraphs have been discussed in the literature. Most of the hypergraph products can be viewed as generalizations of one of the four standard graph products. The most widely studied variant, the socalled square product, does not have this property, however. Here we survey the literature on hypergraph products with an emphasis on comparing the alternative generalizations of graph products and the relationships among them. In this context the socalled 2sections and L2sections are considered. These constructions are closely linked to related colored graph structures that seem to be a useful tool for the prime factor decompositions w.r.t. specific hypergraph products. We summarize the current knowledge on the propagation of hypergraph invariants under the different hypergraph multiplications. While the overwhelming majority of the material concerns finite (undirected) hypergraphs, the survey also covers a summary of the few results on products of infinite and directed hypergraphs.
Biomedical Literature Mining with Transitive Closure and Maximum Network Flow
"... Is approved by the final examining committee: ..."
Feature Diagrams: a Formalization and extensible Metamodel Proposals
"... Abstract: Feature models are used to represent the variability and commonality of software product lines, and permit the configuration of specific applications. However, universally accepted definitions of feature and feature diagrams are missing. This paper proposes the use of hypergraphs to integr ..."
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Abstract: Feature models are used to represent the variability and commonality of software product lines, and permit the configuration of specific applications. However, universally accepted definitions of feature and feature diagrams are missing. This paper proposes the use of hypergraphs to integrate the different versions of these concepts in an extensible characterization. The definition, validation and selection of feature configurations are based on hypergraph properties and existing algorithms. Once the formalism is stated, the definition of a feature metamodel is straightforward and a set of modeling tools, compatible with the different flavors of feature diagrams, can be readily built. Finally, configuration and transformation of feature diagrams into UML models are defined as algebraic and QVT transformations.
A Formal Model Of SystemC Components Using
"... Abstract — In this paper, we introduce a new mathematical structure: fractal hypergraph. Due to the hierarchical and compositional nature of fractal hypergraphs, representations based on fractal hypergraphs can capture and abstract the objectoriented nature of SystemC. We propose a formal semantics ..."
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Abstract — In this paper, we introduce a new mathematical structure: fractal hypergraph. Due to the hierarchical and compositional nature of fractal hypergraphs, representations based on fractal hypergraphs can capture and abstract the objectoriented nature of SystemC. We propose a formal semantics of SystemC components based on fractal hypergraphs that has already be used in a formal debugger of SystemC components.
Dashboard byExample: A Hypergraphbased approach to Ondemand Data warehousing systems
"... Abstract—The usefulness and ease of use of dashboards are essential elements in supporting interactive queries in data warehousing systems, as they provide the analysts the view of critical business metrics that reflect the business performance. However, ondemand dashboard development presents a ch ..."
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Abstract—The usefulness and ease of use of dashboards are essential elements in supporting interactive queries in data warehousing systems, as they provide the analysts the view of critical business metrics that reflect the business performance. However, ondemand dashboard development presents a challenging task for linking semantic equivalent data facts, discovering structural dependencies between and within data sources. In this paper, we introduce an improved approach for dashboard development that is supported by byexample framework and semanticbased data linkage management. In this Dashboardbyexample (DBE) framework, hypergraphbased techniques are adopted to acquire knowledge from heterogeneous and disparate data into homogeneous ontological clusters and partitions. Moreover, the use of hypergraphguided data linkage provides multiple perspectives on the knowledge space, supporting interaction model to explore, contextualize and aggregate the data depending on the application needs. The applicability of our approach is discussed in a case study scenario, highlight the flexibility and efficiency in handling ondemand requirements in data warehousing systems. Index Terms—Data warehousing, byexample, query processing, dashboard, hypergraphbased I.