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18
Computing knockout strategies in metabolic networks
 JOURNAL OF COMP. BIOLOGY
, 2008
"... Given a metabolic network in terms of its metabolites and reactions, our goal is to efficiently compute the minimal knock out sets of reactions required to block a given behaviour. We describe an algorithm which improves the computation of these knock out sets when the elementary modes (minimal fun ..."
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Given a metabolic network in terms of its metabolites and reactions, our goal is to efficiently compute the minimal knock out sets of reactions required to block a given behaviour. We describe an algorithm which improves the computation of these knock out sets when the elementary modes (minimal functional subsystems) of the network are given. We also describe an algorithm which computes both the knock out sets and the elementary modes containing the blocked reactions directly from the description of the network and whose worstcase computational complexity is better than the algorithms currently in use for these problems. Computational results are included.
Semantic composition of lecture subparts for a personalized elearning
 In Proc. of ESWC 2007
, 2007
"... Abstract. In this paper we propose an algorithm for personalized learning based on a user’s query and a repository of lecture subparts —i.e., learning objects — both are described in a subset of OWLDL. It works in two steps. First, it retrieves lecture subparts that cover as much as possible the u ..."
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Cited by 7 (1 self)
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Abstract. In this paper we propose an algorithm for personalized learning based on a user’s query and a repository of lecture subparts —i.e., learning objects — both are described in a subset of OWLDL. It works in two steps. First, it retrieves lecture subparts that cover as much as possible the user’s query. The solution is based on the concept covering problem for which we present a modified algorithm. Second, an appropriate sequence of lecture subparts is generated. Indeed, the different lecture subparts are only reachable when a given prerequisite is fulfilled, i.e., the learner must have a minimal background knowledge to be able to assimilate the requested learning object. Therefore, our algorithm takes into account the user’s knowledge to generate a personalized lecture composition and suggests a flow of learning objects to the user. 1
Lower bounds for three algorithms for transversal hypergraph generation
 Discrete Appl. Math
"... Abstract. The computation of all minimal transversals of a given hypergraph in outputpolynomial time is a long standing open question known as the transversal hypergraph generation. One of the first attempts on this problem—the sequential method [Ber89]—is not outputpolynomial as was shown by Takat ..."
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Cited by 6 (2 self)
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Abstract. The computation of all minimal transversals of a given hypergraph in outputpolynomial time is a long standing open question known as the transversal hypergraph generation. One of the first attempts on this problem—the sequential method [Ber89]—is not outputpolynomial as was shown by Takata [Tak02]. Recently, three new algorithms improving the sequential method were published and experimentally shown to perform very well in practice [BMR03, DL05, KS05]. Nevertheless, a theoretical worstcase analysis has been pending. We close this gap by proving lower bounds for all three algorithms. Thereby, we show that none of them is outputpolynomial. 1
A Data Mining Formalization to Improve Hypergraph
 Minimal Transversal Computation”, Fundamental Informaticae
, 2007
"... Abstract. Finding hypergraph transversals is a major algorithmic issue which was shown having many connections with the data mining area. In this paper, by defining a new Galois connection, we show that this problem is closely related to the mining of the socalled condensed representations of freq ..."
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Abstract. Finding hypergraph transversals is a major algorithmic issue which was shown having many connections with the data mining area. In this paper, by defining a new Galois connection, we show that this problem is closely related to the mining of the socalled condensed representations of frequent patterns. This data mining formalization enables us to benefit from efficient algorithms dedicated to the extraction of condensed representations. More precisely, we demonstrate how it is possible to use the levelwise framework to improve the hypergraph minimal transversal computation by exploiting an antimonotone constraint to safely prune the search space. We propose a new algorithm MTMINER to extract minimal transversals and provide experiments showing that our method is efficient in practice.
On the fixedparameter tractability of the equivalence test of monotone normal forms
 Information Processing Letters
"... We consider the problem Monet—given two monotone formulas ϕ in DNF and ψ in CNF, decide whether they are equivalent. While Monet is probably not coNPhard, it is a long standing open question whether it has a polynomial time algorithm and thus belongs to P. In this paper we examine the parameterized ..."
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We consider the problem Monet—given two monotone formulas ϕ in DNF and ψ in CNF, decide whether they are equivalent. While Monet is probably not coNPhard, it is a long standing open question whether it has a polynomial time algorithm and thus belongs to P. In this paper we examine the parameterized complexity of Monet. We show that Monet is in FPT by giving fixedparameter algorithms for different parameters.
On Berge multiplication for monotone boolean dualization
"... Given the prime CNF representation φ of a monotone Boolean function f: {0, 1} n ↦ → {0, 1}, the dualization problem calls for finding the corresponding prime DNF representation ψ of f. A very simple method (called Berge multiplication [3, Page 52–53]) works by multiplying out the clauses of φ from ..."
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Given the prime CNF representation φ of a monotone Boolean function f: {0, 1} n ↦ → {0, 1}, the dualization problem calls for finding the corresponding prime DNF representation ψ of f. A very simple method (called Berge multiplication [3, Page 52–53]) works by multiplying out the clauses of φ from left to right in some order, simplifying whenever possible using the absorption law. We show that for any monotone CNF φ, Berge multiplication can be done in subexponential time, and for many interesting subclasses of monotone CNF’s such as CNF’s with bounded size, bounded degree, bounded intersection, bounded conformality, and readonce formula, it can be done in polynomial or quasipolynomial time.
Masking Patterns in Sequences: A New Class of Motif Discovery with Don’t Cares
, 2009
"... In this paper, we introduce a new notion of motifs, called masks, that succinctly represent the repeated patterns for an input sequence T of n symbols drawn from an alphabet Σ. We show how to build the set of all maximal masks of length L and quorum q, in O(2 L n) time and space in the worst case. W ..."
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In this paper, we introduce a new notion of motifs, called masks, that succinctly represent the repeated patterns for an input sequence T of n symbols drawn from an alphabet Σ. We show how to build the set of all maximal masks of length L and quorum q, in O(2 L n) time and space in the worst case. We analytically show that our algorithms perform better than constanttime enumerating and checking all the potential (Σ  + 1) L candidate patterns in T after a polynomialtime preprocessing of T. Our algorithms are also cachefriendly, attaining O(2 L sort(n)) block transfers, where sort(n) is the cache oblivious complexity of sorting n items. Key words: Motif inference, motifs with don’t care, motif partial order, motifs with masks. 1.
Experimental comparison of the two FredmanKhachiyanalgorithms
"... Abstract. We experimentally compare the two algorithms A and B by Fredman and Khachiyan [FK96] for the problem Monet—given two monotone Boolean formulas ϕ in DNF and ψ in CNF, decide whether they are equivalent. Currently, algorithm B is the Monet algorithm with the best known worstcase performance ..."
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Abstract. We experimentally compare the two algorithms A and B by Fredman and Khachiyan [FK96] for the problem Monet—given two monotone Boolean formulas ϕ in DNF and ψ in CNF, decide whether they are equivalent. Currently, algorithm B is the Monet algorithm with the best known worstcase performance. However, there is no experimental evaluation of its practical performance yet, mainly due to the following two reasons. Firstly, implementation of algorithm B is usually considered to be more involved than for algorithm A. Secondly and probably more importantly, there is the assumption that the operations performed by algorithm B to ensure recursion on smaller subproblems do only pay off theoretically. In this paper, we contrast this assumption by experimentally showing algorithm B to be competitive and even superior to algorithm A on many instances. 1
POLYNOMIAL DELAY ALGORITHM FOR LISTING MINIMAL EDGE DOMINATING SETS IN GRAPHS
"... Abstract. A hypergraph is a pair pV, Eq where V is a finite set and E Ď 2V is called the set of hyperedges. An outputpolynomial algorithm for C Ď 2V is an algorithm that lists without repetitions all the elements of C in time polynomial in the sum of the size of H and the accumulated size of all t ..."
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Abstract. A hypergraph is a pair pV, Eq where V is a finite set and E Ď 2V is called the set of hyperedges. An outputpolynomial algorithm for C Ď 2V is an algorithm that lists without repetitions all the elements of C in time polynomial in the sum of the size of H and the accumulated size of all the elements in C. Whether there exists an outputpolynomial algorithm to list all the inclusionwise minimal hitting sets of hyperedges of a given hypergraph (the TransEnum problem) is a fifty years old open problem, and up to now there are few tractable examples of hypergraph classes. An inclusionwise minimal hitting set of the closed neighborhoods of a graph is called a minimal dominating set. A closed neighborhood of a vertex is the set composed of the vertex itself with all its neighbors. It is known that there exists an outputpolynomial algorithm for the set of minimal dominating sets in graphs if and only if there is one for the minimal hitting sets in hypergraphs. Hoping this equivalence can help to get new insights in the TransEnum problem, it is natural to look at graph classes. It was proved independently and with different techniques in [Golovach et al. ICALP 2013] and [Kanté et al. ISAAC 2012] that there exists an incremental outputpolynomial algorithm for the set of minimal edge dominating sets in graphs (i.e. minimal dominating sets in line graphs). We provide the first polynomial delay and polynomial space algorithm that lists all the minimal edge dominating sets in graphs, answering an open problem of [Golovach et al.ICALP 2013]. Besides the result, we hope the used techniques that are a mix of a modification of the wellknown Berge’s algorithm and a strong use of the structure of line graphs, are of great interest and could be used to get new outputpolynomial algorithms. 1.