257 research outputs found
The Graph Motif problem parameterized by the structure of the input graph
The Graph Motif problem was introduced in 2006 in the context of biological
networks. It consists of deciding whether or not a multiset of colors occurs in
a connected subgraph of a vertex-colored graph. Graph Motif has been mostly
analyzed from the standpoint of parameterized complexity. The main parameters
which came into consideration were the size of the multiset and the number of
colors. Though, in the many applications of Graph Motif, the input graph
originates from real-life and has structure. Motivated by this prosaic
observation, we systematically study its complexity relatively to graph
structural parameters. For a wide range of parameters, we give new or improved
FPT algorithms, or show that the problem remains intractable. For the FPT
cases, we also give some kernelization lower bounds as well as some ETH-based
lower bounds on the worst case running time. Interestingly, we establish that
Graph Motif is W[1]-hard (while in W[P]) for parameter max leaf number, which
is, to the best of our knowledge, the first problem to behave this way.Comment: 24 pages, accepted in DAM, conference version in IPEC 201
Complexity of Grundy coloring and its variants
The Grundy number of a graph is the maximum number of colors used by the
greedy coloring algorithm over all vertex orderings. In this paper, we study
the computational complexity of GRUNDY COLORING, the problem of determining
whether a given graph has Grundy number at least . We also study the
variants WEAK GRUNDY COLORING (where the coloring is not necessarily proper)
and CONNECTED GRUNDY COLORING (where at each step of the greedy coloring
algorithm, the subgraph induced by the colored vertices must be connected).
We show that GRUNDY COLORING can be solved in time and WEAK
GRUNDY COLORING in time on graphs of order . While GRUNDY
COLORING and WEAK GRUNDY COLORING are known to be solvable in time
for graphs of treewidth (where is the number of
colors), we prove that under the Exponential Time Hypothesis (ETH), they cannot
be solved in time . We also describe an
algorithm for WEAK GRUNDY COLORING, which is therefore
\fpt for the parameter . Moreover, under the ETH, we prove that such a
running time is essentially optimal (this lower bound also holds for GRUNDY
COLORING). Although we do not know whether GRUNDY COLORING is in \fpt, we
show that this is the case for graphs belonging to a number of standard graph
classes including chordal graphs, claw-free graphs, and graphs excluding a
fixed minor. We also describe a quasi-polynomial time algorithm for GRUNDY
COLORING and WEAK GRUNDY COLORING on apex-minor graphs. In stark contrast with
the two other problems, we show that CONNECTED GRUNDY COLORING is
\np-complete already for colors.Comment: 24 pages, 7 figures. This version contains some new results and
improvements. A short paper based on version v2 appeared in COCOON'1
Designing RNA secondary structures is hard
An RNA sequence is a word over an alphabet on four elements {A, C, G, U} called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can be represented as well-parenthesized expressions with additional dots, where pairs of matching parentheses symbolize paired bases and dots, unpaired bases. The two fundamental problems in RNA algorithmic are to predict how sequences fold within some model of energy and to design sequences of bases which will fold into targeted secondary structures. Predicting how a given RNA sequence folds into a pseudoknot-free secondary structure is known to be solvable in cubic time since the eighties and in truly subcubic time by a recent result of Bringmann et al. (FOCS 2016), whereas Lyngsø has shown it is NP-complete if pseudoknots are allowed (ICALP 2004). As a stark contrast, it is unknown whether or not designing a given RNA secondary structure is a tractable task; this has been raised as a challenging open question by Anne Condon (ICALP 2003). Because of its crucial importance in a number of fields such as pharmaceutical research and biochemistry, there are dozens of heuristics and software libraries dedicated to RNA secondary structure design. It is therefore rather surprising that the computational complexity of this central problem in bioinformatics has been unsettled for decades.
In this paper we show that, in the simplest model of energy which is the Watson-Crick model the design of secondary structures is NP-complete if one adds natural constraints of the form: index i of the sequence has to be labeled by base b. This negative result suggests that the same lower bound holds for more realistic models of energy. It is noteworthy that the additional constraints are by no means artificial: they are provided by all the RNA design pieces of software and they do correspond to the actual practice (see for example the instances of the EteRNA project). Our reduction from a variant of 3-Sat has as main ingredients: arches of parentheses of different widths, a linear order interleaving variables and clauses, and an intended rematching strategy which increases the number of pairs iff the three literals of a same clause are not satisfied. The correctness of the construction is also quite intricate; it relies on the polynomial algorithm for the design of saturated structures – secondary structures without dots – by Haleš et al. (Algorithmica 2016), counting arguments, and a concise case analysis
Parameterized Exact and Approximation Algorithms for Maximum -Set Cover and Related Satisfiability Problems
Given a family of subsets over a set of elements~ and two
integers~ and~, Max k-Set Cover consists of finding a subfamily~ of cardinality at most~, covering at least~
elements of~. This problem is W[2]-hard when parameterized by~, and FPT
when parameterized by . We investigate the parameterized approximability of
the problem with respect to parameters~ and~. Then, we show that Max
Sat-k, a satisfiability problem generalizing Max k-Set Cover, is also FPT with
respect to parameter~.Comment: Accepted in RAIRO - Theoretical Informatics and Application
On the Complexity of Various Parameterizations of Common Induced Subgraph Isomorphism
In the Maximum Common Induced Subgraph problem (henceforth MCIS), given two
graphs and , one looks for a graph with the maximum number of
vertices being both an induced subgraph of and . MCIS is among the
most studied classical NP-hard problems. It remains NP-hard on many graph
classes including forests. In this paper, we study the parameterized complexity
of MCIS. As a generalization of \textsc{Clique}, it is W[1]-hard parameterized
by the size of the solution. Being NP-hard even on forests, most structural
parameterizations are intractable. One has to go as far as parameterizing by
the size of the minimum vertex cover to get some tractability. Indeed, when
parameterized by the sum of the vertex
cover number of the two input graphs, the problem was shown to be
fixed-parameter tractable, with an algorithm running in time .
We complement this result by showing that, unless the ETH fails, it cannot be
solved in time . This kind of tight lower bound has been shown
for a few problems and parameters but, to the best of our knowledge, not for
the vertex cover number. We also show that MCIS does not have a polynomial
kernel when parameterized by , unless .
Finally, we study MCIS and its connected variant MCCIS on some special graph
classes and with respect to other structural parameters.Comment: This version introduces new result
Interpretation of precision tests in the Higgs sector in terms of physics beyond the Standard Model
We demonstrate how the measurements of the Higgs-fermion and Higgs-gauge
boson couplings can be interpreted in terms of physics beyond the Standard
Model in a model-independent way. That is, we describe deviations from the
Standard Model by effective operators made of Higgs fields and gauge
fields, under the hypothesis that the new physics may show up in the Higgs
sector only and the effective operators are generated at tree level. While the
effective operator coefficients are independent in general, the completion of
the theory at high energies will lead to specific correlations which will be
recovered between Higgs-fermion and Higgs-gauge boson couplings. We demonstrate
that the current measurement of these couplings in terms of tree-level new
physics requires several new mediators with specific relationships among
different couplings. New insights in the effective theory and mediator spaces
can be expected for improved measurements from the inclusive and the exclusive vector boson fusion-dominated search channels, as well as the measurement of the Higgs
self-couplings, including higher order couplings which do not exist in the
Standard Model.Comment: 12 pages, 2 figures; v2: some discussions extended, conclusions
unchanged; version to appear in PR
Designing RNA Secondary Structures is Hard
International audienceAn RNA sequence is a word over an alphabet on four elements {A, C, G, U } called bases. RNA sequences fold into secondary structures where some bases pair with one another while others remain unpaired. Pseudoknot-free secondary structures can be represented as well-parenthesized expressions with additional dots, where pairs of matching parentheses symbolize paired bases and dots, unpaired bases. The two fundamental problems in RNA algorithmic are to predict how sequences fold within some model of energy and to design sequences of bases which will fold into targeted secondary structures. Predicting how a given RNA sequence folds into a pseudoknot-free secondary structure is known to be solvable in cubic time since the eighties and in truly subcubic time by a recent result of Bringmann et al. (FOCS 2016), whereas Lyngsø has shown it is NP-complete if pseudoknots are allowed (ICALP 2004). As a stark contrast, it is unknown whether or not designing a given RNA secondary structure is a tractable task; this has been raised as a challenging open question by Anne Condon (ICALP 2003). Because of its crucial importance in a number of fields such as pharmaceutical research and biochemistry, there are dozens of heuristics and software libraries dedicated to RNA secondary structure design. It is therefore rather surprising that the computational complexity of this central problem in bioinformatics has been unsettled for decades. In this paper we show that, in the simplest model of energy which is the Watson-Crick model the design of secondary structures is NP-complete if one adds natural constraints of the form: index i of the sequence has to be labeled by base b. This negative result suggests that the same lower bound holds for more realistic models of energy. It is noteworthy that the additional constraints are by no means artificial: they are provided by all the RNA design pieces of software and they do correspond to the actual practice (see for example the instances of the EteRNA project). Our reduction from a variant of 3-Sat has as main ingredients: arches of parentheses of different widths, a linear order interleaving variables and clauses, and an intended rematching strategy which increases the number of pairs iff the three literals of a same clause are false. The correctness of the construction is also quite intricate; it relies on the polynomial algorithm for the design of saturated structures-secondary structures without dots-by Haleš et al. (Algorithmica 2016), counting arguments, and a concise case analysis
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