18,465 research outputs found
Hybrid Algorithms Based on Integer Programming for the Search of Prioritized Test Data in Software Product Lines
In Software Product Lines (SPLs) it is not possible, in general, to test all products of the family. The number of products denoted by a SPL is very high due to the combinatorial explosion of features. For this reason, some coverage criteria have been proposed which try to test at least all feature interactions without the necessity to test all products, e.g., all pairs of features (pairwise coverage). In addition, it is desirable to first test products composed by a set of priority features. This problem is known as the Prioritized Pairwise Test Data Generation Problem. In this work we propose two hybrid algorithms using Integer Programming (IP) to generate a prioritized test suite. The first one is based on an integer linear formulation and the second one is based on a integer quadratic (nonlinear) formulation. We compare these techniques with two state-of-the-art algorithms, the Parallel Prioritized Genetic Solver (PPGS) and a greedy algorithm called prioritized-ICPL. Our study reveals that our hybrid nonlinear approach is clearly the best in both, solution quality and computation time. Moreover, the nonlinear variant (the fastest one) is 27 and 42 times faster than PPGS in the two groups of instances analyzed in this work.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. Partially funded by the Spanish Ministry of Economy and Competitiveness and FEDER under contract TIN2014-57341-R, the University of Málaga, Andalucía Tech and the Spanish Network TIN2015-71841-REDT (SEBASENet)
BeWith: A Between-Within Method to Discover Relationships between Cancer Modules via Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions
The analysis of the mutational landscape of cancer, including mutual
exclusivity and co-occurrence of mutations, has been instrumental in studying
the disease. We hypothesized that exploring the interplay between
co-occurrence, mutual exclusivity, and functional interactions between genes
will further improve our understanding of the disease and help to uncover new
relations between cancer driving genes and pathways. To this end, we designed a
general framework, BeWith, for identifying modules with different combinations
of mutation and interaction patterns. We focused on three different settings of
the BeWith schema: (i) BeME-WithFun in which the relations between modules are
enriched with mutual exclusivity while genes within each module are
functionally related; (ii) BeME-WithCo which combines mutual exclusivity
between modules with co-occurrence within modules; and (iii) BeCo-WithMEFun
which ensures co-occurrence between modules while the within module relations
combine mutual exclusivity and functional interactions. We formulated the
BeWith framework using Integer Linear Programming (ILP), enabling us to find
optimally scoring sets of modules. Our results demonstrate the utility of
BeWith in providing novel information about mutational patterns, driver genes,
and pathways. In particular, BeME-WithFun helped identify functionally coherent
modules that might be relevant for cancer progression. In addition to finding
previously well-known drivers, the identified modules pointed to the importance
of the interaction between NCOR and NCOA3 in breast cancer. Additionally, an
application of the BeME-WithCo setting revealed that gene groups differ with
respect to their vulnerability to different mutagenic processes, and helped us
to uncover pairs of genes with potentially synergetic effects, including a
potential synergy between mutations in TP53 and metastasis related DCC gene
OEDIPUS: Onium Evolution, Dipole Interaction and Perturbative Unitarisation Simulation
A Monte Carlo simulation program is presented which can be used to determine
the small- evolution of a heavy onium using Mueller's colour dipole
formulation, giving the full distribution of dipoles in rapidity and impact
parameter. Routines are also provided which calculate onium-onium scattering
amplitudes between individual pairs of onium configurations, making it possible
to establish the contribution of multiple pomeron exchange terms to onium-onium
scattering (the unitarisation corrections).Comment: 21 pages LaTeX2e. Postscript available from
http://www.hep.phy.cam.ac.uk/theory/papers and program available from
ftp://axpf.hep.phy.cam.ac.uk/pub/theory/oedipus.tar.g
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