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Computing and Information Systems - Research Publications
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ItemPrincipal type inference for GHC-style multi-parameter type classesSulzmann, M ; Schrijvers, T ; Stuckey, PJ ; Kobayashi, N (SPRINGER-VERLAG BERLIN, 2006)
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ItemTelecommunications feature subscription as a partial order constraint problemCODISH, M. ; LAGOON, V. ; STUCKEY, P. (Springer Verlag, 2008)
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ItemDiscovery of minimal unsatisfiable subsets of constraints using hitting set dualizationBailey, J ; Stuckey, PJ ; Hermenegildo, M ; Cabeza, D (SPRINGER-VERLAG BERLIN, 2005)
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ItemPropagating Dense Systems of Integer Linear EquationsFeydy, T ; Stuckey, PJ (ASSOC COMPUTING MACHINERY, 2007)
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ItemPropagation = Lazy Clause GenerationOHRIMENKO, O. ; STUCKEY, P. ; CODISH, M. (Springer Verlag, 2007)
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ItemDynamic Analysis of Bounds Versus Domain PropagationSchulte, C ; Stuckey, PJ ; DelaBanda, MG ; Pontelli, E (Springer, 2008-12-01)Constraint propagation solvers interleave propagation (removing impossible values from variable domains) with search. Previously, Schulte and Stuckey introduced the use of static analysis to determine where in a constraint program domain propagators can be replaced by more efficient bounds propagators and still ensure that the same search space is traversed. This paper introduces a dynamic yet considerably simpler approach to uncover the same information. The information is obtained by a linear time traversal of an analysis graph that straightforwardly reflects the properties of propagators implementing constraints. Experiments confirm that the simple dynamic method is efficient and that it can be used interleaved with search, taking advantage of the simplification of the constraint graph that arises from search.
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ItemFast node overlap removalDwyer, T ; Marriott, K ; Stuckey, PJ ; Healy, P ; Nikolov, NS (SPRINGER-VERLAG BERLIN, 2006)
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ItemIncremental connector routingWybrow, M ; Marriott, K ; Stuckey, PJ ; Healy, P ; Nikolov, NS (SPRINGER-VERLAG BERLIN, 2006)
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ItemMUSTANG: A multiple structural alignment algorithmKonagurthu, AS ; Whisstock, JC ; Stuckey, PJ ; Lesk, AM (WILEY, 2006-08-15)Multiple structural alignment is a fundamental problem in structural genomics. In this article, we define a reliable and robust algorithm, MUSTANG (MUltiple STructural AligNment AlGorithm), for the alignment of multiple protein structures. Given a set of protein structures, the program constructs a multiple alignment using the spatial information of the C(alpha) atoms in the set. Broadly based on the progressive pairwise heuristic, this algorithm gains accuracy through novel and effective refinement phases. MUSTANG reports the multiple sequence alignment and the corresponding superposition of structures. Alignments generated by MUSTANG are compared with several handcurated alignments in the literature as well as with the benchmark alignments of 1033 alignment families from the HOMSTRAD database. The performance of MUSTANG was compared with DALI at a pairwise level, and with other multiple structural alignment tools such as POSA, CE-MC, MALECON, and MultiProt. MUSTANG performs comparably to popular pairwise and multiple structural alignment tools for closely related proteins, and performs more reliably than other multiple structural alignment methods on hard data sets containing distantly related proteins or proteins that show conformational changes.
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ItemThe island confinement method for reducing search space in local search methodsFang, H ; Kilani, Y ; Lee, JHM ; Stuckey, PJ (SPRINGER, 2007-12)