Computing and Information Systems - Research Publications

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2006 11
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Author: Stuckey, Peter × End date: 2006 × Start date: 2006 ×

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    Principal type inference for GHC-style multi-parameter type classes
    Sulzmann, M ; Schrijvers, T ; Stuckey, PJ ; Kobayashi, N (SPRINGER-VERLAG BERLIN, 2006)
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    A framework for extended algebraic data types
    Sulzmann, M ; Wazny, J ; Stuckey, PJ ; Hagiya, M ; Wadler, P (SPRINGER, 2006)
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    Solving partial order constraints for LPO termination
    Codish, M ; Lagoon, V ; Stuckey, PJ ; Pfenning, F (SPRINGER-VERLAG BERLIN, 2006)
    This paper introduces a new kind of propositional encoding for reasoning about partial orders. The symbols in an unspecified partial order are viewed as variables which take integer values and are interpreted as indices in the order. For a partial order statement on n symbols each index is represented in log2 n propositional variables and partial order constraints between symbols are modeled on the bit representations. We illustrate the application of our approach to determine LPO termination for term rewrite systems. Experimental results are unequivocal, indicating orders of magnitude speedups in comparison with current implementations for LPO termination. The proposed encoding is general and relevant to other applications which involve propositional reasoning about partial orders.
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    Size-change termination analysis in κ-bits
    Codish, M ; Lagoon, V ; Schachte, P ; Stuckey, PJ ; Sestoft, P (SPRINGER-VERLAG BERLIN, 2006)
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    Type processing by constraint reasoning
    Stuckey, PJ ; Sulzmann, M ; Wazny, J ; Kobayashi, N (SPRINGER-VERLAG BERLIN, 2006)
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    Adding constraint solving to Mercury
    Becket, R ; de la Banda, MG ; Marriott, K ; Somogyi, Z ; Stuckey, PJ ; Wallace, M ; VanHentenryck, P (SPRINGER-VERLAG BERLIN, 2006)
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    ACD Term Rewriting
    Duck, GJ ; Stuckey, PJ ; Brand, S ; Etalle, S ; Truszczynski, M (SPRINGER-VERLAG BERLIN, 2006)
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    Fast node overlap removal
    Dwyer, T ; Marriott, K ; Stuckey, PJ ; Healy, P ; Nikolov, NS (SPRINGER-VERLAG BERLIN, 2006)
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    Incremental connector routing
    Wybrow, M ; Marriott, K ; Stuckey, PJ ; Healy, P ; Nikolov, NS (SPRINGER-VERLAG BERLIN, 2006)
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    MUSTANG: A multiple structural alignment algorithm
    Konagurthu, 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.