Computing and Information Systems - Research Publications
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ItemAbstract Interpretation over Non-Lattice Abstract Domains(Springer, 2013)The classical theoretical framework for static analysis of programs is abstract interpretation. Much of the power and elegance of that framework rests on the assumption that an abstract domain is a lattice. Nonetheless, and for good reason, the literature on program analysis provides many examples of non-lattice domains, including non-convex numeric domains. The lack of domain structure, however, has negative consequences, both for the precision of program analysis and for the termination of standard Kleene iteration. In this paper we explore these consequences and present general remedies.
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ItemSearch combinators(SPRINGER, 2013-04)
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ItemSolving RCPSP/max by lazy clause generation(SPRINGER, 2013-06)
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ItemDiscovery and analysis of consistent active subnetworks in cancers(BMC, 2013-01-21)Gene expression profiles can show significant changes when genetically diseased cells are compared with non-diseased cells. Biological networks are often used to identify active subnetworks (ASNs) of the diseases from the expression profiles to understand the reason behind the observed changes. Current methodologies for discovering ASNs mostly use undirected PPI networks and node centric approaches. This can limit their ability to find the meaningful ASNs when using integrated networks having comprehensive information than the traditional protein-protein interaction networks. Using appropriate scoring functions to assess both genes and their interactions may allow the discovery of better ASNs. In this paper, we present CASNet, which aims to identify better ASNs using (i) integrated interaction networks (mixed graphs), (ii) directions of regulations of genes, and (iii) combined node and edge scores. We simplify and extend previous methodologies to incorporate edge evaluations and lessen their sensitivity to significance thresholds. We formulate our objective functions using mixed integer programming (MIP) and show that optimal solutions may be obtained. We compare the ASNs obtained by CASNet and similar other approaches to show that CASNet can often discover more meaningful and stable regulatory ASNs. Our analysis of a breast cancer dataset finds that the positive feedback loops across 7 genes, AR, ESR1, MYC, E2F2, PGR, BCL2 and CCND1 are conserved across the basal/triple negative subtypes in multiple datasets that could potentially explain the aggressive nature of this cancer subtype. Furthermore, comparison of the basal subtype of breast cancer and the mesenchymal subtype of glioblastoma ASNs shows that an ASN in the vicinity of IL6 is conserved across the two subtypes. This result suggests that subtypes of different cancers can show molecular similarities indicating that the therapeutic approaches in different types of cancers may be shared.
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ItemFast and accurate protein substructure searching with simulated annealing and GPUs(BMC, 2010-09-03)BACKGROUND: Searching a database of protein structures for matches to a query structure, or occurrences of a structural motif, is an important task in structural biology and bioinformatics. While there are many existing methods for structural similarity searching, faster and more accurate approaches are still required, and few current methods are capable of substructure (motif) searching. RESULTS: We developed an improved heuristic for tableau-based protein structure and substructure searching using simulated annealing, that is as fast or faster and comparable in accuracy, with some widely used existing methods. Furthermore, we created a parallel implementation on a modern graphics processing unit (GPU). CONCLUSIONS: The GPU implementation achieves up to 34 times speedup over the CPU implementation of tableau-based structure search with simulated annealing, making it one of the fastest available methods. To the best of our knowledge, this is the first application of a GPU to the protein structural search problem.
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ItemStructuring Documents Efficiently(University of Sydney, 2005)
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ItemPrincipal type inference for GHC-style multi-parameter type classes(SPRINGER-VERLAG BERLIN, 2006)
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ItemLazy Clause Generation: Combining the Power of SAT and CP (and MIP?) Solving(SPRINGER-VERLAG BERLIN, 2010)
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ItemOptimizing compilation of CHR with rule priorities(Springer, 2008-05-14)
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ItemObservable confluence for constraint handling rules(SPRINGER-VERLAG BERLIN, 2007)