Browsing Research Articles (Mathematical Sciences) by Title

Now showing items 1-20 of 41

    • The asymptotic number of binary codes and binary matroids 

      Wild, Marcel (Society for Industrial and Applied Mathematics (SIAM), 2006-08)
      The asymptotic number of nonequivalent binary n-codes is determined. This is also the asymptotic number of nonisomorphic binary matroids on n elements.

    • Benchmarking multi-rate codon models 

      Delport, Wayne; Scheffler, Konrad; Gravenor, Mike B.; Muse, Spencer V.; Pond, Sergei Kosakovsky (Public Library of Science, 2010-07-21)
      The single rate codon model of non-synonymous substitution is ubiquitous in phylogenetic modeling. Indeed, the use of a non-synonymous to synonymous substitution rate ratio parameter has facilitated the interpretation of ...

    • Calculating the output distribution of stack filters that are erosion-dilation cascades, in particular LULU-filters 

      Anguelov, R.; Butler, P. W.; Rohwer, C. H.; Wild, Marcel (Cornell University Library, 2011)
      ENGLISH ABSTRACT: Two procedures to compute the output distribution 0S of certain stack filters S (so called erosion-dilation cascades) are given. One rests on the disjunctive normal form of S and also yields the rank ...

    • Codon test : modeling amino acid substitution preferences in coding sequences 

      Delport, Wayne; Scheffler, Konrad; Botha, Gordon; Gravenor, Mike B.; Muse, Spencer V.; Pond, Sergei L. Kosakovsky (PLOS Computational Biology, 2010-08)
      Codon models of evolution have facilitated the interpretation of selective forces operating on genomes. These models, however, assume a single rate of non-synonymous substitution irrespective of the nature of amino acids ...

    • Compactly generating all satisfying truth assignments of a horn formula 

      Wild, Marcel (Delft University in cooperation with IOS Press, 2012-01)
      ENGLISH ABSTRACT: While it was known that all models of a Horn formula can be generated in outputpolynomial time, here we present an explicit algorithm as opposed to the rather vague oracle-scheme suggested in the proof ...

    • Computational and theoretical analysis of human diseases associated with infectious pathogens 

      Noutchie, Suares Clovis Oukouomi; Kwuimy, Cedrick Aurelien Kitio; Tewa, Jean Jules; Nyabadza, Farai; Bildik, Necdet (Hindawi, 2015)
      Mathematical models and computer simulations are useful experimental tools for building and testing theories, assessing quantitative conjectures, answering specific questions, determining sensitivities to changes in parameter ...

    • Computing the output distribution of a stack filter from the DNF of its positive Boolean function 

      Wild, Marcel (Cornell University Library, 2010)
      ENGLISH ABSTRACT: The majority of nonlinear filters used in practise are stack filters. An algorithm is presented which calculates the output distribution of an arbitrary stack filter S from the disjunctive normal form ...

    • Computing various types of lattices freely generated by posets 

      Wild, Marcel (Edizioni CERFIM Centro di Ricerche in Fisica e MatematicaResearch Center for Mathematics and Physics - Locarno - Switzerland, 2000)
      see item for abstract

    • Correcting the bias of empirical frequency parameter estimators in codon models 

      Kosakovsky Pond, Sergei; Delport, Wayne; Muse, Spencer V.; Scheffler, Konrad (Public Library of Science -- PLOS, 2010-07)
      Markov models of codon substitution are powerful inferential tools for studying biological processes such as natural selection and preferences in amino acid substitution. The equilibrium character distributions of these ...

    • Decomposing the hypercube Qn into n isomorphic edge-disjoint trees 

      Wagner, Stephan; Wild, Marcel (Elsevier, 2012-02)
      The problem of finding edge-disjoint trees in a hypercube arises for example in the context of parallel computing [3]. Independently of applications it is of high aesthetic appeal. The hypercube of dimension n, denoted ...

    • Detecting individual sites subject to episodic diversifying selection 

      Murrell, Ben; Wertheim, Joel O.; Moola, Sasha; Weighill, Thomas; Scheffler, Konrad; Pond, Sergei L. Kosakovsky (Public Library of Science, 2012-07-02)
      The imprint of natural selection on protein coding genes is often difficult to identify because selection is frequently transient or episodic, i.e. it affects only a subset of lineages. Existing computational techniques, ...

    • Entropy generation in a couple stress fluid flow through a vertical channel filled with saturated porous media 

      Makinde, Oluwole Daniel; Eegunjobi, Adetayo Samuel (MDPI, 2013-10-25)
      The present work investigates numerically the inherent irreversibility in a steady flow of a couple stress fluid through a vertical channel packed with saturated porous substances. The First and Second Laws of Thermodynamics ...

    • Francis Guthrie : a colourful life 

      Maritz, Pieter; Mouton, Sonja (Springer, 2012-09)
      In 1852, in London, Francis Guthrie posed the question of colouring a map with four colours only, the question that eventually became known as the Four Colour Problem. The problem is famous, but what else do we know of ...

    • Frequent toggling between alternative amino acids Is driven by selection in HIV-1 

      Delport, Wayne; Scheffler, Konrad; Seoighe, Cathal (Public Library of Science, 2008)
      Host immune responses against infectious pathogens exert strong selective pressures favouring the emergence of escape mutations that prevent immune recognition. Escape mutations within or flanking functionally conserved ...

    • A geometrical model for testing bilateral symmetry of bamboo leaf with a simplified Gielis equation 

      Lin, Shuyan; Zhang, Li; Reddy, Gadi V. P.; Hui, Cang; Gielis, Johan; Ding, Yulong; Shi, Peijian (Wiley Open Access, 2016)
      The size and shape of plant leaves change with growth, and an accurate description of leaf shape is crucial for describing plant morphogenesis and development. Bilateral symmetry, which has been widely observed but poorly ...

    • The geometry of unitary 2-representations of finite groups and their 2-characters 

      Bartlett, Bruce (Springer Link, 2011-02)
      Motivated by topological quantum field theory, we investigate the geometric aspects of unitary 2-representations of finite groups on 2-Hilbert spaces, and their 2-characters. We show how the basic ideas of geometric ...

    • Invading a mutualistic network : to be or not to be similar 

      Minoarivelo, Henintsoa Onivola; Hui, Cang (Wiley Open Access, 2016)
      Biological invasion remains a major threat to biodiversity in general and a disruptor to mutualistic interactions in particular. While a number of empirical studies have directly explored the role of invasion in mutualistic ...

    • Left ventricular segmentation from MRI datasets with edge modelling conditional random fields 

      Dreijer, Janto F.; Herbst, Ben M.; Du Preez, Johan A. (BioMed Central, 2013-07)
      Background: This paper considers automatic segmentation of the left cardiac ventricle in short axis magnetic resonance images. Various aspects, such as the presence of papillary muscles near the endocardium border, makes ...

    • Model checking rational agents 

      Bordini, Rafael H.; Fisher, Michael; Wooldridge, Michael; Visser, Willem (IEEE - -Institute of Electrical and Electronics Engineers, 2004-10)
      Agent-oriented programming techniques seem appropriate for developing systems that operate in complex, dynamic, and unpredictable environments. We aim to address this requirement by developing model-checking techniques for ...

    • Modeling HIV-1 drug resistance as episodic directional selection 

      Murrell, Ben; De Oliveira, Tulio; Seebregts, Chris; Pond, Sergei L. Kosakovsky; Scheffler, Konrad (PLOS Computational Biology, 2011-05)
      The evolution of substitutions conferring drug resistance to HIV-1 is both episodic, occurring when patients are on antiretroviral therapy, and strongly directional, with site-specific resistant residues increasing in ...