Regulatory motif discovery using a population clustering evolutionary algorithm

This paper describes a novel evolutionary algorithm for regulatory motif discovery in DNA promoter sequences. The algorithm uses data clustering to logically distribute the evolving population across the search space. Mating then takes place within local regions of the population, promoting overall solution diversity and encouraging discovery of multiple solutions. Experiments using synthetic data sets have demonstrated the algorithm's capacity to find position frequency matrix models of known regulatory motifs in relatively long promoter sequences. These experiments have also shown the algorithm's ability to maintain diversity during search and discover multiple motifs within a single population. The utility of the algorithm for discovering motifs in real biological data is demonstrated by its ability to find meaningful motifs within muscle-specific regulatory sequences

On the Computation of Clebsch-Gordan Coefficients and the Dilation Effect

We investigate the problem of computing tensor product multiplicities for complex semisimple Lie algebras. Even though computing these numbers is #P-hard in general, we show that if the rank of the Lie algebra is assumed fixed, then there is a polynomial time algorithm, based on counting the lattice points in polytopes. In fact, for Lie algebras of type A_r, there is an algorithm, based on the ellipsoid algorithm, to decide when the coefficients are nonzero in polynomial time for arbitrary rank. Our experiments show that the lattice point algorithm is superior in practice to the standard techniques for computing multiplicities when the weights have large entries but small rank. Using an implementation of this algorithm, we provide experimental evidence for conjectured generalizations of the saturation property of Littlewood--Richardson coefficients. One of these conjectures seems to be valid for types B_n, C_n, and D_n.Comment: 21 pages, 6 table

Vertices of Gelfand-Tsetlin Polytopes

This paper is a study of the polyhedral geometry of Gelfand-Tsetlin patterns arising in the representation theory \mathfrak{gl}_n \C and algebraic combinatorics. We present a combinatorial characterization of the vertices and a method to calculate the dimension of the lowest-dimensional face containing a given Gelfand-Tsetlin pattern. As an application, we disprove a conjecture of Berenstein and Kirillov about the integrality of all vertices of the Gelfand-Tsetlin polytopes. We can construct for each $n\geq5$ a counterexample, with arbitrarily increasing denominators as $n$ grows, of a non-integral vertex. This is the first infinite family of non-integral polyhedra for which the Ehrhart counting function is still a polynomial. We also derive a bound on the denominators for the non-integral vertices when $n$ is fixed.Comment: 14 pages, 3 figures, fixed attribution

Singing synthesis with an evolved physical model

A two-dimensional physical model of the human vocal tract is described. Such a system promises increased realism and control in the synthesis. of both speech and singing. However, the parameters describing the shape of the vocal tract while in use are not easily obtained, even using medical imaging techniques, so instead a genetic algorithm (GA) is applied to the model to find an appropriate configuration. Realistic sounds are produced by this method. Analysis of these, and the reliability of the technique (convergence properties) is provided

Image processing applications using a novel parallel computing machine based on reconfigurable logic

Zelig is a 32 physical node fine-grained computer employing field-programmable gate arrays. Its application to the high speed implementation of various image pre-processing operations (in particular binary morphology) is described together with typical speed-up result

Are They Listening?: Revisiting Male Privilege and Defensive Learning in a Feminist Classroom

Privileged students, particularly male-identified students, in women’s studies classrooms have been a population of study previously. Many feminist educators have encountered resistance from a male-identified student in their classroom. Scholarship has been done that analyzes the discourses around how male privilege is invoked by men in women’s studies classrooms. This study defined defensive learning with specific acts of disengagement that hinder privileged students, particularly male-identified students in Gender and Women’s Studies, from taking classes that are considered “feminist,” and from learning about systems of privilege. A series of semi-structured interviews with six male-identified students who were enrolled in women’s studies classes was conducted. The purpose of this study was to go in-depth on how privileged students learned and thought about privilege, privilege’s role in defensive learning, and men’s participation in feminism. The findings suggest that the participants identified as feminists, thought privilege should be widely taught to all students, particularly more privileged students, and that they would benefit from Gender and Women’s Studies course content. Conversely, my study suggests that feminism being demonized in popular culture and misinformation about Gender and Women’s Studies, as an academic discipline, can dissuade many privileged students from enrolling or participating in feminist and social justice projects. Recommendations for increasing enrollment in Gender and Women’s Studies, teaching privilege, and avenues for future research are also discussed

Examining the Practices and Quality of Preschool Teachers’ Practices Managing the Challenging Behaviors of Young Children

All teachers have to manage a classroom environment and meet the needs of their students. In early childhood educational settings, challenging behaviors have been found to be a significant responsibility. The variables involved in effectively intervening in challenging behavior, and developing behavior support plans, are often determined by various factors. Previous research into challenging behaviors of young children have focused on the effectiveness of certain behavioral interventions, professional development opportunities, and curriculum such as the Pyramid Model. This proposed qualitative study centered the practices teachers reported using interceding in problem behavior, and inquired about the influences behind why teachers used certain classroom management practices. A multi-case study design across four classrooms within one type of educational facility sought depth of understanding about potential links between the practices teachers reported using and the quality of the classroom environment, using the Teaching Pyramid Observation Tool (TPOT) as an additional procedure in data collection

Hierarchical strategies for efficient fault recovery on the reconfigurable PAnDA device

A novel hierarchical fault-tolerance methodology for reconfigurable devices is presented. A bespoke multi-reconfigurable FPGA architecture, the programmable analogue and digital array (PAnDA), is introduced allowing fine-grained reconfiguration beyond any other FPGA architecture currently in existence. Fault blind circuit repair strategies, which require no specific information of the nature or location of faults, are developed, exploiting architectural features of PAnDA. Two fault recovery techniques, stochastic and deterministic strategies, are proposed and results of each, as well as a comparison of the two, are presented. Both approaches are based on creating algorithms performing fine-grained hierarchical partial reconfiguration on faulty circuits in order to repair them. While the stochastic approach provides insights into feasibility of the method, the deterministic approach aims to generate optimal repair strategies for generic faults induced into a specific circuit. It is shown that both techniques successfully repair the benchmark circuits used after random faults are induced in random circuit locations, and the deterministic strategies are shown to operate efficiently and effectively after optimisation for a specific use case. The methods are shown to be generally applicable to any circuit on PAnDA, and to be straightforwardly customisable for any FPGA fabric providing some regularity and symmetry in its structure