1,721,108 research outputs found
Computational Science for Undergraduate Biologists via QUT.Bio.Excel
No full textAbstractMolecular biology is a scientific discipline which has changed fundamentally in character over the past decade to rely on large scale datasets – public and locally generated - and their computational analysis and annotation. Undergraduate education of biologists must increasingly couple this domain context with a data-driven computational scientific method. Yet modern programming and scripting languages and rich computational environments such as R and MATLAB present significant barriers to those with limited exposure to computer science, and may require substantial tutorial assistance over an extended period if progress is to be made. In this paper we report our experience of undergraduate bioinformatics education using the familiar, ubiquitous spreadsheet environment of Microsoft Excel. We describe a configurable extension called QUT.Bio.Excel, a custom ribbon, supporting a rich set of data sources, external tools and interactive processing within the spreadsheet, and a range of problems to demonstrate its utility and success in addressing the needs of students over their studies
"Equation missing" : A Cross-Platform Programming Framework for Quantum-Accelerated Scientific Computing
No full textThis paper introduces a new cross-platform programming framework for developing quantum-accelerated scientific computing applications and executing them on most of today’s cloud-based quantum computers and simulators. It makes use of C++ template meta-programming techniques to implement quantum algorithms as generic, platform-independent expressions, which get automatically synthesized into device-specific compute kernels upon execution. Our software framework supports concurrent and asynchronous execution of multiple quantum kernels via a CUDA-inspired stream concept.Accepted Author ManuscriptNumerical Analysi
Strategic Use of Data Assimilation for Dynamic Data-Driven Simulation
No full textDynamic data-driven simulation (DDDS) incorporates real-time measurement data to improve simulation models during model run-time. Data assimilation (DA) methods aim to best approximate model states with imperfect measurements, where particle Filters (PFs) are commonly used with discrete-event simulations. In this paper, we study three critical conditions of DA using PFs: (1) the time interval of iterations, (2) the number of particles and (3) the level of actual and perceived measurement errors (or noises), and provide recommendations on how to strategically use data assimilation for DDDS considering these conditions. The results show that the estimation accuracy in DA is more constrained by the choice of time intervals than the number of particles. Good accuracy can be achieved without many particles if the time interval is sufficiently short. An over estimation of the level of measurement errors has advantages over an under estimation. Moreover, a slight over estimation has better estimation accuracy and is more responsive to system changes than an accurate perceived level of measurement errors.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.System EngineeringPolicy Analysi
Agent based modeling of viral infections: an investigation across several spatio-temporal scales
Get PDFFinite element simulation of stress evolution in a frictional contact system
No full textA 3-dimensional finite element algorithm for modeling nonlinear frictional contact behaviours between deformable bodies with the node-to-point contact element strategy has been proposed and applied here to investigate stress evolution processes of a nonlinear frictional contact system. The numerical results of a typical intra-plate fault bend model demonstrate the efficiency and usefulness of this algorithm
Dense Temporal Subgraphs in Protein-Protein Interaction Networks
No full textTemporal networks have been successfully applied to represent the dynamics of protein-protein interactions. In this paper we focus on the identification of dense subgraphs in temporal protein-protein interaction networks, a relevant problem to find group of proteins related to a given functionality. We consider a drawback of an existing approach for this problem that produce large time intervals over which temporal subgraphs are defined. We propose a problem to deal with this issue and we design (1) an exact algorithm based on dynamic programming which solves the problem in polynomial time and (2) a heuristic, based on a segmentation of the time domain and the computation of a refinement. The experimental results we present on seven protein-protein interaction networks show that in many cases our heuristic is able to reduce the time intervals with respect to those computed by the existing methods
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Enabling Non-Linear Quantum Operations through Variational Quantum Splines
Get PDFThe postulates of quantum mechanics impose only unitary transformations on
quantum states, which is a severe limitation for quantum machine learning
algorithms. Quantum Splines (QSplines) have recently been proposed to
approximate quantum activation functions to introduce non-linearity in quantum
algorithms. However, QSplines make use of the HHL as a subroutine and require a
fault-tolerant quantum computer to be correctly implemented. This work proposes
the Generalised Hybrid Quantum Splines (GHQSplines), a novel method for
approximating non-linear quantum activation functions using hybrid
quantum-classical computation. The GHQSplines overcome the highly demanding
requirements of the original QSplines in terms of quantum hardware and can be
implemented using near-term quantum computers. Furthermore, the proposed method
relies on a flexible problem representation for non-linear approximation and it
is suitable to be embedded in existing quantum neural network architectures. In
addition, we provide a practical implementation of the GHQSplines using
Pennylane and show that our model outperforms the original QSplines in terms of
quality of fitting
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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