546 research outputs found

    Differential Evolution Approach to Detect Recent Admixture

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    The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools that can infer multiple origins. Misclassification of such individuals can lead to incorrect and costly misinterpretations of genomic data, primarily in disease studies and drug trials. We present an advanced tool to infer ancestry that can identify the biogeographic origins of highly mixed individuals. reAdmix is an online tool available at http://chcb.saban-chla.usc.edu/reAdmix/.Comment: presented at ISMB 2014, VariSI

    Comparative Study of Some Population-based Optimization Algorithms on Inverse Scattering of a Two-Dimensional Perfectly Conducting Cylinder in Slab Medium

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    [[abstract]]The application of four techniques for the shape reconstruction of a 2-D metallic cylinder buried in dielectric slab medium by measured the cattered fields outside is studied in the paper. The finite-difference time-domain (FDTD) technique is employed for electromagnetic analyses for both the forward and inverse scattering problems, while the shape reconstruction problem is transformed into optimization one during the course of inverse scattering. Then, four techniques including asynchronous particle swarm optimization (APSO), PSO, dynamic differential evolution (DDE) and self-adaptive DDE (SADDE) are applied to reconstruct the location and shape of the 2-Dmetallic cylinder for comparative purposes. The statistical performances of these algorithms are compared. The results show that SADDE outperforms PSO, APSO and DDE in terms of the ability of exploring the optima. However, these results are considered to be indicative and do not generally apply to all optimization problems in electromagnetics.[[incitationindex]]SCI[[incitationindex]]EI[[booktype]]紙本[[booktype]]電子

    Enhanced Parallel Sine Cosine Algorithm for Constrained and Unconstrained Optimization

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    The sine cosine algorithm’s main idea is the sine and cosine-based vacillation outwards or towards the best solution. The first main contribution of this paper proposes an enhanced version of the SCA algorithm called as ESCA algorithm. The supremacy of the proposed algorithm over a set of state-of-the-art algorithms in terms of solution accuracy and convergence speed will be demonstrated by experimental tests. When these algorithms are transferred to the business sector, they must meet time requirements dependent on the industrial process. If these temporal requirements are not met, an efficient solution is to speed them up by designing parallel algorithms. The second major contribution of this work is the design of several parallel algorithms for efficiently exploiting current multicore processor architectures. First, one-level synchronous and asynchronous parallel ESCA algorithms are designed. They have two favors; retain the proposed algorithm’s behavior and provide excellent parallel performance by combining coarse-grained parallelism with fine-grained parallelism. Moreover, the parallel scalability of the proposed algorithms is further improved by employing a two-level parallel strategy. Indeed, the experimental results suggest that the one-level parallel ESCA algorithms reduce the computing time, on average, by 87.4% and 90.8%, respectively, using 12 physical processing cores. The two-level parallel algorithms provide extra reductions of the computing time by 91.4%, 93.1%, and 94.5% with 16, 20, and 24 processing cores, including physical and logical cores. Comparison analysis is carried out on 30 unconstrained benchmark functions and three challenging engineering design problems. The experimental outcomes show that the proposed ESCA algorithm behaves outstandingly well in terms of exploration and exploitation behaviors, local optima avoidance, and convergence speed toward the optimum. The overall performance of the proposed algorithm is statistically validated using three non-parametric statistical tests, namely Friedman, Friedman aligned, and Quade tests.This research was supported by the Spanish Ministry of Science, Innovation and Universities and the Research State Agency under Grant RTI2018-098156-B-C54 cofinanced by FEDER funds and the Ministry of Science and Innovation and the Research State Agency under Grant PID2020-120213RB-I00 cofinanced by FEDER funds

    Differential Evolution in Wireless Communications: A Review

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    Differential Evolution (DE) is an evolutionary computational method inspired by the biological processes of evolution and mutation. DE has been applied in numerous scientific fields. The paper presents a literature review of DE and its application in wireless communication. The detailed history, characteristics, strengths, variants and weaknesses of DE were presented. Seven broad areas were identified as different domains of application of DE in wireless communications. It was observed that coverage area maximisation and energy consumption minimisation are the two major areas where DE is applied. Others areas are quality of service, updating mechanism where candidate positions learn from a large diversified search region, security and related field applications. Problems in wireless communications are often modelled as multiobjective optimisation which can easily be tackled by the use of DE or hybrid of DE with other algorithms. Different research areas can be explored and DE will continue to be utilized in this contex

    Advanced techniques for rated speed increment in industrial drives

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    Studio, analisi, implementazione e simulazione di vari algoritmi di controllo per azionamenti elettrici di motori high-spee

    Hybrid Intelligent Optimization Methods for Engineering Problems

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    The purpose of optimization is to obtain the best solution under certain conditions. There are numerous optimization methods because different problems need different solution methodologies; therefore, it is difficult to construct patterns. Also mathematical modeling of a natural phenomenon is almost based on differentials. Differential equations are constructed with relative increments among the factors related to yield. Therefore, the gradients of these increments are essential to search the yield space. However, the landscape of yield is not a simple one and mostly multi-modal. Another issue is differentiability. Engineering design problems are usually nonlinear and they sometimes exhibit discontinuous derivatives for the objective and constraint functions. Due to these difficulties, non-gradient-based algorithms have become more popular in recent decades. Genetic algorithms (GA) and particle swarm optimization (PSO) algorithms are popular, non-gradient based algorithms. Both are population-based search algorithms and have multiple points for initiation. A significant difference from a gradient-based method is the nature of the search methodologies. For example, randomness is essential for the search in GA or PSO. Hence, they are also called stochastic optimization methods. These algorithms are simple, robust, and have high fidelity. However, they suffer from similar defects, such as, premature convergence, less accuracy, or large computational time. The premature convergence is sometimes inevitable due to the lack of diversity. As the generations of particles or individuals in the population evolve, they may lose their diversity and become similar to each other. To overcome this issue, we studied the diversity concept in GA and PSO algorithms. Diversity is essential for a healthy search, and mutations are the basic operators to provide the necessary variety within a population. After having a close scrutiny of the diversity concept based on qualification and quantification studies, we improved new mutation strategies and operators to provide beneficial diversity within the population. We called this new approach as multi-frequency vibrational GA or PSO. They were applied to different aeronautical engineering problems in order to study the efficiency of these new approaches. These implementations were: applications to selected benchmark test functions, inverse design of two-dimensional (2D) airfoil in subsonic flow, optimization of 2D airfoil in transonic flow, path planning problems of autonomous unmanned aerial vehicle (UAV) over a 3D terrain environment, 3D radar cross section minimization problem for a 3D air vehicle, and active flow control over a 2D airfoil. As demonstrated by these test cases, we observed that new algorithms outperform the current popular algorithms. The principal role of this multi-frequency approach was to determine which individuals or particles should be mutated, when they should be mutated, and which ones should be merged into the population. The new mutation operators, when combined with a mutation strategy and an artificial intelligent method, such as, neural networks or fuzzy logic process, they provided local and global diversities during the reproduction phases of the generations. Additionally, the new approach also introduced random and controlled diversity. Due to still being population-based techniques, these methods were as robust as the plain GA or PSO algorithms. Based on the results obtained, it was concluded that the variants of the present multi-frequency vibrational GA and PSO were efficient algorithms, since they successfully avoided all local optima within relatively short optimization cycles

    On FPGA implementations for bioinformatics, neural prosthetics and reinforcement learning problems.

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    Mak Sui Tung Terrence.Thesis (M.Phil.)--Chinese University of Hong Kong, 2005.Includes bibliographical references (leaves 132-142).Abstracts in English and Chinese.Abstract --- p.iList of Tables --- p.ivList of Figures --- p.vAcknowledgements --- p.ixChapter 1. --- Introduction --- p.1Chapter 1.1 --- Bioinformatics --- p.1Chapter 1.2 --- Neural Prosthetics --- p.4Chapter 1.3 --- Learning in Uncertainty --- p.5Chapter 1.4 --- The Field Programmable Gate Array (FPGAs) --- p.7Chapter 1.5 --- Scope of the Thesis --- p.10Chapter 2. --- A Hybrid GA-DP Approach for Searching Equivalence Sets --- p.14Chapter 2.1 --- Introduction --- p.16Chapter 2.2 --- Equivalence Set Criterion --- p.18Chapter 2.3 --- Genetic Algorithm and Dynamic Programming --- p.19Chapter 2.3.1 --- Genetic Algorithm Formulation --- p.20Chapter 2.3.2 --- Bounded Mutation --- p.21Chapter 2.3.3 --- Conditioned Crossover --- p.22Chapter 2.3.4 --- Implementation --- p.22Chapter 2.4 --- FPGAs Implementation of GA-DP --- p.24Chapter 2.4.1 --- System Overview --- p.25Chapter 2.4.2 --- Parallel Computation for Transitive Closure --- p.26Chapter 2.4.3 --- Genetic Operation Realization --- p.28Chapter 2.5 --- Discussion --- p.30Chapter 2.6 --- Limitation and Future Work --- p.33Chapter 2.7 --- Conclusion --- p.34Chapter 3. --- An FPGA-based Architecture for Maximum-Likelihood Phylogeny Evaluation --- p.35Chapter 3.1 --- Introduction --- p.36Chapter 3.2 --- Maximum-Likelihood Model --- p.39Chapter 3.3 --- Hardware Mapping for Pruning Algorithm --- p.41Chapter 3.3.1 --- Related Works --- p.41Chapter 3.3.2 --- Number Representation --- p.42Chapter 3.3.3 --- Binary Tree Representation --- p.43Chapter 3.3.4 --- Binary Tree Traversal --- p.45Chapter 3.3.5 --- Maximum-Likelihood Evaluation Algorithm --- p.46Chapter 3.4 --- System Architecture --- p.49Chapter 3.4.1 --- Transition Probability Unit --- p.50Chapter 3.4.2 --- State-Parallel Computation Unit --- p.51Chapter 3.4.3 --- Error Computation --- p.54Chapter 3.5 --- Discussion --- p.56Chapter 3.5.1 --- Hardware Resource Consumption --- p.56Chapter 3.5.2 --- Delay Evaluation --- p.57Chapter 3.6 --- Conclusion --- p.59Chapter 4. --- Field Programmable Gate Array Implementation of Neuronal Ion Channel Dynamics --- p.61Chapter 4.1 --- Introduction --- p.62Chapter 4.2 --- Background --- p.63Chapter 4.2.1 --- Analog VLSI Model for Hebbian Synapse --- p.63Chapter 4.2.2 --- A Unifying Model of Bi-directional Synaptic Plasticity --- p.64Chapter 4.2.3 --- Non-NMDA Receptor Channel Regulation --- p.65Chapter 4.3 --- FPGAs Implementation --- p.65Chapter 4.3.1 --- FPGA Design Flow --- p.65Chapter 4.3.2 --- Digital Model of NMD A and AMPA receptors --- p.65Chapter 4.3.3 --- Synapse Modification --- p.67Chapter 4.4 --- Results --- p.68Chapter 4.4.1 --- Simulation Results --- p.68Chapter 4.5 --- Discussion --- p.70Chapter 4.6 --- Conclusion --- p.71Chapter 5. --- Continuous-Time and Discrete-Time Inference Networks for Distributed Dynamic Programming --- p.72Chapter 5.1 --- Introduction --- p.74Chapter 5.2 --- Background --- p.77Chapter 5.2.1 --- Markov decision process (MDPs) --- p.78Chapter 5.2.2 --- Learning in the MDPs --- p.80Chapter 5.2.3 --- Bellman Optimal Criterion --- p.80Chapter 5.2.4 --- Value Iteration --- p.81Chapter 5.3 --- A Computational Framework for Continuous-Time Inference Network --- p.82Chapter 5.3.1 --- Binary Relation Inference Network --- p.83Chapter 5.3.2 --- Binary Relation Inference Network for MDPs --- p.85Chapter 5.3.3 --- Continuous-Time Inference Network for MDPs --- p.87Chapter 5.4 --- Convergence Consideration --- p.88Chapter 5.5 --- Numerical Simulation --- p.90Chapter 5.5.1 --- Example 1: Random Walk --- p.90Chapter 5.5.2 --- Example 2: Random Walk on a Grid --- p.94Chapter 5.5.3 --- Example 3: Stochastic Shortest Path Problem --- p.97Chapter 5.5.4 --- Relationships Between λ and γ --- p.99Chapter 5.6 --- Discrete-Time Inference Network --- p.100Chapter 5.6.1 --- Results --- p.101Chapter 5.7 --- Conclusion --- p.102Chapter 6. --- On Distributed g-Learning Network --- p.104Chapter 6.1 --- Introduction --- p.105Chapter 6.2 --- Distributed Q-Learniing Network --- p.108Chapter 6.2.1 --- Distributed Q-Learning Network --- p.109Chapter 6.2.2 --- Q-Learning Network Architecture --- p.111Chapter 6.3 --- Experimental Results --- p.114Chapter 6.3.1 --- Random Walk --- p.114Chapter 6.3.2 --- The Shortest Path Problem --- p.116Chapter 6.4 --- Discussion --- p.120Chapter 6.4.1 --- Related Work --- p.121Chapter 6.5 --- FPGAs Implementation --- p.122Chapter 6.5.1 --- Distributed Registering Approach --- p.123Chapter 6.5.2 --- Serial BRAM Storing Approach --- p.124Chapter 6.5.3 --- Comparison --- p.125Chapter 6.5.4 --- Discussion --- p.127Chapter 6.6 --- Conclusion --- p.128Chapter 7. --- Summary --- p.129Bibliography --- p.132AppendixChapter A. --- Simplified Floating-Point Arithmetic --- p.143Chapter B. --- "Logarithm, Exponential and Division Implementation" --- p.144Chapter B.1 --- Introduction --- p.144Chapter B.2 --- Approximation Scheme --- p.145Chapter B.2.1 --- Logarithm --- p.145Chapter B.2.2 --- Exponentiation --- p.147Chapter B.2.3 --- Division --- p.148Chapter C. --- Analog VLSI Implementation --- p.150Chapter C.1 --- Site Function --- p.150Chapter C.1.1 --- Multiplication Cell --- p.150Chapter C.2 --- The Unit Function --- p.153Chapter C.3 --- The Inference Network Computation --- p.154Chapter C.4 --- Layout --- p.157Chapter C.5 --- Fabrication --- p.159Chapter C.5.1 --- Testing and Characterization --- p.16

    Optimization of Tapered Composite Beams

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    A study on the optimization of tapered composite beams for vibration is conducted. Designers of tapered rotating structural components such as wind mill, helicopter or turbine blades are increasingly considering composite materials as an option to create lighter structures without compromising structural stiffness and to significantly increase their efficiency. In the design of composite material structures, a challenge arises due to a large number of design variables, therefore numerical optimization is required for a better design. Given this, the purpose of this study is to propose an optimization methodology for the design of a tapered beam, considering the vibration constrains present in rotating components. This is achieved by coupling a numerical model which considers the bending modes of vibration, with an optimization algorithm, both coded in MATLAB. Five optimization algorithms, heuristic and deterministic, are coded and compared and the most efficient method is selected. Because the ply orientation angles can assume an infinite number of possible angles, or follow the regular 0 / ±45 / 90 degrees approach, four possible tuning approaches are defined. The beam is optimized for the following design cases of boundary conditions and design requirements: the presence or absence of a tensile axial force, the presence or absence of a taper, three taper configurations, four proposed structural tuning approaches and four boundary conditions. Two of these structural tuning approaches are compared for its influence in the dynamic behavior of the structural component and in achieving better values of in-plane and out-of-plane stresses. The results demonstrate the Genetic Algorithm is an efficient method for optimization, a design analysis is an important step in optimization, and an appropriate tuning approach can improve the overall efficiency of the optimized structure

    ASPM and CITK regulate spindle orientation by affecting the dynamics of astral microtubules.

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    Correct orientation of cell division is considered an important factor for the achievement of normal brain size, as mutations in genes that affect this process are among the leading causes of microcephaly. Abnormal spindle orientation is associated with reduction of the neuronal progenitor symmetric divisions, premature cell cycle exit, and reduced neurogenesis. This mechanism has been involved in microcephaly resulting from mutation of ASPM, the most frequently affected gene in autosomal recessive human primary microcephaly (MCPH), but it is presently unknown how ASPM regulates spindle orientation. In this report, we show that ASPM may control spindle positioning by interacting with citron kinase (CITK), a protein whose loss is also responsible for severe microcephaly in mammals. We show that the absence of CITK leads to abnormal spindle orientation in mammals and insects. In mouse cortical development, this phenotype correlates with increased production of basal progenitors. ASPM is required to recruit CITK at the spindle, and CITK overexpression rescues ASPM phenotype. ASPM and CITK affect the organization of astral microtubules (MT), and low doses of MT-stabilizing drug revert the spindle orientation phenotype produced by their knockdown. Finally, CITK regulates both astral-MT nucleation and stability. Our results provide a functional link between two established microcephaly proteins
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