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Comparisons of improved genomic predictions generated by different imputation methods for genotyping by sequencing data in livestock populations

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Journal of Animal science and Biotechnology 2020年第2期11卷 316-326页

作者： Xiao Wang Guosheng Su Dan Hao Mogens SandøLund Haja N.Kadarmideen Quantitative Genomics Bioinformatics and Computational Biology GroupDepartment of Applied Mathematics and Computer ScienceTechnical University of DenmarkRichard Peterson PladsBuilding 3242800 Kongens LyngbyDenmark Center for Quantitative Genetics and Genomics Department of Molecular Biology and GeneticsAarhus University8830 TjeleDenmark Department of Molecular Biology and Genetics Aarhus University8000 Aarhus CDenmark College of Animal Science and Technology Northwest A&F UniversityYangling 712100ShannxiChina

Background:Genotyping by sequencing(GBS)still has problems with missing *** is important for using GBS for genomic predictions,especially for low depths,due to the large number of missing *** allele frequency(MAF)is widely used as a marker data editing criteria for genomic *** this study,three imputation methods(Beagle,IMPUTE2 and FImpute software)based on four MAF editing criteria were investigated with regard to imputation accuracy of missing genotypes and accuracy of genomic predictions,based on simulated data of livestock ***:Four MAFs(no MAF limit,MAF≥0.001,MAF≥0.01 and MAF≥0.03)were used for editing marker data before ***,IMPUTE2 and FImpute software were applied to impute the original ***,IMPUTE2 also imputed the expected genotype dosage after genotype correction(GcIM).The reliability of genomic predictions was calculated using GBS and imputed GBS *** results showed that imputation accuracies were the same for the three imputation methods,except for the data of sequencing read depth(depth)=2,where FImpute had a slightly lower imputation accuracy than Beagle and *** was observed to be the best for all of the imputations at depth=4,5 and 10,but the worst for depth=*** genomic prediction,retaining more SNPs with no MAF limit resulted in higher *** the depth increased to 10,the prediction reliabilities approached those using true genotypes in the GBS *** and IMPUTE2 had the largest increases in prediction reliability of 5 percentage points,and FImpute gained 3 percentage points at depth=*** best prediction was observed at depth=4,5 and 10 using GcIM,but the worst prediction was also observed using GcIM at depth=***:The current study showed that imputation accuracies were relatively low for GBS with low depths and high for GBS with high *** resulted in larger gains in the reliability of genomic predictions for GBS with lowe

关键词： Genomic prediction Genotyping by sequencing Imputation MAF Simulation

Quantum Computing: Vision and Challenges

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arXiv 2024年

作者： Gill, Sukhpal Singh Cetinkaya, Oktay Marrone, Stefano Claudino, Daniel Haunschild, David Schlote, Leon Wu, Huaming Ottaviani, Carlo Liu, Xiaoyuan Machupalli, Sree Pragna Kaur, Kamalpreet Arora, Priyansh Liu, Ji Farouk, Ahmed Song, Houbing Herbert Uhlig, Steve Ramamohanarao, Kotagiri School of Electronic Engineering and Computer Science Queen Mary University of London London United Kingdom Department of Engineering Science University of Oxford Oxford United Kingdom Dipartimento di Matematica e Fisica Università della Campania "Luigi Vanvitelli" Italy Quantum Information Science Section Oak Ridge National Laboratory Oak RidgeTN United States Detecon International GmbH Munich Germany DB Cargo Berlin Germany Center for Applied Mathematics Tianjin University Tianjin China Department of Computer Science York Centre for Quantum Technologies University of York York United Kingdom Quantum Laboratory Fujitsu Research of America Inc. Santa ClaraCA United States Information Networking Institute Carnegie Mellon University PittsburghPA United States Cymax Group Technologies BurnabyBC Canada Microsoft Schiphol Netherlands Mathematics and Computational Research Division Argonne National Laboratory IL United States Department of Computer Science Faculty of Computers and Artificial Intelligence South Valley University Hurghada Egypt Baltimore United States The University of Melbourne MelbourneVIC Australia

The recent development of quantum computing, which uses entanglement, superposition, and other quantum fundamental concepts, can provide substantial processing advantages over traditional computing. These quantum features help solve many complex problems that cannot be solved otherwise with conventional computing methods. These problems include modeling quantum mechanics, logistics, chemical-based advances, drug design, statistical science, sustainable energy, banking, reliable communication, and quantum chemical engineering. The last few years have witnessed remarkable progress in quantum software and algorithm creation and quantum hardware research, which has significantly advanced the prospect of realizing quantum computers. It would be helpful to have comprehensive literature research on this area to grasp the current status and find outstanding problems that require considerable attention from the research community working in the quantum computing industry. To better understand quantum computing, this paper examines the foundations and vision based on current research in this area. We discuss cutting-edge developments in quantum computer hardware advancement and subsequent advances in quantum cryptography, quantum software, and high-scalability quantum computers. Many potential challenges and exciting new trends for quantum technology research and development are highlighted in this paper for a broader debate. Copyright © 2024, The Authors. All rights reserved.

关键词： Qubits

Multilevel approximation of Gaussian random fields: Covariance compression, estimation and spatial prediction

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arXiv 2021年

作者： Harbrecht, Helmut Herrmann, Lukas Kirchner, Kristin Schwab, Christoph Department of Mathematics and Computer Science University of Basel Spiegelgasse 1 Basel4051 Switzerland Johann Radon Institute for Computational and Applied Mathematics Austrian Academy of Sciences Altenbergerstrasse 69 Linz4040 Austria Delft Institute of Applied Mathematics Delft University of Technology P.O. Box 5031 Delft2600 GA Netherlands Seminar for Applied Mathematics ETH Zürich Rämistrasse 101 ZürichCH-8092 Switzerland

Centered Gaussian random fields (GRFs) indexed by compacta such as smooth, bounded domains in Euclidean space or smooth, compact and orientable manifolds are determined by their covariance operators. We consider centered GRFs given sample-wise as variational solutions to coloring operator equations driven by spatial white noise, with pseudodifferential coloring operator being elliptic, self-adjoint and positive from the Hörmander class. This includes the Matérn class of GRFs as a special case. Using microlocal tools and biorthogonal multiresolution analyses on the manifold, we prove that the precision and covariance operators, respectively, may be identified with bi-infinite matrices and finite sections may be diagonally preconditioned rendering the condition number independent of the dimension p of this section. We prove that a tapering strategy by thresholding as e.g. in [Bickel, P.J. and Levina, E. Covariance regularization by thresholding, Ann. Statist., 36 (2008), 2577–2604] applied on finite sections of the bi-infinite precision and covariance matrices results in optimally numerically sparse approximations. Numerical sparsity signifies that only asymptotically linearly many nonzero matrix entries are sufficient to approximate the original section of the bi-infinite covariance or precision matrix using this tapering strategy to arbitrary precision. This tapering strategy is non-adaptive and the locations of these nonzero matrix entries are known a priori. The tapered covariance or precision matrices may also be optimally diagonal preconditioned. Analysis of the relative size of the entries of the tapered covariance matrices motivates novel, multilevel Monte Carlo (MLMC) oracles for covariance estimation, in sample complexity that scales log-linearly with respect to the number p of parameters. This extends [Bickel, P.J. and Levina, E. Regularized Estimation of Large Covariance Matrices, Ann. Stat., 36 (2008), pp. 199–227] to estimation of (finite sections of) ps

关键词： Kriging

Extended Fayans energy density functional: optimization and analysis

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arXiv 2024年

作者： Reinhard, Paul-Gerhard O'Neal, Jared Wild, Stefan M. Nazarewicz, Witold Institut für Theoretische Physik II Universität Erlangen-Nürnberg ErlangenD-91058 Germany Mathematics and Computer Science Division Argonne National Laboratory LemontIL60439 United States Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Department of Industrial Engineering and Management Sciences Northwestern University EvanstonIL60208 United States Facility for Rare Isotope Beams Michigan State University East LansingMI48824 United States Department of Physics and Astronomy Michigan State University East LansingMI48824 United States

The Fayans energy density functional (EDF) has been very successful in describing global nuclear properties (binding energies, charge radii, and especially differences of radii) within nuclear density functional theory. In a recent study, supervised machine learning methods were used to calibrate the Fayans EDF. Building on this experience, in this work we explore the effect of adding isovector pairing terms, which are responsible for different proton and neutron pairing fields, by comparing a 13D model without the isovector pairing term against the extended 14D model. At the heart of the calibration is a carefully selected heterogeneous dataset of experimental observables representing ground-state properties of spherical even-even nuclei. To quantify the impact of the calibration dataset on model parameters and the importance of the new terms, we carry out advanced sensitivity and correlation analysis on both models. The extension to 14D improves the overall quality of the model by about 30%. The enhanced degrees of freedom of the 14D model reduce correlations between model parameters and enhance sensitivity. Copyright © 2024, The Authors. All rights reserved.

关键词： Density functional theory

Generalized forbidding matrix grammars and their membrane computing perspective 21

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Generalized forbidding matrix grammars and their membrane co...

21st International Conference on Membrane Computing, CMC 2020

作者： Fernau, Henning Kuppusamy, Lakshmanan Raman, Indhumathi Fachbereich 4 – Abteilung Informatikwissenschaften Universität Trier Trier54286 Germany School of Computer Science and Engineering VIT University Vellore632 014 India Department of Applied Mathematics and Computational Sciences PSG College of Technology Coimbatore641 004 India

ISBN: (纸本)9783030771010

Matrix grammars are one of the first approaches ever proposed in regulated rewriting, prescribing that rules have to be applied in a certain order. In traditional regulated rewriting, the most interesting case shows up when all rules are context-free. Typical descriptional complexity measures incorporate the number of nonterminals or the length, i.e., the number of rules per matrix. When viewing matrices as program fragments, it becomes natural to consider additional applicability conditions for such matrices. Here, we focus on forbidding sets, i.e., a matrix is applicable to a sentential form w only if none of the words in its forbidding set occurs as a subword in w. This gives rise to further natural descriptional complexity measures: How long could words in forbidding sets be? How many words could be in any forbidding set? How many matrices contain non-empty forbidding contexts? As context-free grammars with forbidding sets are known as generalized forbidding grammars, we call this variant of matrix grammars also generalized forbidding. In this paper, we attempt to answer the above four questions while studying the computational completeness of generalized forbidding matrix grammars. We also link our research to processing strings with membrane computing and discuss appropriate variations of P systems. © Springer Nature Switzerland AG 2021.

关键词： Matrix algebra

Digital Quantum Simulation of Cavity Quantum Electrodynamics: Insights from Superconducting and Trapped Ion Quantum Testbeds

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arXiv 2024年

作者： Rubin, Alex H. Marinelli, Brian Norman, Victoria A. Rizvi, Zainab Burch, Ashlyn D. Naik, Ravi K. Kreikebaum, John Mark Chow, Matthew N.H. Lobser, Daniel S. Revelle, Melissa C. Yale, Christopher G. Ivory, Megan Santiago, David I. Spitzer, Christopher Krstic-Marinkovic, Marina Clark, Susan M. Siddiqi, Irfan Radulaski, Marina Department of Electrical and Computer Engineering University of California DavisCA95616 United States Department of Physics University of California DavisCA95616 United States Quantum Nanoelectronics Laboratory Department of Physics University of California at Berkeley BerkeleyCA94720 United States Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Department of Computer Science University of California DavisCA95616 United States Sandia National Laboratories AlbuquerqueNM87123 United States Materials Science Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Institute for Theoretical Physics ETH Zurich Zurich8093 Switzerland

We explore the potential for hybrid development of quantum hardware where currently available quantum computers simulate open Cavity Quantum Electrodynamical (CQED) systems for applications in optical quantum communication, simulation and computing. Our simulations make use of a recent quantum algorithm that maps the dynamics of a singly excited open Tavis-Cummings model containing N atoms coupled to a lossy cavity. We report the results of executing this algorithm on two noisy intermediate-scale quantum computers: a superconducting processor and a trapped ion processor, to simulate the population dynamics of an open CQED system featuring N = 3 atoms. By applying technology-specific transpilation and error mitigation techniques, we minimize the impact of gate errors, noise, and decoherence in each hardware platform, obtaining results which agree closely with the exact solution of the system. These results can be used as a recipe for efficient and platform-specific quantum simulation of cavity-emitter systems on contemporary and future quantum computers. Copyright © 2024, The Authors. All rights reserved.

关键词： Quantum computers

Sequences in overpartitions

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arXiv 2021年

作者： Andrews, George E. Uncu, ALI Kemal Pennsylvania State University Department of Mathematics University ParkPA16802 United States Johann Radon Institute for Computational and Applied Mathematics Austrian Academy of Science Altenbergerstraße 69 LinzA-4040 Austria University of Bath Faculty of Science Department of Computer Science BathBA2 7AY United Kingdom

This paper is devoted to the study of sequences in overpartitions and their relation to 2-color partitions. An extensive study of a general class of double series is required to achieve these *** Codes Primary 11B65, Secondary 11C08, 11C20, 11P81, 11P84, 05A10, 05A15, 05A17 Copyright © 2021, The Authors. All rights reserved.

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A nuclear mass model rooted in chiral effective field theory

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arXiv 2025年

作者： Mishra, C. Ekström, A. Hagen, G. Menickelly, M. Papenbrock, T. Wild, S.M. Department of Physics and Astronomy University of Tennessee KnoxvilleTN37996 United States Lawrence Livermore National Laboratory LivermoreCA94551 United States Department of Physics Chalmers University of Technology GöteborgSE-412 96 Sweden Physics Division Oak Ridge National Laboratory Oak RidgeTN37831 United States Mathematics and Computer Science Division Argonne National Laboratory LemontIL60439 United States Applied Math & Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States

We develop a nuclear mass model that is based on chiral effective field theory at next-to-next-to leading order. Nuclear binding energies are computed via the Hartree-Fock method using a Hamiltonian from delta-full chiral effective field theory. We employ Hartree-Fock emulators to adjust 11 low-energy constants in the chiral interaction to binding energies of 18 even-even nuclei. When applied to 107 even-even nuclei with mass numbers 16 ≤ A ≤ 56 the chiral mass model exhibits an overall root-mean-square deviation of 3.5 MeV. © 2025, CC BY.

关键词： Binding energy

Reflecting (ON) the modulo 9 kanade-russell (conjectural) identities

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arXiv 2021年

作者： Uncu, Ali Zudilin, Wadim University of Bath Faculty of Science Department of Computer Science BathBA2 7AY United Kingdom Johann Radon Institute for Computational and Applied Mathematics Austrian Academy of Science Altenbergerstraße 69 LinzA-4040 Austria Department of Mathematics IMAPP Radboud University PO Box 9010 Nijmegen 6500 GL Netherlands

We examine complexity and versatility of five modulo 9 Kanade- Russell identities through their finite (aka polynomial) versions and images under the q → 1/q *** Codes Primary 11P84, Secondary 05A15, 05A17, 11B65 Cop... 详细信息

关键词： Functions