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Quantifying the local reliability of a sequence alignment

PROTEIN ENGINEERING 1996年第2期9卷 127-132页

作者： Mevissen, HT Vingron, M German National Research Center for Computer Science (GMD) Institute for Algorithms and Scientific Computing (SCAI) SchlossBirlinghoven D-53754 St Augustin Germany

We present a method for attributing a measure of reliability to a residue pair in an optimal alignment of two protein sequences. Validation based on a database of structurally correct alignments [Pascarella and Argos (1992) Protein Engng, 5, 121-137] shows that correctly aligned parts of a sequence alignment systematically receive high scores in this measure, The higher the sequence similarity between two sequences, the larger is the fraction found of the correct parts of the alignment, We used these observations to design a program that draws a reliability curve along an optimal alignment reflecting the chances for each residue pair to be aligned correctly.

关键词： alignment reliability protein sequence alignment

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On the use of simplex methods in constructing quadratic models

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science China Mathematics 2007年第7期50卷 913-924页

作者： Qing-hua ZHOU 1 College of Mathematics and computer,Hebei University,Baoding 071002,China 2 State Key Laboratory of scientific and Engineering computing,Institute of Computational Mathematics and scientific/Engineering computing,Academy of Mathematics and Systems science,Chinese Academy of sciences,Beijing 100080,China College of Mathematics Computer Hebei University Baoding 071002 China State Key Laboratory of Scientific Engineering Computing Institute of Computational Mathematics Scientific/Engineering Computing Academy of Mathematics Systems Science Chinese Academy of Sciences Beijing 100080 China

In this paper, we investigate the quadratic approximation methods. After studying the basic idea of simplex methods, we construct several new search directions by combining the local information progressively obtained during the iterates of the algorithm to form new subspaces. And the quadratic model is solved in the new subspaces. The motivation is to use the information disclosed by the former steps to construct more promising directions. For most tested problems, the number of functions evaluations have been reduced obviously through our algorithms.

关键词： unconstrained optimization trust region method quadratic model Lagrange function simplex methods direct methods 90C56

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High order finite volume methods for singular perturbation problems

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science China Mathematics 2008年第8期51卷 1391-1400页

作者： CHEN ZhongYing HE ChongNan WU Bin Department of Scientific Computing and Computer Applications Sun Yat-Sen UniversityGuangzhou 510275China College of Mathematics and Computer Science Guangxi University for NationalitiesNanning 530006China

In this paper we establish a high order finite volume method for the fourth order singular perturbation *** conjunction with the optimal meshes,the numerical solutions resulting from the method have optimal convergenc... 详细信息

关键词： finite volume methods optimal meshes singular perturbation problems 65L10 65L12 65L60

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Using unified parallel C to parallelize the FDTD method of computational electrodynamics

Using unified parallel C to parallelize the FDTD method of c...

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2009 IEEE 13th International Multitopic Conference, INMIC 2009

作者： Hussain, A. Shafi, A. Raza, J. Center for High Performance Scientific Computing Department of Computing NUST School of Electrical Engineering and Computer Science Pakistan

ISBN: (纸本)9781424448722

This paper discusses a parallel implementation of the Finite-Difference Time-Domain (FDTD) method using Unified Parallel C (UPC). UPC is an extension of ANSI C - primarily designed for programming distributed memory parallel hardware. The FDTD method is a powerful and widely used numerical technique in computational electromagnetics community. It is a resource - CPU cycles and memory - hungry technique. Consequently, a parallel implementation is highly desirable to decrease time-to-solution and be able to study larger problems with limited resources. To the best of our knowledge, this is the first attempt to exploit UPC to parallelize the FDTD method. We evaluate the performance of our implementation on a cluster of four SunFire v890 compute nodes-each equipped with 16 processing cores - and report impressive speedups. ©2009 IEEE.

关键词： Finite difference time domain method

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MAP-based Problem-Agnostic Diffusion Model for Inverse Problems

arXiv

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arXiv 2025年

作者： Tao, Pingping Liu, Haixia Su, Jing Yang, Xiaochen Tan, Hongchen Shandong University Library No. 180 West Culture Road Shandong Weihai264209 China School of Mathematics and Statistics Hubei Key Laboratory of Engineering Modeling and Scientific Computing Institute of Interdisciplinary Research for Mathematics and Applied Science Huazhong University of Science and Technology No. 1037 Luoyu road Hubei Wuhan430074 China Dapartment of Basic Sciences Dalian University of Science and Technology No. 999-26 Harbor Road Liaoning Dalian116052 China School of Computer Science and Technology Harbin Institute of Technology No. 2 West Culture Road Shandong Weihai264209 China Institute of Future Technology Dalian University of Technology No. 2 Lingong Road Liaoning Dalian116081 China

Diffusion models have indeed shown great promise in solving inverse problems in image processing. In this paper, we propose a novel, problem-agnostic diffusion model called the maximum a posteriori (MAP)-based guided term estimation method for inverse problems. To leverage unconditionally pretrained diffusion models to address conditional generation tasks, we divide the conditional score function into two terms according to Bayes’ rule: an unconditional score function (approximated by a pretrained score network) and a guided term, which is estimated using a novel MAP-based method that incorporates a Gaussian-type prior of natural images. This innovation allows us to better capture the intrinsic properties of the data, leading to improved performance. Numerical results demonstrate that our method preserves contents more effectively compared to state-of-the-art methods—for example, maintaining the structure of glasses in super-resolution tasks and producing more coherent results in the neighborhood of masked regions during inpainting. Our numerical implementation is available at https://***/liuhaixias1/ MAP-DIFFUSION-IP. Copyright © 2025, The Authors. All rights reserved.

关键词： Inverse problems

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A Performance Analysis of Task Scheduling for UQ Workflows on HPC Systems

arXiv

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arXiv 2025年

作者： Loi, Chung Ming Reinarz, Anne Lykkegaard, Mikkel Hornsby, William Buchanan, James Seelinger, Linus Danish Technological Institute Aarhus Denmark UKAEA-CCFE Abingdon United Kingdom Scientific Computing Center Karlsruhe Institute of Technology Karlsruhe Germany Department of Computer Science Durham University Durham United Kingdom

Uncertainty Quantification (UQ) workloads are becoming increasingly common in science and engineering. They involve the submission of thousands or even millions of similar tasks with potentially unpredictable runtimes, where the total number is usually not known a priori. A static one-size-fits-all batch script would likely lead to suboptimal scheduling, and native schedulers installed on High-Performance computing (HPC) systems such as SLURM often struggle to efficiently handle such workloads. In this paper, we introduce a new load balancing approach suitable for UQ workflows. To demonstrate its efficiency in a real-world setting, we focus on the GS2 gyrokinetic plasma turbulence simulator. Individual simulations can be computationally demanding, with runtimes varying significantly—from minutes to hours—depending on the high-dimensional input parameters. Our approach uses the UQ and Modelling Bridge, which offers a language-agnostic interface to a simulation model, combined with HyperQueue which works alongside the native scheduler. In particular, deploying this framework on HPC systems does not require system-level changes. We benchmark our proposed framework against a standalone SLURM approach using GS2 and a Gaussian Process surrogate thereof. Our results demonstrate a reduction in scheduling overhead by up to three orders of magnitude and a maximum reduction of 38% in CPU time for long-running simulations compared to the naïve SLURM approach, while making no assumptions about the job submission patterns inherent to UQ workflows. © 2025, CC BY.

关键词： Fusion reactions

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Stabilized approximate inverse preconditioners for indefinite matrices 46

Stabilized approximate inverse preconditioners for indefinit...

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46th Annual Southeast Regional Conference on XX, ACM-SE 46

作者： Lee, Eun-Joc Laboratory for High Performance Scientific Computing and Computer Simulation Department of Computer Science University of Kentucky United States

ISBN: (纸本)9781605581057

A two-phase preconditioning strategy based on a factored sparse approximate inverse is proposed for solving sparse indefinite matrices. In each phase, the strategy first makes the original matrix diagonally dominant to enhance the stability by a shifting method, and constructs an inverse approximation of the shifted matrix by utilizing a factored sparse approximate inverse preconditioner. The two inverse approximation matrices produced from each phase are then combined to be used as a preconditioner. Experimental results show that the presented strategy improves the accuracy and the stability of the preconditioner on solving indefinite sparse matrices. Furthermore, the strategy ensures that convergence rate of the preconditioned iterations of the two-phase preconditioning strategy is much better than that of the standard sparse approximate inverse ones for solving indefinite matrices. Copyright 2008 ACM.

关键词： Matrix algebra

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A SPARSE-GRID METHOD FOR MULTI-DIMENSIONAL BACKWARD STOCHASTIC DIFFERENTIAL EQUATIONS

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Journal of Computational Mathematics 2013年第3期31卷 221-248页

作者： Guannan Zhang Max Gunzburger Weidong Zhao Department of Scientific Computing Florida State University Tallahassee FL 32306Computer Science and Mathematics Division Oak Ridge National Lab Oak Ridge TN 37831 Department of Scientific Computing Florida State University Tallahassee FL 32306 School of Mathematics Shandong University Jinan Shandong 250100 China

A sparse-grid method for solving multi-dimensional backward stochastic differential equations （BSDEs） based on a multi-step time discretization scheme [31] is presented. In the multi-dimensional spatial domain, i.e. the Brownian space, the conditional mathe- matical expectations derived from the original equation are approximated using sparse-grid Gauss-Hermite quadrature rule and （adaptive） hierarchical sparse-grid interpolation. Error estimates are proved for the proposed fully-discrete scheme for multi-dimensional BSDEs with certain types of simplified generator functions. Finally, several numerical examples are provided to illustrate the accuracy and efficiency of our scheme.

关键词： Backward stochastic differential equations Multi-step scheme Gauss-Hermite quadrature rule Adaptive hierarchical basis Sparse grids.

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Modular Autonomous Virtualization System for Two-Dimensional Semiconductor Quantum Dot Arrays

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Physical Review X 2025年第2期15卷 021034-021034页

作者： Anantha S. Rao Donovan Buterakos Barnaby van Straaten Valentin John Cécile X. Yu Stefan D. Oosterhout Lucas Stehouwer Giordano Scappucci Menno Veldhorst Francesco Borsoi Justyna P. Zwolak Joint Center for Quantum Information and Computer Science University of Maryland College Park Maryland 20742 USA Department of Physics University of Maryland College Park Maryland 20742 USA National Institute of Standards and Technology Gaithersburg Maryland 20899 USA QuTech and Kavli Institute of Nanoscience Delft University of Technology P.O. Box 5046 2600 GA Delft The Netherlands QuTech and Netherlands Organisation for Applied Scientific Research (TNO) Delft The Netherlands Present address: NNF Quantum Computing Programme Niels Bohr Institute University of Copenhagen Blegdamsvej 17 2100 Copenhagen Denmark.

Arrays of gate-defined semiconductor quantum dots are among the leading candidates for building scalable quantum processors. High-fidelity initialization, control, and readout of spin qubit registers require exquisite and targeted control over key Hamiltonian parameters that define the electrostatic environment. However, due to the tight gate pitch, capacitive crosstalk between gates hinders independent tuning of chemical potentials and interdot couplings. While virtual gates offer a practical solution, determining all the required cross-capacitance matrices accurately and efficiently in large quantum dot registers is an open challenge. Here, we establish a modular automated virtualization system (MAViS)—a general and modular framework for autonomously constructing a complete stack of multilayer virtual gates in real time. Our method employs machine learning techniques to rapidly extract features from two-dimensional charge stability diagrams. We then utilize computer vision and regression models to self-consistently determine all relative capacitive couplings necessary for virtualizing plunger and barrier gates in both low- and high-tunnel-coupling regimes. Using MAViS, we successfully demonstrate accurate virtualization of a dense two-dimensional array comprising ten quantum dots defined in a high-quality Ge/SiGe heterostructure. Our work offers an elegant and practical solution for the efficient control of large-scale semiconductor quantum dot systems.

关键词： Semiconductor quantum dots

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Enactment engine independent provenance recording for e-science infrastructures

Enactment engine independent provenance recording for e-Scie...

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2010 4th International Conference on Research Challenges in Information science, RCIS 2010

作者： Khanl, Fakhri Alam Hussain, Sardar Janciakl, Ivan Brezanyl, Peter Department of Scientific Computing Faculty of Computer Science University of Vienna Austria Glasgow United Kingdom

ISBN: (纸本)9781424448401

Researchers are becoming more effective in their work with the automation of scientific discovery processes and experiments in dry-labs rather than through wet-labs experiments. The automation of these processes requires complex workflows, which is one of the promising techniques to help collaborating scientists to share their experimental results and achieve them via a distributed software infrastructure. Subsequently, the history of the findings needs to be recorded - so called provenance - in order to be reproducible and re-provable. Various solutions and techniques have been elaborated for provenance data collection and analysis. In this paper we propose a taxonomy to categorize existing solutions for run-time and execution provenance of workflows into workflow enactment engine dependent, so called listener mode provenance category, and enactment engine independent, so called monitoring mode provenance category. Additionally, our novel solution for a monitoring mode provenance concept at the middleware level is introduced and the design, architecture and performance evaluation of our prototype implementation are discussed. © 2010 IEEE.

关键词： Engines

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