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arXiv 2021年

作者： Torquato, Salvatore Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

The study of hyperuniform states of matter is an emerging multidisciplinary field, impinging on topics in the physical sciences, mathematics and biology. The focus of this work is the exploration of quantitative descriptors that herald when a many-particle system in d-dimensional Euclidean space Rd approaches a hyperuniform state as a function of the relevant control parameter. We establish quantitative criteria to ascertain the extent of hyperuniform and nonhyperuniform distance-scaling regimes as well as the crossover point between them in terms of the "volume" coefficient A and "surface-area" coefficient B associated with the local number variance σ2(R) for a spherical window of radius R. The larger the ratio B/A, the larger the hyperuniform scaling regime, which becomes of infinite extent in the limit B/A → ∞. To complement the known direct-space representation of the coefficient B in terms of the total correlation function h(r), we derive its corresponding Fourier representation in terms of the structure factor S(k), which is especially useful when scattering information is available experimentally or theoretically. We also demonstrate that the free-volume theory of the pressure of equilibrium packings of identical hard spheres that approach a strictly jammed state either along the stable crystal or metastable disordered branch dictates that such end states be exactly hyperuniform. Using the ratio B/A, as well as other diagnostic measures of hyperuniformity, including the hyperuniformity index H and the direct-correlation function length scale ξc, we study three different exactly solvable models as a function of the relevant control parameter, either density or temperature, with end states that are perfectly hyperuniform. Specifically, we analyze equilibrium systems of hard rods and "sticky" hard-sphere systems in arbitrary space dimension d as a function of density. We also examine low-temperature excited states of many-particle systems interacting with "steal

关键词： Temperature

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COVID-19 Infected Lung Computed Tomography Segmentation and Supervised Classification Approach

引用

Computers, Materials & Continua 2021年第7期68卷 391-407页

作者： Aqib Ali Wali Khan Mashwani Samreen Naeem Muhammad Irfan Uddin Wiyada Kumam Poom Kumam Hussam Alrabaiah Farrukh Jamal Christophe Chesneau Department of Computer Science Concordia College BahawalpurBahawalpur63100Pakistan Department of Computer Science&IT Glim Institute of Modern StudiesBahawalpur63100Pakistan Institute of Numerical Sciences Kohat University of Science&TechnologyKohat26000Pakistan Institute of Computing Kohat University of Science and TechnologyKohat26000Pakistan Program in Applied Statistics Department of Mathematics and Computer ScienceFaculty of Science and TechnologyRajamangala University of Technology ThanyaburiThanyaburi12110Thailand Departments of Mathematics Faculty of ScienceCenter of Excellence in Theoretical and Computational Science(TaCS-CoE)&KMUTT Fixed Point Research LaboratoryRoom SCL 802 Fixed Point LaboratoryScience Laboratory BuildingKing Mongkut’s University of Technology Thonburi(KMUTT)Bangkok10140Thailand Department of Medical Research China Medical University HospitalTaichung40402Taiwan College of Engineering Al Ain UniversityAl Ain64141United Arab Emirates Department of Mathematics Tafila Technical UniversityTafila66110Jordan Department of Statistics The Islamia University of BahawalpurBahawalpur63100Pakistan 11Department of MathematicsUniversitéde CaenLMNOCaen14032France

The purpose of this research is the segmentation of lungs computed tomography(CT)scan for the diagnosis of COVID-19 by using machine learning *** dataset contains data from patients who are prone to the *** contains three types of lungs CT images(Normal,Pneumonia,and COVID-19)collected from two different sources;the first one is the Radiology Department of Nishtar Hospital Multan and Civil Hospital Bahawalpur,Pakistan,and the second one is a publicly free available medical imaging database known as *** the preprocessing,a novel fuzzy c-mean automated region-growing segmentation approach is deployed to take an automated region of interest(ROIs)and acquire 52 hybrid statistical features for each ***,12 optimized statistical features are selected via the chi-square feature reduction *** the classification,five machine learning classifiers named as deep learning J4,multilayer perceptron,support vector machine,random forest,and naive Bayes are deployed to optimize the hybrid statistical features *** is observed that the deep learning J4 has promising results(sensitivity and specificity:0.987;accuracy:98.67%)among all the deployed *** a complementary study,a statistical work is devoted to the use of a new statistical model to fit the main datasets of COVID-19 collected in Pakistan.

关键词： COVID-19 machine learning fuzzy c-mean deep learning J4

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The bourque distances for mutation trees of cancers 20

The bourque distances for mutation trees of cancers

引用

20th International Workshop on Algorithms in Bioinformatics, WABI 2020

作者： Jahn, Katharina Beerenwinkel, Niko Zhang, Louxin Department of Biosystems Science and Engineering ETH Zurich Basel Switzerland SIB Swiss Institute of Bioinformatics Basel Switzerland Department of Mathematics and Computational Biology Program National University of Singapore Singapore

ISBN: (纸本)9783959771610

Mutation trees are rooted trees of arbitrary node degree in which each node is labeled with a mutation set. These trees, also referred to as clonal trees, are used in computational oncology to represent the mutational history of tumours. Classical tree metrics such as the popular RobinsonFoulds distance are of limited use for the comparison of mutation trees. One reason is that mutation trees inferred with different methods or for different patients often contain different sets of mutation labels. Here, we generalize the RobinsonFoulds distance into a set of distance metrics called Bourque distances for comparing mutation trees. A connection between the RobinsonFoulds distance and the nearest neighbor interchange distance is also presented. © Katharina Jahn, Niko Beerenwinkel, and Louxin Zhang;licensed under Creative Commons License CC-BY

关键词： Bourque distance Clonal trees Mutation trees Phylogenetic trees Robinson–Foulds distance Tree distance Tree metric

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Study of self-interaction-errors in barrier heights using locally scaled and Perdew-Zunger self-interaction methods

arXiv

引用

arXiv 2022年

作者： Mishra, Prakash Yamamoto, Yoh Johnson, J. Karl Jackson, Koblar A. Zope, Rajendra R. Baruah, Tunna Computational Science Program University of Texas at El Paso El PasoTX79968 United States Department of Physics University of Texas El PasoTX79968 United States Department of Chemical & Petroleum Engineering University of Pittsburgh PittsburghPA15261 United States Physics Department Science of Advanced Materials Program Central Michigan University Mt. PleasantMI48859 United States

We study the effect of self-interaction errors on the barrier heights of chemical reactions. For this purpose we use the well-known Perdew-Zunger [J. P. Perdew and A. Zunger, Phys. Rev. B, 23, 5048 (1981)] self-interaction-correction (PZSIC), as well as two variations of the recently developed, locally scaled self-interaction correction (LSIC) [R. R. Zope et al., J. Chem. Phys. 151, 214108 (2019)] to study the barrier heights of the BH76 benchmark dataset. Our results show that both PZSIC and especially the LSIC methods improve the barrier heights relative to the local density approximation (LDA). The version of LSIC that uses the iso-orbital indicator z as a scaling factor gives a more consistent improvement than an alternative version that uses an orbital-dependent factor w based on the ratio of orbital densities to the total electron density. We show that LDA energies evaluated using the self-consistent and self-interaction-free PZSIC densities can be used to assess density-driven errors. The LDA reaction barrier errors for the BH76 set are found to contain significant density-driven errors for all types of reactions contained in the set, but the corrections due to adding SIC to the functional are much larger than those stemming from the density for the hydrogen transfer reactions and of roughly equal size for the non-hydrogen transfer reactions. Copyright © 2022, The Authors. All rights reserved.

关键词： Local density approximation

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A Sparse DAE Solver in Maple

arXiv

引用

arXiv 2022年

作者： Jang, Taejin Uppaluri, Maitri Subramanian, Venkat R. Materials Science and Engineering Program Texas Materials Institute The University of Texas at Austin AustinTX78712 United States Walker Department of Mechanical Engineering The University of Texas at Austin AustinTX78712 United States Oden Institute for Computational Science and Engineering The University of Texas at Austin AustinTX United States

In this paper, some adaptive single-step methods like Trapezoid (TR), Implicit-mid point (IMP), Euler-backward (EB), and Radau IIA (Rad) methods are implemented in Maple to solve index-1 nonlinear Differential Algebraic Equations (DAEs). Maple's robust and efficient ability to search within a list/set is exploited to identify the sparsity pattern and the analytic Jacobian. The algorithm and implementation were found to be robust and efficient for index-1 DAE problems and scales well for finite difference/finite element discretization of two-dimensional models with system size up to 10,000 nonlinear DAEs and solves the same in few seconds. © 2022, CC BY-NC-ND.

关键词： Differential equations

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CAUCHY MARKOV RANDOM FIELD PRIORS FOR BAYESIAN INVERSION

arXiv

引用

arXiv 2021年

作者： Suuronen, Jarkko Chada, Neil K. Roininen, Lassi School of Engineering Science Lappeenranta-Lahti University of Technology PO Box 20 LappeenrantaFI-53851 Finland Applied Mathematics and Computational Science Program King Abdullah University of Science and Technology Thuwal23955 Saudi Arabia

The use of Cauchy Markov random field priors in statistical inverse problems can potentially lead to posterior distributions which are non-Gaussian, high-dimensional, multimodal and heavy-tailed In order to use such priors successfully, sophisticated optimization and Markov chain Monte Carlo (MCMC) methods are usually required In this paper, our focus is largely on reviewing recently developed Cauchy difference priors, while introducing interesting new variants, whilst providing a comparison We firstly propose a one-dimensional second order Cauchy difference prior, and construct new first and second order two-dimensional isotropic Cauchy difference priors Another new Cauchy prior is based on the stochastic partial differential equation approach, derived from Matérn type Gaussian presentation The comparison also includes Cauchy sheets Our numerical computations are based on both maximum a posteriori and conditional mean estimation We exploit state-of-the-art MCMC methodologies such as Metropolis-within-Gibbs, Repelling-Attracting Metropolis, and No-U-Turn sampler variant of Hamiltonian Monte Carlo We demonstrate the models and methods constructed for one-dimensional and two-dimensional deconvolution problems Thorough MCMC statistics are provided for all test cases, including potential scale reduction factors. Copyright © 2021, The Authors. All rights reserved.

关键词： Bayesian networks

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TERMinator: A Neural Framework for Structure-Based Protein Design using Tertiary Repeating Motifs

arXiv

引用

arXiv 2022年

作者： Li, Alex J. Sundar, Vikram Grigoryan, Gevorg Keating, Amy E. Department of Chemistry Massachusetts Institute of Technology United States Computational and Systems Biology Program Massachusetts Institute of Technology United States Department of Computer Science Dartmouth College United States Departments of Biology and Biological Engineering Massachusetts Institute of Technology United States

computational protein design has the potential to deliver novel molecular structures, binders, and catalysts for myriad applications. Recent neural graph-based models that use backbone coordinate-derived features show exceptional performance on native sequence recovery tasks and are promising frameworks for design. A statistical framework for modeling protein sequence landscapes using Tertiary Motifs (TERMs), compact units of recurring structure in proteins, has also demonstrated good performance on protein design tasks. In this work, we investigate the use of TERM-derived data as features in neural protein design frameworks. Our graph-based architecture, TERMinator, incorporates TERM-based and coordinate-based information and outputs a Potts model over sequence space. TERMinator outperforms state-of-the-art models on native sequence recovery tasks, suggesting that utilizing TERM-based and coordinate-based features together is beneficial for protein design. © 2022, CC BY.

关键词： Potts model

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A gas-only bioreactor system maintains stable culture environments and reveals that moderate pH deviations trigger transcriptome-wide responses in human cells cultured in physioxia and physiological buffers

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Life Medicine 2023年第2期1卷 236-240页

作者： Silvia Arossa Samhan M. Alsolami Shannon G. Klein Yingzi Zhang Gerardo Ramos-Mandujano Alexandra Steckbauer Anieka J. Parry Juan Carlos Izpisúa-Belmonte Carlos M. Duarte Mo Li Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC) King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia Bioscience Program Biological and Environmental Science and Engineering Division (BESE) King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia Gene Expression Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Rd. La Jolla CA 92037 USA Altos Labs Inc. 5510 Morehouse Drive Suite 300 San Diego CA 92121 USA

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Mean-field theory for double-well systems on degree-heterogeneous networks

arXiv

引用

arXiv 2022年

作者： Kundu, Prosenjit MacLaren, Neil G. Kori, Hiroshi Masuda, Naoki Department of Mathematics State University of New York BuffaloNY14260-2900 United States Department of Complexity Science and Engineering The University of Tokyo Chiba277-8561 Japan Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY14260-5030 United States

Many complex dynamical systems in the real world, including ecological, climate, financial, and power-grid systems, often show critical transitions, or tipping points, in which the system’s dynamics suddenly transit into a qualitatively different state. In mathematical models, tipping points happen as a control parameter gradually changes and crosses a certain threshold. Tipping elements in such systems may interact with each other as a network, and understanding the behavior of interacting tipping elements is a challenge because of the high dimensionality originating from the network. Here we develop a degree-based mean-field theory for a prototypical double-well system coupled on a network with the aim of understanding coupled tipping dynamics with a low-dimensional description. The method approximates both the onset of the tipping point and the position of equilibria with a reasonable accuracy. Based on the developed theory and numerical simulations, we also provide evidence for multistage tipping point transitions in networks of double-well systems. © 2022, CC BY.

关键词： Mean field theory

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An Island-Based Hybrid Evolutionary Algorithm for Caloric-Restricted Diets

Research Square

引用

Research Square 2021年

作者： Silva, João Gabriel R. Duarte, Grasiele R. Carvalho, Iago A. Goliatt, Leonardo Vieira, Vinicius F. Xavier, Carolina R. IFMT Brazil Computational Modeling Federal University of Juiz de Fora Brazil Civil Engineering Program COPPE Federal University of Rio de Janeiro Brazil Computer Science Program Federal University of Minas Gerais Brazil Computer Science Program Federal University of Sao Joao del Rei Brazil

The most popular and successful way to maintain a healthy body is to have a rich and balanced diet, combined with physical exercise. Since it was proposed the diet dilemma, several works in the literature suggested calculating a diet that respects an individual’s nutritional needs. In the Caloric-Restricted Diet Problem (CRDP), the goal is to find a reduced-calorie diet that meets an individual’s dietary needs aiming for weight loss. This paper proposes a Hybrid Island-Based Evolutionary Algorithm (IBHEA) that combines a Genetic Algorithm (GA) with a Differential Evolution (DE) communicating through a migration policy to solve the CRDP. computational experiments showed that IBHEA outperforms the non-distributed and non-hybrid implementations, generating a greater variety of diets with a small calorie count. © 2021, CC BY.

关键词： Nutrition

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