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Imaging atomic-scale chemistry from fused multi-modal electron microscopy

npj Computational Materials 2022年第1期8卷 164-171页

作者： Jonathan Schwartz Zichao Wendy Di Yi Jiang Alyssa J.Fielitz Don-Hyung Ha Sanjaya D.Perera Ismail El Baggari Richard D.Robinson Jeffrey A.Fessler Colin Ophus Steve Rozeveld Robert Hovden Department of Materials Science and Engineering University of MichiganAnn ArborMIUSA Mathematics and Computer Science Division Argonne National LaboratoryLemontILUSA Advanced Photon Source Facility Argonne National LaboratoryLemontILUSA Dow Chemical Co. MidlandMIUSA Department of Material Science and Engineering Cornell UniversityIthacaNew YorkUSA School of Integrative Engineering Chung-Ang UniversitySeoulRepublic of Korea Department of Physics Cornell UniversityIthacaNYUSA The Rowland Institute at Harvard CambridgeMAUSA Department of Electrical Engineering and Computer Science University of MichiganAnn ArborMIUSA National Center for Electron Microscopy Lawrence Berkeley National LaboratoryMolecular FoundryBerkeleyCAUSA Applied Physics Program University of MIchiganAnn ArborMIUnited States

Efforts to map atomic-scale chemistry at low doses with minimal noise using electron microscopes are fundamentally limited by inelastic ***,fused multi-modal electron microscopy offers high signal-to-noise ratio(SNR)recovery of material chemistry at nano-and atomic-resolution by coupling correlated information encoded within both elastic scattering(high-angle annular dark-field(HAADF))and inelastic spectroscopic signals(electron energy loss(EELS)or energy-dispersive x-ray(EDX)).By linking these simultaneously acquired signals,or modalities,the chemical distribution within nanomaterials can be imaged at significantly lower doses with existing detector *** many cases,the dose requirements can be reduced by over one order of *** high SNR recovery of chemistry is tested against simulated and experimental atomic resolution data of heterogeneous nanomaterials.

关键词： materials chemistry fused

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Correction to: Analysis of the dynamics of anthrax epidemic model with delay

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Discover applied Sciences 2024年第11期6卷 1-1页

作者： Raza, Ali Abdella, Kenzu Department of Physical Sciences The University of Chenab Gujrat Pakistan Mathematics Research Center Department of Mathematics Near East University Mersin 10 Türkiye Department of Computer Science and Mathematics Lebanese American University Beirut Lebanon Department of Mathematics Applied Modelling Graduate Program Trent University Peterborough Canada

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Ecumenical Modal Logic 1

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3rd International Workshop on Dynamic Logic, DaLí 2020

作者： Marin, Sonia Pereira, Luiz Carlos Pimentel, Elaine Sales, Emerson Department of Computer Science University College London London United Kingdom Philosophy Department PUC-Rio Rio de Janeiro Brazil Department of Mathematics UFRN Natal Brazil Graduate Program in Applied Mathematics and Statistics UFRN Natal Brazil

ISBN: (数字)9783030658403

ISBN: (纸本)9783030658397

The discussion about how to put together Gentzen’s systems for classical and intuitionistic logic in a single unified system is back in fashion. Indeed, recently Prawitz and others have been discussing the so called ecumenical Systems, where connectives from these logics can co-exist in peace. In Prawitz’ system, the classical logician and the intuitionistic logician would share the universal quantifier, conjunction, negation, and the constant for the absurd, but they would each have their own existential quantifier, disjunction, and implication, with different meanings. Prawitz’ main idea is that these different meanings are given by a semantical framework that can be accepted by both parties. In this work we extend Prawitz’ ecumenical idea to alethic K -modalities. © 2020, Springer Nature Switzerland AG.

关键词： Computer circuits

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Precise determination of pair interactions from pair statistics of many-body systems in and out of equilibrium

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Physical Review E 2022年第4期106卷 044122-044122页

作者： Salvatore Torquato Haina Wang Department of Chemistry Department of Physics Princeton Institute of Materials and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study 1 Einstein Drive Princeton New Jersey 08540 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA

The determination of the pair potential v(r) that accurately yields an equilibrium state at positive temperature T with a prescribed pair correlation function g2(r) or corresponding structure factor S(k) in d-dimensional Euclidean space Rd is an outstanding inverse statistical mechanics problem with far-reaching implications. Recently, Zhang and Torquato [Phys. Rev. E 101, 032124 (2020)] conjectured that any realizable g2(r) or S(k) corresponding to a translationally invariant nonequilibrium system can be attained by a classical equilibrium ensemble involving only (up to) effective pair interactions. Testing this conjecture for nonequilibrium systems as well as for nontrivial equilibrium states requires improved inverse methodologies. We have devised an optimization algorithm to precisely determine effective pair potentials that correspond to pair statistics of general translationally invariant disordered many-body equilibrium or nonequilibrium systems at positive temperatures. This methodology utilizes a parameterized family of pointwise basis functions for the potential function whose initial form is informed by small-, intermediate- and large-distance behaviors dictated by statistical-mechanical theory. Subsequently, a nonlinear optimization technique is utilized to minimize an objective function that incorporates both the target pair correlation function g2(r) and structure factor S(k) so that the small intermediate- and large-distance correlations are very accurately captured. To illustrate the versatility and power of our methodology, we accurately determine the effective pair interactions of the following four diverse target systems: (1) Lennard-Jones system in the vicinity of its critical point, (2) liquid under the Dzugutov potential, (3) nonequilibrium random sequential addition packing, and (4) a nonequilibrium hyperuniform “cloaked” uniformly randomized lattice. We found that the optimized pair potentials generate corresponding pair statistics that accur

关键词： Nonequilibrium statistical mechanics Optimization problems Structural properties Complex materials

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Moment-based metrics for molecules computable from cryogenic electron microscopy images

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Biological imaging 2024年 4卷 e3页

作者： Andy Zhang Oscar Mickelin Joe Kileel Eric J Verbeke Nicholas F Marshall Marc Aurèle Gilles Amit Singer Program in Applied and Computational Mathematics Princeton University Princeton NJ USA. Department of Mathematics and Oden Institute University of Texas at Austin Austin TX USA. Department of Mathematics Oregon State University Corvallis OR USA. Department of Mathematics Princeton University Princeton NJ USA.

Single-particle cryogenic electron microscopy (cryo-EM) is an imaging technique capable of recovering the high-resolution three-dimensional (3D) structure of biological macromolecules from many noisy and randomly oriented projection images. One notable approach to 3D reconstruction, known as Kam's method, relies on the moments of the two-dimensional (2D) images. Inspired by Kam's method, we introduce a rotationally invariant metric between two molecular structures, which does not require 3D alignment. Further, we introduce a metric between a stack of projection images and a molecular structure, which is invariant to rotations and reflections and does not require performing 3D reconstruction. Additionally, the latter metric does not assume a uniform distribution of viewing angles. We demonstrate the uses of the new metrics on synthetic and experimental datasets, highlighting their ability to measure structural similarity.

关键词： Kam’s method alignment-free metric method of moments protein structural similarity rotationally invariant distance structural search

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Designer Pair Statistics of Disordered Many-Particle Systems with Novel Properties

arXiv

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arXiv 2023年

作者： Wang, Haina Torquato, Salvatore Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Chemistry Department of Physics Princeton Materials Institute Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States School of Natural Sciences Institute for Advanced Study 1 Einstein Drive PrincetonNJ08540 United States

Knowledge of exact analytical functional forms for the pair correlation function g2(r) and its corresponding structure factor S(k) of disordered many-particle systems is limited. For fundamental and practical reasons, it is highly desirable to add to the existing data base of analytical functional forms for such pair statistics. Here, we design a plethora of such pair functions in direct and Fourier spaces across the first three Euclidean space dimensions that are realizable by diverse many-particle systems with varying degrees of correlated disorder across length scales, spanning a wide spectrum of hyperuniform, typical nonhyperuniform and antihyperuniform ones. This is accomplished by utilizing an efficient inverse algorithm that determines equilibrium states with up to pair interactions at positive temperature that precisely match targeted forms for both g2(r) and S(k). Among other results, we realize an example with the strongest hyperuniform property among known positive-temperature equilibrium states, critical-point systems (implying unusual 1D systems with phase transitions) that are not in the Ising universality class, systems that attain self-similar pair statistics under Fourier transformation, and an experimentally feasible polymer model. We show that our pair functions enable one to achieve systems with a wide range of translational order and self-diffusion coefficients D, which are inversely related to one another. One can design other realizable pair statistics via linear combinations of our functions or by applying our inverse procedure to other desirable functional forms. Our approach facilitates the inverse design of materials with desirable physical and chemical properties by tuning their pair statistics. © 2023, CC BY.

关键词： Statistics

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Scaling positive random matrices: Concentration and asymptotic convergence

arXiv

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arXiv 2020年

作者： Landa, Boris Program in Applied Mathematics Department of Mathematics Yale University United States

It is well known that any positive matrix can be scaled to have prescribed row and column sums by multiplying its rows and columns by certain positive scaling factors (which are unique up to a positive scalar). This procedure is known as matrix scaling, and has found numerous applications in operations research, economics, image processing, and machine learning. In this work, we investigate the behavior of the scaling factors and the resulting scaled matrix when the matrix to be scaled is random. Specifically, letting Ã∈ RM×N be a positive and bounded random matrix whose entries assume a certain type of independence, we provide a concentration inequality for the scaling factors of Ã around those of A = E[Ã]. This result is employed to bound the convergence rate of the scaling factors of Ã to those of A, as well as the concentration of the scaled version of Ã around the scaled version of A in operator norm, as M, N → ∞. When the entries of Ã are independent, M = N, and all prescribed row and column sums are 1 (i.e., doubly-stochastic matrix scaling), both of the previously-mentioned bounds are O(√log N/N) with high probability. We demonstrate our results in several *** Codes 60B20, 60F10, 65F35 Copyright © 2020, The Authors. All rights reserved.

关键词： Operations research

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Optimizing Hammerstein-Wiener Model for Forecasting Confirmed Cases of Covid-19

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IAENG International Journal of applied mathematics 2022年第1期52卷 1页

作者： Abdullahi, Sunusi Bala Ibrahim, Abdulkarim Hassan Abubakar, Auwal Bala Kambheera, Abhiwat General Investigation Zonal Criminal Investigation Section Force Criminal Investigation and Intelligence Department Nigeria Police Abuja900211 Nigeria Department of Applied Mathematics King Mongkut’s University of Technology Thonburi Bangkok Thailand Department of Mathematical Sciences Faculty of Physical Sciences Bayero University Kano700241 Nigeria Mathematics and Computing Science Program Faculty of Science and Technology Phetchabun Rajabhat University Phetchabun 67000 Thailand

Noise poses challenge to nonlinear Hammerstein-Wiener (HW) subsystem model application, because HW subsystem need large number of parameter interactions. However, flexibility, soft computing, and automatic adjustment to dynamic observation for best model fitting make it potential for forecasting nonlinear data. In this article, we adopted improved HW inference from Levenberg-Marquardt optimization algorithm to optimize HW subsystem and to select best model parameters. Therefore, the adopted model is tested on COVID-19 confirmed reported cases, to estimate transmission rate of COVID-19 virus for period from 15th March 2020 to 29th April 2020. Model validation is carried out on small dataset, which outperforms some existing models. The adopted model is further evaluated using statistical metrics and reported best accuracy of 0.127 and 0.998 for Mean Absolute percentage error (MAPE) and coefficient of determination (R2) respectively, with best model complexity of 1.86. The obtained results are promising enough in predicting spread of COVID-19 virus and may inspire as guidance to relax lockdown restriction policies. © 2022, IAENG International Journal of applied mathematics. All Rights Reserved.

关键词： COVID-19

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Position: Bayesian Deep Learning is Needed in the Age of Large-Scale AI 41

Position: Bayesian Deep Learning is Needed in the Age of Lar...

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41st International Conference on Machine Learning, ICML 2024

作者： Papamarkou, Theodore Skoularidou, Maria Palla, Konstantina Aitchison, Laurence Arbel, Julyan Dunson, David Filippone, Maurizio Fortuin, Vincent Hennig, Philipp Hernández-Lobato, José Miguel Hubin, Aliaksandr Immer, Alexander Karaletsos, Theofanis Khan, Mohammad Emtiyaz Kristiadi, Agustinus Li, Yingzhen Mandt, Stephan Nemeth, Christopher Osborne, Michael A. Rudner, Tim G.J. Rügamer, David Teh, Yee Whye Welling, Max Wilson, Andrew Gordon Zhang, Ruqi Department of Mathematics The University of Manchester Manchester United Kingdom Eric and Wendy Schmidt Center Broad Institute of MIT and Harvard Cambridge United States Spotify London United Kingdom Computational Neuroscience Unit University of Bristol Bristol United Kingdom Centre Inria de l'Université Grenoble Alpes Grenoble France Department of Statistical Science Duke University United States Statistics Program KAUST Saudi Arabia Helmholtz AI Munich Germany Department of Computer Science Technical University of Munich Munich Germany Munich Center for Machine Learning Munich Germany Tübingen AI Center University of Tübingen Tübingen Germany Department of Engineering University of Cambridge Cambridge United Kingdom Department of Mathematics University of Oslo Oslo Norway Bioinformatics and Applied Statistics Norwegian University of Life Sciences Ås Norway Department of Computer Science ETH Zurich Switzerland Chan Zuckerberg Initiative CA United States Center for Advanced Intelligence Project RIKEN Tokyo Japan Vector Institute Toronto Canada Department of Computing Imperial College London London United Kingdom Department of Computer Science UC Irvine Irvine United States Department of Mathematics and Statistics Lancaster University Lancaster United Kingdom Department of Engineering Science University of Oxford Oxford United Kingdom Center for Data Science New York University New York United States Department of Statistics LMU Munich Munich Germany DeepMind London United Kingdom Department of Statistics University of Oxford Oxford United Kingdom Informatics Institute University of Amsterdam Amsterdam Netherlands Courant Institute of Mathematical Sciences Center for Data Science Computer Science Department New York University New York United States Department of Computer Science Purdue University West Lafayette United States

In the current landscape of deep learning research, there is a predominant emphasis on achieving high predictive accuracy in supervised tasks involving large image and language datasets. However, a broader perspective reveals a multitude of overlooked metrics, tasks, and data types, such as uncertainty, active and continual learning, and scientific data, that demand attention. Bayesian deep learning (BDL) constitutes a promising avenue, offering advantages across these diverse settings. This paper posits that BDL can elevate the capabilities of deep learning. It revisits the strengths of BDL, acknowledges existing challenges, and highlights some exciting research avenues aimed at addressing these obstacles. Looking ahead, the discussion focuses on possible ways to combine large-scale foundation models with BDL to unlock their full potential. Copyright 2024 by the author(s)

关键词： Contrastive Learning

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Recent Methodological Advances in Federated Learning for Healthcare

arXiv

引用

arXiv 2023年

作者： Zhang, Fan Kreuter, Daniel Chen, Yichen Dittmer, Sören Tull, Samuel Shadbahr, Tolou Preller, Jacobus Rudd, James H.F. Aston, John A.D. Schönlieb, Carola-Bibiane Gleadall, Nicholas Roberts, Michael Department of Applied Mathematics and Theoretical Physics University of Cambridge Cambridge United Kingdom ZeTeM University of Bremen Bremen Germany Research Program in Systems Oncology Faculty of Medicine University of Helsinki Helsinki Finland Addenbrooke’s Hospital Cambridge University Hospitals NHS Trust Cambridge United Kingdom Department of Medicine University of Cambridge Cambridge United Kingdom Department of Pure Mathematics and Mathematical Statistics University of Cambridge Cambridge United Kingdom Department of Haematology University of Cambridge Cambridge United Kingdom

For healthcare datasets, it is often not possible to combine data samples from multiple sites due to ethical, privacy or logistical concerns. Federated learning allows for the utilisation of powerful machine learning algorithms without requiring the pooling of data. Healthcare data has many simultaneous challenges which require new methodologies to address, such as highly-siloed data, class imbalance, missing data, distribution shifts and non-standardised variables. Federated learning adds significant methodological complexity to conventional centralised machine learning, requiring distributed optimisation, communication between nodes, aggregation of models and redistribution of models. In this systematic review, we consider all papers on Scopus that were published between January 2015 and February 2023 and which describe new federated learning methodologies for addressing challenges with healthcare data. We performed a detailed review of the 89 papers which fulfilled these criteria. Significant systemic issues were identified throughout the literature which compromise the methodologies in many of the papers reviewed. We give detailed recommendations to help improve the quality of the methodology development for federated learning in healthcare. © 2023, CC BY.

关键词： Paper

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