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arXiv 2023年

作者： De Vente, Coen Vermeer, Koenraad A. Jaccard, Nicolas Wang, He Sun, Hongyi Khader, Firas Truhn, Daniel Aimyshev, Temirgali Zhanibekuly, Yerkebulan Le, Tien-Dung Galdran, Adrian Ballester, Miguel Ángel González Carneiro, Gustavo Devika, R.G. Hrishikesh, P.S. Puthussery, Densen Liu, Hong Yang, Zekang Kondo, Satoshi Kasai, Satoshi Wang, Edward Durvasula, Ashritha Heras, Jónathan Zapata, Miguel Ángel Araújo, Teresa Aresta, Guilherme Bogunović, Hrvoje Arikan, Mustafa Lee, Yeong Chan Cho, Hyun Bin Choi, Yoon Ho Qayyum, Abdul Razzak, Imran Van Ginneken, Bram Lemij, Hans G. Sánchez, Clara I. Group Informatics Institute Universiteit Van Amsterdam Noord-Holland Amsterdam Netherlands The Department of Biomedical Engineering and Physics Amsterdam Umc Locatie Amc Noord-Holland Amsterdam Netherlands Department of Radiology and Nuclear Medicine Radboudumc Gelderland Nijmegen Netherlands The Rotterdam Ophthalmic Institute Rotterdam Eye Hospital Rotterdam Netherlands Project Orbis International Inc. New York United States The Peking Union Medical College Hospital Beijing China The Xuanwu Hospital Capital Medical University Beijing100053 China The Tsinghua University Beijing China The Department of Diagnostic and Interventional Radiology University Hospital Aachen Aachen Germany Cmc Technologies Llp Nur-Sultan Kazakhstan Kbc Belgium Universitat Pompeu Fabra Barcelona Spain The Australian Institute for Machine Learning Aiml University of Adelaide Australia Icrea Barcelona Spain The Centre for Vision Speech and Signal Processing University of Surrey United Kingdom The College of Engineering Trivandrum India Founding Minds Software India The Institute of Computing Technology Chinese Academy of Sciences China The Muroran Institute of Technology Japan The Niigata University of Health and Welfare Japan The Schulich School of Medicine and Dentistry University of Western Ontario London Canada The Department of Mathematics and Computer Science University of la Rioja Spain Hospital Vall Hebron Passeig Roser 126 Sant Cugat del Vallès Barcelona08195 Spain UPRetina Barcelona Spain The Christian Doppler Laboratory for Artificial Intelligence in Retina Department of Ophthalmology and Optometry Medical University of Vienna Vienna Austria The Institute of Ophthalmology University College London London United Kingdom The Research Institute for Future Medicine Samsung Medical Center Seoul Korea Republic of Sungkyunkwan University Samsung Medical Center Seoul Korea Republic of The Department of Artificial Intelligence and Informatics Mayo Clinic Jacks

The early detection of glaucoma is essential in preventing visual impairment. Artificial intelligence (AI) can be used to analyze color fundus photographs (CFPs) in a cost-effective manner, making glaucoma screening more accessible. While AI models for glaucoma screening from CFPs have shown promising results in laboratory settings, their performance decreases significantly in realworld scenarios due to the presence of out-of-distribution and low-quality images. To address this issue, we propose the Artificial Intelligence for Robust Glaucoma Screening (AIROGS) challenge. This challenge includes a large dataset of around 113,000 images from about 60,000 patients and 500 different screening centers, and encourages the development of algorithms that are robust to ungradable and unexpected input data. We evaluated solutions from 14 teams in this paper, and found that the best teams performed similarly to a set of 20 expert ophthalmologists and optometrists. The highest-scoring team achieved an area under the receiver operating characteristic curve of 0.99 (95% CI: 0.98-0.99) for detecting ungradable images on-the-fly. Additionally, many of the algorithms showed robust performance when tested on three other publicly available datasets. These results demonstrate the feasibility of robust AI-enabled glaucoma screening. Copyright © 2023, The Authors. All rights reserved.

关键词： Diagnosis

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Code-aware combinatorial interaction testing

arXiv

引用

arXiv 2019年

作者： Ahmed, Bestoun S. Gargantini, Angelo Zamli, Kamal Z. Yilmaz, Cemal Bures, Miroslav Szeles, Marek Department of Mathematics and Computer Science Karlstad University Karlstad651 88 Sweden Department of Management Information and Production Engineering University of Bergamo Italy Faculty of Computer Systems and Software Engineering University Malaysia Pahang Faculty of Engineering and Natural Sciences Sabanci University Istanbul Turkey Department of Computer Science Faculty of Electrical Engineering Czech Technical University in Prague Karlovo nam. 13 Praha 2121 35 Czech Republic

Combinatorial interaction testing (CIT) is a useful testing technique to ad- dress the interaction of input parameters in software systems. In many ap- plications, the technique has been used as a systematic sampling technique to sample the enormous possibilities of test cases. In the last decade, most of the research activities focused on the generation of CIT test suites as it is a computationally complex problem. Although promising, less effort has been paid for the application of CIT. In general, to apply the CIT, practitioners must identify the input parameters for the software-under-test (SUT), feed these parameters to the CIT tool to generate the test suite, and then run those tests on the application with some pass and fail criteria for verification. Using this approach, CIT is used as a black-box testing technique without knowing the effect of the internal code. Although useful, practically, not all the parameters having the same impact on the SUT. This paper intro- duces a different approach to use the CIT as a gray-box testing technique by considering the internal code structure of the SUT to know the impact of each input parameter and thus use this impact in the test generation stage. We applied our approach to five reliable case studies. The results showed that this approach would help to detect new faults as compared to the equal impact parameter approach. Copyright © 2019, The Authors. All rights reserved.

关键词： Black-box testing

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Optimal verification of two-qubit pure states

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Physical Review A 2019年第3期100卷 032315-032315页

作者： Kun Wang Masahito Hayashi Department of Computer Science and Technology State Key Laboratory for Novel Software Technology Nanjing University Nanjing 210093 China Shenzhen Institute for Quantum Science and Engineering Southern University of Science and Technology Shenzhen 518055 China Graduate School of Mathematics Nagoya University Nagoya 464-8602 Japan Centre for Quantum Technologies National University of Singapore 3 Science Drive 2 117542 Singapore

In a recent work [Pallister, Linden, and Montanaro, Phys. Rev. Lett. 120, 170502 (2018)], Pallister et al. proposed an optimal strategy to verify nonmaximally entangled two-qubit pure states under the constraint that the accessible measurements are locally projective and nonadaptive. Their good result leads naturally to the following question: What is the optimal strategy among general local operations and classical communication (LOCC) measurements? In this paper, we answer this problem completely for two-qubit pure states. To be specific, we give the optimal strategy for each of the following available classes of measurements: (i) local operations and one-way classical communication (one-way LOCC) measurements; (ii) local operations and two-way classical communication (two-way LOCC) measurements; and (iii) separable measurements. Surprisingly, our results reveal that for the two-qubit pure state verification problem two-way LOCC measurements remarkably outperform one-way LOCC measurements and have the same power as the separable measurements.

关键词： Quantum benchmarking Quantum entanglement Quantum information processing Quantum measurements Quantum protocols Quantum tomography

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Energetic electron precipitation driven by electromagnetic ion cyclotron waves from ELFIN’s low altitude perspective

arXiv

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arXiv 2022年

作者： Angelopoulos, V. Zhang, X.-J. Artemyev, A.V. Mourenas, D. Tsai, E. Wilkins, C. Runov, A. Liu, J. Turner, D.L. Li, W. Khurana, K. Wirz, R.E. Sergeev, V.A. Meng, X. Wu, J. Hartinger, M.D. Raita, T. Shen, Y. An, X. Shi, X. Bashir, M.F. Shen, X. Gan, L. Qin, M. Capannolo, L. Ma, Q. Russell, C.L. Masongsong, E.V. Caron, R. He, I. Iglesias, L. Jha, S. King, J. Kumar, S. Le, K. Mao, J. McDermott, A. Nguyen, K. Norris, A. Palla, A. Roosnovo Tam, J. Xie, E. Yap, R.C. Ye, S. Young, C. Adair, L.A. Shaffer, C. Chung, M. Cruce, P. Lawson, M. Leneman, D. Allen, M. Anderson, M. Arreola-Zamora, M. Artinger, J. Asher, J. Branchevsky, D. Cliffe, M. Colton, K. Costello, C. Depe, D. Domae, B.W. Eldin, S. Fitzgibbon, L. Flemming, A. Frederick, D.M. Gilbert, A. Hesford, B. Krieger, R. Lian, K. McKinney, E. Miller, J.P. Pedersen, C. Qu, Z. Rozario, R. Rubly, M. Seaton, R. Subramanian, A. Sundin, S.R. Tan, A. Thomlinson, D. Turner, W. Wing, G. Wong, C. Zarifian, A. Earth Planetary and Space Sciences Department Institute of Geophysics and Planetary Physics University of California Los Angeles Los AngelesCA90095 United States University of Texas at Dallas RichardsonTX75080 United States CEA DAM DIF Arpajon France Atmospheric and Oceanic Sciences Departments University of California Los AngelesCA United States Johns Hopkins University Applied Physics Laboratory LaurelMD United States Department of Astronomy Center for Space Physics Boston University BostonMA United States Mechanical and Aerospace Engineering Department Henry Samueli School of Engineering University of California Los AngelesCA90095 United States School of Mechanical Industrial Manufacturing Engineering Oregon State University CorvallisOR97331 United States University of St. Petersburg St. Petersburg Russia Jet Propulsion Laboratory California Institute of Technology PasadenaCA91109 United States Space Science Institute BoulderCO80301 United States Sodankylä Geophysical Observatory University of Oulu Sodankylä Finland Materials Science and Engineering Department Henry Samueli School of Engineering University of California Los AngelesCA90095 United States Deloitte Consulting New YorkNY10112 United States Computer Science Department Henry Samueli School of Engineering University of California Los AngelesCA90095 United States Microsoft RedmondWA98052 United States Physics and Astronomy Department University of California Los AngelesCA90095 United States Department of Astronomy and Astrophysics The University of Chicago ChicagoIL60637 United States Raybeam Inc. Mountain ViewCA94041 United States SpaceX HawthorneCA90250 United States Reliable Robotics Corporation Mountain ViewCA94043 United States Los Alamos National Laboratory Los AlamosNM87545 United States Mathematics Department University of California Los AngelesCA90095 United States Planet Labs PBC San FranciscoCA94107 United States KSAT Inc. De

We review comprehensive observations of electromagnetic ion cyclotron (EMIC) wave-driven energetic electron precipitation using data from the energetic electron detector on the Electron Losses and Fields InvestigatioN (ELFIN) mission, two polar-orbiting low-altitude spinning CubeSats, measuring 50-5000 keV electrons with good pitch-angle and energy resolution. EMIC wave-driven precipitation exhibits a distinct signature in energy-spectrograms of the precipitating-to-trapped flux ratio: peaks at >0.5 MeV which are abrupt (bursty) (lasting ∼17s, or ∆L ∼ 0.56) with significant substructure (occasionally down to sub-second timescale). We attribute the bursty nature of the precipitation to the spatial extent and structuredness of the wave field at the equator. Multiple ELFIN passes over the same MLT sector allow us to study the spatial and temporal evolution of the EMIC wave - electron interaction region. Case studies employing conjugate ground-based or equatorial observations of the EMIC waves reveal that the energy of moderate and strong precipitation at ELFIN approximately agrees with theoretical expectations for cyclotron resonant interactions in a cold plasma. Using 2 years of ELFIN data uniformly distributed in local time, we assemble a statistical database of ∼50 events of strong EMIC wave-driven precipitation. Most reside at L ∼ 5 − 7 at dusk, while a smaller subset exists at L ∼ 8 − 12 at post-midnight. The energies of the peak-precipitation ratio and of the half-peak precipitation ratio (our proxy for the minimum resonance energy) exhibit an L-shell dependence in good agreement with theoretical estimates based on prior statistical observations of EMIC wave power spectra. The precipitation ratio’s spectral shape for the most intense events has an exponential falloff away from the peak (i.e., on either side of ∼ 1.45 MeV). It too agrees well with quasi-linear diffusion theory based on prior statistics of wave spectra. It should be noted though that this diffusive

关键词： Radiation belts

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A perspective on deep learning for molecular modeling and simulations

arXiv

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arXiv 2020年

作者： Zhang, Jun Lei, Yao-Kun Zhang, Zhen Chang, Junhan Li, Maodong Han, Xu Yang, Lijiang Yang, Yi Isaac Gao, Yi Qin Institute of Systems Biology Shenzhen Bay Laboratory Shenzhen518055 China Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 6 Berlin14195 Germany Beijing National Laboratory for Molecular Sciences College of Chemistry and Molecular Engineering Peking University Beijing100871 China Department of Physics Tangshan Normal University Tangshan063000 China Beijing Advanced Innovation Center for Genomics Peking University Beijing100871 China Biomedical Pioneering Innovation Center Peking University Beijing100871 China

Deep learning is transforming many areas in science, and it has great potential in modeling molecular systems. However, unlike the mature deployment of deep learning in computer vision and natural language processing, its development in molecular modeling and simulations is still at an early stage, largely because the inductive biases of molecules are completely different from those of images or texts. Footed on these differences, we first reviewed the limitations of traditional deep learning models from the perspective of molecular physics, and wrapped up some relevant technical advancement at the interface between molecular modeling and deep learning. We do not focus merely on the ever more complex neural network models, instead, we emphasize the theories and ideas behind modern deep learning. We hope that transacting these ideas into molecular modeling will create new opportunities. For this purpose, we summarized several representative applications, ranging from supervised to unsupervised and reinforcement learning, and discussed their connections with the emerging trends in deep learning. Finally, we outlook promising directions which may help address the existing issues in the current framework of deep molecular modeling. © 2020, CC BY.

关键词： Molecular dynamics

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How much information is needed in quantized nonlinear control?

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中国科学（信息科学） 2018年第9期61卷 199-211页

作者： Chuang ZHENG Lin LI Leyi WANG Chanying LI School of Mathematical Sciences Beijing Normal University Beijing 100875 China Department of Electrical and Computer Engineering Wayne State University Detroit 48202 USA Key Laboratory of Systems and Control Academy of Mathematics and Systems ScienceChinese Academy of Sciences Beijing 100190 China

Quantization rate is a crucial measure of complexity in determining stabilizability of control systems subject to quantized state *** paper investigates quantization complexity for a class of nonlinear systems which are subjected to disturbances of unknown statistics and unknown *** class of systems includes linear stablizable systems as special *** lower bounds on the quantization rates are derived which guarantee input-to-state stabilizability for continuous-time and sampled-data feedback strategies,*** examples are provided to validate the results.

关键词： nonlinear systems disturbances input-to-state stabilizability sampled systems quantization rate

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DRIFT-PRESERVING NUMERICAL INTEGRATORS FOR STOCHASTIC HAMILTONIAN systems

arXiv

引用

arXiv 2019年

作者： Chen, Chuchu Cohen, David D'Ambrosio, Raffaele Lang, Annika 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 Beijing100190 China Department of Mathematics and Mathematical Statistics Umeå University Umeå90187 Sweden Department of Engineering and Computer Science and Mathematics University of L'Aquila AQ L'Aquila Italy Department of Mathematical Sciences Chalmers University of Technology University of Gothenburg Göteborg41296 Sweden

The paper deals with numerical discretizations of separable nonlinear Hamiltonian systems with additive noise. For such problems, the expected value of the total energy, along the exact solution, drifts linearly with time. We present and analyze a time integrator having the same property for all times. Furthermore, strong and weak convergence of the numerical scheme along with efficient multilevel Monte Carlo estimators are studied. Finally, extensive numerical experiments illustrate the performance of the proposed numerical *** Codes 65C20. 65C30. 60H10. 60H35 Copyright © 2019, The Authors. All rights reserved.

关键词： Additive noise

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Single-cell stochastic gene expression kinetics with coupled positive-plus-negative feedback

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Physical Review E 2019年第5期100卷 052406-052406页

作者： Chen Jia Le Yi Wang George G. Yin Michael Q. Zhang Division of Applied and Computational Mathematics Beijing Computational Science Research Center Beijing 100193 China Department of Mathematics Wayne State University Detroit Michigan 48202 USA Department of Electrical and Computer Engineering Wayne State University Detroit Michigan 48202 USA Department of Biological Sciences Center for Systems Biology University of Texas at Dallas Richardson Texas 75080 USA MOE Key Laboratory of Bioinformatics Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China

Here we investigate single-cell stochastic gene expression kinetics in a minimal coupled gene circuit with positive-plus-negative feedback. A triphasic stochastic bifurcation is observed upon increasing the ratio of the positive and negative feedback strengths, which reveals a strong synergistic interaction between positive and negative feedback loops. We discover that coupled positive-plus-negative feedback amplifies gene expression mean but reduces gene expression noise over a wide range of feedback strengths when promoter switching is relatively slow, stabilizing gene expression around a relatively high level. In addition, we study two types of macroscopic limits of the discrete chemical master equation model: the Kurtz limit applies to proteins with large burst frequencies and the Lévy limit applies to proteins with large burst sizes. We derive the analytic steady-state distributions of the protein abundance in a coupled gene circuit for both the discrete model and its two macroscopic limits, generalizing the results obtained by Liu et al. [Chaos 26, 043108 (2016)]. We also obtain the analytic time-dependent protein distribution for the classical Friedman-Cai-Xie random bursting model [Friedman, Cai, and Xie, Phys. Rev. Lett. 97, 168302 (2006)]. Our analytic results are further applied to study the structure of gene expression noise in a coupled gene circuit, and a complete decomposition of noise in terms of five different biophysical origins is provided.

关键词： Gene expression Stochastic processes Gene regulatory networks Markovian processes

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Master stability functions for complete, intralayer, and interlayer synchronization in multiplex networks of coupled Rössler oscillators

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Physical Review E 2019年第1期99卷 012304-012304页

作者： Longkun Tang Xiaoqun Wu Jinhu Lü Jun-an Lu Raissa M. D'Souza Fujian Province University Key Laboratory of Computation Science School of Mathematical Science Huaqiao University Quanzhou 362021 China School of Mathematics and Statistics Wuhan University Wuhan 430072 China Department of Computer Science University of California Davis California 95616 USA School of Automation Science and Electrical Engineering State Key Laboratory of Software Development Environment and Beijing Advanced Innovation Center for Big Data and Brain Computing Beihang University Beijing 100191 China

Synchronization phenomena are of broad interest across disciplines and increasingly of interest in a multiplex network setting. For the multiplex network of coupled Rössler oscillators, here we show how the master stability function, a celebrated framework for analyzing synchronization on a single network, can be extended to certain classes of multiplex networks with different intralayer and interlayer coupling functions. We derive three master stability equations that determine, respectively, the necessary regions of complete synchronization, intralayer synchronization, and interlayer synchronization. We calculate these three regions explicitly for the case of a two-layer network of Rössler oscillators and show that the overlap of the regions determines the type of synchronization achieved. In particular, if the interlayer or intralayer coupling function is such that the interlayer or intralayer synchronization region is empty, complete synchronization cannot be achieved regardless of the coupling strength. Furthermore, for any network structure, the occurrence of intralayer and interlayer synchronization depends mainly on the coupling functions of nodes within a layer and across layers, respectively. Our mathematical analysis requires that the intralayer and interlayer supra-Laplacians commute. But, we show this is only a sufficient, and not necessary, condition and that the results can be applied more generally.

关键词： Collective dynamics Synchronization Synchronization transition

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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

arXiv

引用

arXiv 2023年

作者： Eastman, Peter Galvelis, Raimondas Peláez, Raúl P. Abreu, Charlles R.A. Farr, Stephen E. Gallicchio, Emilio Gorenko, Anton Henry, Michael M. Hu, Frank Huang, Jing Krämer, Andreas Michel, Julien Mitchell, Joshua A. Pande, Vijay S. Rodrigues, João P.G.L.M. Rodriguez-Guerra, Jaime Simmonett, Andrew C. Singh, Sukrit Swails, Jason Turner, Philip Wang, Yuanqing Zhang, Ivy Chodera, John D. De Fabritiis, Gianni Markland, Thomas E. Department of Chemistry Stanford University StanfordCA94305 United States Acellera Labs C Dr Trueta 183 Barcelona08005 Spain C Dr. Aiguader 88 Barcelona08003 Spain Chemical Engineering Department School of Chemistry Federal University of Rio de Janeiro Rio de Janeiro68542 Brazil Redesign Science Inc. 180 Varick St. New YorkNY10014 United States EaStCHEM School of Chemistry University of Edinburgh EH9 3FJ United Kingdom Department of Chemistry and Biochemistry Brooklyn College The City University of New York NY United States Ph.D. Program in Chemistry Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New YorkNY United States Stream HPC Koningin Wilhelminaplein 1 - 40601 Amsterdam1062 HG Netherlands Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Zhejiang Hangzhou310024 China Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 12 Berlin14195 Germany The Open Force Field Initiative Open Molecular Software Foundation DavisCA95616 United States Andreessen Horowitz 2865 Sand Hill Rd Menlo ParkCA94025 United States Department of Structural Biology Stanford University StanfordCA94305 United States Charité Universitätsmedizin Berlin In silico Toxicology and Structural Bioinformatics Virchowweg 6 Berlin10117 Germany Laboratory of Computational Biology National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Entos Inc. 9310 Athena Circle La Jolla CA92037 United States College of Engineering Virginia Polytechnic Institute State University BlacksburgVA24061 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University 24 Waverly Place New YorkNY10004 United States T

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost. Copyright © 2023, The Authors. All rights reserved.

关键词： Machine learning

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