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Machine learning framework to segment sarcomeric structures in SMLM data

SCIENTIFIC REPORTS 2023年第1期13卷 1-10页

作者： Varga, Daniel Szikora, Szilard Novak, Tibor Pap, Gergely Leko, Gabor Mihaly, Jozsef Erdelyi, Miklos Univ Szeged Dept Opt & Quantum Elect Dom Ter 9 H-6720 Szeged Hungary Biol Res Ctr Inst Genet Temesvar Korut 62 H-6726 Szeged Hungary Univ Szeged Dept Comp Algorithms & Artificial Intelligence Arpad Ter 2 H-6720 Szeged Hungary Univ Szeged Dept Software Engn Dugon Ter 13 H-6720 Szeged Hungary Univ Szeged Dept Genet Kozep Fasor 52 H-6726 Szeged Hungary

Object detection is an image analysis task with a wide range of applications, which is difficult to accomplish with traditional programming. Recent breakthroughs in machine learning have made significant progress in this area. However, these algorithms are generally compatible with traditional pixelated images and cannot be directly applied for pointillist datasets generated by single molecule localization microscopy (SMLM) methods. Here, we have improved the averaging method developed for the analysis of SMLM images of sarcomere structures based on a machine learning object detection algorithm. The ordered structure of sarcomeres allows us to determine the location of the proteins more accurately by superimposing SMLM images of identically assembled proteins. However, the area segmentation process required for averaging can be extremely time-consuming and tedious. In this work, we have automated this process. The developed algorithm not only finds the regions of interest, but also classifies the localizations and identifies the true positive ones. For training, we used simulations to generate large amounts of labelled data. After tuning the neural network's internal parameters, it could find the localizations associated with the structures we were looking for with high accuracy. We validated our results by comparing them with previous manual evaluations. It has also been proven that the simulations can generate data of sufficient quality for training. Our method is suitable for the identification of other types of structures in SMLM data.

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quantum guessing games with posterior information

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REPORTS ON PROGRESS IN PHYSICS 2022年第7期85卷 074001-074001页

作者： Carmeli, Claudio Heinosaari, Teiko Toigo, Alessandro Univ Genoa DIME Via Magliotto 2 I-17100 Savona Italy VTT Tech Res Ctr Finland Ltd Quantum Algorithms & Software Jyvaskyla Finland Univ Turku Dept Phys & Astron Turku Finland Politecn Milan Dipartimento Matemat Piazza Leonardo da Vinci 32 I-20133 Milan Italy INFN Sez Milano Via Celoria 16 I-20133 Milan Italy

quantum guessing games form a versatile framework for studying different tasks of information processing. A quantum guessing game with posterior information uses quantum systems to encode messages and classical communication to give partial information after a quantum measurement has been performed. We present a general framework for quantum guessing games with posterior information and derive structure and reduction theorems that enable to analyze any such game. We formalize symmetry of guessing games and characterize the optimal measurements in cases where the symmetry is related to an irreducible representation. The application of guessing games to incompatibility detection is reviewed and clarified. All the presented main concepts and results are demonstrated with examples.

关键词： quantum guessing game state discrimination quantum incompatibility

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RANDOM ACCESS TEST AS AN IDENTIFIER OF NONCLASSICALITY

arXiv

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arXiv 2021年

作者： Heinosaari, Teiko Leppäjärvi, Leevi Department of Physics and Astronomy University of Turku Finland Quantum Algorithms and Software VTT Technical Research Centre of Finland Ltd. Finland RCQI Institute of Physics Slovak Academy of Sciences Dúbravská cesta 9 Bratislava84511 Slovakia

Random access codes are an intriguing class of communication tasks that reveal an operational and quantitative difference between classical and quantum information processing. We formulate a natural generalization of random access codes and call them random access tests, defined for any finite collection of measurements in an arbitrary finite dimensional general probabilistic theory. These tests can be used to examine collective properties of collections of measurements. We show that the violation of a classical bound in a random access test is a signature of either measurement incompatibility or super information storability. The polygon theories are exhaustively analyzed and a critical difference between even and odd polygon theories is revealed. Copyright © 2021, The Authors. All rights reserved.

关键词： quantum optics

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Anticipative measurements in hybrid quantum-classical computation

arXiv

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arXiv 2022年

作者： Heinosaari, Teiko Reitzner, Daniel Toigo, Alessandro Quantum Algorithms and Software VTT Technical Research Centre of Finland Ltd Espoo Finland Department of Physics and Astronomy University of Turku Turku20014 Finland Dipartimento di Matematica Politecnico di Milano Piazza Leonardo da Vinci 32 Milano20133 Italy Istituto Nazionale di Fisica Nucleare Sezione di Milano Via Celoria 16 Milano20133 Italy

Before the availability of large scale fault-tolerant quantum devices, one has to find ways to make the most of current noisy intermediate-scale quantum devices. One possibility is to seek smaller repetitive hybrid quantum-classical tasks with higher fidelity, rather than directly pursuing large complex tasks. We present an approach in this direction where the quantum computation is supplemented by a classical result. While the presence of the supplementary classical information helps alone, taking advantage of its anticipation also leads to a new type of quantum measurements, which we call anticipative. Anticipative quantum measurements lead to improved success rate over cases where we would use quantum measurements optimized without assuming the later arriving supplementing information. Importantly, in an anticipative quantum measurement the combination of the results from classical and quantum computations happens only in the end, without the need for feedback from the one to the other computation, a feature which hence allows for running both computations in parallel. We demonstrate the method using an IBMQ device and show that it leads to an improved success rate even in a real noisy setting. © 2022, CC BY-NC-ND.

关键词： quantum computers

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A many-body approach to transport in quantum systems: from the transient regime to the stationary state

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JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL 2022年第27期55卷 273001-273001页

作者： Ridley, M. Talarico, N. W. Karlsson, D. Lo Gullo, N. Tuovinen, R. Tel Aviv Univ Sch Phys & Astron IL-69978 Tel Aviv Israel Technol Innovat Inst Quantum Res Ctr Abu Dhabi U Arab Emirates Aalto Univ Sch Sci Dept Appl Phys QTF Ctr ExcellenceCtr Quantum Engn FIN-00076 Aalto Finland Algorithmiq Ltd Kanavakatu 3c Helsinki 00160 Finland Univ Jyvaskyla Nanosci Ctr Dept Phys Jyvaskyla 40014 Finland CSC IT Ctr Sci POB 405 Espoo 02101 Finland VTT Tech Res Ctr Finland Ltd Quantum Algorithms & Software POB 1000 Espoo 02044 Finland Univ Turku Turku Ctr Quantum Phys Dept Phys & Astron QTF Ctr Excellence Turku 20014 Finland Univ Helsinki QTF Ctr Excellence Dept Phys POB 64 Helsinki 00014 Finland

We review one of the most versatile theoretical approaches to the study of time-dependent correlated quantum transport in nano-systems: the non-equilibrium Green's function (NEGF) formalism. Within this formalism, one can treat, on the same footing, inter-particle interactions, external drives and/or perturbations, and coupling to baths with a (piece-wise) continuum set of degrees of freedom. After a historical overview on the theory of transport in quantum systems, we present a modern introduction of the NEGF approach to quantum transport. We discuss the inclusion of inter-particle interactions using diagrammatic techniques, and the use of the so-called embedding and inbedding techniques which take the bath couplings into account non-perturbatively. In various limits, such as the non-interacting limit and the steady-state limit, we then show how the NEGF formalism elegantly reduces to well-known formulae in quantum transport as special cases. We then discuss non-equilibrium transport in general, for both particle and energy currents. Under the presence of a time-dependent drive-encompassing pump-probe scenarios as well as driven quantum systems-we discuss the transient as well as asymptotic behavior, and also how to use NEGF to infer information on the out-of-equilibrium system. As illustrative examples, we consider model systems general enough to pave the way to realistic systems. These examples encompass one- and two-dimensional electronic systems, systems with electron-phonon couplings, topological superconductors, and optically responsive molecular junctions where electron-photon couplings are relevant.

关键词： quantum transport many-body correlation non-equilibrium Green's function

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A many-body approach to transport in quantum systems: From the transient regime to the stationary state

arXiv

引用

arXiv 2022年

作者： Ridley, M. Talarico, N.W. Karlsson, D. Lo Gullo, N. Tuovinen, Riku School of Physics and Astronomy Tel-Aviv University Tel-Aviv69978 Israel Quantum Research Centre Technology Innovation Institute Abu Dhabi United Arab Emirates QTF Centre of Excellence Center for Quantum Engineering Department of Applied Physics Aalto University School of Science AaltoFIN-00076 Finland Algorithmiq Ltd. Kanavakatu 3c Helsinki00160 Finland Department of Physics Nanoscience Center University of Jyväskylä Jyväskylä40014 Finland CSC-IT Center for Science P.O. Box 405 Espoo02101 Finland Quantum Algorithms and Software VTT Technical Research Centre of Finland Ltd. Finland QTF Centre of Excellence Turku Centre for Quantum Physics Department of Physics and Astronomy University of Turku Turku20014 Finland QTF Centre of Excellence Department of Physics University of Helsinki P.O. Box 64 00014 Finland

We review one of the most versatile theoretical approaches to the study of time-dependent correlated quantum transport in nano-systems: the non-equilibrium Green’s function (NEGF) formalism. Within this formalism, one can treat, on the same footing, inter-particle interactions, external drives and/or perturbations, and coupling to baths with a (piece-wise) continuum set of degrees of freedom. After a historical overview on the theory of transport in quantum systems, we present a modern introduction of the NEGF approach to quantum transport. We discuss the inclusion of inter-particle interactions using diagrammatic techniques, and the use of the so-called embedding and inbedding techniques which take the bath couplings into account non-perturbatively. In various limits, such as the non-interacting limit and the steady-state limit, we then show how the NEGF formalism elegantly reduces to well-known formulae in quantum transport as special cases. We then discuss non-equilibrium transport in general, for both particle and energy currents. Under the presence of a time-dependent drive – encompassing pump–probe scenarios as well as driven quantum systems – we discuss the transient as well as asymptotic behavior, and also how to use NEGF to infer information on the out-of-equilibrium system. As illustrative examples, we consider model systems general enough to pave the way to realistic systems. These examples encompass one- and two-dimensional electronic systems, systems with electron–phonon couplings, topological superconductors, and optically responsive molecular junctions where electron–photon couplings are relevant. Copyright © 2022, The Authors. All rights reserved.

关键词： quantum optics

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General measurements with limited resources and their application to quantum unambiguous state discrimination

arXiv

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arXiv 2020年

作者： Reitzner, Daniel Bouda, Jan Quantum Algorithms and Software VTT Technical Research Centre of Finland VTT P.O. Box 1000 FI-02044 Finland Faculty of Informatics Masaryk University Botanická 68a Brno602 00 Czech Republic RCQI Institute of Physics Slovak Academy of Sciences Dúbravská cesta 9 Bratislava845 11 Slovakia

In this report, we present a framework for implementing an arbitrary n-outcome generalized quantum measurement (POVM) on an m-qubit register as a sequence of two-outcome measurements requiring only single ancillary qubit. Our procedure offers a particular construction for the two-outcome partial measurements which can be composed into a full implementation of the measurement on any gate architecture. This implementation in general requires classical feedback;we present specific cases when this is not the case. We apply this framework on the unambiguous state discrimination and analyze possible strategies. In the simplest case, it gives the same construction as is known, if we opt for performing conclusiveness measurement first. However, it also offers possibility of performing measurement for one of the state outcomes first, leaving conclusiveness measurement for later. This shows flexibility of presented framework and opens possibilities for further optimization. We present discussion also on biased qubit case as well as general case of unambiguous quantum state discrimination in higher dimension. Copyright © 2020, The Authors. All rights reserved.

关键词： Qubits

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DPA-2:a large atomic model as a multitask learner

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npj Computational Materials 2024年第1期10卷 185-199页

作者： Duo Zhang Xinzijian Liu Xiangyu Zhang Chengqian Zhang Chun Cai Hangrui Bi Yiming Du Xuejian Qin Anyang Peng Jiameng Huang Bowen Li Yifan Shan Jinzhe Zeng Yuzhi Zhang Siyuan Liu Yifan Li Junhan Chang Xinyan Wang Shuo Zhou Jianchuan Liu Xiaoshan Luo Zhenyu Wang Wanrun Jiang Jing Wu Yudi Yang Jiyuan Yang Manyi Yang Fu-Qiang Gong Linshuang Zhang Mengchao Shi Fu-Zhi Dai Darrin M.York Shi Liu Tong Zhu Zhicheng Zhong Jian Lv Jun Cheng Weile Jia Mohan Chen Guolin Ke Weinan E Linfeng Zhang Han Wang AI for Science Institute BeijingP.R.China DP Technology BeijingP.R.China Academy for Advanced Interdisciplinary Studies Peking UniversityBeijingP.R.China State Key Lab of Processors Institute of Computing TechnologyChinese Academy of SciencesBeijingP.R.China University of Chinese Academy of Sciences BeijingP.R.China HEDPS CAPTCollege of EngineeringPeking UniversityBeijingP.R.China Ningbo Institute of Materials Technology and Engineering Chinese Academy of SciencesNingboP.R.China CAS Key Laboratory of Magnetic Materials and Devices and Zhejiang Province Key Laboratory of Magnetic Materials and Application Technology Chinese Academy of SciencesNingboP.R.China School of Electronics Engineering and Computer Science Peking UniversityBeijingP.R.China Shanghai Engineering Research Center of Molecular Therapeutics&New Drug Development School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghaiP.R.China Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine and Department of Chemistry and Chemical BiologyRutgers UniversityPiscatawayNJUSA Department of Chemistry Princeton UniversityPrincetonNJUSA College of Chemistry and Molecular Engineering Peking UniversityBeijingP.R.China Yuanpei College Peking UniversityBeijingP.R.China School of Electrical Engineering and Electronic Information Xihua UniversityChengduP.R.China State Key Laboratory of Superhard Materials College of PhysicsJilin UniversityChangchunP.R.China Key Laboratory of Material Simulation Methods&Software of Ministry of Education College of PhysicsJilin UniversityChangchunP.R.China International Center of Future Science Jilin UniversityChangchunP.R.China Key Laboratory for Quantum Materialsof Zhejiang Province Department of PhysicsSchool of ScienceWestlake UniversityHangzhouP.R.China Atomistic Simulations Italian Institute of TechnologyGenovaItaly State Key Laboratory of Physical Chemistry of Solid Surface iChEMCollege of Chemistry and Chemical EngineeringXiame

The rapid advancements in artificial intelligence(AI)are catalyzing transformative changes in atomic modeling,simulation,and ***-driven potential energy models havedemonstrated the capability to conduct large-scale,long-duration simulations with the accuracy of ab initio electronic structure ***,the model generation process remains a bottleneck for large-scale *** propose a shift towards a model-centric ecosystem,wherein a large atomic model(LAM),pretrained across multiple disciplines,can be efficiently fine-tuned and distilled for various downstream tasks,thereby establishing a new framework for molecular *** this study,we introduce the DPA-2 architecture as a prototype for ***-trained on a diverse array of chemical and materials systemsusing a multi-task approach,DPA-2demonstrates superior generalization capabilities across multiple downstream tasks compared to the traditional single-task pre-training and fine-tuning *** approach sets the stage for the development and broad application of LAMs in molecular and materials simulation research.

关键词： DPA establishing thereby

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DPA-2: a large atomic model as a multi-task learner

arXiv

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arXiv 2023年

作者： Zhang, Duo Liu, Xinzijian Zhang, Xiangyu Zhang, Chengqian Cai, Chun Bi, Hangrui Du, Yiming Qin, Xuejian Peng, Anyang Huang, Jiameng Li, Bowen Shan, Yifan Zeng, Jinzhe Zhang, Yuzhi Liu, Siyuan Li, Yifan Chang, Junhan Wang, Xinyan Zhou, Shuo Liu, Jianchuan Luo, Xiaoshan Wang, Zhenyu Jiang, Wanrun Wu, Jing Yang, Yudi Yang, Jiyuan Yang, Manyi Gong, Fu-Qiang Zhang, Linshuang Shi, Mengchao Dai, Fu-Zhi York, Darrin M. Liu, Shi Zhu, Tong Zhong, Zhicheng Lv, Jian Cheng, Jun Jia, Weile Chen, Mohan Ke, Guolin Weinan, E. Zhang, Linfeng Wang, Han AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing100871 China University of Chinese Academy of Sciences Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China Ningbo Institute of Materials Technology and Engineering Chinese Academy of Sciences Ningbo315201 China CAS Key Laboratory of Magnetic Materials and Devices Zhejiang Province Key Laboratory of Magnetic Materials and Application Technology Chinese Academy of Sciences Ningbo315201 China School of Electronics Engineering and Computer Science Peking University Beijing100871 China Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai200062 China Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States Department of Chemistry Princeton University PrincetonNJ08540 United States College of Chemistry and Molecular Engineering Peking University Beijing100871 China Yuanpei College Peking University Beijing100871 China School of Electrical Engineering and Electronic Information Xihua University Chengdu610039 China State Key Laboratory of Superhard Materials College of Physics Jilin University Changchun130012 China Key Laboratory of Material Simulation Methods & Software of Ministry of Education College of Physics Jilin University Changchun130012 China International Center of Future Science Jilin University Changchun130012 China Key Laboratory for Quantum Materials of Zhejiang Province Department of Physics School of Science Westlake University Zhejiang Hangzhou310030 China Atomistic Simulations Italia

The rapid advancements in artificial intelligence (AI) are catalyzing transformative changes in atomic modeling, simulation, and design. AI-driven potential energy models have demonstrated the capability to conduct large-scale, long-duration simulations with the accuracy of ab initio electronic structure methods. However, the model generation process remains a bottleneck for large-scale applications. We propose a shift towards a model-centric ecosystem, wherein a large atomic model (LAM), pre-trained across multiple disciplines, can be efficiently fine-tuned and distilled for various downstream tasks, thereby establishing a new framework for molecular modeling. In this study, we introduce the DPA-2 architecture as a prototype for LAMs. Pre-trained on a diverse array of chemical and materials systems using a multi-task approach, DPA-2 demonstrates superior generalization capabilities across multiple downstream tasks compared to the traditional single-task pre-training and fine-tuning methodologies. Our approach sets the stage for the development and broad application of LAMs in molecular and materials simulation research. Copyright © 2023, The Authors. All rights reserved.

关键词： Multi-task learning

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