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arXiv 2020年

作者： Ren, Xinguo Merz, Florian Jiang, Hong Yao, Yi Rampp, Markus Lederer, Hermann Blum, Volker Scheffler, Matthias Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences 3rd South Str. 8 Beijing100190 China Lenovo HPC Innovation Center Meitnerstr. 9 StuttgartD-70563 Germany Beijing National Laboratory for Molecular Sciences College of Chemistry and Molecular Engineering Peking University Beijing100871 China Department of Chemistry University of North Carolina Chapel HillNC27599 United States Department of Mechanical Engineering and Materials Science Duke University DurhamNC27708 United States Max Planck Computing and Data Facility Giessenbachstrasse 2 GarchingD-85748 Germany Department of Chemistry Duke University DurhamNC27708 United States Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 BerlinD-14195 Germany Physics Department Humboldt-Universität zu Berlin Zum Großen Windkanal 6 BerlinD-12489 Germany

We present an all-electron, periodic G0W0 implementation within the numerical atomic orbital (NAO) basis framework. A localized variant of the resolution-of-the-identity (RI) approximation is employed to significantly reduce the computational cost of evaluating and storing the two-electron Coulomb repulsion integrals. We demonstrate that the error arising from localized RI approximation can be reduced to an insignificant level by enhancing the set of auxiliary basis functions, used to expand the products of two single-particle NAOs. An efficient algorithm is introduced to deal with the Coulomb singularity in the Brillouin zone sampling that is suitable for the NAO framework. We perform systematic convergence tests and identify a set of computational parameters, which can serve as the default choice for most practical purposes. Benchmark calculations are carried out for a set of prototypical semiconductors and insulators, and compared to independent reference values obtained from an independent G0W0 implementation based on linearized augmented plane waves (LAPW) plus high-energy localized orbitals (HLOs) basis set, as well as experimental results. With a moderate (FHI-aims tier 2) NAO basis set, our G0W0 calculations produce band gaps that typically lie in between the standard LAPW and the LAPW+HLO results. Complementing tier 2 with highly localized Slater-type orbitals (STOs), we find that the obtained band gaps show an overall convergence towards the LAPW+HLO results. The algorithms and techniques developed in this work pave the way for efficient implementations of correlated methods within the NAO framework. Copyright © 2020, The Authors. All rights reserved.

关键词： Quantum chemistry

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Tau-PET signal in Alzheimer’s disease is related to immune activation and synaptic signaling measured with CSF proteomics

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Alzheimer's & Dementia 2023年第S17期19卷

作者： Roos M. Rikken Eleonora M. Vromen Emma M. Coomans Denise Visser Frederik Barkhof Ronald Boellaard Sandeep S.V. Golla Bart N.M. van Berckel Rik Ossenkoppele Anouk den Braber Everard G.B. Vijverberg Wiesje M. van der Flier Yolande A.L. Pijnenburg Charlotte E. Teunissen Pieter Jelle Visser Elsmarieke van de Giessen Betty M. Tijms Amsterdam Neuroscience Brain Imaging Amsterdam Netherlands Radiology & Nuclear Medicine Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Netherlands Correspondece Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Netherlands Amsterdam Neuroscience Neurodegeneration Amsterdam Netherlands Queen Square Institute of Neurology and Centre for Medical Image Computing University College London United Kingdom Clinical Memory Research Unit Lund University Lund Sweden Biological Psychiatry Vrije Universiteit Amsterdam Amsterdam Netherlands Epidemiology and Data Science Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Netherlands Amsterdam Neuroscience Neurodegeneration Amsterdam Noord-Holland Netherlands Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Noord-Holland Netherlands Alzheimer Center Amsterdam Neurology Amsterdam UMC Amsterdam Netherlands Neurochemistry laboratory Clinical Chemistry Amsterdam UMC location VUmc Amsterdam Netherlands Center for Alzheimer Research Karolinska Institutet Division of Clinical Geriatrics Department of Neurobiology Care Sciences and Society Stockholm Sweden Alzheimer Center Limburg School for Mental Health and Neuroscience (MHeNs) Maastricht University Maastricht Netherlands

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Improving individual predictions using social networks assortativity 12

Improving individual predictions using social networks assor...

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12th International Workshop on Self-Organizing Maps and Learning Vector Quantization, Clustering and data Visualization, WSOM 2017

作者： Mulders, Dounia De Bodt, Cyril Bjelland, Johannes Pentland, Alex Sandy Verleysen, Michel De Montjoye, Yves-Alexandre ICTEAM institute Université catholique de Louvain Belgium Telenor Research Norway MIT Media Lab Massachusetts Institute of Technology United States Data Science Institute Department of Computing Imperial College London United Kingdom

ISBN: (纸本)9781509066384

Social networks are known to be assortative with respect to many attributes, such as age, weight, wealth, level of education, ethnicity and gender. This can be explained by influences and homophilies. Independently of its origin, this assortativity gives us information about each node given its neighbors. Assortativity can thus be used to improve individual predictions in a broad range of situations, when data are missing or inaccurate. This paper presents a general framework based on probabilistic graphical models to exploit social network structures for improving individual predictions of node attributes. Using this framework, we quantify the assortativity range leading to an accuracy gain in several situations. We finally show how specific characteristics of the network can improve performances further. For instance, the gender assortativity in real-world mobile phone data changes significantly according to some communication attributes. In this case, individual predictions with 75% accuracy are improved by up to 3%. © 2017 IEEE.

关键词： Belief propagation

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VerSe: A Vertebrae Labelling and Segmentation Benchmark for Multi-detector CT Images

arXiv

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arXiv 2020年

作者： Sekuboyina, Anjany Kumar Husseini, Malek E. Bayat, Amirhossein Löffler, Maximilian Liebl, Hans Li, Hongwei Tetteh, Giles Kukačka, Jan Payer, Christian Štern, Darko Urschler, Martin Chen, Maodong Cheng, Dalong Lessmann, Nikolas Hu, Yujin Wang, Tianfu Yang, Dong Xu, Daguang Ambellan, Felix Amiranashvili, Tamaz Ehlke, Moritz Lamecker, Hans Lehnert, Sebastian Lirio, Marilia de Olaguer, Nicolás Pérez Ramm, Heiko Sahu, Manish Tack, Alexander Zachow, Stefan Jiang, Tao Ma, Xinjun Angerman, Christoph Wang, Xin Brown, Kevin Kirszenberg, Alexandre Puybareau, Élodie Chen, Di Bai, Yiwei Rapazzo, Brandon H. Yeah, Timyoas Zhang, Amber Xu, Shangliang Hou, Feng He, Zhiqiang Zeng, Chan Xiangshang, Zheng Liming, Xu Netherton, Tucker J. Mumme, Raymond P. Court, Laurence E. Huang, Zixun He, Chenhang Wang, Li-Wen Ling, Sai Ho Huynh, Lê Duy Boutry, Nicolas Jakubicek, Roman Chmelik, Jiri Mulay, Supriti Sivaprakasam, Mohanasankar Paetzold, Johannes C. Shit, Suprosanna Ezhov, Ivan Wiestler, Benedikt Glocker, Ben Valentinitsch, Alexander Rempfler, Markus Menze, Björn H. Kirschke, Jan S. Department of Informatics Technical University of Munich Germany Munich School of BioEngineering Technical University of Munich Germany Department of Neuroradiology Klinikum Rechts der Isar Germany Department for Quantitative Biomedicine University of Zurich Switzerland Friedrich Miescher Institute for Biomedical Engineering Switzerland Institute of Biological and Medical Imaging Helmholtz Zentrum München Germany Department of Computing Imperial College London United Kingdom Institute of Computer Graphics and Vision Graz University of Technology Austria Gottfried Schatz Research Center: Biophysics Medical University of Graz Austria School of Computer Science The University of Auckland New Zealand Computer Vision Group iFLYTEK Research South China China Department of Radiology and Nuclear Medicine Radboud University Medical Center Nijmegen Netherlands Shenzhen Research Institute of Big Data China School of Biomedical Engineering Health Science Center Shenzhen University China NVIDIA Corporation United States Zuse Institute Berlin Germany 1000shapes GmbH Berlin Germany Damo Academy Alibaba Group China Department of Mathematics University of Innsbruck Austria Department of Electronic Engineering Fudan University China New York University United States France Deep Reasoning AI Inc United States Technical University of Munich Germany East China Normal University China Chinese Academy of Sciences China Lenovo Group China Ping An Technologies China College of Computer Science and Technology Zhejiang University China Real Doctor AI Research Centre Zhejiang University China The University of Texas MD Anderson Cancer Center United States Department of Electronic and Information Engineering The Hong Kong Polytechnic University China Department of Computing The Hong Kong Polytechnic University China The School of Biomedical Engineering University of Technology Sydney Australia Department of Biomedical Engineering Brno University of Technology Czech Republic India

Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision support systems for diagnosis, surgery planning, and population-based analysis of spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms tackling the labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel level by a human-machine hybrid algorithm (https://***/nqjyw/, https://***/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the results of this evaluation and further investigate the performance variation at the vertebra level, scan level, and different fields of view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top-performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The VerSe content and code can be accessed at: https://***/anjany/verse. © 2020, CC BY-NC-ND.

关键词： Computerized tomography

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Not just privacy: Improving performance of private deep learning in mobile cloud

arXiv

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arXiv 2018年

作者： Wang, Ji Zhang, Jianguo Bao, Weidong Zhu, Xiaomin Cao, Bokai Yu, Philip S. College of Systems Engineering National University of Defense Technology Changsha China Department of Computer Science University of Illinois at Chicago Chicago United States College of Systems Engineering State Key Laboratory of High Performance Computing National University of Defense Technology Changsha China Facebook Inc. Menlo Park United States Department of Computer Science University of Illinois at Chicago Chicago United States Institute for Data Science Tsinghua University Beijing China

The increasing demand for on-device deep learning services calls for a highly efficient manner to deploy deep neural networks (DNNs) on mobile devices with limited capacity. The cloud-based solution is a promising approach to enabling deep learning applications on mobile devices where the large portions of a DNN are offloaded to the cloud. However, revealing data to the cloud leads to potential privacy risk. To benefit from the cloud data center without the privacy risk, we design, evaluate, and implement a cloud-based framework Arden which partitions the DNN across mobile devices and cloud data centers. A simple data transformation is performed on the mobile device, while the resource-hungry training and the complex inference rely on the cloud data center. To protect the sensitive information, a lightweight privacy-preserving mechanism consisting of arbitrary data nullification and random noise addition is introduced, which provides strong privacy guarantee. A rigorous privacy budget analysis is given. Nonetheless, the private perturbation to the original data inevitably has a negative impact on the performance of further inference on the cloud side. To mitigate this influence, we propose a noisy training method to enhance the cloud-side network robustness to perturbed data. Through the sophisticated design, Arden can not only preserve privacy but also improve the inference performance. To validate the proposed Arden, a series of experiments based on three image datasets and a real mobile application are conducted. The experimental results demonstrate the effectiveness of Arden. Finally, we implement Arden on a demo system to verify its practicality. Copyright © 2018, The Authors. All rights reserved.

关键词： Deep neural networks

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Corrigendum: Old-growth forest loss and secondary forest recovery across Amazonian countries (2021 Environ. Res. Lett. 16 085009)

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Environmental Research Letters 2022年第10期17卷 109501-109501页

作者： Charlotte C Smith John R Healey Erika Berenguer Paul J Young Ben Taylor Fernando Elias Fernando Espírito-Santo Jos Barlow Lancaster Environment Centre Lancaster University LA1 4YQ Lancaster United Kingdom School of Natural Sciences College of Environmental Sciences and Engineering Bangor University Bangor LL57 2DG United Kingdom Environmental Change Institute School of Geography and the Environment University of Oxford OX1 3QY Oxford United Kingdom Centre of Excellence for Environmental Data Science Lancaster University and the UK Centre for Ecology and Hydrology Lancaster United Kingdom Institute for Social Futures Lancaster University Lancaster United Kingdom School of Computing and Communications Lancaster University LA1 4YQ Lancaster United Kingdom Embrapa Amazônia Oriental Rede Amazônia Sustentável 66095-903 Belém PA Brazil Leicester Institute of Space and Earth Observation Centre for Landscape and Climate Research School of Geography Geology and Environment University of Leicester University Road Leicester LE1 7RH United Kingdom

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From FAIR to CURE: Guidelines for Computational Models of Biological Systems

arXiv

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arXiv 2025年

作者： Sauro, Herbert M. Agmon, Eran Blinov, Michael L. Gennari, John H. Hellerstein, Joe Heydarabadipour, Adel Hunter, Peter Jardine, Bartholomew E. May, Elebeoba Nickerson, David P. Smith, Lucian P. Bader, Gary D. Bergmann, Frank Boyle, Patrick M. Dräger, Andreas Faeder, James R. Feng, Song Freire, Juliana Fröhlich, Fabian Glazier, James A. Gorochowski, Thomas E. Helikar, Tomas Hoops, Stefan Imoukhuede, Princess Keating, Sarah M. Konig, Matthias Laubenbacher, Reinhard Loew, Leslie M. Lopez, Carlos F. Lytton, William W. McCulloch, Andrew Mendes, Pedro Myers, Chris J. Myers, Jerry G. Mulugeta, Lealem Niarakis, Anna van Niekerk, David D. Olivier, Brett G. Patrie, Alexander A. Quardokus, Ellen M. Radde, Nicole Rohwer, Johann M. Sahle, Sven Schaff, James C. Sego, T.J. Shin, Janis Snoep, Jacky L. Vadigepalli, Rajanikanth Wiley, H. Steve Waltemath, Dagmar Moraru, Ion Department of Bioengineering University of Washington SeattleWA98195-5061 United States Intelligent Systems Engineering and Biocomplexity Institute Indiana University Street BloomingtonIN47408 United States Center for Cardiovascular Biology University of Washington SeattleWA98195-5061 United States eScience Institute University of Washington SeattleWA98195-5061 United States Institute for Stem Cell and Regenerative Medicine University of Washington SeattleWA98195-5061 United States School of Biological Sciences University of Bristol 24 Tyndall Avenue BristolBS8 1TQ United Kingdom Departments of Physiology & Pharmacology Neurology Downstate Health Science University BrooklynNY11203 United States Department of Neurology Kings County Hospital BrooklynNY11203 United States NASA-John H. Glenn Research Center MS 110-3 21000 Brookpark Road ClevelandOH44135 United States Center for Cell Analysis and Modeling UConn Health 263 Farmington Avenue FarmingtonCT06030-6406 United States Amsterdam Institute for Life and Environment Vrije Universiteit Amsterdam De Boelelaan 1108 Amsterdam1081 HZ Netherlands Department of Pathology and Genomic Medicine Thomas Jefferson University 1020 Locust St PhiladelphiaPA19107 United States Biological Sciences Division Pacific Northwest National Laboratory 902 Battelle Blvd RichlandWA99354 United States Auckland Bioengineering Institute University of Auckland Auckland1010 New Zealand Center of Integrative Biology University of Toulouse III-Paul Sabatier 165 Rue Marianne Grunberg-Manago Toulouse31400 France Lifeware Group Inria Building Alan Turing 1 Rue Honoré d’Estienne d’Orves Palaiseau91120 France Multiscale Modeling Group Altos Labs Redwood CityCA94065 United States partner site Tübingen Tübingen Germany Ottfried-Müller-Str. 37 Tübingen72076 Germany 06120 Germany Department of Computer Science Center for Data Science New York University New YorkNY11201 United States Department of Bi

Guidelines for managing scientific data have been established under the FAIR principles requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific disciplines, especially computational biology, both data and models are key to progress. For this reason, and recognizing that such models are a very special type of "data", we argue that computational models, especially mechanistic models prevalent in medicine, physiology and systems biology, deserve a complementary set of guidelines. We propose the CURE principles, emphasizing that models should be Credible, Understandable, Reproducible, and Extensible. We delve into each principle, discussing verification, validation, and uncertainty quantification for model credibility;the clarity of model descriptions and annotations for understandability;adherence to standards and open science practices for reproducibility;and the use of open standards and modular code for extensibility and reuse. We outline recommended and baseline requirements for each aspect of CURE, aiming to enhance the impact and trustworthiness of computational models, particularly in biomedical applications where credibility is paramount. Our perspective underscores the need for a more disciplined approach to modeling, aligning with emerging trends such as Digital Twins and emphasizing the importance of data and modeling standards for interoperability and reuse. Finally, we emphasize that given the non-trivial effort required to implement the guidelines, the community moves to automate as many of the guidelines as possible. © 2025, CC BY.

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Segregated interactions in urban and online spaces

arXiv

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arXiv 2019年

作者： Dong, Xiaowen Morales, Alfredo J. Jahani, Eaman Moro, Esteban Lepri, Bruno Bozkaya, Burcin Sarraute, Carlos Bar-Yam, Yaneer Pentland, Alex Department of Engineering Science University of Oxford Oxford United Kingdom MIT Media Lab CambridgeMA United States New England Complex Systems Institute CambridgeMA United States MIT Institute for Data Systems and Society CambridgeMA United States Department of Mathematics and GISC Universidad Carlos III de Madrid Leganés Spain Mobile and Social Computing Lab Fondazione Bruno Kessler Trento Italy Behavioral Analytics & Visualization Lab Sabancı University Istanbul Turkey New College of Florida SarasotaFL United States Grandata Labs Buenos Aires Argentina

Urban income segregation is a widespread phenomenon that challenges societies across the globe. Classical studies on segregation have largely focused on the geographic distribution of residential neighborhoods rather than on patterns of social behaviors and interactions. In this study, we analyze segregation in economic and social interactions by observing credit card transactions and Twitter mentions among thousands of individuals in three culturally different metropolitan areas. We show that segregated interaction is amplified relative to the expected effects of geographic segregation in terms of both shopping activity and online communication. Furthermore, we find that segregation increases with difference in socio-economic status but is asymmetric, i.e., the amount of interaction from poorer to wealthier neighborhoods is considerably larger than vice versa. Our results provide novel insights into the understanding of behavioral segregation in human interactions with significant socio-political and economic implications. Copyright © 2019, The Authors. All rights reserved.

关键词： Geographical distribution

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Private model compression via knowledge distillation

arXiv

引用

arXiv 2018年

作者： Wang, Ji Bao, Weidong Sun, Lichao Zhu, Xiaomin Cao, Bokai Yu, Philip S. College of Systems Engineering National University of Defense Technology Changsha China Department of Computer Science University of Illinois at Chicago Chicago United States State Key Laboratory of High Performance Computing National University of Defense Technology Changsha China Facebook Inc. Menlo Park United States Institute for Data Science Tsinghua University Beijing China

The soaring demand for intelligent mobile applications calls for deploying powerful deep neural networks (DNNs) on mobile devices. However, the outstanding performance of DNNs notoriously relies on increasingly complex models, which in turn is associated with an increase in computational expense far surpassing mobile devices' capacity. What is worse, app service providers need to collect and utilize a large volume of users' data, which contain sensitive information, to build the sophisticated DNN models. Directly deploying these models on public mobile devices presents prohibitive privacy risk. To benefit from the on-device deep learning without the capacity and privacy concerns, we design a private model compression framework RONA. Following the knowledge distillation paradigm, we jointly use hint learning, distillation learning, and self learning to train a compact and fast neural network. The knowledge distilled from the cumbersome model is adaptively bounded and carefully perturbed to enforce differential privacy. We further propose an elegant query sample selection method to reduce the number of queries and control the privacy loss. A series of empirical evaluations as well as the implementation on an Android mobile device show that RONA can not only compress cumbersome models efficiently but also provide a strong privacy guarantee. For example, on SVHN, when a meaningful (9:83;10-6)-differential privacy is guaranteed, the compact model trained by RONA can obtain 20× compression ratio and 19× speed-up with merely 0.97% accuracy loss. Copyright © 2018, The Authors. All rights reserved.

关键词： Deep neural networks

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Editorial: SPECIAL ISSUE on ADVANCED FRACTAL computing THEOREM and APPLICATION

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Fractals 2017年第4期25卷

作者： Liu, Shuai Key Laboratory of Social Computing and Data Processing of Inner Mongolia College of Computer Science Inner Mongolia University Hohhot010021 China

Fractal represents a special feature of nature and functional objects. However, fractal based computing can be applied to many research domains because of its fixed property resisted deformation, variable parameters and many unpredictable changes. Theoretical research and practical application of fractal based computing have been hotspots for 30 years and will be continued. There are many pending issues awaiting solutions in this domain, thus this thematic issue containing 14 papers publishes the state-of-the-art developments in theorem and application of fractal based computing, including mathematical analysis and novel engineering applications. The topics contain fractal and multifractal features in application and solution of nonlinear odes and equation. © 2017 The Author(s).

关键词： Fractals

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