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arXiv 2017年

作者： Avella-Medina, Marco Parise, Francesca Schaub, Michael T. Segarra, Santiago Department of Statistics Columbia University Laboratory for Information and Decision Systems MIT Institute for Data Systems and Society MIT Department of Engineering Science University of Oxford United Kingdom Department of Electrical and Computer Engineering Rice University

As relational datasets modeled as graphs keep increasing in size and their data-acquisition is permeated by uncertainty, graph-based analysis techniques can become computationally and conceptually challenging. In particular, node centrality measures rely on the assumption that the graph is perfectly known - a premise not necessarily fulfilled for large, uncertain networks. Accordingly, centrality measures may fail to faithfully extract the importance of nodes in the presence of uncertainty. To mitigate these problems, we suggest a statistical approach based on graphon theory: we introduce formal definitions of centrality measures for graphons and establish their connections to classical graph centrality measures. A key advantage of this approach is that centrality measures defined at the modeling level of graphons are inherently robust to stochastic variations of specific graph realizations. Using the theory of linear integral operators, we define degree, eigenvector, Katz and PageRank centrality functions for graphons and establish concentration inequalities demonstrating that graphon centrality functions arise naturally as limits of their counterparts defined on sequences of graphs of increasing size. The same concentration inequalities also provide high-probability bounds between the graphon centrality functions and the centrality measures on any sampled graph, thereby establishing a measure of uncertainty of the measured centrality score. Copyright © 2017, The Authors. All rights reserved.

关键词： Graphic methods

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Highly accurate model for prediction of lung nodule malignancy with ct scans

arXiv

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arXiv 2018年

作者： Causey, Jason Zhang, Junyu Ma, Shiqian Jiang, Bo Qualls, Jake Politte, David G. Prior, Fred Zhang, Shuzhong Huang, Xiuzhen Department of Computer Science Arkansas State University JonesboroAR72467 United States Department of Industrial and Systems Engineering University of Minnesota MinneapolisMN55455 United States Department of Systems Engineering and Engineering Management Chinese University of Hong Kong Shatin N.T. Hong Kong Research Center for Management Science and Data Analytics School of Information Management and Engineering Shanghai University of Finance and Economics Shanghai200433 China Mallinckrodt Institute of Radiology Washington University St. LouisMO63110 United States Department of Biomedical Informatics University of Arkansas for Medical Sciences Little RockAR72205 United States UALR/UAMS Joint Graduate Program in Bioinformatics Little RockAR72204 United States

Computed tomography (CT) examinations are commonly used to predict lung nodule malignancy in patients, which are shown to improve noninvasive early diagnosis of lung cancer. It remains challenging for computational approaches to achieve performance comparable to experienced radiologists. Here we present NoduleX, a systematic approach to predict lung nodule malignancy from CT data, based on deep learning convolutional neural networks (CNN). For training and validation, we analyze >1000 lung nodules in images from the LIDC/IDRI cohort. All nodules were identified and classified by four experienced thoracic radiologists who participated in the LIDC project. NoduleX achieves high accuracy for nodule malignancy classification, with an AUC of ~0.99. This is commensurate with the analysis of the dataset by experienced radiologists. Our approach, NoduleX, provides an effective framework for highly accurate nodule malignancy prediction with the model trained on a large patient population. Our results are replicable with software available at http://***/NoduleX. Copyright © 2018, The Authors. All rights reserved.

关键词： Forecasting

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Synergistic interactions promote behavior spreading and alter phase transition on multiplex Networks

arXiv

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arXiv 2018年

作者： Liu, Quan-Hui Wang, Wei Cai, Shi-Min Tang, Ming Lai, Ying-Cheng Web Sciences Center School of Computer Science and Engineering University of Electronic Science and Technology of China Chengdu611731 China Big Data Research Center University of Electronic Science and Technology of China Chengdu611731 China Laboratory for Modeling of Biological and Socio-technical Systems Northeastern University BostonMA02115 United States College of Computer Science and Technology Chongqing University of Posts and Telecommunications Chongqing400065 China Center for Polymer Studies and Department of Physics Boston University BostonMA02215 United States School of Information Science Technology East China Normal University Shanghai200241 China School of Electrical Arizona State University Computer and Energy Engineering TempeAZ85287 United States

Synergistic interactions are ubiquitous in the real world. Recent studies have revealed that, for a single-layer network, synergy can enhance spreading and even induce an explosive contagion. There is at the present a growing interest in behavior spreading dynamics on multiplex networks. What is the role of synergistic interactions in behavior spreading in such networked systems? To address this question, we articulate a synergistic behavior spreading model on a double layer network, where the key manifestation of the synergistic interactions is that the adoption of one behavior by a node in one layer enhances its probability of adopting the behavior in the other layer. A general result is that synergistic interactions can greatly enhance the spreading of the behaviors in both layers. A remarkable phenomenon is that the interactions can alter the nature of the phase transition associated with behavior adoption or spreading dynamics. In particular, depending on the transmission rate of one behavior in a network layer, synergistic interactions can lead to a discontinuous (first-order) or a continuous (second-order) transition in the adoption scope of the other behavior with respect to its transmission rate. A surprising two-stage spreading process can arise: Due to synergy, nodes having adopted one behavior in one layer adopt the other behavior in the other layer and then prompt the remaining nodes in this layer to quickly adopt the behavior. Analytically, we develop an edge-based compartmental theory and perform a bifurcation analysis to fully understand, in the weak synergistic interaction regime where the dynamical correlation between the network layers is negligible, the role of the interactions in promoting the social behavioral spreading dynamics in the whole system. Copyright © 2018, The Authors. All rights reserved.

关键词： Network layers

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Diagnosis of epilepsy after first seizure. Introducing the SWISS FIRST study

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Clinical and Translational Neuroscience 2020年第2期4卷

作者： Baudouin Zongxin Jin Pia De Stefano Valentina Petroulia Christian Rummel Claus Kiefer Mauricio Reyes Kaspar Schindler Pieter van Mierlo Margitta Seeck Roland Wiest Support Center for Advanced Neuroimaging Inselspital University of Bern Bern SwitzerlandSleep-Wake-Epilepsy Center and Center for Experimental Neurology Department of Neurology Inselspital University Hospital University of Bern Bern Switzerland Electroencephalography and Epilepsy Unit Department of Neurology University Hospitals of Geneva Geneva Switzerland Support Center for Advanced Neuroimaging Inselspital University of Bern Bern Switzerland ARTORG Center for Biomedical Engineering University of Bern/Insel Data Science Center Inselspital Bern Switzerland Sleep-Wake-Epilepsy Center and Center for Experimental Neurology Department of Neurology Inselspital University Hospital University of Bern Bern Switzerland Department of Electronics and Information Systems Ghent University Ghent Belgium

Diagnosis of epilepsy after a first unprovoked seizure is possible according to the guidelines by the International League Against Epilepsy, if the risk recurrence of a second unprovoked seizure is exceeding 60%. However, this cutoff constitutes only a proxy depending on the patients’ history, magnetic resonance imaging (MRI), and electroencephalography (EEG) findings but nevertheless also from the treating neurologists’ individual experience. In a Switzerland-wide observational study, we aim to recruit patients that were admitted to the emergency department with the referral diagnosis of a first and unprovoked seizure. We make use of optimized MRI protocols to identify potential structural epileptogenic lesions, introduce new imaging-based markers of epileptogenecity, and use most recent postprocessing methods as automatic morphometry, spike map analysis, and functional connectivity. With these diagnostic tools, we aim to segregate patients that present with epileptic seizures versus mimicks and non-epileptic seizures and stratify for every finding in MRI and EEG its predictive value for a second unprovoked seizure. These findings shall support neurologists to calculate and not only estimate the seizure recurrence rate in future.

关键词： Epilepsy neuroimaging automatic morphometry functional connectivity spike maps

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Inside Cover: A novel in vivo Cerenkov luminescence image-guided surgery on primary and metastatic colorectal cancer (J. Biophotonics 3/2020)

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Journal of Biophotonics 2020年第3期13卷

作者： Zeyu Zhang Yawei Qu Yu Cao Xiaojing Shi Hongbo Guo Xiaojun Zhang Sheng Zheng Haifeng Liu Zhenhua Hu Jie Tian Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education School of Life Science and Technology Xidian University Xi'an China CAS Key Laboratory of Molecular Imaging Beijing Key Laboratory of Molecular Imaging The State Key Laboratory of Management and Control for Complex Systems Institute of Automation Chinese Academy of Sciences Beijing China Department of Gastroenterology the Third Medical Centre Chinese PLA General Hospital Beijing China Department of Control Science and Engineering Harbin Institute of Technology Harbin China Department of Anorectal the Third medical Centre Chinese PLA General Hospital Beijing China University of Chinese Academy of Sciences Beijing China School of Information Sciences and Technology Northwest University Xi'an China Department of Nuclear Medicine Chinese PLA General Hospital Beijing China Beijing Advanced Innovation Center for Big Data-Based Precision Medicine School of Medicine Beihang University Beijing China

This study presents a novel intraoperative in vivo imaging approach which harnessed Cerenkov luminescence (CL) to detect primary and metastatic colorectal cancer (CRC) using clinically approved radiopharmaceuticals. In the mice and swine experiments, the proposed approach effectively improved the effect of CRC surgery. The approach is believed to be promising for utilizing CL in open surgery. Further details can be found in the article by Zeyu Zhang, Yawei Qu, Yu Cao et al. ( e201960152 )

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A note on semidefinite programming relaxations for polynomial optimization over a single sphere

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science China Mathematics 2016年第8期59卷 1543-1560页

作者： HU Jiang JIANG Bo LIU Xin WEN ZaiWen Beijing International Center for Mathematical Research Peking University Research Center for Management Science and Data Analytics School of Information Management and EngineeringShanghai University of Finance and Economics LSEC Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and Systems Science Chinese Academy of Sciences

We study two instances of polynomial optimization problem over a single sphere. The first problem is to compute the best rank-1 tensor approximation. We show the equivalence between two recent semidefinite relaxations methods. The other one arises from Bose-Einstein condensates(BEC), whose objective function is a summation of a probably nonconvex quadratic function and a quartic term. These two polynomial optimization problems are closely connected since the BEC problem can be viewed as a structured fourth-order best rank-1 tensor approximation. We show that the BEC problem is NP-hard and propose a semidefinite relaxation with both deterministic and randomized rounding procedures. Explicit approximation ratios for these rounding procedures are presented. The performance of these semidefinite relaxations are illustrated on a few preliminary numerical experiments.

关键词： polynomial optimization over a single sphere semidefinite programming best rank-1 tensor ap-proximation Bose-Einstein condensates

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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

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NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

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The repertoire of mutational signatures in human cancer (vol 578, pg 94, 2020)

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NATURE 2023年第7948期614卷 E41-E41页

作者： Alexandrov, Ludmil B. Kim, Jaegil Haradhvala, Nicholas J. Huang, Mi Ni Ng, Alvin Wei Tian Wu, Yang Boot, Arnoud Covington, Kyle R. Gordenin, Dmitry A. Bergstrom, Erik N. Islam, S. M. Ashiqul Lopez-Bigas, Nuria Klimczak, Leszek J. McPherson, John R. Morganella, Sandro Sabarinathan, Radhakrishnan Wheeler, David A. Mustonen, Ville Getz, Gad Rozen, Steven G. Stratton, Michael R. Department of Cellular and Molecular Medicine Department of Bioengineering Moores Cancer Center University of California San Diego CA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Cellular and Molecular Medicine and Department of Bioengineering University of California San Diego La Jolla CA USA UC San Diego Moores Cancer Center San Diego CA USA University of California San Diego San Diego CA USA Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Massachusetts General Hospital Boston MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama Japan Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada Programme in Cancer & Stem Cell Biology Duke-NUS Medical School Singapore Singapore Centre for Computational Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Centre for Computational Biology Duke-NUS Medical School Singapore Singapore SingHealth Duke-NUS Institute of Precision Medicine National Heart Centre Singapore Singapore Singapore Cancer Science Institute of Singapore National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Singapore Singapore Laboratory of Cancer Epigenome Division of Medical Science National Cancer Centre Singapore Singapore Singapore Duke-NUS Medical School Singapore Singapore Human Genome Sequencing Center Baylor College of Medicine Houston TX USA Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Genome Integrity and Structural Biology Laboratory National Ins

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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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The complete mitochondrial genome sequence and phylogenetic analysis ofLuciola lateralis, one of the most famous firefly in Japan (Coleoptera: Lampyridae)

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Mitochondrial DNA Part B 2017年第2期2卷 546-547页

作者： Juri Maeda Dai-Ichiro Kato Kazunari Arima Yuji Ito Atsushi Toyoda Hideki Noguchi Department of Chemistry and Biosciences Graduate School of Science and Engineering Kagoshima University Kagoshima Japan Advanced Genomics Center National Institute of Genetics Mishima Japan Center for Genome Informatics Joint Support-Center for Data Science Research Research Organization of Information and Systems Mishima Japan

We will report the complete mitochondrial genome sequence of Japanese firefly ‘Heike Botaru’,Luciola lateralis(Coleoptera: Lampyridae). Total length of this mitogenome was 16,719 bp and the composition of each base was A (42.50%), C (9.01%), G (14.16%), T (34.33%), respectively. The obtained sequence fulfils general mitogenome composition of metazoan (13 protein coding sequences (CDSs), 22 tRNA genes, two rRNA subunits, and an AT-rich region). From the phylogenetic tree analysis using 25 kinds of insect mitogenome including firefly family was found thatL. lateralisis the closest to the genusAquatica.

关键词： Luciola lateralis firefly Lampyridae mitochondrial genome Coleoptera

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