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

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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Structural Effects and Aggregation in a Social-Network Model of Natural Resource Consumption

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IFAC-PapersOnLine 2017年第1期50卷 7675-7680页

作者： Manzoor T. Rovenskaya E. Muhammad A. Department of Electrical Engineering Lahore University of Management Sciences (LUMS) Lahore Pakistan Center for Water Informatics & Technology (WIT) Lahore University of Management Sciences (LUMS) Pakistan Advanced Systems Analysis Program International Institute for Applied Systems Analysis (IIASA) Laxenburg Austria Faculty of Computational Mathematics and Cybernetics Lomonosov Moscow State University Moscow Russian Federation

In this paper we consider a networked system of natural-resource consumption, where the agents are governed by a recently reported model of consumer psychology Dynamics of the consumption for each agent are influenced by the state of the resource and consumption of her neighbors. The process is parameterized by the psychological characteristics of each agent. This study extends the original model to incorporate the underlying network topology and explores the effects of aggregation via densely-connected communities present in the network. The exercise yields new interpretations of the predictions made by the original model in context of the influence network. We present aggregation mechanisms first for certain canonical structures of the consuming population and later on for a class of non-canonically structured populations. In the end we present an approximate aggregation scheme for populations where only some inaccurate information of the consumer characteristics is available. © 2017

关键词： Control in economics identification of environmental systems Modeling Multi-agent systems Natural resources management Social Networks

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Cluster synchronization of diffusively-coupled nonlinear systems: A contraction based approach

arXiv

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arXiv 2017年

作者： Aminzare, Zahra Dey, Biswadip Davison, Elizabeth N. Leonard, Naomi Ehrich Program in Applied and Computational Mathematics Princeton University NJ08544 United States Department of Mechanical and Aerospace Engineering Princeton University NJ08540 United States

Finding the conditions that foster synchronization in networked oscillatory systems is critical to understanding a wide range of biological and mechanical systems. However, the conditions proved in the literature for synchronization in nonlinear systems with linear coupling, such as has been used to model neuronal networks, are in general not strict enough to accurately determine the system behavior. We leverage contraction theory to derive new sufficient conditions for cluster synchronization in terms of the network structure, for a network where the intrinsic nonlinear dynamics of each node may differ. Our result requires that network connections satisfy a cluster-input-equivalence condition, and we explore the influence of this requirement on network dynamics. For application to networks of nodes with neuronal spiking dynamics, we show that our new sufficient condition is tighter than those found in previous analyses which used nonsmooth Lyapunov functions. Improving the analytical conditions for when cluster synchronization will occur based on network configuration is a significant step toward facilitating understanding and control of complex oscillatory systems. Copyright © 2017, The Authors. All rights reserved.

关键词： Synchronization

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Local-order metric for condensed-phase environments

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Physical Review B 2018年第6期97卷 064105-064105页

作者： Fausto Martelli Hsin-Yu Ko Erdal C. Oğuz Roberto Car Department of Chemistry Princeton University Princeton New Jersey 08544 USA Institut für Theoretische Physik II Heinrich-Heine-Universität D-40225 Düsseldorf Germany Department of Physics Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

We introduce a local order metric (LOM) that measures the degree of order in the neighborhood of an atomic or molecular site in a condensed medium. The LOM maximizes the overlap between the spatial distribution of sites belonging to that neighborhood and the corresponding distribution in a suitable reference system. The LOM takes a value tending to zero for completely disordered environments and tending to one for environments that perfectly match the reference. The site-averaged LOM and its standard deviation define two scalar order parameters, S and δS, that characterize with excellent resolution crystals, liquids, and amorphous materials. We show with molecular dynamics simulations that S, δS, and the LOM provide very insightful information in the study of structural transformations, such as those occurring when ice spontaneously nucleates from supercooled water or when a supercooled water sample becomes amorphous upon progressive cooling.

关键词： Glass transition Nucleation Order parameters Phase transitions

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Data-driven model reduction and transfer operator approximation

arXiv

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arXiv 2017年

作者： Klus, Stefan Nüske, Feliks Koltai, Péter Wu, Hao Kevrekidis, Ioannis Schütte, Christof Noé, Frank Department of Mathematics and Computer Science Freie Universität Berlin Germany Department of Chemical and Biological Engineering & Program in Applied and Computational Mathematics Princeton University United States Zuse Institute Berlin Germany

In this review paper, we will present different data-driven dimension reduction techniques for dynamical systems that are based on transfer operator theory as well as methods to approximate transfer operators and their eigenvalues, eigenfunctions, and eigenmodes. The goal is to point out similarities and differences between methods developed independently by the dynamical systems, fluid dynamics, and molecular dynamics communities such as time-lagged independent component analysis (TICA), dynamic mode decomposition (DMD), and their respective generalizations. As a result, extensions and best practices developed for one particular method can be carried over to other related methods. Copyright © 2017, The Authors. All rights reserved.

关键词： Dynamical systems

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Classical many-particle systems with unique disordered ground states

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Physical Review E 2017年第4期96卷 042146-042146页

作者： G. Zhang F. H. Stillinger S. Torquato Department of Chemistry Princeton University Princeton New Jersey 08544 USA Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Classical ground states (global energy-minimizing configurations) of many-particle systems are typically unique crystalline structures, implying zero enumeration entropy of distinct patterns (aside from trivial symmetry operations). By contrast, the few previously known disordered classical ground states of many-particle systems are all high-entropy (highly degenerate) states. Here we show computationally that our recently proposed “perfect-glass” many-particle model [Sci. Rep. 6, 36963 (2016)] possesses disordered classical ground states with a zero entropy: a highly counterintuitive situation . For all of the system sizes, parameters, and space dimensions that we have numerically investigated, the disordered ground states are unique such that they can always be superposed onto each other or their mirror image. At low energies, the density of states obtained from simulations matches those calculated from the harmonic approximation near a single ground state, further confirming ground-state uniqueness. Our discovery provides singular examples in which entropy and disorder are at odds with one another. The zero-entropy ground states provide a unique perspective on the celebrated Kauzmann-entropy crisis in which the extrapolated entropy of a supercooled liquid drops below that of the crystal. We expect that our disordered unique patterns to be of value in fields beyond glass physics, including applications in cryptography as pseudorandom functions with tunable computational complexity.

关键词： Nonequilibrium statistical mechanics Pattern formation

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Benchmark problems for phase retrieval

arXiv

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arXiv 2017年

作者： Elser, Veit Lan, Ti-Yen Bendory, Tamir Department of Physics Cornell University IthacaNY14853-2501 United States Program in Applied and Computational Mathematics Princeton University Princeton08544-1000 United States

In recent years, the mathematical and algorithmic aspects of the phase retrieval problem have received considerable attention. Many papers in this area mention crystallography as a principal application. In crystallography, the signal to be recovered is periodic and comprised of atomic distributions arranged homogeneously in the unit cell of the crystal. The crystallographic problem is both the leading application and one of the hardest forms of phase retrieval. We have constructed a graded set of benchmark problems for evaluating algorithms that perform this type of phase retrieval. The data, publicly available online1, is provided in an easily interpretable format. We also propose a simple and unambiguous success/failure criterion based on the actual needs in crystallography. Baseline runtimes were obtained with an iterative algorithm that is similar but more transparent than those used in crystallography. Empirically,the runtimes grow exponentially with respect to a new hardness parameter: the sparsity of the signal autocorrelation. We also review the algorithms used by the leading software packages. This set of benchmark problems, we hope, will encourage the development of new algorithms for the phase retrieval problem in general, and crystallography in particular. Copyright © 2017, The Authors. All rights reserved.

关键词： Benchmarking

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A fourth-order accurate finite volume method for ideal mhd via upwind constrained transport

arXiv

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arXiv 2017年

作者： Felker, Kyle Gerard Stone, James Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Astrophysical Sciences Princeton University PrincetonNJ08544 United States

We present a fourth-order accurate finite volume method for the solution of ideal magnetohydrodynamics (MHD). The numerical method combines high-order quadrature rules in the solution of semi-discrete formulations of hyperbolic conservation laws with the upwind constrained transport (UCT) framework to ensure that the divergence-free constraint of the magnetic field is satisfied. A novel implementation of UCT that uses the piecewise parabolic method (PPM) for the reconstruction of magnetic fields at cell corners in 2D is introduced. The resulting scheme can be expressed as the extension of the second-order accurate constrained transport (CT) Godunov-type scheme that is currently used in the Athena astrophysics code. After validating the base algorithm on a series of hydrodynamics test problems, we present the results of multidimensional MHD test problems which demonstrate formal fourth-order convergence for smooth problems, robustness for discontinuous problems, and improved accuracy relative to the second-order scheme. Copyright © 2017, The Authors. All rights reserved.

关键词： Numerical methods

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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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Pre-processing and classification of hyperspectral imagery via selective inpainting

Pre-processing and classification of hyperspectral imagery v...

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IEEE International Conference on Acoustics, Speech and Signal Processing

作者： Victoria Chayes Kevin Miller Rasika Bhalerao Jiajie Luo Wei Zhu Andrea L. Bertozzi Wenzhi Liao Stanley Osher California Research Training Program in Computational and Applied Mathematics United States of America University of California Los Angeles Department of Mathematics United States of America Ghent University Department of Telecommunications and Information Processing Belgium

ISBN: (纸本)9781509041183

We propose a semi-supervised algorithm for processing and classification of hyperspectral imagery. For initialization, we keep 20% of the data intact, and use Principal Component Analysis to discard voxels from noisier bands and pixels. Then, we use either an Accelerated Proximal Gradient algorithm (APGL), or a modified APGL algorithm with a penalty term for distance between inpainted pixels and endmembers (APGL Hyp), on the initialized datacube to inpaint the missing data. APGL and APGL Hyp are distinguished by performance on datasets with full pixels removed or extreme noise. This inpainting technique results in band-by-band datacube sharpening and removal of noise from individual spectral signatures. We can also classify the inpainted cube by assigning each pixel to its nearest endmember via Euclidean distance. We demonstrate improved accuracy in classification over data-mining techniques like k-means, unmixing techniques like Hierarchical Non-Negative Matrix Factorization, and graph-based methods like Non-Local Total Variation.

关键词： Hyperspectral imagery (HSI) data preprocessing image inpainting image classification image enhancement Data preprocessing hyperspectral imagery Image classification image enhancement pixel Pretreatment matrix decomposition initialization Euclidean distance

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