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Author Correction: Effect of de novo transcriptome assembly on transcript quantification

Scientific reports 2019年第1期9卷 18041页

作者： Ping-Han Hsieh Yen-Jen Oyang Chien-Yu Chen Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei 10617 Taiwan. Department of Computer Science and Information Engineering National Taiwan University Taipei 10617 Taiwan. Department of Bio-Industrial Mechatronics Engineering National Taiwan University Taipei 10617 Taiwan. chienyuchen@ntu.edu.tw. Genome and Systems Biology Program National Taiwan University and Academia sinica Taipei 10617 Taiwan. chienyuchen@ntu.edu.tw.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Quantized memory-augmented neural networks

arXiv

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arXiv 2017年

作者： Park, Seongsik Kim, Seijoon Lee, Seil Bae, Ho Yoon, Sungroh Department of Electrical and Computer Engineering Seoul National University Seoul08826 Korea Republic of Interdisciplinary Program in Bioinformatics Seoul National University Seoul08826 Korea Republic of

Memory-augmented neural networks (MANNs) refer to a class of neural network models equipped with external memory (such as neural Turing machines and memory networks). These neural networks outperform conventional recurrent neural networks (RNNs) in terms of learning long-term dependency, allowing them to solve intriguing AI tasks that would otherwise be hard to address. This paper concerns the problem of quantizing MANNs. Quantization is known to be effective when we deploy deep models on embedded systems with limited resources. Furthermore, quantization can substantially reduce the energy consumption of the inference procedure. These benefits justify recent developments of quantized multilayer perceptrons, convolutional networks, and RNNs. However, no prior work has reported the successful quantization of MANNs. The in-depth analysis presented here reveals various challenges that do not appear in the quantization of the other networks. Without addressing them properly, quantized MANNs would normally suffer from excessive quantization error which leads to degraded performance. In this paper, we identify memory addressing (specifically, content-based addressing) as the main reason for the performance degradation and propose a robust quantization method for MANNs to address the challenge. In our experiments, we achieved a computation-energy gain of 22× with 8-bit fixed-point and binary quantization compared to the floating-point implementation. Measured on the bAbI dataset, the resulting model, named the quantized MANN (Q-MANN), improved the error rate by 46% and 30% with 8-bit fixed-point and binary quantization, respectively, compared to the MANN quantized using conventional techniques. Copyright © 2017, The Authors. All rights reserved.

关键词： Recurrent neural networks

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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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Modeling helium segregation to the surfaces of plasma-exposed tungsten as a function of temperature and surface orientation

Modeling helium segregation to the surfaces of plasma-expose...

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作者： Blondel, Sophie Hammond, Karl D. Hu, Lin Maroudas, Dimitrios Wirth, Brian D. University of Tennessee Department of Nuclear Engineering KnoxvilleTN37996 United States Oak Ridge National Laboratory Computer Sciences and Mathematics Division Oak RidgeTN37831 United States University of Missouri Department of Chemical Engineering ColumbiaMO65211 United States University of Missouri Nuclear Engineering Program ColumbiaMO65211 United States University of Massachusetts Department of Chemical Engineering AmherstMA01003-9303 United States Oak Ridge National Laboratory Fusion and Materials for Nuclear Systems Division Oak RidgeTN37831 United States

We provide a description of the dependence on surface crystallographic orientation and temperature of the segregation of helium implanted with energies consistent with low-energy plasma exposure to tungsten surfaces. Here, we describe multiscale modeling results based on a hierarchical approach to scale bridging that incorporates atomistic studies based on a reliable interatomic potential to parameterize a spatially dependent drift-diffusion-reaction cluster-dynamics code. An extensive set of molecular dynamics (MD) simulations has been performed at 933 K and/or 1200 K to determine the probabilities of desorption and modified trap mutation that occurs as small, mobile Hen (1 ≥ n ≥ 7) clusters diffuse from the near-surface region toward surfaces of varying crystallographic orientation due to an elastic interaction force that provides the thermodynamic driving force for surface segregation. These near-surface cluster dynamics have significant effects on the surface morphology, the near-surface defect structures, and the amount of helium retained in the material upon plasma exposure, for which we have developed an extensive MD database of cumulative evolution during high-flux helium implantation at 933 K, which we compare to our properly parameterized cluster-dynamics model. This validated model is then used to evaluate the effects of temperature on helium retention and subsurface helium clustering. © 2017 American Nuclear Society.

关键词： Helium

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Benchmarks and tests of a multidimensional cluster dynamics model of helium implantation in tungsten

Benchmarks and tests of a multidimensional cluster dynamics ...

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作者： Blondel, Sophie Bernholdt, David E. Hammond, Karl D. Hu, Lin Maroudas, Dimitrios Wirth, Brian D. University of Tennessee Department of Nuclear Engineering KnoxvilleTN37996 United States Oak Ridge National Laboratory Computer Sciences and Mathematics Division Oak RidgeTN37831 United States University of Missouri Department of Chemical Engineering ColumbiaMO65211 United States University of Missouri Nuclear Engineering Program ColumbiaMO65211 United States University of Massachusetts Department of Chemical Engineering AmherstMA01003 United States Oak Ridge National Laboratory Fusion and Materials for Nuclear Systems Division Oak RidgeTN37831 United States

We present a hierarchical multiscale modeling study of implanted helium (He) segregation near grain boundaries (GBs) of tungsten. We extend our spatially dependent cluster dynamics model to two spatial dimensions in order to take into account the biased drift of mobile He clusters toward the GBs observed in atomic-scale simulations. We are able to reproduce the results from large-scale molecular dynamics simulations near and away from the GBs at low fluence with the extended cluster dynamics model. We suggest and verify that the sink (surface and GB) strengths are attenuated by the increasing concentration of He clusters at high fluence. This cluster dynamics model continues to set the stage for development of fully atomistically informed, coarse-grained models for computationally efficient predictions of He retention and surface morphological evolution, advancing progress toward the goal of efficient and optimal design of plasma-facing components. © 2017 American Nuclear Society.

关键词： Grain boundaries

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Multistatic microwave holography: Initial results on anthropomorphic phantoms 10

Multistatic microwave holography: Initial results on anthrop...

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10th European Conference on Antennas and Propagation, EuCAP 2016

作者： Tapia, Daniel Flores Nepote, Mario Solis Herrera, Diego Rodriguez Lei, Fu Yonsheng, Gui Benyon, Valerie Can-Min, Hu Pistorius, Stephen Latif, Saeed Department of Physics and Astronomy Biomedical Engineering Program Department of Electrical and Computer Engineering University of Manitoba WinnipegManitoba Canada Department of Electrical and Computer Engineering University of South Alabama MobileAlabama United States

ISBN: (纸本)9788890701863

Ultra Wide Band Radar is a novel technology used for breast cancer detection. This imaging modality uses ultra wide band waveforms to form a reflectivity map of the breast region in which tumors can potentially been clearly distinguished. In this study, the authors assess the use of a novel Breast UWBR reconstruction approach, microwave holography, on anthropomorphic phantoms. These phantoms mimic both the shape and dielectric properties of human breast. The images formed using microwave holography are consistent with the location of the synthetic breast structures and show signal to clutter level above 3dB. © 2016 European Association of Antennas and Propagation.

关键词： Microwave holography

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Development of a prototype of an automatic system for shrimp farming using telecontrol as a viable proposal for small producers

Development of a prototype of an automatic system for shrimp...

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European Conference on Electrical engineering and computer Science (EECS)

作者： Ivan Daniel Oviedo Carlos A. Altamirano Marcos E. Millan Nestor X. Arreaga Vladimir Sanchez Padilla Escuela Superior Politécnica del Litoral ESPOL Faculty of Electrical and Computer Engineering Guayaquil Ecuador Escuela Superior Politécnica del Litoral ESPOL ReDIT Group Telematics Engineering Program Guayaquil Ecuador

ISBN: (纸本)9781538620861

This paper presents a solution for different activities concerning shrimp farming, especially focused on the middle-class artisanal productive sector, using both open source hardware and open source software. The proposal aims to optimize monitoring during shrimp farming, measuring parameters, such as dissolved oxygen, water temperature and food levels inside reservoirs, in order to have a real-time reading of parameters. In case critical values appear, an alarm activates by control center, notifying by either electronic mail or web interface. The attractiveness of the proposal consists in the automation of the feeding system, which provides food supply to shrimps at certain daily periods, controlling by web interface the different options the breeder has available, a process that can be even managed remotely.

关键词： Temperature measurement Temperature sensors Monitoring Servomotors Reservoirs Wires

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Effect of node attributes on the temporal dynamics of network structure

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Physical Review E 2017年第3期95卷 032304-032304页

作者： Naghmeh Momeni Babak Fotouhi Department of Electrical and Computer Engineering McGill University Montréal Québec Canada Program for Evolutionary Dynamics Harvard University Cambridge Massachusetts 02138 USA Institute for Quantitative Social Sciences Harvard University Cambridge Massachusetts 02138 USA

Many natural and social networks evolve in time and their structures are dynamic. In most networks, nodes are heterogeneous, and their roles in the evolution of structure differ. This paper focuses on the role of individual attributes on the temporal dynamics of network structure. We focus on a basic model for growing networks that incorporates node attributes (which we call “quality”), and we focus on the problem of forecasting the structural properties of the network in arbitrary times for an arbitrary initial network. That is, we address the following question: If we are given a certain initial network with given arbitrary structure and known node attributes, then how does the structure change in time as new nodes with given distribution of attributes join the network? We solve the model analytically and obtain the quality-degree joint distribution and degree correlations. We characterize the role of individual attributes in the position of individual nodes in the hierarchy of connections. We confirm the theoretical findings with Monte Carlo simulations.

关键词： Degree correlations Degree distributions Dynamics of networks Network formation & growth Preferential attachment Stochastic processes Probability theory

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Polaritonic frequency-comb generation and breather propagation in a negative-index metamaterial with a cold four-level atomic medium

arXiv

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arXiv 2019年

作者： Asgarnezhad-Zorgabad, Saeid Berini, Pierre Sanders, Barry C. Department of Physics Sharif University of Technology Tehran11365 11155 Iran Institute for Quantum Science and Technology University of Calgary CalgaryABT2N 1N4 Canada Department of Physics University of Ottawa 150 Louis-Pasteur OttawaONK1N 6N5 Canada Centre for Research in Photonics University of Ottawa 25 Templeton St. OttawaONK1N 6N5 Canada School of Electrical Engineering and Computer Science 700 King Edward St. OttawaONK1N 6N5 Canada Program in Quantum Information Science Canadian Institute for Advanced Research TorontoONM5G 1M1 Canada

We develop a concept for a waveguide that exploits spatial control of nonlinear surface-polaritonic waves. Our scheme includes an optical cavity with four-level N-type atoms in a lossless dielectric placed above a negative-index metamaterial layer. We propose exciting a polaritonic Akhmediev breather at a certain position of the interface between the atomic medium and the metamaterial by modifying laser-field intensities and detunings. Furthermore, we propose generating position-dependent polaritonic frequency combs by engineering widths of the electromagnetically induced transparency window commensurate with the surface-polaritonic modulation instability. Therefore, this waveguide acts as a high-speed polaritonic modulator and position-dependent frequency-comb generator, which can be applied to compact photonic chips. Copyright © 2019, The Authors. All rights reserved.

关键词： Metamaterials

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Glial responses to implanted electrodes in the brain (vol 1, pg 862, 2017)

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NATURE BIOMEDICAL engineering 2018年第1期2卷 52-52页

作者： Salatino, Joseph W. Ludwig, Kip A. Kozai, Takashi D. Y. Purcell, Erin K. Department of Biomedical Engineering Michigan State University East Lansing MI USA. Institute for Quantitative Health Science and Engineering Michigan State University East Lansing MI USA. Department of Neurologic Surgery Mayo Clinic Rochester MN USA. Department of Bioengineering University of Pittsburgh Pittsburgh PA USA. Center for the Neural Basis of Cognition University of Pittsburgh Pittsburgh PA USA. McGowan Institute of Regenerative Medicine University of Pittsburgh Pittsburgh PA USA. Neurotech Center University of Pittsburgh Brain Institute Pittsburgh PA USA. Department of Electrical and Computer Engineering Michigan State University East Lansing MI USA. Neuroscience Program Michigan State University East Lansing MI USA.

The use of implants that can electrically stimulate or record electrophysiological or neurochemical activity in nervous tissue is rapidly expanding. Despite remarkable results in clinical studies and increasing market approvals, the mechanisms underlying the therapeutic effects of neuroprosthetic and neuromodulation devices, as well as their side effects and reasons for their failure, remain poorly understood. A major assumption has been that the signal-generating neurons are the only important target cells of neural-interface technologies. However, recent evidence indicates that the supporting glial cells remodel the structure and function of neuronal networks and are an effector of stimulation-based therapy. Here, we reframe the traditional view of glia as a passive barrier, and discuss their role as an active determinant of the outcomes of device implantation. We also discuss the implications that this has on the development of bioelectronic medical devices.

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