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A Graphical Model for Fusing Diverse Microbiome Data

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arXiv 2022年

作者： Aktukmak, Mehmet Zhu, Haonan Chevrette, Marc G. Nepper, Julia Magesh, Shruthi Handelsman, Jo Hero, Alfred Department of Electrical and Computer Engineering University of Michigan United States Department of Plant Pathology University of Wisconsin-Madison United States Wisconsin Institute for Discovery United States Microbiology Doctoral Training Program University of Wisconsin-Madison United States

This paper develops a Bayesian graphical model for fusing disparate types of count data. The motivating application is the study of bacterial communities from diverse high dimensional features, in this case transcripts, collected from different treatments. In such datasets, there are no explicit correspondences between the communities and each correspond to different factors, making data fusion challenging. We introduce a flexible multinomial-Gaussian generative model for jointly modeling such count data. This latent variable model jointly characterizes the observed data through a common multivariate Gaussian latent space that parameterizes the set of multinomial probabilities of the transcriptome counts. The covariance matrix of the latent variables induces a covariance matrix of co-dependencies between all the transcripts, effectively fusing multiple data sources. We present a computationally scalable variational Expectation-Maximization (EM) algorithm for inferring the latent variables and the parameters of the model. The inferred latent variables provide a common dimensionality reduction for visualizing the data and the inferred parameters provide a predictive posterior distribution. In addition to simulation studies that demonstrate the variational EM procedure, we apply our model to a bacterial microbiome dataset.1 © 2022, CC BY.

关键词： Covariance matrix

The behavior of internet traffic for internet services during COVID-19 pandemic scenario

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arXiv 2021年

作者： da Silva, Carlos Alexandre Gouvea Ferrari, Allan Christian Krainski Osinski, Cristiano Pelacini, Douglas Antonio Firmino Computer Science Department State University of Parana Midwest Unicentro Guarapuava Brazil Centro Universitário Unicuritiba Curitiba Brazil Department of Electrical Engineering Electrical Engineering Graduate Program Federal University of Paraná Curitiba Brazil

Since the end of 2019, the SARS-CoV-2 virus known as COVID-19 has spread rapidly around the world, forcing many governments to impose restrictive blocking or lockdown to combat the pandemic. With locomotion restriction of people in almost of countries of the world, workers and students needed to keep their activities at home. As a result, people's behavior, habits, and the way they started using the Internet changed significantly. Like professionals of offices, the younger played an important role in this behavior, especially in the type of resources used by them. As result, the characterization and traffic of communication networks were affected in some way. In this perspective article, we join from many available studies about the COVID-19 effect at networks and investigate the effects on the Internet traffic of using services such as video streaming, video conferencing, and gaming during 2020's months of the pandemic. © 2021, CC BY.

关键词： Diseases

COEM: Cross-Modal Embedding for MetaCell Identification

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arXiv 2022年

作者： Mao, Haiyi Jia, Minxue Dou, Jason Xiaotian Zhang, Haotian Benos, Panayiotis V. Department of Computational and Systems Biology University of Pittsburgh PA United States Joint Carnegie Mellon University University of Pittsburgh PhD Program in Computational Biology United States Department of Electrical and Computer Engineering University of Pittsburgh PA United States

Metacells are disjoint and homogeneous groups of single-cell profiles, representing discrete and highly granular cell states. Existing metacell algorithms tend to use only one modality to infer metacells, even though single-cell multi-omics datasets profile multiple molecular modalities within the same cell. Here, we present Cross-MOdal Embedding for MetaCell Identification (COEM), which utilizes an embedded space leveraging the information of both scATAC-seq and scRNA-seq to perform aggregation, balancing the trade-off between fine resolution and sufficient sequencing coverage. COEM outperforms the state-of-the-art method SEACells by efficiently identifying accurate and well-separated metacells across datasets with continuous and discrete cell types. Furthermore, COEM significantly improves peak-to-gene association analyses, and facilitates complex gene regulatory inference tasks. © 2022, CC BY.

关键词： Embeddings

Performance limits due to thermal transport in graphene single-photon bolometers

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Physical Review Applied 2024年第1期21卷 014006-014006页

作者： Caleb Fried B. Jordan Russell Ethan G. Arnault Bevin Huang Gil-Ho Lee Dirk Englund Erik A. Henriksen Kin Chung Fong Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge Massachusetts 02139 Department of Earth and Planetary Sciences Harvard University Cambridge Massachusetts 02138 USA Department of Physics Harvard University Cambridge Massachusetts 02138 USA Raytheon BBN Quantum Engineering and Computing Group Cambridge Massachusetts 02138 USA Department of Physics Washington University in St. Louis St. Louis Missouri USA Intelligence Community Postdoctoral Research Fellowship Program Massachusetts Institute of Technology Cambridge Massachusetts 02139 Department of Physics Pohang University of Science and Technology Pohang 790-784 Republic of Korea

In high-sensitivity bolometers and calorimeters, the photon absorption often occurs at a finite distance from the temperature sensor to accommodate antennas or avoid the degradation of superconducting circuitry exposed to radiation. As a result, thermal propagation from the input to the temperature readout can critically affect detector performance. In this paper we model the performance of a graphene bolometer, accounting for electronic thermal diffusion and dissipation via electron-phonon coupling at low temperatures in three regimes: clean, supercollision, and resonant scattering. Our results affirm the feasibility of a superconducting readout without Cooper-pair breaking by mid- and near-infrared photons, and provide a recipe for designing graphene absorbers for calorimetric single-photon detectors. We investigate the trade-off between the input-readout distance and detector efficiency, and predict an intrinsic timing jitter of approximately 2.7 ps. Based on our result, we propose a spatial-mode-resolving photon detector to increase the communication bandwidth.

关键词： Heat transfer Metrology Optical quantum information processing Graphene Josephson junctions Bolometers Calorimetry Single-photon detectors

Meaningful human control: actionable properties for AI system development

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AI and Ethics 2022年第1期3卷 241-255页

作者： Cavalcante Siebert, Luciano Lupetti, Maria Luce Aizenberg, Evgeni Beckers, Niek Zgonnikov, Arkady Veluwenkamp, Herman Abbink, David Giaccardi, Elisa Houben, Geert-Jan Jonker, Catholijn M. van den Hoven, Jeroen Forster, Deborah Lagendijk, Reginald L. AiTech Interdisciplinary Research Program on Meaningful Human Control Delft University of Technology Delft The Netherlands Faculty of Electrical Engineering Mathematics and Computer Science Delft University of Technology Delft The Netherlands Faculty of Industrial Design Engineering Delft University of Technology Delft The Netherlands Faculty of Mechanical Maritime and Materials Engineering Delft University of Technology Delft The Netherlands Faculty of Technology Policy and Management Delft University of Technology Delft The Netherlands

How can humans remain in control of artificial intelligence (AI)-based systems designed to perform tasks autonomously? Such systems are increasingly ubiquitous, creating benefits - but also undesirable situations where moral responsibility for their actions cannot be properly attributed to any particular person or group. The concept of meaningful human control has been proposed to address responsibility gaps and mitigate them by establishing conditions that enable a proper attribution of responsibility for humans; however, clear requirements for researchers, designers, and engineers are yet inexistent, making the development of AI-based systems that remain under meaningful human control challenging. In this paper, we address the gap between philosophical theory and engineering practice by identifying, through an iterative process of abductive thinking, four actionable properties for AI-based systems under meaningful human control, which we discuss making use of two applications scenarios: automated vehicles and AI-based hiring. First, a system in which humans and AI algorithms interact should have an explicitly defined domain of morally loaded situations within which the system ought to operate. Second, humans and AI agents within the system should have appropriate and mutually compatible representations. Third, responsibility attributed to a human should be commensurate with that human’s ability and authority to control the system. Fourth, there should be explicit links between the actions of the AI agents and actions of humans who are aware of their moral responsibility. We argue that these four properties will support practically minded professionals to take concrete steps toward designing and engineering for AI systems that facilitate meaningful human control.

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Effects of Fir-Wood Biochar on Ch4 Oxidation Rates and Methanotrophs in Landfill Cover Soils Packed at Three Different Proctor Compaction Levels

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SSRN

SSRN 2023年

作者： Yi, Susan C. Heijbroek, Anne Cutz, Luis Pillay, Stephanie de Jong, Wiebren Abeel, Thomas Gebert, Julia Delft University of Technology Faculty of Mechanical Maritime and Materials Engineering Leeghwaterstraat 39 Delft2628 CB Netherlands Delft University of Technology Faculty of Electrical Engineering Mathematics and Computer Science Van Mourik Broekmanweg 6 Delft2628 XE Netherlands Broad Institute of MIT and Harvard Infectious Disease and Microbiome Program 415 Main St. CambridgeMA02142 United States

Application of biochar to landfill cover soils can purportedly improve methane (CH4) oxidation rates. However, understanding of the combined effects of soil texture, compaction, and biochar on activity and composition of the methanotrophs is limited. The amendment of wood biochar on two differently textured landfill cover soils at three compaction levels of the Proctor density were explored by analyzing changes in soil physical properties relevant to methane oxidation, the effects on CH4 oxidation rates and on the composition of the methanotrophic community. Loose soils with and without biochar were pre-incubated to equally elevate the CH4 oxidation rates. Hereafter, soils were compacted and re-incubated. Methane oxidation rates, gas diffusivity, water retention characteristics and pore size distribution were analyzed on the compacted soils. Abundance of methanotrophic bacteria (MOB) was determined at the end of both the pre-incubation tests and the incubation tests of the packed samples. Biochar significantly increased porosity at all compaction levels, resulting in enhanced diffusion coefficients. Also, a re-distribution in pore sizes was observed. Increased gas diffusivity from low compaction and amendment of biochar, however, did not reflect higher methane oxidation rates due to high diffusive oxygen fluxes over the limited height of the compacted soil specimens. All soils, with and without biochar, were strongly dominated by type II methanotrophs. In the sandy soil, biochar amendment strongly increased MOB abundance, which could be attributed to a corresponding increase in the abundance of Methylocystis species, while in the clayey soil no such response was observed. Compaction did not change the community composition in either soil. Biochar addition to landfill cover soils may not always enhance methanotrophic activity and hence reduce fugitive methane emissions with the effect being soil-specific. However, especially in finer and more compacted soils, biochar

关键词： Compaction

An exploration of neural dynamics of motor imagery for people with amyotrophic lateral sclerosis

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An exploration of neural dynamics of motor imagery for peopl...

作者： Hosni, Sarah M. Deligani, R.J. Zisk, A. McLinden, J. Borgheai, S.B. Shahriari, Y. Department of Electrical Computer and Biomedical Engineering University of Rhode Island KingstonRI United States Interdisciplinary Neuroscience Program University of Rhode Island KingstonRI United States

Objective. Studies of the neuropathological effects of amyotrophic lateral sclerosis (ALS) on the underlying motor system have investigated abnormalities in the magnitude and timing of the event-related desynchronization (ERD) and synchronization (ERS) during motor execution (ME). However, the spatio-spectral-temporal dynamics of these sensorimotor oscillations during motor imagery (MI) have not been fully explored for these patients. This study explores the neural dynamics of sensorimotor oscillations for ALS patients during MI by quantifying ERD/ERS features in frequency, time, and space. Approach. Electroencephalogram (EEG) data were recorded from six patients with ALS and 11 age-matched healthy controls (HC) while performing a MI task. ERD/ERS features were extracted using wavelet-based time-frequency analysis and compared between the two groups to quantify the abnormal neural dynamics of ALS in terms of both time and frequency. Topographic correlation analysis was conducted to compare the localization of MI activity between groups and to identify subject-specific frequencies in the µ and β frequency bands. Main results. Overall, reduced and delayed ERD was observed for ALS patients, particularly during right-hand MI. ERD features were also correlated with ALS clinical scores, specifically disease duration, bulbar, and cognitive functions. Significance. The analyses in this study quantify abnormalities in the magnitude and timing of sensorimotor oscillations for ALS patients during MI tasks. Our findings reveal notable differences between MI and existing results on ME in ALS. The observed alterations are speculated to reflect disruptions in the underlying cortical networks involved in MI functions. Quantifying the neural dynamics of MI plays an important role in the study of EEG-based cortical markers for ALS. © 2019 IOP Publishing Ltd.

关键词： Electroencephalography

Fine Particulate Matter Emissions from Electric Vehicle Fast Charging Stations

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SSRN

SSRN 2025年

作者： Li, Liqiao Yao, Yuan Niu, Muchuan Chen, Haoxuan Yu, Qiao Wu, Qingyang Li, Yuhang Zhang, Yijie Ozcan, Aydogan Jerrett, Michael Zhu, Yifang Department of Environmental Health Sciences Jonathan and Karin Fielding School of Public Health University of California Los Angeles Los AngelesCA United States Institute of Environment and Sustainability University of California Los Angeles Los AngelesCA United States Electrical and Computer Engineering Department University of California Los Angeles Los AngelesCA United States RAND Health Sciences Program United States

The global shift to electric vehicles necessitates the expansion of Direct Current Fast Charging (DCFC) stations, yet the related environmental and public health impacts remain unclear. Here, we report that the power cabinet at DCFC stations emit fine particulate matter (PM2.5). We collected integrated filter samples from 50 DCFC stations across 47 cities in Los Angeles County, California. The daily PM2.5 concentrations were between 7.3 and 39.0 µg m-3, significantly higher than urban background sites (p = 0.02) and the nearest U.S. EPA monitoring stations (p © 2025, The Authors. All rights reserved.

关键词： Air quality

Increasing the mobility and power-electronics figure of merit of AlGaN with atomically thin AlN/GaN digital-alloy superlattices

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arXiv 2022年

作者： Pant, Nick Lee, Woncheol Sanders, Nocona Kioupakis, Emmanouil Applied Physics Program University of Michigan Ann ArborMI48109 United States Department of Materials Science and Engineering University of Michigan Ann ArborMI48109 United States Department of Electrical Engineering and Computer Science University of Michigan Ann ArborMI48109 United States

Alloy scattering in random AlGaN alloys drastically reduces the electron mobility and therefore the power-electronics figure of merit. As a result, Al compositions greater than 75% are required to obtain even a two-fold increase of the Baliga figure of merit compared to GaN. However, beyond approximately 80% Al composition, donors in AlGaN undergo the DX transition which makes impurity doping increasingly more difficult. Moreover, the contact resistance increases exponentially with increasing Al content, and integration with dielectrics becomes difficult due to the upward shift of the conduction band. Atomically thin superlattices of AlN and GaN, also known as digital alloys, are known to grow experimentally under appropriate growth conditions. These chemically ordered nanostructures could offer significantly enhanced figure of merit compared to their random-alloy counterparts due to the absence of alloy scattering, as well as better integration with contact metals and dielectrics. In this work, we investigate the electronic structure and phonon-limited electron mobility of atomically thin AlN/GaN digital-alloy superlattices using first-principles calculations based on density-functional and many-body perturbation theory. The band gap of the atomically thin superlattices reaches 4.8 eV, and the in-plane (out-of-plane) mobility is 369 (452) cm2 V-1 s-1. Using the modified Baliga figure of merit that accounts for the dopant ionization energy, we demonstrate that atomically thin AlN/GaN superlattices with a monolayer sublattice periodicity have the highest modified Baliga figure of merit among several technologically relevant ultra-wide band-gap materials, including random AlGaN, β-Ga2O3, cBN, and diamond. Copyright © 2022, The Authors. All rights reserved.

关键词： Aluminum gallium nitride