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2020 IEEE International Conference on Informatics, IoT, and Enabling Technologies, ICIoT 2020

作者： Antoun, Wissam Baly, Fady Achour, Rim Hussein, Amir Hajj, Hazem American University of Beirut Electrical and Computer Engineering Department Beirut Lebanon Graduate Program in Computational Science American University of Beirut Beirut Lebanon

ISBN: (数字)9781728148212

ISBN: (纸本)9781728148212

This paper presents state of the art methods for addressing three important challenges in automated fake news detection: fake news detection, domain identification, and bot identification in tweets. The proposed solutions achieved first place in a recent international competition on fake news. For fake news detection, we present two models. The winning model in the competition combines similarity between the embedding of each article's title and the embedding of the top five corresponding google search results. The new model relies on advances in Natural Language Understanding (NLU) end to end deep learning models to identify stylistic differences between legitimate and fake news articles. This second model was developed after the competition and outperforms the winning approach. For news domain detection, the winning model is a hybrid approach composed of named entity features concatenated with semantic embeddings derived from end to end models. For twitter bot detection, we propose to use the following features: duration between account creation and tweet date, presence of a tweet's link, presence of user's location, other tweet's features, and the tweets' metadata. Experiments include insights into the importance of the different features and the results indicate the superior performances of all proposed models. © 2020 IEEE.

关键词： Competition

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Multimodal identification of the mouse brain using simultaneous Ca²⁺ imaging and fMRI

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Communications Biology 2025年第1期8卷 1-14页

作者： Mandino, Francesca Horien, Corey Shen, Xilin Desrosiers-Grégoire, Gabriel Luo, Wendy Markicevic, Marija Constable, R. Todd Papademetris, Xenophon Chakravarty, Mallar M. Betzel, Richard F. Lake, Evelyn M. R. Department of Radiology and Biomedical Imaging Yale University School of Medicine New Haven CT United States Interdepartmental Neuroscience Program Yale University School of Medicine New Haven CT United States MD/PhD program Yale University School of Medicine New Haven CT United States Computational Brain Anatomy Laboratory Douglas Mental Health University Institute Montreal QC Canada Integrated Program in Neuroscience McGill University Montreal QC Canada Department of Biomedical Engineering Yale University School of Medicine New Haven CT United States Department of Neurosurgery Yale University School of Medicine New Haven CT United States Deparment of Biomedical Informatics and Data Science Yale University New Haven CT United States Department of Psychological and Brain Sciences Indiana University Bloomington IN United States Wu Tsai Institute Yale University New Haven CT United States

Individual differences in neuroimaging are of interest to clinical and cognitive neuroscientists based on their potential for guiding the personalized treatment of various heterogeneous neurological conditions and diseases. Despite many advantages, the prevailing modality in this field—blood-oxygen-level-dependent (BOLD) functional magnetic resonance imaging (fMRI)—suffers from low spatiotemporal resolution and specificity as well as a propensity for noise and spurious signal corruption. To better understand individual differences in BOLD-fMRI data, we can use animal models where fMRI, alongside complementary but more invasive contrasts, can be accessed. Here, we apply simultaneous wide-field fluorescence calcium imaging and BOLD-fMRI in mice to interrogate individual differences using a connectome-based identification framework adopted from the human fMRI literature. This approach yields high spatiotemporal resolution cell-type specific signals (here, from glia, excitatory, as well as inhibitory interneurons) from the whole cortex. We found mouse multimodal connectome-based identification to be successful and explored various features of these data. © The Author(s) 2025.

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Regulation of regeneration in Arabidopsis thaliana

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aBIOTECH 2023年第4期4卷 332-351页

作者： Md Khairul Islam Sai Teja Mummadi Sanzhen Liu Hairong Wei Computational Science and Engineering Program Michigan Technological UniversityHoughtonMI 49931USA Computer Science Michigan Technological UniversityHoughtonMI 49931USA Department of Plant Pathology Kansas State UniversityManhattanKS 66506USA College of Forest Resources and Environmental Science Michigan Technological UniversityHoughtonMI 49931USA

We employed several algorithms with high efficacy to analyze the public transcriptomic data,aiming to identify key transcription factors(TFs)that regulate regeneration in Arabidopsis ***,we utilized CollaborativeNet,also known as TF-Cluster,to construct a collaborative network of all TFs,which was subsequently decomposed into many subnetworks using the Triple-Link and Compound Spring Embedder(CoSE)*** analysis of these subnetworks led to the identification of nine subnetworks closely associated with *** further applied principal component analysis and gene ontology(GO)enrichment analysis to reduce the subnetworks from nine to three,namely subnetworks 1,12,and *** for TF-binding sites in the promoters of the co-expressed and co-regulated(CCGs)genes of all TFs in these three subnetworks and Triple-Gene Mutual Interaction analysis of TFs in these three subnetworks with the CCGs involved in regeneration enabled us to rank the TFs in each ***,six potential candidate TFs-WOx9A,LEC2,PGA37,WIP5,PEI1,and AIL1 from subnetwork 1-were identified,and their roles in somatic embryogenesis(GO:0010262)and regeneration(GO:0031099)were discussed,so were the TFs in Subnetwork 12 and 17 associated with *** TFs identified were also assessed using the CIS-BP database and Expression *** analyses suggest some novel TFs that may have regulatory roles in regeneration and embryogenesis and provide valuable data and insights into the regulatory mechanisms related to *** tools and the procedures used here are instrumental for analyzing high-throughput transcriptomic data and advancing our understanding of the regulation of various biological processes of interest.

关键词： Regeneration Pluripotency Transcription factor Collaborative network

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Quantifying random variability in decision-making in pediatric cardiac surgery

JTCVS Open

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JTCVS Open 2025年

作者： Dlugos, Kayla V. Mazwi, Mjaye Signorile, Marisa Steve Fan, Chun-Po Trbovich, Patricia Honjo, Osami Institute of Medical Science University of Toronto ON Canada Division of Cardiovascular Surgery The Labatt Family Heart Centre The Hospital for Sick Children Toronto ON Canada Department of Surgery University of Toronto ON Canada Division of Cardiac Critical Care Seattle Children's Hospital Seattle Wash United States Ted Rogers Computational Program Ted Rogers Centre for Heart Research Peter Munk Cardiac Centre UHN Toronto ON Canada Institute of Health Policy Management and Evaluation University of Toronto Toronto ON Canada North York General Hospital Toronto ON Canada Institute of Biomedical Engineering University of Toronto Toronto ON Canada

Objective: Random variability in day-to-day decision-making referred to as “noise” is associated with variation that negatively affects both the reproducibility and quality of decision-making. Although well described in other fields, the prevalence and significance of noise in medical decision-making are understudied and largely unknown. The goal of this study was to quantify noise in medical decision-making using a noise audit. Methods: A noise audit was completed by 71 (n = 71) Heart Centre staff at the Hospital for Sick Children and Seattle Children's Hospital and involved a series of cases and questions surrounding decisions commonly encountered in the care for patients with transposition of the great arteries and critical aortic stenosis. Entropy was used to quantify total variation in responses. Because absolute entropy was not immediately comparable across audit questions with a different number of prespecified options, we reported a standardized version of entropy, which was calculated by dividing the absolute entropy by its theoretical maximum for each case. To compare responses in easy to hard questions across years of experience (<10 years and >10 years) and role, we reported aggregate entropy ratios. Aggregate entropy ratios were calculated by first stratifying by group of comparison and then calculating the standardized entropy for each question and taking the average of standardized entropies for easy questions and hard questions. Finally, to determine the ratio (easy to hard), we divided the average standardized entropy of the easy questions by the average standardized entropy of the hard questions. Results: The overall audit aggregate entropy ratio was 0.85 less than 1, indicating lower-complexity questions had less variation than higher-complexity questions. The aggregate entropy ratio for those with more than 10 years of experience was 0.8 and 0.87, respectively, for those with less than 10 years of experience. The aggregate entropy ratios for thos

关键词： congenital heart surgery entropy medical decision-making noise noise audit random variability

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Deciphering DNA variant-associated aberrant splicing with the aid of RNA sequencing (vol 55, pg 732, 2023)

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NATURE GENETICS 2023年第7期55卷 1251-1251页

作者： Zhang, Bin Gao, Xin Computer Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia KAUST Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia

Aberrant RNA splicing events resulting from DNA variations are common causes of genetic disorders. Two studies published in Nature Genetics independently describe methods to decipher DNA-variant-associated aberrant sp... 详细信息

关键词： Data mining High-throughput screening

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KLF2 maintains lineage fidelity and suppresses CD8 T cell exhaustion during acute LCMV infection

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science (New York, N.Y.) 2025年第6735期387卷 eadn2337页

作者： Fagerberg, Eric Attanasio, John Dien, Christine Singh, Jaiveer Kessler, Emily A. Abdullah, Leena Shen, Jian Hunt, Brian G. Connolly, Kelli A. De Brouwer, Edward He, Jiaming Iyer, Nivedita R. Buck, Jessica Borr, Emily R. Damo, Martina Foster, Gena G. Giles, Josephine R. Huang, Yina H. Tsang, John S. Krishnaswamy, Smita Cui, Weiguo Joshi, Nikhil S. Department of Immunobiology Yale University School of Medicine New Haven CT United States Program in Computational Biology & Bioinformatics Yale University New Haven CT United States Department of Microbiology and Immunology Geisel School of Medicine at Dartmouth NH United States Department of Pathology Feinberg School of Medicine at Northwestern University Chicago IL United States Department of Genetics and Computer Science Yale University School of Medicine New Haven CT United States Department of Medicine University of Chicago Chicago IL United States Section of Hematology Department of Internal Medicine Yale University School of Medicine New Haven CT United States Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania Philadelphia PA United States Institute for Immunology Perelman School of Medicine University of Pennsylvania Philadelphia PA United States Parker Institute for Cancer Immunotherapy Perelman School of Medicine University of Pennsylvania Philadelphia PA United States Yale Center for Systems and Engineering Immunology Yale University School of Medicine New Haven CT United States New Haven CT United States Department of Biomedical Engineering Yale University New Haven CT United States Computational Biology and Bioinformatics Program Yale University CT USA New Haven United States Applied Math Program Yale University New Haven CT United States

Naïve CD8 T cells have the potential to differentiate into a spectrum of functional states during an immune response. How these developmental decisions are made and what mechanisms exist to suppress differentiation toward alternative fates remains unclear. We employed in vivo CRISPR-Cas9-based perturbation sequencing to assess the role of ~40 transcription factors (TFs) and epigenetic modulators in T cell fate decisions. Unexpectedly, we found that knockout of the TF Klf2 resulted in aberrant differentiation to exhausted-like CD8 T cells during acute infection. KLF2 was required to suppress the exhaustion-promoting TF TOX and to enable the TF TBET to drive effector differentiation. KLF2 was also necessary to maintain a polyfunctional tumor-specific progenitor state. Thus, KLF2 provides effector CD8 T cell lineage fidelity and suppresses the exhaustion program.

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Observation of dark edge states in parity-time-symmetric quantum dynamics

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National science Review 2023年第8期10卷 156-165页

作者： Peng Xue Xingze Qiu Kunkun Wang Barry C. Sanders Wei Yi Beijing Computational Science Research Center Key Laboratory of Quantum Information University of Science and Technology of China Chinese Academy of Sciences Synergetic Innovation Center in Quantum Information and Quantum Physics University of Science and Technology of China Chinese Academy of Sciences School of Physics and Optoelectronic Engineering Anhui University Shanghai Branch National Laboratory for Physical Sciences at MicroscaleUniversity of Science and Technology of China Institute for Quantum Science and Technology University of Calgary Program in Quantum Information Science Canadian Institute for Advanced Research

Topological edge states arise in non-Hermitian parity-time(PT)-symmetric systems, and manifest themselves as bright or dark edge states, depending on the imaginary components of their eigenenergies. As the spatial probabilities of dark edge states are suppressed during the non-unitary dynamics, it is a challenge to observe them experimentally. Here we report the experimental detection of dark edge states in photonic quantum walks with spontaneously broken PT symmetry, thus providing a complete description of the topological phenomena therein. We experimentally confirm that the global Berry phase in PT-symmetric quantum-walk dynamics unambiguously defines topological invariants of the system in both the PT-symmetry-unbroken and-broken regimes. Our results establish a unified framework for characterizing topology in PT-symmetric quantum-walk dynamics, and provide a useful method to observe topological phenomena in PT-symmetric non-Hermitian systems in general.

关键词： parity-time symmetry photonic quantum walks dark edge states topological invariants

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Applications of compressed sensing for sar moving-target velocity estimation and image compression

Applications of compressed sensing for sar moving-target vel...

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作者： Khwaja, Ahmed Shaharyar Ma, Jianwei School of Aerospace Tsinghua University Beijing 100084 China Program in Computational Science and Engineering Florida State University Tallahassee FL 32306-4510 United States

Compressed sensing (CS) is a recently introduced concept that enables the recovery of signals sampled below the Nyquist rate. A prerequisite for its application is the sparsity of the concerned signals in a certain basis. The concept has been applied to medical imaging, seismic imaging, optical remote sensing, and, recently, radar. This paper describes two possible applications of CS for synthetic aperture radar (SAR): 1) estimation of moving-target velocities in the case of high and low signal-to-clutter ratios, as well as more than one scatterer in a single pixel making use of clutter cancellation, and 2) online compression of processed SAR images with the help of curvelet sparsity-promoting offline decoding. CS for SAR offers the possibility of using lesser amount of data, as well as a convenient way of knowing motion and position parameters of multiple moving targets. The CS technique is useful for simplification of hardware or reduction of data that are useful in the case of limited onboard data storage capacity. The results are demonstrated by means of numerical experiments using simulated data for moving-target velocity estimation and MiniSAR data for SAR image compression. © 2011 IEEE.

关键词： Compressed sensing

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RJSSim: A reconfigurable job scheduling simulator for parallel processing learning 33

RJSSim: A reconfigurable job scheduling simulator for parall...

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33rd Annual Frontiers in Education, FIE 2003

作者： Góes, Luís F.W. Martins, Carlos A.P.S. Pontifical Catholic University of Minas Gerais Post-Graduation Program in Electrical Engineering Computational and Digital Systems Laboratory Belo HorizonteMG Brazil Pontifical Catholic University of Minas Gerais Computer Science Department Post-Graduation Program in Electrical Engineering Computational and Digital Systems Laboratory Belo HorizonteMG Brazil

ISBN: (纸本)0780379616

In this work, we present and analyze the use of a reconfigurable job scheduling simulator called RJSSim as an aid tool for parallel processing learning. This software is a functional and performance Java-based simulator of job scheduling policies. Our objectives are: to present RJSSim;to show the use of RJSSim and reconfigurability concepts for parallel processing learning. First, we present a prototype of RJSSim and the reconfigurability concept. Then we describe two case studies remarking the main parallel processing concepts and skills students can learn. In the first case study, we analyze two parallel algorithm models. In the second, we do some performance tests among parallel (reconfigurable) scheduling policies and architectures. Then, we analyze the performance through some metrics like response time, idle time etc. Finally we discuss and analyze the use of RJSSim for parallel processing learning. Our main contribution is: an implementation of RJSSim for parallel processing learning. © 2003 IEEE.

关键词： Parallel algorithms

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Sub- And supercritical bifurcations and turning points in a simple BWR model

Sub- And supercritical bifurcations and turning points in a ...

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2000 ANS International Topical Meeting on Advances in Reactor Physics and Mathematics and Computation into the Next Millennium, PHYSOR 2000

作者： Rizwan-Uddin Department of Nuclear Plasma and Radiological Engineering University of Illinois at Urbana-Champaign UrbanaIL61801 United States Computational Science and Engineering Program University of Illinois at Urbana-Champaign United States

ISBN: (纸本)0894486551

Stability and bifurcation analyses of BWRs have been performed using a reduced order, nuclear-coupled thermal hydraulics model. This has been carried out using a bifurcation analysis code, BIFDD. A large segment of the parameter space has been investigated using this very efficient tool. Stability boundaries are obtained in several two-dimensional parameter spaces. In addition, the nature of bifurcation along these stability boundaries has also been determined. Results indicate that both subcritical as well as supercritical Poincaré-Andronov-Hopf bifurcations are likely to occur in regions of interest in parameter space. In addition to the semi-analytical bifurcation studies, the governing equations have also been integrated numerically. Results confirm the findings of the bifurcation analysis. Numerical integrations, carried out for parameter values away from the stability boundary, further show that the bifurcation curves, in many cases of subcritical bifurcations, have a turning point. The bifurcation curve in these cases extends back into the unstable region. These results show that it is possible to experience large amplitude stable oscillations in the unstable region infinitesimally close to the stability boundary. Moreover, large amplitude stable oscillations are also possible in the stable region of the parameter space near the stability boundary, following large but finite perturbations. These findings provide alternate explanation for the experimental and operational observations in BWRs that indicate the existence of stable limit cycle oscillations and the possibility of growing amplitude oscillations. Results obtained here using a simple model suggest that further work along these lines, with more detailed models, is needed to identify operating conditions and perturbation amplitudes that might lead to stable limit cycles or growing amplitude oscillations in current and next generation of BWRs. © 2000 Proceedings of the PHYSOR 2000 - ANS International To

关键词： Curve fitting

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