Article
Computer Science, Artificial Intelligence
Bin Gu, Zhiyuan Dang, Zhouyuan Huo, Cheng Deng, Heng Huang
Summary: This paper introduces a general sparse kernel learning formulation based on random feature approximation to tackle the challenge of big data era. A new large-scale sparse kernel learning algorithm (AsyDSSKL) is proposed using techniques of asynchronous parallel computation and doubly stochastic optimization. Experimental results demonstrate that AsyDSSKL has significant superiority in computational efficiency over existing kernel methods.
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
(2022)
Article
Physics, Particles & Fields
Ladislav Hlavaty, Ivo Petr
Summary: This paper investigates the Poisson-Lie transformation of dilaton and vector field J in generalized supergravity equations. While existing formulas work well for isometric sigma models, examples presented in the paper show that these formulas do not preserve the generalized supergravity equations. Therefore, the paper suggests modifying these formulas.
EUROPEAN PHYSICAL JOURNAL C
(2021)
Article
Astronomy & Astrophysics
Parita Shah
Summary: This sentence introduces the method of embedding the geometries of generalized lambda deformations into the framework of double field theory.
Article
Mathematics
Zsigmond Tarcsay, Tamas Titkos
Summary: The paper generalizes the classical concept of positive operators and develops a general extension theory that overcomes the lack of a Hilbert space structure and normable topology. The concept of anti-duality is used to define positivity in a natural way and cover areas where Hilbert space theory is not applicable. The main theorem characterizes operators that admit a continuous positive extension to the whole space.
MATHEMATISCHE NACHRICHTEN
(2021)
Review
Ecology
Abelardo Montesinos-Lopez, Osval Antonio Montesinos-Lopez, Jose Cricelio Montesinos-Lopez, Carlos Alberto Flores-Cortes, Roberto de la Rosa, Jose Crossa
Summary: This paper provides a guide on implementing Bayesian generalized kernel regression methods for genomic prediction in R, showcasing the construction process of seven kernel methods and providing specific examples. The strengths, limitations, and contributions of kernel methods are discussed.
Article
Automation & Control Systems
Yue Chen, Song Zhu, Chaoxu Mu, Xiaoyang Liu, Shiping Wen
Summary: This article investigates the global asymptotic stability of a class of recurrent neural networks (RNNs) with generalized piecewise constant argument (GPCA). By utilizing the Banach fixed point theorem (BFPT) and comparison principle, a set of improved criteria are proposed to ensure the existence and uniqueness (EU) of the solutions and the global asymptotic stability of equilibrium point for the considered RNNs. Compared to existing results, this article reduces the requirements for system parameters and provides more criteria in different forms, significantly expanding the feasible range of the obtained criteria. The effectiveness of the obtained results is demonstrated through numerical examples.
IEEE TRANSACTIONS ON SYSTEMS MAN CYBERNETICS-SYSTEMS
(2023)
Article
Mathematics
Jorge Lauret, Cynthia Will
Summary: A fixed point of the generalized Ricci flow on a generalized metric space is Bismut Ricci flat, where H is g-harmonic and Rc(g) = 14Hg2, and we show the uniqueness of Bismut Ricci flat G-invariant generalized metric on a homogeneous space under certain conditions. We also provide a one-parameter family of Bismut Ricci flat G-invariant generalized metrics on G/K when K is simple and the standard metric is Einstein on both G1/K and G2/K.
TRANSACTIONS OF THE AMERICAN MATHEMATICAL SOCIETY
(2023)
Article
Statistics & Probability
Zongyuan Shang, Alan Ker
Summary: This article introduces two generalized nonparametric methods for estimating multiple, possibly like, densities. These methods do not require knowledge of the form or extent of likeness between the unknown densities, making them attractive in empirical applications. Numerical simulations demonstrate that these two generalized methods lead to significant efficiency gains.
COMPUTATIONAL STATISTICS
(2021)
Article
Engineering, Electrical & Electronic
Yu-Qi Liu, Xin Du, Hui-Liang Shen, Shu-Jie Chen
Summary: This study proposes a more accurate method for describing out-of-focus blur, modeling the blur kernel using a generalized Gaussian (GG) function and simplifying it to a single-parameter model. Experimental results demonstrate the advantages of this method in image deblurring.
IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS FOR VIDEO TECHNOLOGY
(2021)
Article
Mathematics, Applied
Jong-Do Park
Summary: This paper focuses on computing the reproducing kernel for the generalized Fock space and establishing a connection between the reproducing kernel and the error function. It provides closed forms for specific parameters and proves a specific property as z approaches infinity.
JOURNAL OF FUNCTION SPACES
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Tim Schmidt, Zoltan Nagy
Summary: The study aimed to develop and test a sensitive, reliable, and widely applicable measure of temporal instability (TIM) for fMRI quality assurance. The results showed that the proposed TIM provides a reliable test for ascertaining scanner stability for fMRI experiments.
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2023)
Article
Computer Science, Interdisciplinary Applications
Manh Hong Duong, Xiaocheng Shang
Summary: This article studies numerical methods for the generalized Langevin equation (GLE) with a positive Prony series memory kernel. A new splitting method is proposed, which is easy to implement and significantly improves the accuracy and robustness of GLE simulations. The superiority of the method is demonstrated through error analysis and numerical experiments.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Automation & Control Systems
Jose M. Bernal-de-Lazaro, Carlos Cruz -Corona, Antonio J. Silva-Neto, Orestes Llanes-Santiago
Summary: This paper provides a comprehensive literature survey on the importance of selecting the kernel function and their parameters in fault diagnosis applications, and proposes a kernel evaluation framework to assist in the selection and adjustment of kernel functions.
Article
Computer Science, Artificial Intelligence
Eufrasio de A. Lima Neto, Paulo C. Rodrigues
Summary: SVD is a widely used algorithm for dimensionality reduction and principal component analysis, but it is not suitable for data contaminated with outlying observations. To overcome this limitation, a kernel robust SVD algorithm is proposed, which operates in the original space and applies a robust linear regression framework to obtain robust estimates for the singular values and singular vectors. Simulation results show that the proposed algorithm outperforms classical and robust SVD algorithms. The merits of the proposed algorithm are also illustrated in an image recovery application.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Mathematics, Applied
Haoming Sun, Haizhang Zhang
Summary: Learning theory aims to establish a strong mathematical foundation for machine learning and, in particular, estimates the learning rates of different learning algorithms to assess their generalization ability. However, most research in this area has focused on single-task kernel methods, neglecting the study of multitask kernel methods. In our study, we analyze the learning rates for multitask regularization networks and l2-norm coefficient regularization, which are both new areas of research. Our findings demonstrate a quantitative relationship between the learning rates and the number of tasks, which has not been explored in previous literature.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2023)
Article
Immunology
Jessica A. Grembi, Audrie Lin, Md Abdul Karim, Md Ohedul Islam, Rana Miah, Benjamin F. Arnold, Elizabeth T. Rogawski McQuade, Shahjahan Ali, Md Ziaur Rahman, Zahir Hussain, Abul K. Shoab, Syeda L. Famida, Md Saheen Hossen, Palash Mutsuddi, Mahbubur Rahman, Leanne Unicomb, Rashidul Haque, Mami Taniuchi, Jie Liu, James A. Platts-Mills, Susan P. Holmes, Christine P. Stewart, Jade Benjamin-Chung, John M. Colford Jr, Eric R. Houpt, Stephen P. Luby
Summary: We evaluated the impact of water, sanitation, and handwashing (WSH) and nutrition interventions on enteropathogens in children in Bangladesh. WSH interventions were associated with fewer enteric viruses compared to controls. There was no difference in bacterial and protozoan pathogens for WSH or nutrition interventions.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Statistics & Probability
Claire Donnat, Susan Holmes
Summary: This study examines the evaluation of the reproductive number R for COVID-19 from a Bayesian perspective, explores the impact of heterogeneity on uncertainty quantification, and demonstrates the significant effects of heterogeneity through simulations of transmission and the impact of social distancing strategies.
JOURNAL OF APPLIED STATISTICS
(2023)
Article
Immunology
Sonwabile Dzanibe, Katie Lennard, Agano Kiravu, Melanie S. S. Seabrook, Berenice Alinde, Susan P. Holmes, Catherine A. Blish, Heather B. Jaspan, Clive M. Gray
Summary: This study evaluated the dynamics of Treg and Th17 cell populations in the first 36 weeks of human life. It found distinct differences between cord blood and peripheral blood phenotypes and observed a disruption in the balance of Th17 to Treg cells at birth, likely due to gut damage and the migration of newborn Treg cells to the gut. The study highlights the importance of studying immune cell ontogeny in the early pediatric period.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Immunology
Geoffrey T. Ivison, Elena Vendrame, Giovanny J. Martinez-Colon, Thanmayi Ranganath, Rosemary Vergara, Nancy Q. Zhao, Maureen P. Martin, Sean C. Bendall, Mary Carrington, Joshua C. Cyktor, Deborah K. McMahon, Joseph Eron, R. Brad Jones, John W. Mellors, Ronald J. Bosch, Rajesh T. Gandhi, Susan Holmes, Catherine A. Blish
Summary: This study examines the role of Natural Killer (NK) cells in controlling HIV-1 persistence during long-term antiretroviral therapy (ART). The findings suggest that certain NK cell receptors and ligands are associated with HIV-1 persistence, as measured by various markers. Additionally, specific NK cell phenotypes were found to be related to HIV-1 persistence.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Statistics & Probability
Saskia Comess, Hannah Wang, Susan Holmes, Claire Donnat
Summary: Pooled testing offers an efficient solution to COVID-19 testing demands with considerations of sample correlations and infection risk heterogeneity. This paper presents statistical modeling and real data analysis to optimize sensitivity and efficiency at low cost, and provides an interactive tool for selecting the optimal pool size.
STATISTICAL SCIENCE
(2022)
Article
Computer Science, Information Systems
Laura Symul, Susan Holmes
Summary: In this study, a hierarchical approach based on hidden semi-Markov models is proposed to identify reproductive events and quantify uncertainty in multivariate time series with frequent missing data. The method adapts to changes in tracking behavior, captures variable- and state-dependent missingness, and accurately predicts cycle length.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2022)
Article
Cell Biology
Morteza Roodgar, Fabian P. Suchy, Lan H. Nguyen, Vivek K. Bajpai, Rahul Sinha, Jose G. Vilches-Moure, Kevin Van Bortle, Joydeep Bhadury, Ahmed Metwally, Lihua Jiang, Ruiqi Jian, Rosaria Chiang, Angelos Oikonomopoulos, Joseph C. Wu, Irving L. Weissman, Joseph L. Mankowski, Susan Holmes, Kyle M. Loh, Hiromitsu Nakauchi, Catherine A. VandeVoort, Michael P. Snyder
Summary: The study focuses on the generation and characterization of induced pluripotent stem cells (iPSCs) from non-human primate species, specifically chimpanzees and pig-tailed macaques. The researchers establish improved culture methods for these iPSCs and demonstrate their potential by injecting them into the embryos of rhesus macaques. The findings provide valuable resources for non-human primate iPSCs research.
Article
Mathematics, Interdisciplinary Applications
Kris Sankaran, Susan P. Holmes
Summary: By linking conceptual theories with observed data, generative models serve as a crucial tool in various fields such as molecular biology, particle physics, and epidemiology. This article introduces the underlying concepts of generative models and discusses their applications in experimental design, model refinement, goodness-of-fit evaluation, and agent based simulation. The article emphasizes the flexibility of recombining generative mechanisms in different problem contexts and provides practical illustrations and code examples.
ANNUAL REVIEW OF STATISTICS AND ITS APPLICATION
(2023)
Article
Immunology
Kaiming Tao, Soo-Yon Rhee, Philip L. Tzou, Susan P. Holmes, Robert W. Shafer
Summary: During population-based genotypic drug resistance testing, HIV-1 pol nucleotide ambiguities that encode amino acid mixtures are common. This study examines the validity of sequences with fully ambiguous codons (FACs), which can translate to more than four amino acids. The findings indicate a strong correlation between FACs and HLA-associated positions as well as drug-resistance positions, suggesting that FACs are likely to result from antiviral or immune selection pressure in the context of population-based genotypic resistance testing.
AIDS RESEARCH AND HUMAN RETROVIRUSES
(2023)
Article
Pharmacology & Pharmacy
Soo-Yon Rhee, Neil Parkin, P. Richard Harrigan, Susan Holmes, Robert W. Shafer
Summary: This study reviewed the genetic mechanisms of resistance to Cabotegravir (CAB). The results showed that the most commonly selected mutations in patients developing virological failure while receiving CAB included Q148R, N155H, and E138K. The study also identified 14 drug resistance mutations significantly associated with reduced CAB susceptibility. The study highlights the importance of careful patient screening and close virological monitoring to prevent the emergence of drug resistance with the use of CAB.
ANTIVIRAL RESEARCH
(2022)
Article
Cell Biology
Madeline J. Lee, Michelle W. Leong, Arjun Rustagi, Aimee Beck, Leiping Zeng, Susan Holmes, Lei S. Qi, Catherine A. Blish
Summary: SARS-CoV-2 evades direct killing by natural killer (NK) cells by downregulating ligands for the activating receptor NKG2D. The viral protein Nsp1 mediates the downregulation of NKG2D ligands and alone is sufficient to confer resistance to NK cell killing.
Article
Multidisciplinary Sciences
Dari Shalon, Rebecca Neal Culver, Jessica A. Grembi, Jacob Folz, Peter V. Treit, Handuo Shi, Florian A. Rosenberger, Les Dethlefsen, Xiandong Meng, Eitan Yaffe, Andres Aranda-Diaz, Philipp E. Geyer, Johannes B. Mueller-Reif, Sean Spencer, Andrew D. Patterson, George Triadafilopoulos, Susan P. Holmes, Matthias Mann, Oliver Fiehn, David A. Relman, Kerwyn Casey Huang
Summary: This study developed an ingestible device that can collect samples from multiple regions of the human intestinal tract during normal digestion. Multi-omics analysis of the collected samples revealed significant differences in bacteria, phages, host proteins, and metabolites between the intestines and stool. The study provides insights into the roles of the gut microbiome and metabolome in human physiology and disease through non-invasive longitudinal profiling of microorganisms, proteins, and bile acids along the intestinal tract.
Article
Biotechnology & Applied Microbiology
Aaron J. Wilk, Alex K. Shalek, Susan Holmes, Catherine A. Blish
Summary: A flexible and scalable framework called Scriabin is presented to analyze cell-cell communication at single-cell resolution. It accurately recovers expected communication edges and uncovers spatial features of interaction. The approach is applicable to various datasets and provides insights into niche-phenotype relationships in health and disease.
NATURE BIOTECHNOLOGY
(2023)
Article
Virology
Kaiming Tao, Soo-Yon Rhee, Philip L. Tzou, Zachary A. Osman, Sergei L. Kosakovsky Pond, Susan P. Holmes, Robert W. Shafer
Summary: In order to manage individuals with detectable viremia and experience with the HIV-1 capsid inhibitor lenacapavir, capsid sequencing is required. By analyzing the published HIV-1 group M capsid sequences, the variability of amino acids at each position and the influence of subtype and cytotoxic T lymphocyte (CTL) selection pressure were characterized.
Article
Multidisciplinary Sciences
Elizabeth K. K. Costello, Daniel B. B. DiGiulio, Anna Robaczewska, Laura Symul, Ronald J. J. Wong, Gary M. M. Shaw, David K. K. Stevenson, Susan P. P. Holmes, Douglas S. S. Kwon, David A. A. Relman
Summary: Childbirth leads to vaginal inflammation and a decrease in Lactobacillus dominance, which continues to affect women for up to one year postpartum. Only 49.4% of women were able to recover from this disturbance by the end of the first postpartum year, indicating a significant impact on women's health and future pregnancies.
NATURE COMMUNICATIONS
(2023)
