Article
Engineering, Mechanical
P. L. Green, L. J. Devlin, R. E. Moore, R. J. Jackson, J. Li, S. Maskell
Summary: This paper discusses the optimization of the 'L-kernel' in Sequential Monte Carlo samplers to improve performance, resulting in reduced variance of estimates and fewer resampling requirements.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2022)
Article
Engineering, Mechanical
Adolphus Lye, Alice Cicirello, Edoardo Patelli
Summary: This tutorial paper reviews the use of advanced Monte Carlo sampling methods in Bayesian model updating for engineering applications, introducing different methods and comparing their performance. Three case studies demonstrate the advantages and limitations of these sampling techniques in parameter identification, posterior distribution sampling, and stochastic identification of model parameters.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2021)
Article
Mathematics
Kai Yin, Anirban Mondal, Martial Ndeffo-Mbah, Paromita Banerjee, Qimin Huang, David Gurarie
Summary: We propose a modified SEIR model to retrospectively study the transmission dynamics of COVID-19 in India. The model considers the complexities of COVID-19 infection and the effects of government controls and individual behaviors. Bayesian method is used to calibrate the model and estimate undetected cases.
Article
Agriculture, Dairy & Animal Science
M. A. Stephen, C. R. Burke, N. Steele, J. E. Pryce, S. Meier, P. R. Amer, C. V. C. Phyn, D. J. Garrick
Summary: In this study, the genetic and phenotypic relationships between anogenital distance (AGD) and body stature and fertility traits in dairy cattle were characterized. The results showed that AGD is a moderately heritable trait and is associated with reproductive success in lactating cows.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Computer Science, Interdisciplinary Applications
Weimin Zhou, Umberto Villa, Mark A. Anastasio
Summary: Medical imaging systems are often evaluated and optimized using objective measures of image quality, with the Bayesian Ideal Observer (IO) representing an upper limit for performance evaluation. A new MCMC method called MCMC-GAN, employing a GAN-based stochastic object model (SOM), shows promise in extending the applicability of MCMC methods for IO analyses of medical imaging systems.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2023)
Article
Computer Science, Artificial Intelligence
Chikezie Chimere Onyekwena, Qi Li, Happiness Ijeoma Umeobi, Xiaying Li, John N. Ng'ombe
Summary: The soil water retention curve is a fundamental concept in unsaturated soil mechanics. Existing prediction models require large datasets, but obtaining such datasets can be costly and time-consuming. To address this issue, a reliability-based approach using a Bayesian framework and Hamiltonian Monte Carlo method is proposed. The method is robust and provides reliable predictions even with limited prior knowledge, while significantly reducing computation time and cost.
EXPERT SYSTEMS WITH APPLICATIONS
(2022)
Review
Statistics & Probability
Christopher Nemeth, Paul Fearnhead
Summary: MCMC algorithms are considered the gold standard technique for Bayesian inference, but the computational cost can be prohibitive for large datasets, leading to the development of scalable Monte Carlo algorithms. One type of these algorithms is SGMCMC, which reduces per-iteration cost by utilizing data subsampling techniques.
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
(2021)
Article
Business
Mike G. Tsionas
Summary: This paper presents results from Bayesian analysis of random switching exponential smoothing models, showing that the new methods are robust and easy to implement. Monte Carlo simulations and real data sets demonstrate the methods' strong performance, especially when extended with a Markov chain assumption on the slope of the trend. Model comparison and selection tools are also provided for out-of-sample behavior analysis.
TECHNOLOGICAL FORECASTING AND SOCIAL CHANGE
(2022)
Article
Mathematics
Samuel Livingstone
Summary: This study investigates the impact of proposal distributions on the ergodicity of the Metropolis-Hastings method, showing that suitable choices can alter the ergodic properties of the algorithm. It is found that allowing the proposal variance to grow unboundedly in the tails of heavy-tailed distributions can establish geometric ergodicity, but the growth rate needs to be carefully controlled to avoid high rejection rates. Furthermore, a judicious choice of proposal distribution can lead to geometric ergodicity in scenarios where probability concentrates on narrower tails, which is not the case for the Random Walk Metropolis.
Review
Green & Sustainable Science & Technology
D. Hou, I. G. Hassan, L. Wang
Summary: Building Energy Model (BEM) calibration is crucial for accuracy, with recent focus on stochastic Bayesian inference calibration. However, confusion remains regarding theory, strengths, limitations, and implementations. Selecting appropriate mathematical models and tools poses a challenge.
RENEWABLE & SUSTAINABLE ENERGY REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Andrew F. Neuwald, Hui Yang, Tracy Nixon
Summary: SPARC helps generate plausible hypotheses about underlying biochemical mechanisms by structurally characterizing protein sequence constraints, analyzing include pairwise sequence correlations, correspondence between directly coupled residue pairs, and interactions among constrained residues.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Immunology
Fang-Chi Hsu, Li-Chern Pan, Yen-Fang Huang, Chin-Hui Yang, Ming-Neng Shiu, Hsiu-Ju Lin
Summary: A study found that neutralizing antibody titers reached their peak within 161 days after vaccination and decreased to lower levels by day 360. This indicates that neutralizing antibody titers decline within 6 months after vaccination, and protection against the Omicron variant may only occur during the peak period.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Computer Science, Interdisciplinary Applications
Arvind K. Saibaba, Pranjal Prasad, Eric de Sturler, Eric Miller, Misha E. Kilmer
Summary: This paper demonstrates how to reduce the computational cost of each log-likelihood evaluation by using randomized techniques and embedding them within MCMC algorithms. The resulting MCMC algorithms are shown to be computationally efficient methods for quantifying uncertainty associated with the reconstructed parameters.
JOURNAL OF COMPUTATIONAL PHYSICS
(2021)
Article
Geosciences, Multidisciplinary
Elizabeth M. Berg, Fan-Chi Lin, Vera Schulte-Pelkum, Amir Allam, Hongrui Qiu, Konstantinos Gkogkas
Summary: The near-surface seismic velocity structure and Vp/Vs ratio have significant impacts on ground motion amplification during large earthquakes. By combining three datasets and using Bayesian joint inversion, this study investigates shallow crustal shear velocity and near-surface Vp/Vs ratio in Southern California. The results indicate a correlation between receiver functions and short-period Rayleigh wave ellipticity measurements, requiring the inclusion of a Vp/Vs parameter. The updated model suggests widespread shallow fracturing and/or groundwater undersaturation, with lower than expected Vp/Vs ratios outside sedimentary basins.
GEOPHYSICAL RESEARCH LETTERS
(2021)
Article
Engineering, Civil
Jia-Hua Yang, Heung-Fai Lam, Yong-Hui An
Summary: The paper proposes a new two-phase adaptive MCMC method to address the problem of determining the posterior probability density function (PDF) in Bayesian model updating. By using a parameter-space search algorithm and a weighted MCMC algorithm, samples in the regions of high probability can be generated adaptively without going through computationally demanding multiple levels.
ENGINEERING STRUCTURES
(2022)
Article
Pediatrics
Flory L. Nkoy, Bernhard A. Fassl, Victoria L. Wilkins, Joseph Johnson, Eun Hea Unsicker, Karmella J. Koopmeiners, Andrea Jensen, Michelle Frazier, Jordan Gaddis, Lis Malmgren, Stacey Williams, Heather Oldroyd, Tom Greene, Xiaoming Sheng, Derek A. Uchida, Christopher G. Maloney, Bryan L. Stone
Article
Peripheral Vascular Disease
Naveen Rathi, Paul K. Whelton, Glenn M. Chertow, William C. Cushman, Alfred K. Cheung, Guo Wei, Robert Boucher, Paul L. Kimmel, Adam P. Bress, Holly J. Kramer, Catreena Al-Marji, Tom Greene, Srinivasan Beddhu
AMERICAN JOURNAL OF HYPERTENSION
(2019)
Article
Health Care Sciences & Services
Adi Gundlapalli, Audrey L. Jones, Andrew Redd, Guy Divita, Emily Brignone, Warren B. P. Pettey, Marjorie E. Carter, Matthew H. Samore, Rebecca K. Blais, Jamison D. Fargo
Article
Urology & Nephrology
Andrew S. Levey, Ron T. Gansevoort, Josef Coresh, Lesley A. Inker, Hiddo L. Heerspink, Morgan E. Grams, Tom Greene, Hocine Tighiouart, Kunihiro Matsushita, Shoshana H. Ballew, Yingying Sang, Edward Vonesh, Jian Ying, Tom Manley, Dick de Zeeuw, Kai-Uwe Eckardt, Adeera Levin, Vlado Perkovic, Luxia Zhang, Kerry Willis
AMERICAN JOURNAL OF KIDNEY DISEASES
(2020)
Article
Urology & Nephrology
Andrew S. Levey, Josef Coresh, Hocine Tighiouart, Tom Greene, Lesley A. Inker
NATURE REVIEWS NEPHROLOGY
(2020)
Article
Surgery
Carl A. Beyer, Eduard Poltavskiy, Lauren E. Walker, Warren Pettey, Ying Suo, Andrew Redd, Alex G. Rittel, William H. Kazanis, Jacob R. Dunham, Lee A. Zarzabal, W. Cliff Rutter, Alan Sim, Jessica R. Watrous, Jeffrey T. Howard, Jud C. Janak, Ian J. Stewart, Adi Gundlapalli
Summary: This study aimed to determine whether persistent opioid use after injury is associated with subsequent long-term development of clinically recognized opioid abuse. The findings showed that nearly a quarter of patients continued to use opioids 3 to 6 months after discharge, and this persistent use was related to the long-term development of opioid abuse.
Letter
Cardiac & Cardiovascular Systems
Christopher P. Cannon, Vlado Perkovic, Rajiv Agarwal, James Baldassarre, George Bakris, David M. Charytan, Dick de Zeeuw, Robert Edwards, Tom Greene, Hiddo J. L. Heerspink, Meg J. Jardine, Adeera Levin, Jing-Wei Li, Bruce Neal, Carol Pollock, David C. Wheeler, Hong Zhang, Bernard Zinman, Kenneth W. Mahaffey
Article
Otorhinolaryngology
Vanessa Torrecillas, Chelsea M. Allen, Tom Greene, Albert Park, Winnie Chung, Tatiana M. Lanzieri, Gail Demmler-Harrison
OTOLARYNGOLOGY-HEAD AND NECK SURGERY
(2020)
Article
Urology & Nephrology
Kalani L. Raphael, Tom Greene, Guo Wei, Tristin Bullshoe, Kunani Tuttle, Alfred K. Cheung, Srinivasan Beddhu
CLINICAL JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2020)
Article
Health Care Sciences & Services
Maria E. Fernandez, Chelsey R. Schlechter, Guilherme Del Fiol, Bryan Gibson, Kensaku Kawamoto, Tracey Siaperas, Alan Pruhs, Tom Greene, Inbal Nahum-Shani, Sandra Schulthies, Marci Nelson, Claudia Bohner, Heidi Kramer, Damian Borbolla, Sharon Austin, Charlene Weir, Timothy W. Walker, Cho Y. Lam, David W. Wetter
IMPLEMENTATION SCIENCE
(2020)
Article
Transplantation
Hiddo J. L. Heerspink, Bergur Stefansson, Glenn M. Chertow, Ricardo Correa-Rotter, Tom Greene, Fan-Fan Hou, Magnus Lindberg, John McMurray, Peter Rossing, Roberto Toto, Anna Maria Langkilde, David C. Wheeler
NEPHROLOGY DIALYSIS TRANSPLANTATION
(2020)
Article
Medicine, General & Internal
Barbara Ellen Jones, Jian Ying, Vanessa Stevens, Candace Haroldsen, Tao He, McKenna Nevers, Matthew A. Christensen, Richard E. Nelson, Gregory J. Stoddard, Brian C. Sauer, Peter M. Yarbrough, Makoto M. Jones, Matthew Bidwell Goetz, Tom Greene, Matthew H. Samore
JAMA INTERNAL MEDICINE
(2020)
Article
Health Care Sciences & Services
Ian J. Stewart, Eduard Poltavskiy, Jeffrey T. Howard, Jud C. Janak, Warren Pettey, Lee Ann Zarzabal, Lauren E. Walker, Carl A. Beyer, Alan Sim, Ying Suo, Andrew Redd, Kevin K. Chung, Adi Gundlapalli
Summary: Severe traumatic injury is associated with the subsequent development of hypertension, diabetes mellitus, and coronary artery disease. The findings have profound implications for the primary care of injured service members and may be applicable to civilian trauma patients. Further exploration of post-trauma changes is needed to guide future intervention strategies.
JOURNAL OF GENERAL INTERNAL MEDICINE
(2021)
Article
Gastroenterology & Hepatology
Judith Staub, Ali Siddiqui, Megan Murphy, Robert Lam, Meet Parikh, Douglas Pleskow, Georgios Papachristou, Reem Sharaiha, Usama Iqbal, David Loren, Thomas Kowalski, Arish Noor, Tayebah Mumtaz, Ichiro Yasuda, Samuel Thomas, Abdul Hsaeeb, Jennifer Herrick, Tom Greene, Douglas G. Adler
ANNALS OF GASTROENTEROLOGY
(2020)
Article
Social Work
Lori M. Gawron, Warren B. P. Pettey, Andrew M. Redd, Ying Suo, David K. Turok, Adi Gundlapalli
JOURNAL OF SOCIAL DISTRESS AND THE HOMELESS
(2019)