21 papers · ranked by Valyu relevance
Xihe Hu
The bootstrap is a technique recently developed to get energy eigenvalues of bound states and correlation functions. There are three crucial steps - recursive equations, positivity constraints, search space. We calculate recursive equations of many representative quantum mechanics systems, such as polynomial potential…
Zhi Yang Tho, Raymond L. Chambers, A. H. Welsh
Clustered data arise naturally in many scientific and applied research settings where units are grouped within clusters. They are commonly analyzed using linear mixed models to account for within-cluster correlations. This article focuses on the scenario in which cluster sizes might be highly unbalanced and proposes a…
Frédéric Lemoine, Olivier Gascuel
Felsenstein’s bootstrap is the most commonly used method to measure branch support in phylogenetics. Current sequencing technologies can result in massive sampling of taxa (e.g. SARS-CoV-2). In this case, the sequences are very close, the trees are short, and the branches correspond to a small number of mutations…
Jinji Pang, Wangqian Ju, Michael Welch, Phillip Gauger + 3 more
'Qijing Zhang' 'Chong Wang'] Developing and evaluating novel diagnostic assays are crucial components of contemporary diagnostic research. The receiver operating characteristic (ROC) curve and the area under the ROC curve (AUC) are frequently used to evaluate diagnostic assays’ performance. The variation in AUC…
Julia Steinmetz, Carsten Jentsch
Mack's distribution-free chain ladder reserving model belongs to the most popular approaches in non-life insurance mathematics. Proposed to determine the first two moments of the reserve, it does not allow to identify the whole distribution of the reserve. For this purpose, Mack's model is usually equipped with a…
Peter C. Austin
Background Healthcare provider profiling involves the comparison of outcomes between patients cared for by different healthcare providers. An important component of provider profiling is risk-adjustment so that providers that care for sicker patients are not unfairly penalized. One method for provider profiling entails…
Muhammad Yahya Matdoan, Muhammad Mashuri, Muhammad Ahsan
Accurate parameter estimation is a critical component of effective process control using g charts. While traditional methods like maximum likelihood and Bayesian estimation are widely used, th ey may exhibit limitations in small sample size scenarios, leading to inaccurate parameter estimates. To address these…
Jared Clark, Richard L. Warr
Bootstrapping was designed to randomly resample data from a fixed sample using Monte Carlo techniques. However, the original sample itself defines a discrete distribution. Convolutional methods are well suited for discrete distributions, and we show the advantages of utilizing these techniques for bootstrapping. The…
Joseph Rich, Lior Pachter
Summary: fastQpick is a command-line tool and Python library for sampling FASTQ reads with replacement. Sampling with replacement turns a single FASTQ file into an arbitrary number of bootstrap replicates, which enables uncertainty quantification and statistical analysis at the level of raw reads. This process answers…
Jared Huzar, Madelyn Shenoy, Maxwell D. Sanderford, Sudhir Kumar + 1 more
'Sayaka Miura'] Bulk sequencing is commonly used to characterize the genetic diversity of cancer cell populations in tumors and the evolutionary relationships of cancer clones. However, bulk sequencing produces aggregate information on nucleotide variants and their sample frequencies, necessitating computational…
Wancen Mu, Eric Davis, Stuart Lee, Mikhail Dozmorov + 2 more
bootRanges provides fast functions for generation of bootstrapped genomic ranges representing the null sets in enrichment analysis. We show that shuffling or permutation schemes may result in overly narrow test statistics null distributions, while creating new ranges sets with a block bootstrap preserves local genomic…
Rory M. Crean, Joanna S. G. Slusky, Peter M. Kasson, Shina Caroline Lynn Kamerlin
Simulation datasets of proteins (e.g., those generated by molecular dynamics simulations) are filled with information about how the non-covalent interaction network within a protein regulates the conformation and thus function of said protein. Most proteins contain thousands of non-covalent interactions, with most of…
Shayan R. Akhavan, Scott T. Kelley
PyBootNet is a user-friendly Python package that integrates bootstrapping analysis and correlation network construction. The package offers functions for generating bootstrapped network metrics, statistically comparing network metrics among datasets, and visualizing bootstrapped networks. PyBootNet is designed to be…
Paul Zaharias, Frédéric Lemoine, Olivier Gascuel
The bootstrap method is based on resampling alignments and re-estimating trees. Felsenstein’s bootstrap proportions (FBP) is the most common approach to assess the reliability and robustness of sequence-based phylogenies. However, when increasing taxon-sampling (i.e., the number of sequences) to hundreds or thousands…
Fumikazu Miwakeichi, Andreas Galka, Hector Zenil, Jiang Zhang + 1 more
'Peng Cui'] In this study, we present a thorough comparison of the performance of four different bootstrap methods for assessing the significance of causal analysis in time series data. For this purpose, multivariate simulated data are generated by a linear feedback system. The methods investigated are uncorrelated…
Vincent Dufour-Decieux, Brandi Ransom, Rodrigo Freitas, Jose Blanchet + 1 more
Molecular Dynamics (MD) simulations are a key tool to understand the mechanism of complex chemical system and observe their outcomes in different conditions. However, such simulations are computationally expensive, which limits their timescales to the nanoseconds. This limitation is inconsequential at high…
Beomsu Baek, Jongkwon Jo, Mingon Kang, Youngsoon Kim
Accurate identification of significant features in high-dimensional data is indispensable in high-throughput genomic analysis and association studies. Least Absolute Shrinkage and Selection Operator (LASSO) and its derivatives have been widely adapted to discover potential biomarkers as a feature selection scheme in…
Owen, Art B.
This article explores combinations of weighted bootstraps, like the Bayesian bootstrap, with the bootstrap t method for setting approximate confidence intervals for the mean of a random variable in small samples. For this problem the usual bootstrap t has good coverage but provides intervals with long and highly…
Sihan Fu, Oucheng Liu, Shiyuan Wang, Jin Shi + 1 more
Code agents increasingly help developers work with unfamiliar repositories, but every such task depends on a costly prerequisite: bootstrapping the repository into a usable development state. This process requires substantial trial-and-error exploration, yet the resulting knowledge--resolved dependencies, repair…
Authors not listed
The rigorous design of adsorption-based separation processes, such as Pressure Swing Adsorption (PSA) and Temperature Swing Adsorption (TSA), is fundamentally dependent on the accuracy of the underlying mathematical models describing equilibrium isotherms and transport kinetics. However, the current state of the art is…
Priyanka Prakash Surve, Oleg Brodt, Mark Yampolskiy, Yuval Elovici + 1 more
'Asaf Shabtai'] Abstract—The Unified Extensible Firmware Interface (UEFI) is a linchpin of modern computing systems, governing secure system initialization and booting. This paper is urgently needed because of the surge in UEFI-related attacks and vulnerabilities in recent years. Motivated by this urgent concern, we…