26 papers · ranked by Valyu relevance
Chris C. Holmes, Stephen G. Walker
In this paper, we start by reviewing exchangeability and its relevance to the Bayesian approach. We highlight the predictive nature of Bayesian models and the symmetry assumptions implied by beliefs of an underlying exchangeable sequence of observations. By taking a closer look at the Bayesian bootstrap, the parametric…
Nils Lid Hjort
Let $X_1,\ldots,X_n$ be a random sample from an unknown probability distribution $P$ on the sample space ${\cal X}$, and let $θ=θ(P)$ be a parameter of interest. The present paper proposes a nonparametric `Bayesian bootstrap' method of obtaining Bayes estimates and Bayesian confidence limits for $θ$. It uses a simple…
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…
Barmak Mostofian, Daniel M. Zuckerman
Recent advances in molecular simulations allow the evaluation of previously unattainable observables, such as rate constants for protein folding. However, these calculations are usually computationally expensive and even significant computing resources may result in a small number of independent estimates spread over…
Ian Osband, Benjamin Van Roy
This technical note presents a new approach to carrying out the kind of exploration achieved by Thompson sampling, but without explicitly maintaining or sampling from posterior distributions. The approach is based on a bootstrap technique that uses a combination of observed and artificially generated data. The latter…
Mohsen Sadatsafavi, Carlo Marra, Shawn Aaron, Stirling Bryan
Background Cost-effectiveness analyses (CEAs) that use patient-specific data from a randomized controlled trial (RCT) are popular, yet such CEAs are criticized because they neglect to incorporate evidence external to the trial. A popular method for quantifying uncertainty in a RCT-based CEA is the bootstrap. The…
Bradley Efron
The parametric bootstrap can be used for the efficient computation of Bayes posterior distributions. Importance sampling formulas take on an easy form relating to the deviance in exponential families and are particularly simple starting from Jeffreys invariant prior. Because of the i.i.d. nature of bootstrap sampling…
Bradley M Broom, Kim-Anh Do, Devika Subramanian
Background Considerable progress has been made on algorithms for learning the structure of Bayesian networks from data. Model averaging by using bootstrap replicates with feature selection by thresholding is a widely used solution for learning features with high confidence. Yet, in the context of limited data many…
Elena Ballante, Pietro Muliere, Silvia Figini
This paper proposes a new class of predictive models for survival analysis called Generalized Bayesian Ensemble Survival Tree (GBEST). It is well known that survival analysis poses many different challenges, in particular when applied to small data or censorship mechanism. Our contribution is the proposal of an…
Simon Lyddon, Chris Holmes, Stephen G. Walker
In this paper we revisit the weighted likelihood bootstrap, a method that generates samples from an approximate Bayesian posterior of a parametric model. We show that the same method can be derived, without approximation, under a Bayesian nonparametric model with the parameter of interest defined as minimising an…
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…
Jonathan H. Huggins, Jeffrey W. Miller
Under model misspecification, it is known that Bayesian posteriors often do not properly quantify uncertainty about true or pseudo-true parameters. Even more fundamentally, misspecification leads to a lack of reproducibility in the sense that the same model will yield contradictory posteriors on independent data sets…
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…
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh + 1 more
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has…
Christoph Dalitz, Felix Lögler
The m-out-of-n bootstrap is a possible workaround to compute confidence intervals for bootstrap inconsistent estimators, because it works under weaker conditions than the n-out-of-n bootstrap. It has the disadvantage, however, that it requires knowledge of an appropriate scaling factor τn and that the coverage…
Elias Chaibub Neto, Kay Hamacher
In this paper we propose a vectorized implementation of the non-parametric bootstrap for statistics based on sample moments. Basically, we adopt the multinomial sampling formulation of the non-parametric bootstrap, and compute bootstrap replications of sample moment statistics by simply weighting the observed data…
D. Samuel Schwarzkopf
The problems with classical frequentist statistics are well established, yet the enthusiasm of researchers to adopt alternatives like Bayesian inference remains modest. Here I present the bootstrapped evidence test, an objective resampling procedure that takes the precision with which both the experimental and null…
F. Lemoine, J.-B. Domelevo Entfellner, E. Wilkinson, T. De Oliveira + 1 more
Felsenstein’s article describing the application of the bootstrap to evolutionary trees, is one of the most cited papers of all time. That statistical method, based on resampling and replications, is used extensively to assess the robustness of phylogenetic inferences. However, increasing numbers of sequences are now…
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…
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…
Wei Wang, Kevin J. Liu
The standard bootstrap method is used throughout science and engineering to perform general-purpose non-parametric resampling and re-estimation. Among the most widely cited and widely used such applications is the phylogenetic bootstrap method, which Felsenstein proposed in 1985 as a means to place statistical…
Robert Arbon, Yanchen Zhu, Antonia S. J. S. Mey
Markov state models (MSM) are a popular statistical method for analyzing the conformational dynamics of proteins, including protein folding. With all statistical and machine learning (ML) models choices must be made about the modeling pipeline that cannot be directly learned from the data. These choices, or…
Authors not listed
Plastic mechanical recycling is the conventional technological step towards circularity. In such aspects, complex mixtures of polyolefin blends are often fed into mechanical recycling systems, resulting in moulded products with uncertain quality. To add to the difficulty of heterogeneous feedstocks, the testing of…
Lucian Chan, Geoffrey Hutchison, Garrett Morris
Generating low-energy molecular conformers is a key task for many areas of computational chemistry, molecular modeling and cheminformatics. Most current conformer generation methods primarily focus on generating geometrically diverse conformers rather than finding the most probable or energetically lowest minima. Here…
Lucian Chan, Geoffrey Hutchison, Garrett Morris
Generating low-energy molecular conformers is a key task for many areas of computational chemistry, molecular modeling and cheminformatics. Most current conformer generation methods primarily focus on generating geometrically diverse conformers rather than finding the most probable or energetically lowest minima. Here…
Sterling Baird, Jason R. Hall, Taylor D. Sparks
Would you rather search for a line inside a cube or a point inside a square? This type of solution degeneracy often exists in physics-based simulations and wet-lab experiments, but constraining these degeneracies is often unsupported or difficult to implement in many optimization packages, requiring additional time and…