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The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by…

In a world with data that change rapidly and abruptly, it is important to detect those changes accurately. In this paper we describe an R package implementing a generalized version of an algorithm recently proposed by Hocking et al. [2020]…

For data with high-dimensional covariates but small to moderate sample sizes, the analysis of single datasets often generates unsatisfactory results. The integrative analysis of multiple independent datasets provides an effective way of…

Methodology · Statistics 2015-01-19 Yuan Huang , Qingzhao Zhang , Sanguo Zhang , Jian Huang , Shuangge Ma

Quantifying the causal effects of continuous exposures on outcomes of interest is critical for social, economic, health, and medical research. However, most existing software packages focus on binary exposures. We develop the CausalGPS R…

Computation · Statistics 2023-10-03 Naeem Khoshnevis , Xiao Wu , Danielle Braun

Skewness plays a relevant role in several multivariate statistical techniques. Sometimes it is used to recover data features, as in cluster analysis. In other circumstances, skewness impairs the performances of statistical methods, as in…

Computation · Statistics 2019-03-26 Cinzia Franceschini , Nicola Loperfido

Studies often estimate associations between an outcome and multiple variates. For example, studies of diagnostic test accuracy estimate sensitivity and specificity, and studies of predictive and prognostic factors typically estimate…

Systematic variation is a common issue in metabolomics data analysis. Therefore, different scaling and normalization techniques are used to preprocess the data for metabolomics data analysis. Although several scaling methods are available…

Machine Learning · Statistics 2022-08-02 Biplab Biswas , Nishith Kumar , Md Aminul Hoque , Md Ashad Alam

One of the fundamental challenges in drawing causal inferences from observational studies is that the assumption of no unmeasured confounding is not testable from observed data. Therefore, assessing sensitivity to this assumption's…

Methodology · Statistics 2024-06-25 Md Abdul Basit , Mahbub A. H. M. Latif , Abdus S Wahed

The R package BigVAR allows for the simultaneous estimation of high-dimensional time series by applying structured penalties to the conventional vector autoregression (VAR) and vector autoregression with exogenous variables (VARX)…

Computation · Statistics 2017-02-24 William Nicholson , David Matteson , Jacob Bien

The R package BNSP provides a unified framework for semiparametric location-scale regression and stochastic search variable selection. The statistical methodology that the package is built upon utilizes basis function expansions to…

Other Statistics · Statistics 2018-10-09 Georgios Papageorgiou

There has been a tremendous methodological development of Bayes factors for hypothesis testing in the social and behavioral sciences, and related fields. This development is due to the flexibility of the Bayes factor for testing multiple…

Individual-based models are complex and they have usually an elevated number of input parameters which must be tuned for reproducing the observed population data or the experimental results as accurately as possible. Thus, one of the…

Neural and Evolutionary Computing · Computer Science 2020-05-27 Antonio Prestes García , Alfonso Rodríguez-Patón

As the adoption of Artificial Intelligence (AI) models expands into critical real-world applications, ensuring the explainability of these models becomes paramount, particularly in sensitive fields such as medicine and finance. Linear…

Machine Learning · Computer Science 2024-10-10 Tuan L. Vo , Uyen Dang , Thu Nguyen

Stacking, a potent ensemble learning method, leverages a meta-model to harness the strengths of multiple base models, thereby enhancing prediction accuracy. Traditional stacking techniques typically utilize established learning models, such…

Machine Learning · Computer Science 2024-10-31 Wei Wu , Liang Tang , Zhongjie Zhao , Chung-Piaw Teo

Uplift modeling aims at predicting the causal effect of an action such as a medical treatment or a marketing campaign on a particular individual, by taking into consideration the response to a treatment. The treatment group contains…

Applications · Statistics 2021-09-14 Mouloud Belbahri , Alejandro Murua , Olivier Gandouet , Vahid Partovi Nia

This contribution presents a guide to the R package multilevLCA, which offers a complete and innovative set of technical tools for the latent class analysis of single-level and multilevel categorical data. We describe the available model…

Computation · Statistics 2024-04-11 Johan Lyrvall , Roberto Di Mari , Zsuzsa Bakk , Jennifer Oser , Jouni Kuha

The R package merlin performs flexible joint modelling of hierarchical multi-outcome data. Increasingly, multiple longitudinal biomarker measurements, possibly censored time-to-event outcomes and baseline characteristics are available.…

Computation · Statistics 2020-07-29 Emma C. Martin , Alessandro Gasparini , Michael J. Crowther

Objective: Radiation therapy treatment planning is a time-consuming process involving iterative adjustments of hyperparameters. To automate the treatment planning process, we propose a meta-optimization framework, called MetaPlanner (MP).…

Medical Physics · Physics 2022-02-22 Charles Huang , Yusuke Nomura , Yong Yang , Lei Xing

Meta-analysis methods have been widely used to combine results from multiple clinical or genomic studies to increase statistical power and ensure robust and accurate conclusion. Adaptively weighted Fisher's method (AW-Fisher) is an…

Methodology · Statistics 2017-08-18 Zhiguang Huo , Shaowu Tang , Yongseok Park , George Tseng

Randomized controlled trials are the gold standard for measuring causal effects. However, they are often not always feasible, and causal treatment effects must be estimated from observational data. Observational studies do not allow robust…