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By introducing a common representational system for metadata that describe the employed simulation workflows, diverse sources of data and platforms in computational molecular engineering, such as workflow management systems, can become…
We present MISTIQS, a Multiplatform Software for Time-dependent Quantum Simulations. MISTIQS delivers end-to-end functionality for simulating the quantum many-body dynamics of systems governed by time-dependent Heisenberg Hamiltonians…
ShinyItemAnalysis (SIA) is an R package and shiny application for an interactive presentation of psychometric methods and analysis of multi-item measurements in psychology, education, and social sciences in general. In this article, we…
The performance of optimization algorithms relies crucially on their parameterizations. Finding good parameter settings is called algorithm tuning. The sequential parameter optimization (SPOT) package for R is a toolbox for tuning and…
Integrated analysis of multi-omics datasets holds great promise for uncovering complex biological processes. However, the large dimension of omics data poses significant interpretability and multiple testing challenges. Simultaneous…
Conducting user studies that involve physiological and behavioral measurements is very time-consuming and expensive, as it not only involves a careful experiment design, device calibration, etc. but also a careful software testing. We…
The task of atom rearrangement has emerged in the last decade as a fundamental building block for the development of neutral atom-based quantum processors. However, despite many recent efforts to develop algorithms with favorable asymptotic…
Computational micromagnetics has become an essential tool in academia and industry to support fundamental research and the design and development of devices. Consequently, computational micromagnetics is widely used in the community, and…
Spike cameras, with their exceptional temporal resolution, are revolutionizing high-speed visual applications. Large-scale synthetic datasets have significantly accelerated the development of these cameras, particularly in reconstruction…
It is critical to accurately simulate data when employing Monte Carlo techniques and evaluating statistical methodology. Measurements are often correlated and high dimensional in this era of big data, such as data obtained in…
Joint modeling has become increasingly popular for characterizing the association between one or more longitudinal biomarkers and competing risks time-to-event outcomes. However, semiparametric multivariate joint modeling for large-scale…
Simulation studies are widely used to evaluate statistical methods. However, new methods are often introduced and evaluated using data-generating mechanisms (DGMs) devised by the same authors. This coupling creates misaligned incentives,…
We present Synthesizer, a fast, flexible, modular and extensible platform for modelling synthetic astrophysical observables. Synthesizer can be used for a number of applications, but is predominantly designed for generating mock observables…
This paper presents a methodological framework for training, self-optimising, and self-organising surrogate models to approximate and speed up multiobjective optimisation of technical systems based on multiphysics simulations. At the hand…
The concept of "tidy data" offers a powerful framework for structuring data to ease manipulation, modeling and visualization. However, most R functions, both those built-in and those found in third-party packages, produce output that is not…
We describe software and a language for quasibiological computations. Its theoretical basis is a unified theory of complex (adaptive) systems where all laws are regularities of relations between things or agents, and dynamics is made from…
Simulation testing is an important approach to evaluating fishery stock assessment methods. In the last decade, the fisheries stock assessment modeling framework Stock Synthesis (SS3) has become widely used around the world. However, there…
Health economic models simulate the costs and effects of health technologies for use in health technology assessment (HTA) to inform efficient use of scarce resources. Models have historically been developed using spreadsheet software…
ArQTiC is an open-source, full-stack software package built for the simulations of materials on quantum computers. It currently can simulate materials that can be modeled by any Hamiltonian derived from a generic, one-dimensional,…
Labelling data is expensive and time consuming especially for domains such as medical imaging that contain volumetric imaging data and require expert knowledge. Exploiting a larger pool of labeled data available across multiple centers,…