Related papers: SimOmics: A Simulation Toolkit for Multivariate an…

This paper is dedicated to the R package FMM which implements a novel approach to describe rhythmic patterns in oscillatory signals. The frequency modulated M\"obius (FMM) model is defined as a parametric signal plus a gaussian noise, where…

The R Package IBMPopSim aims to simulate the random evolution of heterogeneous populations using stochastic Individual-Based Models (IBMs). The package enables users to simulate population evolution, in which individuals are characterized…

Structural equation modelling (SEM) is a multivariate statistical technique for estimating complex relationships between observed and latent variables. Although numerous SEM packages exist, each of them has limitations. Some packages are…

We propose to use agent-based simulation models for the development of statistical methods in Official Statistics, especially in relation with the new digital data sources. We present a mobile network data simulator which is managed through…

We present pyroomacoustics, a software package aimed at the rapid development and testing of audio array processing algorithms. The content of the package can be divided into three main components: an intuitive Python object-oriented…

Metal-organic frameworks (MOFs) offer a vast design space, and as such, computational simulations play a critical role in predicting their structural and physicochemical properties. However, MOF simulations remain difficult to access…

MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…

Interrogation of biological pathways is an integral part of omics data analysis. Large language models (LLMs) enable the generation of custom pathways and gene sets tailored to specific scientific questions. These targeted sets are…

We present a new approach to the simulation and analysis of immune system behavior. The simulations that can be done with our software package called SIMMUNE are based on immunological data that describe the behavior of immune system agents…

The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…

For researchers in electromyography (EMG), and similar biosginals, signal processing is naturally an essential topic. There are a number of excellent tools available. To these one may add the freely available open source statistical…

We rewrite the metric/nonmetric and weighted/unweighted versions of the smacof program for square symmetric data as one monolithic C program. R is used for taking care of the data and parameter setup, the I/O, and of issuing a single call…

Considering the diverse nature of real-world distributed applications that makes it hard to identify a representative subset of distributed benchmarks, we focus on their underlying distributed algorithms. We present and characterize a new…

The synthpop package for R https://www.synthpop.org.uk provides tools to allow data custodians to create synthetic versions of confidential microdata that can be distributed with fewer restrictions than the original. The synthesis can be…

Recent advances in high-throughput sequencing technologies have enabled the extraction of multiple features that depict patient samples at diverse and complementary molecular levels. The generation of such data has led to new challenges in…

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…

With advanced imaging, sequencing, and profiling technologies, multiple omics data become increasingly available and hold promises for many healthcare applications such as cancer diagnosis and treatment. Multimodal learning for integrative…

We present a data simulation package designed to create a series of simulated data samples for a detector with non-destructive sampling capability. The original intent of this software was to provide a method for generating simulated images…

Background and Objective: Computational ultrasound imaging has become a well-established methodology in the ultrasound community. Simulations of ultrasound sequences and images allow the study of innovative techniques in terms of emission…

Developing large-scale foundational datasets is a critical milestone in advancing artificial intelligence (AI)-driven scientific innovation. However, unlike AI-mature fields such as natural language processing, materials science,…