Related papers: BSTModelKit.jl: A Julia Package for Constructing, …
This paper introduces the TulipaProfileFitting.jl package, a tool developed in Julia for generating renewable energy profiles that fit a specified capacity factor. It addresses the limitations of naive methods in adjusting existing profiles…
The demand for high-performance computing (HPC) is ever-increasing for everyday statistical computing purposes. The downside is that we need to write specialized code for each HPC environment. CPU-level parallelization needs to be…
First we shortly review the different kinds of network modelling methods for systems biology with an emphasis on the different subtypes of logical models, which we review in more detail. Then we show the advantages of Boolean networks…
Motivation: Flux balance analysis, and its variants, are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered…
Stochastic dominance is a fundamental concept in decision-making under uncertainty and quantitative finance, yet its practical application is hindered by computational intractability due to infinitely many constraints. We introduce the…
We introduce Metatheory.jl: a lightweight and performant general purpose symbolics and metaprogramming framework meant to simplify the act of writing complex Julia metaprograms and to significantly enhance Julia with a native term rewriting…
Biofilms are communities of microorganisms that grow on virtually all surfaces with sufficient nutrients including aquatic and industrial water systems and medical devices. Biofilms are complex, structured communities where the interplay of…
MicroMagnetic.jl is an open-source Julia package for micromagnetic and atomistic simulations. Using the features of the Julia programming language, MicroMagnetic.jl supports CPU and various GPU platforms, including NVIDIA, AMD, Intel, and…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
In the context of science, the well-known adage "a picture is worth a thousand words" might well be "a model is worth a thousand datasets." In this manuscript we introduce the SciML software ecosystem as a tool for mixing the information of…
Numerical investigations are an important research tool in quantum information theory. There already exists a wide range of computational tools for quantum information theory implemented in various programming languages. However, there is…
Bayesian synthetic likelihood (BSL) is a popular method for estimating the parameter posterior distribution for complex statistical models and stochastic processes that possess a computationally intractable likelihood function. Instead of…
Biochemical reaction models describing subcellular processes generally come with a large uncertainty. To be able to account for this during the modeling process, we have developed the R-package UQSA, performing uncertainty quantification…
The development of new electronic structure methods is a very time consuming and error prone process when done by hand. SpinAdaptedSecondQuantization is an open-source Julia package we have developed for working with automated electronic…
We present Trixi.jl, a Julia package for adaptive high-order numerical simulations of hyperbolic partial differential equations. Utilizing Julia's strengths, Trixi.jl is extensible, easy to use, and fast. We describe the main design choices…
We present JDLL, an agile Java library that offers a comprehensive toolset/API to unify the development of high-end applications of DL for bioimage analysis and to streamline their installation and maintenance. JDLL provides all the…
Biclustering is a data mining technique which searches for local patterns in numeric tabular data with main application in bioinformatics. This technique has shown promise in multiple areas, including development of biomarkers for cancer,…
Along with the emergence and popularity of social communications on the Internet, topic discovery from short texts becomes fundamental to many applications that require semantic understanding of textual content. As a rising research field,…
Topic models provide a flexible and principled framework for exploring hidden structure in high-dimensional co-occurrence data and are commonly used natural language processing (NLP) of text. In this paper, we design and implement a Java…
Scientists construct and analyze computational models to understand the world. That understanding comes from efforts to augment, combine, and compare models of related phenomena. We propose SemanticModels.jl, a system that leverages…