Related papers: BSTModelKit.jl: A Julia Package for Constructing, …
We describe a package realized in the Julia programming language which performs symbolic manipulations applied to nonlinear evolution equations, their flows, and commutators of such objects. This tool was employed to perform contrived…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
We introduce DeePKS-kit, an open-source software package for developing machine learning based energy and density functional models. DeePKS-kit is interfaced with PyTorch, an open-source machine learning library, and PySCF, an ab initio…
Rule-based models are often used for data analysis as they combine interpretability with predictive power. We present RuleKit, a versatile tool for rule learning. Based on a sequential covering induction algorithm, it is suitable for…
We present DataDeps.jl: a julia package for the reproducible handling of static datasets to enhance the repeatability of scripts used in the data and computational sciences. It is used to automate the data setup part of running software…
This paper explores some basic concepts of Biochemical Systems Theory (BST) and Metabolic Control Analysis (MCA), two frameworks developed to understand the behavior of biochemical networks. Initially introduced by Savageau, BST focuses on…
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the…
Interpreting biological networks becomes challenging when molecular components, such as genes or proteins, participate in numerous interactions, resulting in densely connected regions and overlapping interactions that obscure functional…
Stochastic reaction-diffusion processes may be presented in terms of integrable quantum chains and can be used to describe various biological and chemical systems. Exploiting the integrability of the models one finds in some cases good…
We present an efficient numerical implementation of the quasi-classical doorway-window approximation, specifically designed for on-the-fly simulations of time-resolved nonlinear spectroscopic signals in the Julia package WaveMixings.jl. The…
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to…
We introduce the third major version of Metatheory.jl, a Julia library for general-purpose metaprogramming and symbolic computation. Metatheory.jl provides a flexible and performant implementation of e-graphs and Equality Saturation (EqSat)…
We present the W-SLDA Toolkit, a general-purpose software package for simulating ultracold Fermi gases within the framework of density functional theory and its time-dependent extensions. The toolkit enables fully microscopic studies of…
We introduce DiffOpt.jl, a Julia library to differentiate through the solution of optimization problems with respect to arbitrary parameters present in the objective and/or constraints. The library builds upon MathOptInterface, thus…
Classical methods to simulate quantum systems are not only a key element of the physicist's toolkit for studying many-body models but are also increasingly important for verifying and challenging upcoming quantum computers. Pauli…
The modeling of bio-molecular system across molecular scales remains a central challenge in scientific research. Large language models (LLMs) are increasingly applied to bio-molecular discovery, yet systematic evaluation across multi-scale…
We present \texttt{MathOptAI.jl}, an open-source Julia library for embedding trained machine learning predictors into a JuMP model. \texttt{MathOptAI.jl} can embed a wide variety of neural networks, decision trees, and Gaussian Processes…
The open-source software package SolidStateDetectors$.$jl to calculate the fields and simulate the drifts of charge carriers in solid state detectors, together with the corresponding pulses, is introduced. The package can perform all…
We present the preliminary high-level design and features of DynamicPPL.jl, a modular library providing a lightning-fast infrastructure for probabilistic programming. Besides a computational performance that is often close to or better than…
The Smodels system implements the stable model semantics for normal logic programs. It handles a subclass of programs which contain no function symbols and are domain-restricted but supports extensions including built-in functions as well…