Related papers: SBML2Julia: interfacing SBML with efficient nonlin…
Chemellia is an open-source framework for atomistic machine learning in the Julia programming language. The framework takes advantage of Julia's high speed as well as the ability to share and reuse code and interfaces through the paradigm…
AnyMOD.jl is a Julia framework for creating large-scale energy system models with multiple periods of capacity expansion. It applies a novel graphbased approach that was developed to address the challenges in modeling high levels of…
Stochastic process models are now commonly used to analyse complex biological, ecological and industrial systems. Increasingly there is a need to deliver accurate estimates of model parameters and assess model fit by optimizing the timing…
NetworkDynamics.jl is an easy-to-use and computationally efficient package for working with heterogeneous dynamical systems on complex networks, written in Julia, a high-level, high-performance, dynamic programming language. By combining…
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…
In this article, we propose an interval constraint programming method for globally solving catalog-based categorical optimization problems. It supports catalogs of arbitrary size and properties of arbitrary dimension, and does not require…
The growing proliferation of FPGAs and High-level Synthesis (HLS) tools has led to a large interest in designing hardware accelerators for complex operations and algorithms. However, existing HLS toolflows typically require a significant…
Co-developing scientific algorithms and hardware accelerators requires domain-specific knowledge and large engineering resources. This leads to a slow development pace and high project complexity, which creates a barrier to entry that is…
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we…
StateSpaceModels.jl is an open-source Julia package for modeling, forecasting and simulating time series in a state-space framework. The package represents a straightforward tool that can be useful for a wide range of applications that deal…
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…
Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise…
The evergrowing computational complexity of High Performance Computing applications is often met with an horizontal scalling of computing systems. Colaterally, each added node risks being a single point of failure to parallel programs,…
Scientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly complex task, it extremely common that the software is used…
Integrating computational fluid dynamics (CFD) software into optimization and machine-learning frameworks is hampered by the rigidity of classic computational languages and the slow performance of more flexible high-level languages.…
HarmonicBalance.jl is a publicly available Julia package designed to simplify and solve systems of periodic time-dependent nonlinear ordinary differential equations. Time dependence of the system parameters is treated with the harmonic…
Many theoretical works and tools on epidemiological field reflect the emphasis on decision-making Tools by both public health and the scientific community, which continues to increase. Indeed, in the epidemiological field, modeling tools…
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…
The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. This paper discusses enhancements and extensions contained in version…
Dynamic programming languages face semantic and performance challenges in the presence of features, such as eval, that can inject new code into a running program. The Julia programming language introduces the novel concept of world age to…