Related papers: Solving Polynomial Systems with phcpy
Scientific inference is often undermined by the vast but rarely explored "multiverse" of defensible modelling choices, which can generate results as variable as the phenomena under study. We introduce RobustiPy, an open-source Python…
Due to the complex behavior arising from non-uniqueness, symmetry, and bifurcations in the solution space, solving inverse problems of nonlinear differential equations (DEs) with multiple solutions is a challenging task. To address this, we…
Different security issues are a common problem for open source packages archived to and delivered through software ecosystems. These often manifest themselves as software weaknesses that may lead to concrete software vulnerabilities. This…
High Performance Computing~(HPC) software stacks have become complex, with the dependencies of some applications numbering in the hundreds. Packaging, distributing, and administering software stacks of that scale is a complex undertaking…
A Materials Project based open-source Python tool, MPInterfaces, has been developed to automate the high-throughput computational screening and study of interfacial systems. The framework encompasses creation and manipulation of interface…
Computing haplotypes from sequencing data, i.e. haplotype assembly, is an important component of molecular and population genetics problems, including interpreting the effects of genetic variation on complex traits and reconstructing…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
An algorithm is presented here, for discovering Hopf-Bifurcation varieties of polynomial dynamical systems. It is based on the expression of specific polynomials, as sums of products of first degree polynomials, with parametrical…
We introduce VOPy, an open-source Python library designed to address black-box vector optimization, where multiple objectives must be optimized simultaneously with respect to a partial order induced by a convex cone. VOPy extends beyond…
We present the first public version (v0.2) of the open-source and community-developed Python package, Astropy. This package provides core astronomy-related functionality to the community, including support for domain-specific file formats…
Agent-based cellular models simulate tissue evolution by capturing the behavior of individual cells, their interactions with neighboring cells, and their responses to the surrounding microenvironment. An important challenge in the field is…
To compute solutions of sparse polynomial systems efficiently we have to exploit the structure of their Newton polytopes. While the application of polyhedral methods naturally excludes solutions with zero components, an irreducible…
In this article, we describe an implementation of a polynomial system solver to compute the approximate solutions of a 0-dimensional polynomial system with finite precision p-adic arithmetic. We also describe an improvement to an algorithm…
The polyhedral homotopy method of Huber and Sturmfels is a particularly efficient and robust numerical method for solving system of (Laurent) polynomial equations. A central component in an implementation of this method is an efficient and…
We discuss in detail a recently proposed hybrid particle-continuum scheme for complex fluids and evaluate it at the example of a confined homopolymer solution in slit geometry. The hybrid scheme treats polymer chains near the impenetrable…
The last improvements in programming languages, programming models, and frameworks have focused on abstracting the users from many programming issues. Among others, recent programming frameworks include simpler syntax, automatic memory…
Nonlinear two-point boundary value problems arise in numerous areas of application. The existence and number of solutions for various cases has been studied from a theoretical standpoint. These results generally rely upon growth conditions…
We present \code{phaser}, an open-source Python package that provides a unified interface to both conventional and gradient descent-based ptychographic algorithms. Features such as mixed-state probe, probe position correction, and…
Large-scale simulations of plasmas are essential for advancing our understanding of fusion devices, space, and astrophysical systems. Particle-in-Cell (PIC) codes have demonstrated their success in simulating numerous plasma phenomena on…
The Epiphany is a many-core, low power, low on-chip memory architecture and one can very cheaply gain access to a number of parallel cores which is beneficial for HPC education and prototyping. The very low power nature of these…