Related papers: Solving Polynomial Systems with phcpy

Systems biology is an inter-disciplinary field that studies systems of biological components at different scales, which may be molecules, cells or entire organism. In particular, systems biology methods are applied to understand functional…

SpeechPy is an open source Python package that contains speech preprocessing techniques, speech features, and important post-processing operations. It provides most frequent used speech features including MFCCs and filterbank energies…

Recently, contiguous sequential pattern mining (CSPM) gained interest as a research topic, due to its varied potential real-world applications, such as web log and biological sequence analysis. To date, studies on the CSPM problem remain in…

Manapy is a parallel, unstructured, finite-volume based solver for the solution of partial differential equations (PDE). The framework is written using Python, it is object-oriented, and is organized in such a way that it is easy to…

Scientific workflows facilitate computational, data manipulation, and sometimes visualization steps for scientific data analysis. They are vital for reproducing and validating experiments, usually involving computational steps in scientific…

Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…

Integrated information theory provides a mathematical framework to fully characterize the cause-effect structure of a physical system. Here, we introduce PyPhi, a Python software package that implements this framework for causal analysis…

For several computational problems in homotopy theory, we obtain algorithms with running time polynomial in the input size. In particular, for every fixed k>1, there is a polynomial-time algorithm that, for a 1-connected topological space X…

Fanpy is a free and open-source Python library for developing and testing multideterminant wavefunctions and related ab initio methods in electronic structure theory. The main use of Fanpy is to quickly prototype new methods by making it…

GCsnap2 Cluster is a scalable, high performance tool for genomic context analysis, developed to overcome the limitations of its predecessor, GCsnap1 Desktop. Leveraging distributed computing with mpi4py[.]futures, GCsnap2 Cluster achieved a…

DisCoPy (Distributional Compositional Python) is an open source toolbox for computing with string diagrams and functors. In particular, the diagram data structure allows to encode various kinds of quantum processes, with functors for…

Let $\K$ be a field of characteristic zero and $\Kbar$ be an algebraic closure of $\K$. Consider a sequence of polynomials$G=(g\_1,\dots,g\_s)$ in $\K[X\_1,\dots,X\_n]$, a polynomial matrix $\F=[f\_{i,j}] \in \K[X\_1,\dots,X\_n]^{p \times…

We are interested in the fast computation of the exact value of integrals of polynomial functions over convex polyhedra. We present speed ups and extensions of the algorithms presented in previous work. We present the new software…

Compound AI applications, which compose calls to ML models using a general-purpose programming language like Python, are widely used for a variety of user-facing tasks, from software engineering to enterprise automation, making their…

Computational methods are driving high impact microscopy techniques such as ptychography. However, the design and implementation of new algorithms is often a laborious process, as many parts of the code are written in close-to-the-hardware…

Robust estimation provides essential tools for analyzing data that contain outliers, ensuring that statistical models remain reliable even in the presence of some anomalous data. While robust methods have long been available in R, users of…

We propose a new algorithm for numerical path tracking in polynomial homotopy continuation. The algorithm is `robust' in the sense that it is designed to prevent path jumping and in many cases, it can be used in (only) double precision…

Scientific simulation codes are public property sustained by the community. Modern technology allows anyone to join scientific software projects, from anywhere, remotely via the internet. The phonopy and phono3py codes are widely used open…

There are numerous approaches to building analysis applications across the high-energy physics community. Among them are Python-based, or at least Python-driven, analysis workflows. We aim to ease the adoption of a Python-based analysis…

The Phychip project is a collaborative European research initiative to design and implement computation using the organism Physarum polycephalum; it is funded by the Seventh Framework Programme (FP7) by the European Commission within CORDIS…