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The Python package pylimer-tools is a comprehensive toolkit for computational studies of polymer networks, particularly bead-spring networks. The package provides functionality to generate polymer networks using Monte Carlo (MC) procedures…

Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…

GPTIPS is a free, open source MATLAB based software platform for symbolic data mining (SDM). It uses a multigene variant of the biologically inspired machine learning method of genetic programming (MGGP) as the engine that drives the…

As optimization challenges continue to evolve, so too must our tools and understanding. To effectively assess, validate, and compare optimization algorithms, it is crucial to use a benchmark test suite that encompasses a diverse range of…

We introduce giotto-ph, a high-performance, open-source software package for the computation of Vietoris-Rips barcodes. giotto-ph is based on Morozov and Nigmetov's lockfree (multicore) implementation of Ulrich Bauer's Ripser package. It…

Characterizing quantum processes is indispensable for the implementation of any task in quantum information processing. In this paper, we develop an efficient method to fully characterize arbitrary Gaussian processes in continuous-variable…

This article introduces MCNP-GO (https://github.com/afriou/mcnpgo), a Python package designed to manipulate and assemble MCNP input files, allowing users to assemble a set of independent objects, each described by a valid MCNP file, into a…

Bayesian Networks (BNs) are used in various fields for modeling, prediction, and decision making. pgmpy is a python package that provides a collection of algorithms and tools to work with BNs and related models. It implements algorithms for…

Parallelization schemes are essential in order to exploit the full benefits of multi-core architectures. In said architectures, the most comprehensive parallelization API is OpenMP. However, the introduction of correct and optimal OpenMP…

Despite a large corpus of recent work on scaling up Gaussian processes, a stubborn trade-off between computational speed, prediction and uncertainty quantification accuracy, and customizability persists. This is because the vast majority of…

Matrix Distributed Processing (MDP) is a C++ library for fast development of efficient parallel algorithms. It constitues the core of FermiQCD. MDP enables programmers to focus on algorithms, while parallelization is dealt with…

Gaussian mixture models (GMMs) are ubiquitous in statistical learning, particularly for unsupervised problems. While full GMMs suffer from the overparameterization of their covariance matrices in high-dimensional spaces, spherical GMMs…

GeneralizIT is a Python package designed to streamline the application of Generalizability Theory (G-Theory) in research and practice. G-Theory extends classical test theory by estimating multiple sources of error variance, providing a more…

Gaussian Processes (GPs) are flexible, nonparametric Bayesian models widely used for regression and classification because of their ability to capture complex data patterns and quantify predictive uncertainty. However, the O(n^3)…

We introduce and study a multiparameter version of the generalized counting process (GCP), where there is a possibility of finitely many arrivals simultaneously. We call it the multiparameter GCP. In a particular case, it is uniquely…

We study the problem of learning Gaussian Mixture Models (GMMs) and ask: which structural properties govern their sample complexity? Prior work has largely tied this complexity to the minimum pairwise separation between components, but we…

We report the development of a python-based auxiliary-field quantum Monte Carlo (AFQMC) program, ipie, with preliminary timing benchmarks and new AFQMC results on the isomerization of [Cu$_2$O$_2$$]^{2+}$. We demonstrate how implementations…

This paper presents `chipfiring`, a comprehensive Python package for the mathematical analysis of chip-firing games on finite graphs. The package provides a robust toolkit for defining graphs and chip configurations (divisors), performing…

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…

We present a tool for the comparison and validation of the integration packages suitable for Solar System dynamics. iCompare, written in Python, compares the ephemeris prediction accuracy of a suite of commonly-used integration packages…