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In this paper, we present pomdp_py, a general purpose Partially Observable Markov Decision Process (POMDP) library written in Python and Cython. Existing POMDP libraries often hinder accessibility and efficient prototyping due to the…
In this work, we review the theory involved in the Bayesian calibration of complex computer models, with particular emphasis on their use for applications involving computationally expensive simulations and scarce experimental data. In the…
We present dynesty, a public, open-source, Python package to estimate Bayesian posteriors and evidences (marginal likelihoods) using Dynamic Nested Sampling. By adaptively allocating samples based on posterior structure, Dynamic Nested…
We present an open-source simulation framework for optically detected magnetic resonance, developed in Python. The framework allows users to construct, manipulate, and evolve multipartite quantum systems that consist of spins and electronic…
We previously reported on the complex permittivity and dc conductivity of waste-activated sludge. The measurements, spanning a frequency range of 3 MHz to 40 GHz, were made using an open-ended coaxial transmission line. Although this…
The MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix ($C_{ij}$) obtained from any ab-initio density-functional theory (DFT) code. The current version of…
We have built an open-source software system for the modeling of biomolecular reaction networks, SloppyCell, which is written in Python and makes substantial use of third-party libraries for numerics, visualization, and parallel…
We introduce a Python framework designed to automate the most common tasks associated with the extraction and upscaling of the statistics of single-impact crater functions to inform coefficients of continuum equations describing surface…
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…
This paper presents a Python software package, Ph3pyWF, providing a more convenient platform to realize high-throughput analysis of lattice thermal conductivity for ceramic materials. The interface of Ph3pyWF is friendly for users with…
Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…
Accurate force fields are essential for reliable molecular simulations. These models are refined against quantum mechanical calculations and experimental measurements, which are subject to random and systematic errors. Bayesian Inference of…
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…
Software Engineering and the implementation of software has become a challenging task as many tools, frameworks and languages must be orchestrated into one functioning piece. This complexity increases the need for testing and analysis…
Since Lorenz's seminal work on a simplified weather model, the numerical analysis of nonlinear dynamical systems has become one of the main subjects of research in physics. Despite of that, there remains a need for accessible, efficient,…
While the recursive property of entropy is well known in information theory, it is rarely utilized in thermodynamics, despite entropy originating in this field. Moreover, computational tools to implement this concept within first-principles…
As dynamical systems equipped with neural network controllers (neural feedback systems) become increasingly prevalent, it is critical to develop methods to ensure their safe operation. Verifying safety requires extending control theoretic…
Structural Equation Modeling (SEM) is an umbrella term that includes numerous multivariate statistical techniques that are employed throughout a plethora of research areas, ranging from social to natural sciences. Until recently, SEM…
As camera pixel arrays have grown larger and faster, and optical microscopy techniques ever more refined, there has been an explosion in the quantity of data acquired during routine light microcopy. At the single-molecule level, analysis…
This paper presents a 55-line code written in python for 2D and 3D topology optimization (TO) based on the open-source finite element computing software (FEniCS), equipped with various finite element tools and solvers. PETSc is used as the…