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Motivation: Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses. Results: We have developed SimPlot++, an open-source multiplatform application implemented in Python,…
We have developed PyTIE (Python Topological Indices Expressions) which is defined as the collections of Python packages such as PyTIE D, PyTIE DS, PyTIE SMS DE, and PyTIE SMS DSE, which are open-source software packages and cross-platform…
This paper presents a distributed platform for Natural Language Processing called PyPLN. PyPLN leverages a vast array of NLP and text processing open source tools, managing the distribution of the workload on a variety of configurations:…
PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…
Programming modern high-performance computing systems is challenging due to the need to efficiently program GPUs and accelerators and to handle data movement between nodes. The C++ language has been continuously enhanced in recent years…
This paper reports the development of a Python Non-Uniform Fast Fourier Transform (PyNUFFT) package, which accelerates non-Cartesian image reconstruction on heterogeneous platforms. Scientific computing with Python encompasses a mature and…
We develop a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts,…
We announce the public release of PynPoint, a Python package that we have developed for analysing exoplanet data taken with the angular differential imaging observing technique. In particular, PynPoint is designed to model the point spread…
Fuzzy logic is an accepted and well-developed approach for constructing verbal models. Fuzzy based methods are getting more popular, while the engineers deal with more daily life tasks. This paper presents a new Python toolkit for Interval…
Performance assessment is a key issue in the process of proposing new machine learning/statistical estimators. A possible method to complete such task is by using simulation studies, which can be defined as the procedure of estimating and…
Most parallel applications suffer from load imbalance, a crucial performance degradation factor. In particle simulations, this is mainly due to the migration of particles between processing elements, which eventually gather unevenly and…
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…
The Statistical Toolkit is an open source system specialized in the statistical comparison of distributions. It addresses requirements common to different experimental domains, such as simulation validation (e.g. comparison of experimental…
The increase of existing computational capabilities has made simulation emerge as a third discipline of Science, lying midway between experimental and purely theoretical branches [1, 2]. Simulation enables the evaluation of quantities which…
Python is a popular programming language known for its ease of learning and extensive libraries. However, concerns about performance and energy consumption have led to the development of compilers to enhance Python code efficiency. Despite…
PyPOTS is an open-source Python library dedicated to data mining and analysis on multivariate partially-observed time series with missing values. Particularly, it provides easy access to diverse algorithms categorized into five tasks:…
Large language models (LLMs) hold tremendous potential for addressing numerous real-world challenges, yet they typically demand significant computational resources and memory. Deploying LLMs onto a resource-limited hardware device with…
Quantifying simulation uncertainties is a critical component of rigorous predictive simulation. A key component of this is forward propagation of uncertainties in simulation input data to output quantities of interest. Typical approaches…
In this work, we investigate improving the runtime performance of key computational kernels in the Python Tensor Toolbox (pyttb), a package for analyzing tensor data across a wide variety of applications. Recent runtime performance…
Nested parallelism exists in scientific codes that are searching multi-dimensional spaces. However, implementations of nested parallelism often have overhead and load balance issues. The Orbital Analysis code we present exhibits a sparse…