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SBcoyote is an open-source cross-platform biochemical reaction viewer and editor released under the liberal MIT license. It is written in Python and uses wxPython to implement the GUI and the drawing canvas. It supports the visualization…
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…
Multi-modal Large Language Models (MLLMs) have demonstrated strong capabilities in general-purpose perception and reasoning, but they still struggle with tasks that require spatial understanding of the 3D world. To address this, we…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
The package \textsf{clayton} is designed to be intuitive, user-friendly, and efficient. It offers a wide range of copula models, including Archimedean, Elliptical, and Extreme. The package is implemented in pure \textsf{Python}, making it…
This paper introduces GIMP-ML v1.1, a set of Python plugins for the widely popular GNU Image Manipulation Program (GIMP). It enables the use of recent advances in computer vision to the conventional image editing pipeline. Applications from…
A major trend in academia and data science is the rapid adoption of Bayesian statistics for data analysis and modeling, leading to the development of probabilistic programming languages (PPL). A PPL provides a framework that allows users to…
Automated debugging, long pursued in a variety of fields from software engineering to cybersecurity, requires a framework that offers the building blocks for a programmable debugging workflow. However, existing debuggers are primarily…
Theory evaluation is a key problem in many areas: machine learning, scientific discovery, inverse engineering, decision making, software engineering, design, human sciences, etc. If we have a set of theories that are able to explain the…
Python has become the dominant language for general-purpose programming, yet it lacks robust tools for formal verification. In contrast, programmers working in languages such as C benefit from mature model checkers, for example CBMC, which…
In this document, we introduce PyCSP$3$, a Python library that allows us to write models of combinatorial constrained problems in a declarative manner. Currently, with PyCSP$3$, you can write models of constraint satisfaction and…
This paper introduces ROmodel, an open source Python package extending the modeling capabilities of the algebraic modeling language Pyomo to robust optimization problems. ROmodel helps practitioners transition from deterministic to robust…
Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for…
Language Models (LLMs), such as transformer-based neural networks trained on billions of parameters, have become increasingly prevalent in software engineering (SE). These models, trained on extensive datasets that include code…
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…
Stellar abundance analysis relies on flexible, high-performance spectral synthesis. To meet these needs, we present PySME v1.0, an updated Python implementation of Spectroscopy Made Easy (SME) designed for precise and survey-scale modelling…
The deep learning language of choice these days is Python; measured by factors such as available libraries and technical support, it is hard to beat. At the same time, software written in lower-level programming languages like C++ retain…
PyPM is a Python-based domain specific language (DSL) for building rewrite-based optimization passes on machine learning computation graphs. Users define individual optimizations by writing (a) patterns that match subgraphs of a computation…
Software Bills of Material (SBOMs), which improve transparency by listing the components constituting software, are a key countermeasure to the mounting problem of Software Supply Chain attacks. SBOM generation tools take project source…
We contribute a Python client for the Isabelle server, which gives researchers and students using Python as their primary programming language an opportunity to communicate with the Isabelle server through TCP directly from a Python script.…