14 papers · ranked by Valyu relevance
Guillaume Lemaître, Fernando Nogueira, Christos K. Aridas
imbalanced-learn is an open-source python toolbox aiming at providing a wide range of methods to cope with the problem of imbalanced dataset frequently encountered in machine learning and pattern recognition. The implemented state-of-the-art methods can be categorized into 4 groups: (i) under-sampling, (ii)…
Quinn Thibeault, Jacob Anderson, Aniruddh Chandratre, Giulia Pedrielli + 1 more
'Giulia Pedrielli' 'Georgios Fainekos'] Abstract. In this paper, we present the Python package PSY-TaLiRo which is a toolbox for temporal logic robustness guided falsification of Cyber-Physical Systems (CPS). PSY-TaLiRo is a completely modular toolbox supporting multiple temporal logic offline monitors as well as…
Henrik Podéus, Gustav Magnusson, Sasan Keshmiri, Kajsa Tunedal + 3 more
When modeling complex, hierarchical, and time-dynamic systems, such as biological systems, good computational tools are essential. Current tools, while powerful, often lack comprehensive frameworks for modular model composition, hierarchical system building, and time-dependent input handling, particularly within the…
João P. G. L. M. Rodrigues, João M. C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin
The pdb-tools are a collection of Python scripts for working with molecular structure data in the PDB format. They allow users to edit, convert, and validate PDB files, from the command-line, in a simple but efficient manner. The pdb-tools are implemented in Python, without any external dependencies, and are freely…
Paulo Roberto Pereira Santiago, Abel Gonçalves Chinaglia, Kira Flanagan, Bruno L. S. Bedo + 4 more
Multimodal Toolbox Authors: ['Paulo Roberto Pereira Santiago' 'Abel Gonçalves Chinaglia' 'Kira Flanagan' 'Bruno L. S. Bedo' 'Lígia Yumi Mochida' 'Juan Aceros' 'Aline Bononi' 'Guilherme M. Cesar'] Biomechanics and Motor Control Laboratory, School of Physical Education and Sport, USP, Brazil Graduate Program in…
Johnathan Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar + 10 more
Computational Pathology (CPath) has seen rapid growth in recent years, driven by advanced deep learning (DL) algorithms. These algorithms typically share the same sequence of steps. However, due to the sheer size and complexity of handling large multi-gigapixel whole-slide images, there is no open-source software…
Laura Wiggins, Stuart Lacy, Graeme Park, Joanne Marrison + 5 more
We previously developed the CellPhe toolkit^1^, an open-source R package for automated cell phenotyping from ptychography time-lapse videos. To align with the growing adoption of python-based image analysis tools and to enhance interoperability with widely used software for cell segmentation and tracking, we developed…
Kiri Choi, J. Kyle Medley, Caroline Cannistra, Matthias König + 3 more
In this article, we present Tellurium, a powerful Python-based integrated environment designed for model building, analysis, simulation and reproducibility in systems and synthetic biology. Tellurium is a modular, cross-platform, and open-source integrated development environment (IDE) composed of multiple libraries…
Christoph Redies, Ralf Bartho, Lisa Koßmann, Branka Špehar + 3 more
research Authors: ['Christoph Redies' 'Ralf Bartho' 'Lisa Koßmann' 'Branka Špehar' 'Ronald Hübner' 'Johan Wagemans' 'Gregor U. Hayn‐Leichsenring'] Over the past two decades, researchers in the field of visual aesthetics have studied numerous quantitative (objective) image properties and how they relate to visual…
Knut Rand, Ivar Grytten, Milena Pavlovic, Chakravarthi Kanduri + 1 more
Python is a popular and widespread programming language for scientific computing, in large part due to the powerful array programming library NumPy, which makes it easy to write clean, vectorized and efficient code for handling large datasets. A challenge with using array programming for biological data is that the…
Hamed Tahmooresi, Abbas Heydarnoori, Alireza Aghamohammadi
—Python is a popular, widely used, and general-purpose programming language. In spite of its ever-growing community, researchers have not performed much analysis on Python's topics, trends, and technologies which provides insights for developers about Python community trends and main issues. In this article, we examine…
François Moreews, Jean-Baptiste Bougaud, Emmanuelle Becker, Florence Gondret + 1 more
Biological Pathway Exchange (BioPAX) is a standard language, represented in OWL, that aims to enable the integration, exchange, visualization and analysis of biological pathway data. While public databanks increasingly provide datasets in BioPAX format, their use remains below potential. Users may encounter challenges…
Peter K. G. Williams, Casey Law, Geoffrey C. Bower
New and upgraded radio interferometers produce data at massive rates and will require significant improvements in analysis techniques to reach their promised levels of performance in a routine manner. Until these techniques are fully developed, productivity and accessibility in scientific programming environments will…
Chengjie Chen, Hao Chen, Yi Zhang, Hannah R. Thomas + 3 more
The rapid development of high-throughput sequencing (HTS) techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for…