Related papers: Scikit-fingerprints: easy and efficient computatio…
In drug-discovery-related tasks such as virtual screening, machine learning is emerging as a promising way to predict molecular properties. Conventionally, molecular fingerprints (numerical representations of molecules) are calculated…
We introduce SciWING, an open-source software toolkit which provides access to pre-trained models for scientific document processing tasks, inclusive of citation string parsing and logical structure recovery. SciWING enables researchers to…
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…
ORBKIT is a toolbox for post-processing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary…
We describe how Python can be leveraged to streamline the curation, modelling and dissemination of drug discovery data as well as the development of innovative, freely available tools for the related scientific community. We look at various…
EC-KitY is a comprehensive Python library for doing evolutionary computation (EC), licensed under the BSD 3-Clause License, and compatible with scikit-learn. Designed with modern software engineering and machine learning integration in…
Scikit-HEP is a community-driven and community-oriented project with the goal of providing an ecosystem for particle physics data analysis in Python. Scikit-HEP is a toolset of approximately twenty packages and a few "affiliated" packages.…
metric-learn is an open source Python package implementing supervised and weakly-supervised distance metric learning algorithms. As part of scikit-learn-contrib, it provides a unified interface compatible with scikit-learn which allows to…
LensKit is an open-source toolkit for building, researching, and learning about recommender systems. First released in 2010 as a Java framework, it has supported diverse published research, small-scale production deployments, and education…
$\textit{Pymc-learn}$ is a Python package providing a variety of state-of-the-art probabilistic models for supervised and unsupervised machine learning. It is inspired by $\textit{scikit-learn}$ and focuses on bringing probabilistic machine…
Signature-based methods have recently gained significant traction in machine learning for sequential data. In particular, signature kernels have emerged as powerful discriminators and training losses for generative models on time-series,…
As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using…
We present an open source Python 3 library aimed at practitioners of molecular simulation, especially Monte Carlo simulation. The aims of the library are to facilitate the generation of simulation data for a wide range of problems; and to…
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…
There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent…
Scikit-multiflow is a multi-output/multi-label and stream data mining framework for the Python programming language. Conceived to serve as a platform to encourage democratization of stream learning research, it provides multiple state of…
The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…
SciPy is an open source scientific computing library for the Python programming language. SciPy 1.0 was released in late 2017, about 16 years after the original version 0.1 release. SciPy has become a de facto standard for leveraging…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
A large amount of data is produced every second from modern information systems such as mobile devices, the world wide web, Internet of Things, social media, etc. Analysis and mining of this massive data requires a lot of advanced tools and…