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DeeProb-kit is a unified library written in Python consisting of a collection of deep probabilistic models (DPMs) that are tractable and exact representations for the modelled probability distributions. The availability of a representative…
Detecting microbial biomarkers used to predict disease phenotypes and clinical outcomes is crucial for disease early-stage screening and diagnosis. Most methods for biomarker identification are linear-based, which is very limited as…
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of…
We present FlowMO: an open-source Python library for molecular property prediction with Gaussian Processes. Built upon GPflow and RDKit, FlowMO enables the user to make predictions with well-calibrated uncertainty estimates, an output…
SMILES is a linear representation of chemical structures which encodes the connection table, and the stereochemistry of a molecule as a line of text with a grammar structure denoting atoms, bonds, rings and chains, and this information can…
Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in…
SparseChem provides fast and accurate machine learning models for biochemical applications. Especially, the package supports very high-dimensional sparse inputs, e.g., millions of features and millions of compounds. It is possible to train…
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,…
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by…
Structural fingerprints and pharmacophore modeling are methodologies that have been used for at least two decades in various fields of cheminformatics: from similarity searching to machine learning (ML). Advances in silico techniques…
\textsc{Pykat} is a Python package which extends the popular optical interferometer modelling software \textsc{Finesse}. It provides a more modern and efficient user interface for conducting complex numerical simulations, as well as…
Understanding how the brain functions is one of the biggest challenges of our time. The analysis of experimentally recorded neural firing patterns (spike trains) plays a crucial role in addressing this problem. Here, the PySpike library is…
Local governments, as part of 'smart city' initiatives and to promote interoperability, are increasingly incorporating open-source software into their data management, analysis, and visualisation workflows. Python, with its concise and…
The problem of accurately measuring the similarity between graphs is at the core of many applications in a variety of disciplines. Graph kernels have recently emerged as a promising approach to this problem. There are now many kernels, each…
A Materials Project based open-source Python tool, MPInterfaces, has been developed to automate the high-throughput computational screening and study of interfacial systems. The framework encompasses creation and manipulation of interface…
Fingerprint image quality affects heavily the performance of fingerprint recognition systems. This paper reviews existing approaches for fingerprint image quality computation. We also implement, test and compare a selection of them using…
We present nbodykit, an open-source, massively parallel Python toolkit for analyzing large-scale structure (LSS) data. Using Python bindings of the Message Passing Interface (MPI), we provide parallel implementations of many commonly used…
The proliferation of physiological sensors opens new opportunities to explore interactions, conduct experiments and evaluate the user experience with continuous monitoring of bodily functions. Commercial devices, however, can be costly or…
In response to a concerning trend of selectively emphasizing metrics in medical image segmentation (MIS) studies, we introduce \texttt{seg-metrics}, an open-source Python package for standardized MIS model evaluation. Unlike existing…
With the increased availability of rich tactile sensors, there is an equally proportional need for open-source and integrated software capable of efficiently and effectively processing raw touch measurements into high-level signals that can…