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We introduce hyppo, a unified library for performing multivariate hypothesis testing, including independence, two-sample, and k-sample testing. While many multivariate independence tests have R packages available, the interfaces are…
With the continuous rise of malicious campaigns and the exploitation of new attack vectors, it is necessary to assess the efficacy of the defensive mechanisms used to detect them. To this end, the contribution of our work is twofold. First,…
pyssam is a Python library for creating statistical shape and appearance models (SSAMs) for biological (and other) shapes such as bones, lungs or other organs. A point cloud best describing the anatomical 'landmarks' of the organ are…
Python libraries often need to maintain a stable public API even as internal implementations evolve, gain new backends, or depend on heavy optional libraries. In Python, where internal objects are easy to inspect and import, users can come…
Background and Objective: Deep learning enables tremendous progress in medical image analysis. One driving force of this progress are open-source frameworks like TensorFlow and PyTorch. However, these frameworks rarely address issues…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
Automated deidentification of clinical text data is crucial due to the high cost of manual deidentification, which has been a barrier to sharing clinical text and the advancement of clinical natural language processing. However, creating…
Missing or corrupted modalities are common in physiological signal-based medical applications owing to hardware constraints or motion artifacts. However, most existing methods assume the availability of all modalities, resulting in…
We introduce a unified Python package for the prediction of protein biophysical properties, streamlining previous tools developed by the Bio2Byte research group. This suite facilitates comprehensive assessments of protein characteristics,…
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…
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…
Active learning (AL) is a sub-field of ML focused on the development of methods to iteratively and economically acquire data by strategically querying new data points that are the most useful for a particular task. Here, we introduce…
We present a flexible, open-source Python package for the accurate simulation of the $z$-propagation dynamics of ultrashort optical pulses in nonlinear waveguides, especially valid for few-cycle pulses and their interaction. The simulation…
In this work we introduce repro_eval - a tool for reactive reproducibility studies of system-oriented information retrieval (IR) experiments. The corresponding Python package provides IR researchers with measures for different levels of…
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…
DoubleML is an open-source Python library implementing the double machine learning framework of Chernozhukov et al. (2018) for a variety of causal models. It contains functionalities for valid statistical inference on causal parameters when…
PyMilo is an open-source Python package that addresses the limitations of existing Machine Learning (ML) model storage formats by providing a transparent, reliable, and safe method for exporting and deploying trained models. Current…
PyamilySeq is a Python-based tool designed for interpretable gene clustering and pangenomic inference, supporting analyses at both species and genus levels. It facilitates the clustering of gene sequences into families based on sequence…
Information theory, i.e. the mathematical analysis of information and of its processing, has become a tenet of modern science; yet, its use in real-world studies is usually hindered by its computational complexity, the lack of coherent…
This paper presents FauxPy, a fault localization tool for Python programs. FauxPy supports seven well-known fault localization techniques in four families: spectrum-based, mutation-based, predicate switching, and stack trace fault…