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We introduce cellanneal, a python-based software for deconvolving bulk RNA sequencing data. cellanneal relies on the optimization of Spearman's rank correlation coefficient between experimental and computational mixture gene expression…

Magpy is a C++ accelerated Python package for modelling and simulating the magnetic dynamics of nano-sized particles. Nanoparticles are modelled as a system of three-dimensional macrospins and simulated with a set of coupled stochastic…

BLASFEO is a dense linear algebra library providing high-performance implementations of BLAS- and LAPACK-like routines for use in embedded optimization. A key difference with respect to existing high-performance implementations of BLAS is…

Distributed in-memory data processing engines accelerate iterative applications by caching substantial datasets in memory rather than recomputing them in each iteration. Selecting a suitable cluster size for caching these datasets plays an…

DBSCAN is a classical density-based clustering procedure with tremendous practical relevance. However, DBSCAN implicitly needs to compute the empirical density for each sample point, leading to a quadratic worst-case time complexity, which…

We present a reduced-dimension, ballistic deposition, Monte Carlo particle packing algorithm and discuss its application to the analysis of the microstructure of hard-sphere systems with broad particle size distributions. We extend our…

We present SPEAR, an open-source python library for data programming with semi supervision. The package implements several recent data programming approaches including facility to programmatically label and build training data. SPEAR…

Good quality video coding for low bit-rate applications is important for transmission over narrow-bandwidth channels and for storage with limited memory capacity. In this work, we develop a previous analysis for image compression at low…

This document contains the mathematical introduction to RORPack - a Python software library for robust output tracking and disturbance rejection for linear PDE systems. The RORPack library is open-source and freely available at…

BayesPy is an open-source Python software package for performing variational Bayesian inference. It is based on the variational message passing framework and supports conjugate exponential family models. By removing the tedious task of…

As an alternative to variable selection or shrinkage in high dimensional regression, we propose to randomly compress the predictors prior to analysis. This dramatically reduces storage and computational bottlenecks, performing well when the…

The $\texttt{torch-choice}$ is an open-source library for flexible, fast choice modeling with Python and PyTorch. $\texttt{torch-choice}$ provides a $\texttt{ChoiceDataset}$ data structure to manage databases flexibly and…

The bootstrap is a popular and powerful method for assessing precision of estimators and inferential methods. However, for massive datasets which are increasingly prevalent, the bootstrap becomes prohibitively costly in computation and its…

The use of Bayesian adaptive designs for randomised controlled trials has been hindered by the lack of software readily available to statisticians. We have developed a new software package (Bayesian Adaptive Trials Simulator Software -…

Bayesian Optimisation (BO) refers to a suite of techniques for global optimisation of expensive black box functions, which use introspective Bayesian models of the function to efficiently search for the optimum. While BO has been applied…

We present an application, Superplot, for calculating and plotting statistical quantities relevant to parameter inference from a "chain" of samples drawn from a parameter space, produced by e.g. MultiNest. A simple graphical interface…

Binarized Neural Networks, a recently discovered class of neural networks with minimal memory requirements and no reliance on multiplication, are a fantastic opportunity for the realization of compact and energy efficient inference…

Space-filling experimental design techniques are commonly used in many computer modeling and simulation studies to explore the effects of inputs on outputs. This research presents raxpy, a Python package that leverages expressive annotation…

We present nerblackbox, a python library to facilitate the use of state-of-the-art transformer-based models for named entity recognition. It provides simple-to-use yet powerful methods to access data and models from a wide range of sources,…

Fpack is a utility program for optimally compressing images in the FITS (Flexible Image Transport System) data format (see http://fits.gsfc.nasa.gov). The associated funpack program restores the compressed image file back to its original…