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The graphical lasso \citep{FHT2007a} is an algorithm for learning the structure in an undirected Gaussian graphical model, using $\ell_1$ regularization to control the number of zeros in the precision matrix ${\B\Theta}={\B\Sigma}^{-1}$…
Large-scale {\it in vitro} drug sensitivity screens are an important tool in personalized oncology to predict the effectiveness of potential cancer drugs. The prediction of the sensitivity of cancer cell lines to a panel of drugs is a…
Partial least squares (PLS) regression combines dimensionality reduction and prediction using a latent variable model. Since partial least squares regression (PLS-R) does not require matrix inversion or diagonalization, it can be applied to…
We present gradiend, an open-source Python package that operationalizes the GRADIEND method for learning feature directions from factual-counterfactual MLM and CLM gradients in language models. The package provides a unified workflow for…
Motivation: Model selection is a ubiquitous challenge in statistics. For penalized models, model selection typically entails tuning hyperparameters to maximize a measure of fit or minimize out-of-sample prediction error. However, these…
partycls is a Python framework for cluster analysis of systems of interacting particles. By grouping particles that share similar structural or dynamical properties, partycls enables rapid and unsupervised exploration of the system's…
The fitting or parameter estimation of complex ecological models is a challenging optimisation task, with a notable lack of tools for fitting complex, long runtime or stochastic models. calibrar is an R package that is dedicated to the…
This paper introduces ROmodel, an open source Python package extending the modeling capabilities of the algebraic modeling language Pyomo to robust optimization problems. ROmodel helps practitioners transition from deterministic to robust…
One of the most attractive features of R is its linear modeling capabilities. We describe a Python package, salmon, that brings the best of R's linear modeling functionality to Python in a Pythonic way -- by providing composable objects for…
File systems are critical OS components that require constant evolution to support new hardware and emerging application needs. However, the traditional paradigm of developing features, fixing bugs, and maintaining the system incurs…
This article describes lcpy, an open-source python package that allows for advanced parametric Life Cycle Assessment (LCA) and Life Cycle Costing (LCC) analysis. The package is designed to allow the user to model a process with a flexible,…
An algorithm implemented in an open-source python library was developed for building periodic coincidence site lattice (CSL) grain boundary models in a universal fashion. The software framework aims to generate tilt and twist grain…
The $\ell_1$-penalized method, or the Lasso, has emerged as an important tool for the analysis of large data sets. Many important results have been obtained for the Lasso in linear regression which have led to a deeper understanding of…
The generalised linear model (GLM) is a very important tool for analysing real data in biology, sociology, agriculture, engineering and many other application domain where the relationship between the response and explanatory variables may…
Efficient estimation of causal and structural parameters can be automated using the Riesz representation theorem and debiased machine learning (DML). We present genriesz, an open-source Python package that implements automatic DML and…
This paper describes a novel Python package, named causalgraph, for modeling and saving causal graphs embedded in knowledge graphs. The package has been designed to provide an interface between causal disciplines such as causal discovery…
FCMpy is an open source package in Python for building and analyzing Fuzzy Cognitive Maps. More specifically, the package allows 1) deriving fuzzy causal weights from qualitative data, 2) simulating the system behavior, 3) applying machine…
Generalized additive models for location, scale and shape (GAMLSS) are a flexible class of regression models that allow to model multiple parameters of a distribution function, such as the mean and the standard deviation, simultaneously.…
As the use of text-to-image generative models increases, so does the adoption of automatic benchmarking methods used in their evaluation. However, while metrics and datasets abound, there are few unified benchmarking libraries that provide…
Generation and analysis of time-series data is relevant to many quantitative fields ranging from economics to fluid mechanics. In the physical sciences, structures such as metastable and coherent sets, slow relaxation processes, collective…