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Applications are increasingly written as dynamic workflows underpinned by an execution framework that manages asynchronous computations across distributed hardware. However, execution frameworks typically offer one-size-fits-all solutions…

We introduce \texttt{pycobra}, a Python library devoted to ensemble learning (regression and classification) and visualisation. Its main assets are the implementation of several ensemble learning algorithms, a flexible and generic interface…

We introduce rLLM (relationLLM), a PyTorch library designed for Relational Table Learning (RTL) with Large Language Models (LLMs). The core idea is to decompose state-of-the-art Graph Neural Networks, LLMs, and Table Neural Networks into…

We introduce TurboGP, a Genetic Programming (GP) library fully written in Python and specifically designed for machine learning tasks. TurboGP implements modern features not available in other GP implementations, such as island and cellular…

Data grid replication is an effective method to achieve efficient and fault tolerant data access while reducing access latency and bandwidth consumption in grids. Since we have storage limitation, a replica should be created in the best…

Tuning hyperparameters for machine learning algorithms is a tedious task, one that is typically done manually. To enable automated hyperparameter tuning, recent works have started to use techniques based on Bayesian optimization. However,…

We introduce Trove, an easy-to-use open-source retrieval toolkit that simplifies research experiments without sacrificing flexibility or speed. For the first time, we introduce efficient data management features that load and process…

We introduce phylodyn, an R package for phylodynamic analysis based on gene genealogies. The package main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes…

DORAEMON is an open-source PyTorch library that unifies visual object modeling and representation learning across diverse scales. A single YAML-driven workflow covers classification, retrieval and metric learning; more than 1000 pretrained…

Phylogenetics is a classical methodology in computational biology that today has become highly relevant for medical investigation of single-cell data, e.g., in the context of cancer development. The exponential size of the tree space is,…

We present PhasorFlow, an open-source Python library introducing a computational paradigm operating on the $S^1$ unit circle. Inputs are encoded as complex phasors $z = e^{i\theta}$ on the $N$-Torus ($\mathbb{T}^N$). As computation proceeds…

Ordered (key-value) maps are an important and widely-used data type for large-scale data processing frameworks. Beyond simple search, insertion and deletion, more advanced operations such as range extraction, filtering, and bulk updates…

Models can be built directly from input and output data trough a process known as system identification. The Nonlinear AutoRegressive with eXogenous inputs (NARMAX) models are among the most used mathematical representations in the area and…

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…

The Grid Datafarm architecture is designed for global petascale data-intensive computing. It provides a global parallel filesystem with online petascale storage, scalable I/O bandwidth, and scalable parallel processing, and it can exploit…

PyArmadillo is a linear algebra library for the Python language, with the aim of closely mirroring the programming interface of the widely used Armadillo C++ library, which in turn is deliberately similar to Matlab. PyArmadillo hence…

RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficiently exploited by graph theoretical approaches and recent…

This paper describes HyperStream, a large-scale, flexible and robust software package, written in the Python language, for processing streaming data with workflow creation capabilities. HyperStream overcomes the limitations of other…

The challenges in feature selection, particularly in balancing model accuracy, interpretability, and computational efficiency, remain a critical issue in advancing machine learning methodologies. To address these complexities, this study…

We introduce Tree-AMP, standing for Tree Approximate Message Passing, a python package for compositional inference in high-dimensional tree-structured models. The package provides a unifying framework to study several approximate message…