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We present TabMixNN, a flexible PyTorch-based deep learning framework that synthesizes classical mixed-effects modeling with modern neural network architectures for tabular data analysis. TabMixNN addresses the growing need for methods that…

While early AutoML frameworks focused on optimizing traditional ML pipelines and their hyperparameters, a recent trend in AutoML is to focus on neural architecture search. In this paper, we introduce Auto-PyTorch, which brings the best of…

We present a new open source python package, based on PyLightcurve and PyTorch, tailored for efficient computation and automatic differentiation of exoplanetary transits. The classes and functions implemented are fully vectorised, natively…

PyTorch \texttt{2.x} introduces a compiler designed to accelerate deep learning programs. However, for machine learning researchers, adapting to the PyTorch compiler to full potential can be challenging. The compiler operates at the Python…

BlackJAX is a library implementing sampling and variational inference algorithms commonly used in Bayesian computation. It is designed for ease of use, speed, and modularity by taking a functional approach to the algorithms' implementation.…

In this paper, we introduce ChainerRL, an open-source deep reinforcement learning (DRL) library built using Python and the Chainer deep learning framework. ChainerRL implements a comprehensive set of DRL algorithms and techniques drawn from…

In this paper, we introduce si4onnx, a package for performing selective inference on deep learning models. Techniques such as CAM in XAI and reconstruction-based anomaly detection using VAE can be interpreted as methods for identifying…

Multivariate time series data are ubiquitous in the application of machine learning to problems in the physical sciences. Chemiresistive sensor arrays are highly promising in chemical detection tasks relevant to industrial, safety, and…

We introduce DeepDIVA: an infrastructure designed to enable quick and intuitive setup of reproducible experiments with a large range of useful analysis functionality. Reproducing scientific results can be a frustrating experience, not only…

Large language models (LLMs) have made impressive progress in chemistry applications. However, the community lacks an LLM specifically designed for chemistry. The main challenges are two-fold: firstly, most chemical data and scientific…

Prediction of toxicity levels of chemical compounds is an important issue in Quantitative Structure-Activity Relationship (QSAR) modeling. Although toxicity prediction has achieved significant progress in recent times through deep learning,…

We propose HydraScreen, a deep-learning approach that aims to provide a framework for more robust machine-learning-accelerated drug discovery. HydraScreen utilizes a state-of-the-art 3D convolutional neural network, designed for the…

Peptide classification tasks, such as predicting toxicity and HIV inhibition, are fundamental to bioinformatics and drug discovery. Traditional approaches rely heavily on handcrafted encodings of one-dimensional (1D) peptide sequences,…

CHEMSMART (Chemistry Simulation and Modeling Automation Toolkit) is an open-source, Python-based framework designed to streamline quantum chemistry workflows for homogeneous catalysis and molecular modeling. By integrating job preparation,…

In structure-based drug design, accurately estimating the binding affinity between a candidate ligand and its protein receptor is a central challenge. Recent advances in artificial intelligence, particularly deep learning, have demonstrated…

We introduce GPflux, a Python library for Bayesian deep learning with a strong emphasis on deep Gaussian processes (DGPs). Implementing DGPs is a challenging endeavour due to the various mathematical subtleties that arise when dealing with…

pyscreener is a Python library that seeks to alleviate the challenges of large-scale structure-based design using computational docking. It provides a simple and uniform interface that is agnostic to the backend docking engine with which to…

Advances in biomedicine are largely fueled by exploring uncharted territories of human biology. Machine learning can both enable and accelerate discovery, but faces a fundamental hurdle when applied to unseen data with distributions that…

In the field of chemical structure recognition, the task of converting molecular images into machine-readable data formats such as SMILES string stands as a significant challenge, primarily due to the varied drawing styles and conventions…

This paper describes a deep-SDM framework, MALPOLON. Written in Python and built upon the PyTorch library, this framework aims to facilitate training and inferences of deep species distribution models (deep-SDM) and sharing for users with…