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OpenML is an online machine learning platform where researchers can easily share data, machine learning tasks and experiments as well as organize them online to work and collaborate more efficiently. In this paper, we present an R package…

GenoML is a Python package automating machine learning workflows for genomics (genetics and multi-omics) with an open science philosophy. Genomics data require significant domain expertise to clean, pre-process, harmonize and perform…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene…

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded…

In recent years, the concept of automated machine learning has become very popular. Automated Machine Learning (AutoML) mainly refers to the automated methods for model selection and hyper-parameter optimization of various algorithms such…

XML stands for the Extensible Markup Language. It is a markup language for documents, Nowadays XML is a tool to develop and likely to become a much more common tool for sharing data and store. XML can communicate structured information to…

Due to their flexibility and superior performance, machine learning models frequently complement and outperform traditional statistical survival models. However, their widespread adoption is hindered by a lack of user-friendly tools to…

RNA-Seq analysis has revolutionized researchers' understanding of the transcriptome in biological research. Assessing the differences in transcriptomic profiles between tissue samples or patient groups enables researchers to explore the…

In this paper, we introduce XGLUE, a new benchmark dataset that can be used to train large-scale cross-lingual pre-trained models using multilingual and bilingual corpora and evaluate their performance across a diverse set of cross-lingual…

In this paper we describe the main featuress of the Bergm package for the open-source R software which provides a comprehensive framework for Bayesian analysis for exponential random graph models: tools for parameter estimation, model…

The rise of the programmable web offers new opportunities for the empirically driven social sciences. The access, compilation and preparation of data from the programmable web for statistical analysis can, however, involve substantial…

Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, non-standardized spreadsheets, or data repositories. This lack of structure challenges…

In this paper, we describe the Rich Representation Language (RRL) which is used in the NECA system. The NECA system generates interactions between two or more animated characters. The RRL is an XML compliant framework for representing the…

The majority of automated machine learning (AutoML) solutions are developed in Python, however a large percentage of data scientists are associated with the R language. Unfortunately, there are limited R solutions available. Moreover high…

1. A hard stop for the implementation of rigorous conservation initiatives is our lack of key species data, especially occurrence data. Furthermore, researchers have to contend with an accelerated speed at which new information must be…

Dynamically typed programming languages like R allow programmers to write generic, flexible and concise code and to interact with the language using an interactive Read-eval-print-loop (REPL). However, this flexibility has its price: As the…

BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these…

Retrieval-augmented large language models (R-LLMs) combine pre-trained large language models (LLMs) with information retrieval systems to improve the accuracy of factual question-answering. However, current libraries for building R-LLMs…

With growing exchanges of people and merchandise between countries, epidemics have become an issue of increasing importance and huge amounts of data are being collected every day. Hence, analyses that were usually run in personal computers…

Interoperability of potentially heterogeneous databases has been an ongoing research issue for a number of years in the database community. With the trend towards globalization of data location and data access and the consequent requirement…