Related papers: Asterias: a parallelized web-based suite for the a…

Gene innovation is a key mechanism on the evolution and phenotypic diversity of life forms. There is a need for tools able to study gene innovation across an increasingly large number of genomic sequences to maximally capitalise our…

Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene…

The ever increasing complexity of machine learning techniques used more and more in practice, gives rise to the need to explain the predictions and decisions of these models, often used as black-boxes. Explainable AI approaches are either…

Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…

The complex and computationally expensive nature of landscape evolution models pose significant challenges in the inference and optimisation of unknown parameters. Bayesian inference provides a methodology for estimation and uncertainty…

Data sharing ecosystems connect providers, consumers, and intermediaries to facilitate the exchange and use of data for a wide range of downstream tasks. In sensitive domains such as healthcare, privacy is enforced as a hard constraint, any…

Gene expression is significantly stochastic making modeling of genetic networks challenging. We present an approximation that allows the calculation of not only the mean and variance but also the distribution of protein numbers. We assume…

Gaussian processes are a class of flexible nonparametric Bayesian tools that are widely used across the sciences, and in industry, to model complex data sources. Key to applying Gaussian process models is the availability of well-developed…

We demonstrate MaskSearch, a system designed to accelerate queries over databases of image masks generated by machine learning models. MaskSearch formalizes and accelerates a new category of queries for retrieving images and their…

Transparent and standardized documentation is essential for building trustworthy generative AI (GAI) systems. However, existing automated methods for generating model and data cards still face three major challenges: (i) static templates,…

We present an online parallel portfolio selection algorithm based on the island model commonly used for parallelization of evolutionary algorithms. In our case each of the islands runs a different optimization algorithm. The distributed…

Genetic algorithms, computer programs that simulate natural evolution, are increasingly applied across many disciplines. They have been used to solve various optimisation problems from neural network architecture search to strategic games,…

Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…

The apsis toolkit presented in this paper provides a flexible framework for hyperparameter optimization and includes both random search and a bayesian optimizer. It is implemented in Python and its architecture features adaptability to any…

AI coding assistants like GitHub Copilot are rapidly transforming software development, but their safety remains deeply uncertain-especially in high-stakes domains like cybersecurity. Current red-teaming tools often rely on fixed benchmarks…

Cluster analysis of biological samples using gene expression measurements is a common task which aids the discovery of heterogeneous biological sub-populations having distinct mRNA profiles. Several model-based clustering algorithms have…

Evaluating retrieval-augmented generation (RAG) systems traditionally relies on hand annotations for input queries, passages to retrieve, and responses to generate. We introduce ARES, an Automated RAG Evaluation System, for evaluating RAG…

A freely available educational application (a mobile website) is presented. This provides access to educational material and drilling on selected topics within mathematics and statistics with an emphasis on tablets and mobile phones. The…

Detecting parallelizable code regions is a challenging task, even for experienced developers. Numerous recent studies have explored the use of machine learning for code analysis and program synthesis, including parallelization, in light of…

Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or Protein Data Bank (PDB) files, or manual sequence entry, and…