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Statistical analysis of evolutionary-related protein sequences provides insights about their structure, function, and history. We show that Restricted Boltzmann Machines (RBM), designed to learn complex high-dimensional data and their…
Machine learning models have spread to almost every area of life. They are successfully applied in biology, medicine, finance, physics, and other fields. With modern software it is easy to train even a~complex model that fits the training…
The analysis and interpretation of relationships between biological molecules is done with the help of networks. Networks are used ubiquitously throughout biology to represent the relationships between genes and gene products. Network…
In this paper, we introduce a package for semi-supervised learning research in the R programming language called RSSL. We cover the purpose of the package, the methods it includes and comment on their use and implementation. We then show,…
Estimating sample size and statistical power is an essential part of a good study design. This R package allows users to conduct power analysis based on Monte Carlo simulations in settings in which consideration of the correlations between…
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…
Recent advancements in developing Pre-trained Language Models for Code (Code-PLMs) have urged many areas of Software Engineering (SE) and brought breakthrough results for many SE tasks. Though these models have achieved the state-of-the-art…
Probe-level models have led to improved performance in microarray studies but the various sources of probe-level contamination are still poorly understood. Data-driven analysis of probe performance can be used to quantify the uncertainty in…
Probabilistic forecasts in the form of probability distributions over future events have become popular in several fields including meteorology, hydrology, economics, and demography. In typical applications, many alternative statistical…
R is a popular language and programming environment for data scientists. It is increasingly co-packaged with both relational and Hadoop-based data platforms and can often be the most dominant computational component in data analytics…
A complete declarative description of the computational environment is often missing when researchers share their materials. Without such description, software obsolescence and missing system components can jeopardize computational…
The use of open-access software is an option that can be considered by those interested in power system studies. In addition, the combination of two or more of these tools can expand the capabilities and the fields of application of each…
This paper presents maplet, an open-source R package for the creation of highly customizable, fully reproducible statistical pipelines for omics data analysis, with a special focus on metabolomics-based methods. It builds on the…
Protein language models (PLMs) have shown promise in improving the understanding of protein sequences, contributing to advances in areas such as function prediction and protein engineering. However, training these models from scratch…
The reproducibility of scientific research has become a point of critical concern. We argue that openness and transparency are critical for reproducibility, and we outline an ecosystem for open and transparent science that has emerged…
Many interesting data sets available on the Internet are of a medium size---too big to fit into a personal computer's memory, but not so large that they won't fit comfortably on its hard disk. In the coming years, data sets of this…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
This document describes an infra-structure provided by the R package performanceEstimation that allows to estimate the predictive performance of different approaches (workflows) to predictive tasks. The infra-structure is generic in the…
Change in language use is driven by cultural forces; it is unclear whether that extends to programming languages. They are designed to be used by humans, but interaction with computer hardware rather than a human audience may limit…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…