Related papers: Lessons learned to boost a bioinformatics knowledg…

Although many updatable learned indexes have been proposed in recent years, whether they can outperform traditional approaches on disk remains unknown. In this study, we revisit and implement four state-of-the-art updatable learned indexes…

Motivation: The rapid growth of biological data has intensified the need for transparent, reproducible, and well-documented computational workflows. The ability to clearly connect the steps of a workflow in the code with their description…

Several methods have recently been developed for joint structure learning of multiple (related) graphical models or networks. These methods treat individual networks as exchangeable, such that each pair of networks are equally encouraged to…

With the proliferation of simple and complex bioinformatics tools, there is the need to teach researchers how to use these tools effectively. To evaluate the potential of cognitive tutoring in the wide-scale adoption of several…

Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…

Academic medical centers are generating an increasing amount of biomedical data and there is an increasing demand for biomedical data for research purposes by research projects, research consortia, companies, and other third parties. At the…

Achieving complete reproducibility in science, particularly in research fields such as biodiversity, is challenging due to analytical choices, bias and interpretation. Here, we examine examples of reproducibility in biological systematics,…

Computational reproducibility of scientific results, that is, the execution of a computational experiment (e.g., a script) using its original settings (data, code, etc.), should always be possible. However, reproducibility has become a…

This paper introduces the Bayesian Inference Engine (BIE), a general parallel, optimised software package for parameter inference and model selection. This package is motivated by the analysis needs of modern astronomical surveys and the…

Biomedical entity linking and event extraction are two crucial tasks to support text understanding and retrieval in the biomedical domain. These two tasks intrinsically benefit each other: entity linking disambiguates the biomedical…

To develop a knowledge-aware recommender system, a key data problem is how we can obtain rich and structured knowledge information for recommender system (RS) items. Existing datasets or methods either use side information from original…

Nowadays, both the amount of cyberattacks and their sophistication have considerably increased, and their prevention is of concern of most of organizations. Cooperation by means of information sharing is a promising strategy to address this…

Scientific processes rely on software as an important tool for data acquisition, analysis, and discovery. Over the years sustainable software development practices have made progress in being considered as an integral component of research.…

Here we present a holistic approach for data exploration on dense knowledge graphs as a novel approach with a proof-of-concept in biomedical research. Knowledge graphs are increasingly becoming a vital factor in knowledge mining and…

Despite remarkable technological advances, AI systems may still benefit from biological principles, such as recurrent connectivity and energy-efficient mechanisms. Drawing inspiration from the brain, we present a biologically plausible…

While several public institutions provide its data openly, the effort required to access, integrate and query this data is too high, reducing the amount of possible dataset users. The Blended Integrated Open Data (BIOD) project has as…

Reproducibility of computationally-derived scientific discoveries should be a certainty. As the product of several person-years' worth of effort, results -- whether disseminated through academic journals, conferences or exploited through…

Biodiversity data are substantially increasing, spurred by technological advances and community (citizen) science initiatives. To integrate data is, likewise, becoming more commonplace. Open science promotes open sharing and data usage.…

To promote engineering self-aware and self-adaptive software systems in a reusable manner, architectural patterns and the related methodology provide an unified solution to handle the recurring problems in the engineering process. However,…

Objective: In this study, we aim to replicate an artefact-based study on software testing to address the gap. We focus on (a) providing a step by step guide of the replication, reflecting on challenges when replicating artefact-based…