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Bioinformatics (Oxford, England)
Sep 30, 2022
MOTIVATION: Experimental testing and manual curation are the most precise ways for assigning Gene Ontology (GO) terms describing protein functions. However, they are expensive, time-consuming and cannot cope with the exponential growth of data genera...
Bioinformatics (Oxford, England)
Sep 16, 2022
MOTIVATION: Machine-learning-based prediction of compound-protein interactions (CPIs) is important for drug design, screening and repurposing. Despite numerous recent publication with increasing methodological sophistication claiming consistent impro...
Bioinformatics (Oxford, England)
Sep 16, 2022
MOTIVATION: The tremendous success of graphical neural networks (GNNs) already had a major impact on systems biology research. For example, GNNs are currently being used for drug target recognition in protein-drug interaction networks, as well as for...
Bioinformatics (Oxford, England)
Sep 16, 2022
SUMMARY: Recently, deep learning models, initially developed in the field of natural language processing (NLP), were applied successfully to analyze protein sequences. A major drawback of these models is their size in terms of the number of parameter...
Bioinformatics (Oxford, England)
Sep 15, 2022
MOTIVATION: Approaches for the diagnosis and treatment of diseases often adopt the multidrug therapy method because it can increase the efficacy or reduce the toxic side effects of drugs. Using different drugs simultaneously may trigger unexpected ph...
Bioinformatics (Oxford, England)
Sep 15, 2022
MOTIVATION: Recent development of deep-learning methods has led to a breakthrough in the prediction accuracy of 3D protein structures. Extending these methods to protein pairs is expected to allow large-scale detection of protein-protein interactions...
Bioinformatics (Oxford, England)
Sep 15, 2022
MOTIVATION: Knowing the sensitivity of a viral strain versus a monoclonal antibody is of interest for HIV vaccine development and therapy. The HIV strains vary in their resistance to antibodies, and the accurate prediction of virus-antibody sensitivi...
Bioinformatics (Oxford, England)
Sep 15, 2022
MOTIVATION: Biomedical machine reading comprehension (biomedical-MRC) aims to comprehend complex biomedical narratives and assist healthcare professionals in retrieving information from them. The high performance of modern neural network-based MRC sy...
Bioinformatics (Oxford, England)
Sep 15, 2022
MOTIVATION: Genome sequencing experiments have revolutionized molecular biology by allowing researchers to identify important DNA-encoded elements genome wide. Regions where these elements are found appear as peaks in the analog signal of an assay's ...
Bioinformatics (Oxford, England)
Sep 2, 2022
MOTIVATION: Existing computational models can predict single- and double-mutant fitness but they do have limitations. First, they are often tested via evaluation metrics that are inappropriate for imbalanced datasets. Second, all of them only predict...