Related papers: Assigning function to protein-protein interactions…
Domain adaptation is a widely used method in natural language processing (NLP) to improve the performance of a language model within a specific domain. This method is particularly common in the biomedical domain, which sees regular…
This paper presents our participation in the AGAC Track from the 2019 BioNLP Open Shared Tasks. We provide a solution for Task 3, which aims to extract "gene - function change - disease" triples, where "gene" and "disease" are mentions of…
Assessing journal impact is central to scholarly communication, yet existing open resources rarely capture how collaboration structures and artificial intelligence (AI) research jointly shape venue prestige in biomedicine. We present…
Protein interaction networks (PINs) are often used to "learn" new biological function from their topology. Since current PINs are noisy, their computational de-noising via link prediction (LP) could improve the learning accuracy. LP uses…
Developing and discovering new drugs is a complex and resource-intensive endeavor that often involves substantial costs, time investment, and safety concerns. A key aspect of drug discovery involves identifying novel drug-target (DT)…
While most studies emphasize on certain aspects of Pathogen-Host Interactions (PHI), such as the preferential attachment of bacteria or virus to its human receptor homolog, studies have attempted to methodically classify interactions among…
Protein-protein interaction (PPI) networks have been used to investigate the influence of SARS-CoV-2 viral proteins on the function of human cells, laying out a deeper understanding of COVID--19 and providing ground for drug repurposing…
Dietary supplements are used by a large portion of the population, but information on their pharmacologic interactions is incomplete. To address this challenge, we present SUPP.AI, an application for browsing evidence of supplement-drug…
Predicting interactions between proteins is one of the most important yet challenging problems in structural bioinformatics. Intrinsically, potential function sites in protein surfaces are determined by both geometric and chemical features.…
Prediction of protein-ligand interactions (PLI) plays a crucial role in drug discovery as it guides the identification and optimization of molecules that effectively bind to target proteins. Despite remarkable advances in deep…
Proteins execute various activities required by biological cells. Further, they structurally support and pro-mote important biochemical reactions which functionally are sparked by active-sites. Active-sites are regions where reac-tions and…
Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has…
Knowledge of a disease includes information of various aspects of the disease, such as signs and symptoms, diagnosis and treatment. This disease knowledge is critical for many health-related and biomedical tasks, including consumer health…
Information Retrieval (IR) is the task of obtaining pieces of data (such as documents) that are relevant to a particular query or need from a large repository of information. IR is a valuable component of several downstream Natural Language…
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Due to the limitation of the previous database, especially…
The rapid growth in the number of experimental and predicted protein structures and more complicated protein structures challenge users in computational biology for utilizing the structural information and protein surface property…
Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained…
Protein-protein interactions (PPIs) are governed by surface complementarity and hydrophobic interactions at protein interfaces. However, designing diverse and physically realistic protein structure and surfaces that precisely complement…
Biomedical event extraction is an information extraction task to obtain events from biomedical text, whose targets include the type, the trigger, and the respective arguments involved in an event. Traditional biomedical event extraction…
Drug-drug interaction (DDI) is a vital information when physicians and pharmacists intend to co-administer two or more drugs. Thus, several DDI databases are constructed to avoid mistakenly combined use. In recent years, automatically…