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Polypharmacy, most often defined as the simultaneous consumption of five or more drugs at once, is a prevalent phenomenon in the older population. Some of these polypharmacies, deemed inappropriate, may be associated with adverse health…

One of the key requirements for incorporating machine learning into the drug discovery process is complete reproducibility and traceability of the model building and evaluation process. With this in mind, we have developed an end-to-end…

Graph Neural Networks (GNNs) have emerged as a structurally natural approach for molecular toxicity prediction, operating directly on atomic connectivity without the information loss inherent to fixed-length fingerprints. However, the…

Adverse drug reaction (ADR) prediction plays a crucial role in both health care and drug discovery for reducing patient mortality and enhancing drug safety. Recently, many studies have been devoted to effectively predict the drug-ADRs…

In this research, we present our work participation for the DrugProt task of BioCreative VII challenge. Drug-target interactions (DTIs) are critical for drug discovery and repurposing, which are often manually extracted from the…

In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools…

Motivation: Drug combination is a sensible strategy for disease treatment by improving the efficacy and reducing concomitant side effects. Due to the large number of possible combinations among candidate compounds, exhaustive screening is…

Of the 2652 articles considered, 106 met the inclusion criteria. Review of the included papers resulted in identification of 43 chronic diseases, which were then further classified into 10 disease categories using ICD-10. The majority of…

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph…

Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a…

Drug repurposing is an emerging approach for drug discovery involving the reassignment of existing drugs for novel purposes. An alternative to the traditional de novo process of drug development, repurposed drugs are faster, cheaper, and…

Over the years several studies have demonstrated the ability to identify potential drug-drug interactions via data mining from the literature (MEDLINE), electronic health records, public databases (Drugbank), etc. While each one of these…

Drug repositioning-a promising strategy for discovering new therapeutic uses for existing drugs-has been increasingly explored in the computational science literature using biomedical databases. However, the technological potential of drug…

Substance use, substance use disorder, and overdoses related to substance use are major public health problems globally and in the United States. A key aspect of addressing these problems from a public health standpoint is improved…

Background and Objective: It is commonly accepted that accurate monitoring of neurodegenerative diseases is crucial for effective disease management and delivery of medication and treatment. This research develops automatic clinical…

There is a growing interest in using a longitudinal observational databases to detect drug safety signal. In this paper we present a novel method, which we used online during the OMOP Cup. We consider homogeneous ensembling, which is based…

There are a few challenges related to the task of biomedical named entity recognition, which are: the existing methods consider a fewer number of biomedical entities (e.g., disease, symptom, proteins, genes); and these methods do not…

Chemical Mass Casualty Incidents (MCI) place a heavy burden on hospital staff and resources. Machine Learning (ML) tools can provide efficient decision support to caregivers. However, ML models require large volumes of data for the most…

Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. [...] Biomedical literature mining can aid DDI research by extracting relevant DDI signals from either the published literature or large clinical…

The basis of several recent methods for drug repurposing is the key principle that an efficacious drug will reverse the disease molecular 'signature' with minimal side-effects. This principle was defined and popularized by the influential…