Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Conference Object Citation - Scopus: 1Drug Repositioning via Entity Transformation in Biomedical Knowledge Systems(Springer Science and Business Media Deutschland GmbH, 2025) Erkantarci, B.; Bakal, G.The drug discovery process for known diseases is crucial in bioinformatics, given the extensive clinical trials, regulatory approvals, and high costs. Computational in silico methods are essential to mitigate these challenges, as they help identify promising drug candidates, thereby reducing the time and cost associated with drug discovery. An effective strategy in this domain is drug repositioning, where existing drugs, already approved for one disease, are repurposed for treating another. This approach is advantageous as it leverages the established safety profiles of existing drugs, avoiding toxic effects on human metabolism. In this effort, we employed a translational entity embedding-based neural network model to advance drug repositioning efforts. We utilize the Semantic Medline Database (SemMedDB) as the primary source of biomedical entity relationships for model training. The model is validated using repoDB, a gold standard dataset for drug repositioning. Technically, the model will learn to minimize the vector distance between related entities. This distance will serve as the basis for predicting potential drug-disease pairs in drug repositioning, offering a novel computational method to expedite the drug discovery process. © 2025 Elsevier B.V., All rights reserved.Conference Object Citation - Scopus: 3A Computational Drug Repositioning Effort Using Patients' Reviews Dataset(Institute of Electrical and Electronics Engineers Inc., 2023-07-25) Akkaya, Ali; Bakal, GokhanThe drug discovery process is one of the core motivations in both medical and, specifically, pharmaceutical disciplines. Due to the nature of the process, it requires an excessive amount of time, clinical experiments, and budget to cover each discovery phase. In this sense, computational drug discovery efforts can shorten the discovery process by providing plausible candidates since many of the attempts fail for several reasons, such as a lack of participants, financial problems, or ineffective results. In this study, the goal is to identify plausible candidate drugs for diseases. To do that, we utilize a personal experience of drugs dataset generated by patients. Beyond the user-generated comments, the users also give a rate between 1 and 10. Since we want to ensure the dataset quality, we first performed sentiment analysis experiments to prove that the reviews/comments are consistent with the given rating score. Then, only the review pairs having an effectiveness rate of 6 or more are selected as pre-filtered drug-disease pairs. We also build a knowledge graph using treatment-related biomedical relations using predications from Semantic Medline Database to identify drug similarities utilizing the Simrank similarity algorithm. As a result, we reported a list of plausible drugs as repurposing/repositioning candidates for further experiments. © 2023 Elsevier B.V., All rights reserved.