DTiGEMS+: drug–target interaction prediction using graph embedding, graph mining, and similarity-based techniques
Open accessAbstract
In silico prediction of drug–target interactions is a critical phase in the sustainable drug development process, especially when the research focus is to capitalize on the repositioning of existing drugs. However, developing such computational methods is not an easy task, but is much needed, as current methods that predict potential drug–target interactions suffer from high false-positive rates. Here we introduce DTiGEMS+, a computational method that predicts D rug–T arget i nteractions using G raph E mbedding, graph M ining, and S imilarity-based techniques. DTiGEMS+ combines similarity-based as well as feature-based approaches, and models the identification of novel drug–target interactions as a link prediction problem in a heterogeneous network. DTiGEMS+ constructs the heterogeneous network by augmenting the known drug–target interactions graph with two other complementary graphs namely: drug–drug similarity, target–target similarity. DTiGEMS+ combines different computational techniques to provide the final drug target prediction, these techniques include graph embeddings, graph mining, and machine learning. DTiGEMS+ integrates multiple drug–drug similarities and target–target similarities into the final heterogeneous graph construction after applying a similarity selection procedure as well as a similarity fusion algorithm. Using four benchmark datasets, we show DTiGEMS+ substantially improves prediction performance compared to other state-of-the-art in silico methods developed to predict of drug-target interactions by achieving the highest average AUPR across all datasets (0.92), which reduces the error rate by 33.3% relative to the second-best performing model in the state-of-the-art methods comparison.
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- Authors
- Thafar, M. A., Olayan, R. S., Ashoor, H., Albaradei, S., Bajic, V. B., Gao, X., Gojobori, T., & Essack, M.
- Affiliations
- Taif University (SA)
- The Jackson Laboratory for Genomic Medicine (US)
- King Abdulaziz University (SA)
- King Abdullah University of Science and Technology (SA)
- Corresponding author
- Essack, Magbubah
- ORCID
- Venue
- Journal of Cheminformatics
- Published
- 2020-06-29
- Volume
- 12
- Issue
- 1
- Pages
- 44-44
- ISSN
- 1758-2946 (ISSN-L)
- PMC
- PMC7325230
- OpenAlex
- W3039465695
- Cited by
- 143
- References
- 97
- Citations by year
- 2026: 12 · 2025: 18 · 2024: 28 · 2023: 24 · 2022: 15 · 2021: 44 · 2020: 2
- FWCI
- 10.68
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Journal of Cheminformatics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology) (submittedVersion, cc-by)
- Funders
- King Abdullah University of Science and Technology (BAS/1/1606-01-01, BAS/1/1059-01-01, BAS/1/1624-01-01, FCC/1/1976-26-01, FCC/1/1976-17-01)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Computer Science › Information Systems › Recommender Systems and Techniques
- Keywords
- drug-target interaction prediction, graph embedding, graph mining, similarity-based prediction, heterogeneous networks, link prediction, drug-drug similarity, similarity fusion, drug repurposing, false positive reduction
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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