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Gradient Boosting Decision Tree-Based Method for Predicting Interactions Between Target Genes and Drugs
Open accessAbstract
Determining the target genes that interact with drugs—drug–target interactions—plays an important role in drug discovery. Identification of drug–target interactions through biological experiments is time consuming, laborious, and costly. Therefore, using computational approaches to predict candidate targets is a good way to reduce the cost of wet-lab experiments. However, the known interactions (positive samples) and the unknown interactions (negative samples) display a serious class imbalance, which has an adverse effect on the accuracy of the prediction results. To mitigate the impact of class imbalance and completely exploit the negative samples, we proposed a new method, named DTIGBDT, based on gradient boosting decision trees, for predicting candidate drug–target interactions. We constructed a drug–target heterogeneous network that contains the drug similarities based on the chemical structures of drugs, the target similarities based on target sequences, and the known drug–target interactions. The topological information of the network was captured by random walks to update the similarities between drugs or targets. The paths between drugs and targets could be divided into multiple categories, and the features of each category of paths were extracted. We constructed a prediction model based on gradient boosting decision trees. The model establishes multiple decision trees with the extracted features and obtains the interaction scores between drugs and targets. DTIGBDT is a method of ensemble learning, and it effectively reduces the impact of class imbalance. The experimental results indicate that DTIGBDT outperforms several state-of-the-art methods for drug–target interaction prediction. In addition, case studies on Quetiapine, Clozapine, Olanzapine, Aripiprazole, and Ziprasidone demonstrate the ability of DTIGBDT to discover potential drug–target interactions.
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“When compared to other GBM algorithms, XGBoost provides regularized boosting, helping to reduce overfitting with more generalizable results (Torlay et al., 2017; Xuan et al., 2019).”
From Multiclass characterization of frontotemporal dementia variants via multimodal brain network computational inference (2023) · cites this paper as Xuan et al., 2019
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Metadata
- Authors
- Xuan, P., Sun, C., Zhang, T., Ye, Y., Shen, T., & Dong, Y.
- Affiliations
- Heilongjiang University (CN)
- Corresponding author
- Sun, Chang
- Zhang, Tiangang
- Venue
- Frontiers in Genetics
- Publisher
- Frontiers Media SA
- Published
- 2019-05-31
- Volume
- 10
- Pages
- 459-459
- ISSN
- 1664-8021 (ISSN-L)
- PMC
- PMC6555260
- OpenAlex
- W2946853220
- Cited by
- 100
- References
- 78
- Citations by year
- 2026: 7 · 2025: 16 · 2024: 8 · 2023: 19 · 2022: 18 · 2021: 17 · 2020: 11 · 2019: 4
- FWCI
- 8.50
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Natural Science Foundation of China (61702296, 61302139)
- Natural Science Foundation of Heilongjiang Province (LH2019F049, LH2019A029)
- Topics
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- drug-target interaction prediction, gradient boosting decision tree, class imbalance, random walks, ensemble learning, antipsychotic drugs, drug discovery
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