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Cited by 8Computational Drug Discovery MethodsBiomedical Text Mining and OntologiesBioinformatics and Genomic Networks

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A drug repositioning algorithm based on a deep autoencoder and adaptive fusion

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Chen, Peng, Bao, Tianjiazhi, Yu, Xiaosheng, Liu, Zhongtu·2021·BMC Bioinformatics
DOI 10.1186/s12859-021-04406-yPMC PMC8556784
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Abstract

Background: Drug repositioning has caught the attention of scholars at home and abroad due to its effective reduction of the development cost and time of new drugs. However, existing drug repositioning methods that are based on computational analysis are limited by sparse data and classic fusion methods; thus, we use autoencoders and adaptive fusion methods to calculate drug repositioning. Results: In this study, a drug repositioning algorithm based on a deep autoencoder and adaptive fusion was proposed to mitigate the problems of decreased precision and low-efficiency multisource data fusion caused by data sparseness. Specifically, a drug is repositioned by fusing drug-disease associations, drug target proteins, drug chemical structures and drug side effects. First, drug feature data integrated by drug target proteins and chemical structures were processed with dimension reduction via a deep autoencoder to characterize feature representations more densely and abstractly. Then, disease similarity was computed using drug-disease association data, while drug similarity was calculated with drug feature and drug-side effect data. Predictions of drug-disease associations were also calculated using a top-k neighbor method that is commonly used in predictive drug repositioning studies. Finally, a predicted matrix for drug-disease associations was acquired after fusing a wide variety of data via adaptive fusion. Based on experimental results, the proposed algorithm achieves a higher precision and recall rate than the DRCFFS, SLAMS and BADR algorithms with the same dataset. Conclusion: The proposed algorithm contributes to investigating the novel uses of drugs, as shown in a case study of Alzheimer's disease. Therefore, the proposed algorithm can provide an auxiliary effect for clinical trials of drug repositioning.

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Crossref · 10.1186/s12859-021-04406-y

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Fig. 1 Framework of the drug repositioning algorithm based on a deep autoencoder and adaptive fusion, including four types of origin data and three types of data for experiments
Fig. 1 Framework of the drug repositioning algorithm based on a deep autoencoder and adaptive fusion, including four types of origin data and three types of data for experimentsCC BY · PubMed Central
Fig. 2 A schematic diagram of a deep autoencoder framework for drug feature data dimensionality reduction. There are two sections in the overall structure: the encoder, and the decoder. The encoder contains four layers: an input layer, two building layers and an encoding layer. The decoder includes four layers: an encoding layer, two building layers, and an output layer. The building layer is composed of a dense and dropout layer
Fig. 2 A schematic diagram of a deep autoencoder framework for drug feature data dimensionality reduction. There are two sections in the overall structure: the encoder, and the decoder. The encoder contains four layers: an input layer, two building layers and an encoding layer. The decoder includes four layers: an encoding layer, two building layers, and an output layer. The building layer is composed of a dense and dropout layerCC BY · PubMed Central
Fig. 3 Sigmoid function image
Fig. 3 Sigmoid function imageCC BY · PubMed Central
Fig. 4 The number of diseases that can be treated by each drug in the drug-disease associated data
Fig. 4 The number of diseases that can be treated by each drug in the drug-disease associated dataCC BY · PubMed Central
Fig. 5 Changes in the AUCs of the three data sources with different numbers of neighbors (30–120). Via comparison, we find that although the AUC values of three data sources are the highest under 30 neighbors, drug repositioning is a prediction task rather than a simple classification task, and we need more neighbors to provide information. Thus, we choose 50 as the number of neighbors
Fig. 5 Changes in the AUCs of the three data sources with different numbers of neighbors (30–120). Via comparison, we find that although the AUC values of three data sources are the highest under 30 neighbors, drug repositioning is a prediction task rather than a simple classification task, and we need more neighbors to provide information. Thus, we choose 50 as the number of neighborsCC BY · PubMed Central
Fig. 6 a PR curves of the DRDA algorithm and the other three algorithms. The PR curve of DRDA wraps the PR curves of the other three algorithms; thus, the effect is the best. b ROC of the four algorithms. Comparing the curve and AUC value, DADR and DRCFFS have the best effect
Fig. 6 a PR curves of the DRDA algorithm and the other three algorithms. The PR curve of DRDA wraps the PR curves of the other three algorithms; thus, the effect is the best. b ROC of the four algorithms. Comparing the curve and AUC value, DADR and DRCFFS have the best effectCC BY · PubMed Central
Fig. 7 a Correct prediction of the drug-disease associated number with known treatment relationships for the four algorithms at different thresholds. b Proportion of the number of drug-disease associations correctly predicted by the four algorithms with known treatment relationships at different thresholds to all drug-disease with known treatment relationships
Fig. 7 a Correct prediction of the drug-disease associated number with known treatment relationships for the four algorithms at different thresholds. b Proportion of the number of drug-disease associations correctly predicted by the four algorithms with known treatment relationships at different thresholds to all drug-disease with known treatment relationshipsCC BY · PubMed Central

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Citations

Cites

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Metadata

Authors
Chen, P., Bao, T., Yu, X., & Liu, Z.
Affiliations
China Three Gorges University (CN)
Corresponding author
Liu, Zhongtu
ORCID
Venue
BMC Bioinformatics
Publisher
Springer Science and Business Media LLC
Published
2021-10-30
Volume
22
Issue
1
Pages
532-532
ISSN
1471-2105 (ISSN-L)
DOI
10.1186/s12859-021-04406-y
PMC
PMC8556784
OpenAlex
W3116547330
Cited by
8
References
2
Citations by year
2026: 2 · 2025: 3 · 2023: 3
FWCI
1.05
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Bioinformatics (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • The National Key Research and Development Program of China (2016YFC0802500)
  • Research Fund for Excellent Dissertation of China Three Gorges University (2020SSPY075)
Topics
  • Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
  • Health Sciences › Medicine › Health Informatics › Biomedical Text Mining and Ontologies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
drug repurposing, deep autoencoder, adaptive fusion, multi-source data fusion, drug-disease association prediction, drug target proteins, drug chemical structure, adverse drug reactions, disease similarity, drug similarity, Alzheimer's disease, data sparsity
MeSH terms
Algorithms, Alzheimer Disease, Humans, Computational Biology, Drug Repositioning, Drug-Related Side Effects and Adverse Reactions

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