DeepIDC: A Prediction Framework of Injectable Drug Combination Based on Heterogeneous Information and Deep Learning

Yuhe Yang1, Dong Gao2, Xiulan Xie2, Jiaan Qin3,4, Jian Li5, Hao Lin2, Dan Yan4,3, Kejun Deng2
1College of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
2College of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
3Beijing Friendship Hospital, Capital Medical University, Beijing, China
4Beijing Institute of Clinical Pharmacy, Beijing, China
5School of Basic Medical Science, Chengdu University, Chengdu, China

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Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012;489(7414):91–100.

He B, Lu C, Zheng G, He X, Wang M, Chen G, et al. Combination therapeutics in complex diseases. J Cell Mol Med. 2016;20(12):2231–40.

Okada Y, Wu D, Trynka G, Raj T, Terao C, Ikari K, et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature. 2014;506(7488):376.

Cheng FX, Kovacs IA, Barabasi AL. Network-based prediction of drug combinations. Nat Commun. 2019;10(1): 1197.

Jia J, Zhu F, Ma XH, Cao ZWW, Li YXX, Chen YZ. Mechanisms of drug combinations: interaction and network perspectives. Nat Rev Drug Discovery. 2009;8(2):111–28.

Juurlink DN, Mamdani M, Kopp A, Laupacis A, Redelmeier DA. Drug-drug interactions among elderly patients hospitalized for drug toxicity. Jama-J Am Med Assoc. 2003;289(13):1652–8.

Cheng FX, Zhao ZM. Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties. J Am Med Inf Assoc. 2014;21(E2):E278–86.

Wienkers LC, Heath TG. Predicting in vivo drug interactions from in vitro drug discovery data. Nat Rev Drug Discovery. 2005;4(10):825–33.

Maison O, Tardy C, Cabelguenne D, Parat S, Ducastelle S, Piriou V, et al. Drug incompatibilities in intravenous therapy: evaluation and proposition of preventive tools in intensive care and hematology units. Eur J Clin Pharmacol. 2019;75(2):179–87.

Newton DW. Drug incompatibility chemistry. Am J Health-Syst Ph. 2009;66(4):348–57.

Ryu JY, Kim HU, Lee SY. Deep learning improves prediction of drug-drug and drug-food interactions. Proc Natl Acad Sci USA. 2018;115(18):E4304–11.

Cokol M, Chua HN, Tasan M, Mutlu B, Weinstein ZB, Suzuki Y, et al. Systematic exploration of synergistic drug pairs. Mol Syst Biol. 2011;7:544.

Winter GE, Rix U, Carlson SM, Gleixner KV, Grebien F, Gridling M, et al. Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML. Nat Chem Biol. 2012;8(11):905–12.

Yu L, Xia M, An Q. A network embedding framework based on integrating multiplex network for drug combination prediction. Brief Bioinform. 2022;23(1):bbab364.

Zhang P, Wang F, Hu J, Sorrentino R. Label propagation prediction of drug-drug interactions based on clinical side effects. Sci Rep. 2015;5:12339. 

Liu S, Huang Z, Qiu Y, Chen YPP, Zhang W, editors. Structural Network Embedding using Multi-modal Deep Auto-encoders for Predicting Drug-drug Interactions. In: 2019 IEEE international conference on bioinformatics and biomedicine (BIBM); 2019 18–21 Nov. 2019. p. 445-50

Jian-Yu S, Ke G, Xue-Qun S, Siu-Ming Y, editors. LCM-DS: A novel approach of predicting drug-drug interactions for new drugs via Dempster-Shafer theory of evidence. In: 2016 IEEE international conference on bioinformatics and biomedicine (BIBM); 2016 15–18 Dec. 2016. p. 512-5

Yu H, Mao KT, Shi JY, Huang H, Chen Z, Dong K, et al. Predicting and understanding comprehensive drug-drug interactions via semi-nonnegative matrix factorization. BMC Syst Biol. 2018;12(Suppl 1):14.

Zhang W, Chen Y, Li D, Yue X. Manifold regularized matrix factorization for drug-drug interaction prediction. J Biomed Inform. 2018;88:90–7.

Gottlieb A, Stein GY, Oron Y, Ruppin E, Sharan R. INDI: a computational framework for inferring drug interactions and their associated recommendations. Mol Syst Biol. 2012;8:592.

Deng YF, Xu XR, Qiu Y, Xia JB, Zhang W, Liu SC. A multimodal deep learning framework for predicting drug-drug interaction events. Bioinformatics. 2020;36(15):4316–22.

Zhou H. Latest 450 kinds of Chinese and Western medicine injections application compatibility retrieval table. Beijing: Chinese Medical Science and Technology Press; 2013.

Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, et al. PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res. 2021;49(D1):D1388–95.

Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, et al. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 2018;46(D1):D1074–82.

Chen X, Lin Y, Liu M, Gilson MK. The Binding Database: data management and interface design. Bioinformatics. 2002;18(1):130–9.

Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1999;27(1):29–34.

Weininger D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J Chem Inf Comput Sci. 1988;28(1):31–5.

Merlot C, Domine D, Cleva C, Church DJ. Chemical substructures in drug discovery. Drug Discovery Today. 2003;8(13):594–602.

Rogers D, Hahn M. Extended-connectivity fingerprints. J Chem Inf Model. 2010;50(5):742–54.

Morgan HL. The generation of a unique machine description for chemical structures-A technique developed at chemical abstracts service. J Chem Doc. 1965;5(2):107–13.

Greg L, Paolo T, Brian K, et al. rdkit/rdkit: 2022_09_1 (Q3 2022) Release (Release_2022_09_1). Zenodo. https://doi.org/10.5281/zenodo.7235579

Bateman A, Martin MJ, Orchard S, Magrane M, Agivetova R, Ahmad S, et al. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 2021;49(D1):D480–9.

Hochreiter S, Schmidhuber J. Long short-term memory. Neural Comput. 1997;9(8):1735–80.

Srivastava N, Hinton G, Krizhevsky A, Sutskever I, Salakhutdinov R. Dropout: a simple way to prevent neural networks from overfitting. J Mach Learn Res. 2014;15:1929–58.

Fawcett T. An introduction to ROC analysis. Pattern Recogn Lett. 2006;27(8):861–74.

Drugs.com [Internet]. 2018. https://www.drugs.com/. Accessed 13 Feb 2018.

Colucci RD, Cobuzzi LE, Halpern NA. Visual compatibility of labetalol hydrochloride injection with various injectable drugs during simulated Y-site injection. Am J Hosp Pharm. 1988;45(6):1357–8.

Chandler SW, Trissel LA, Weinstein SM. Combined administration of opioids with selected drugs to manage pain and other cancer symptoms: initial safety screening for compatibility. J Pain Symptom Manage. 1996;12(3):168–71.

Smythe MA, Patel MA, Gasloli RA. Visual compatibility of narcotic analgesics with selected intravenous admixtures. Am J Hosp Pharm. 1990;47(4):819–20.

Voytilla KL, Tyler LS, Rusho WJ. Visual compatibility of azithromycin with 24 commonly used drugs during simulated Y-site delivery. Am J Health Syst Pharm. 2002;59(9):853–5.