Current Medicinal Chemistry

Author(s): Zheng Peng, Yanling Ding, Pengfei Zhang, Xiaolan Lv, Zepeng Li*, Xiaoling Zhou* and Shigao Huang*

DOI: 10.2174/0109298673290777240301071513

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Artificial Intelligence Application for Anti-tumor Drug Synergy Prediction

Page: [6572 - 6585] Pages: 14

  • * (Excluding Mailing and Handling)

Abstract

Currently, the main therapeutic methods for cancer include surgery, radiation therapy, and chemotherapy. However, chemotherapy still plays an important role in tumor therapy. Due to the variety of pathogenic factors, the development process of tumors is complex and regulated by many factors, and the treatment of a single drug is easy to cause the human body to produce a drug-resistant phenotype to specific drugs and eventually leads to treatment failure. In the process of clinical tumor treatment, the combination of multiple drugs can produce stronger anti-tumor effects by regulating multiple mechanisms and can reduce the problem of tumor drug resistance while reducing the toxic side effects of drugs. Therefore, it is still a great challenge to construct an efficient and accurate screening method that can systematically consider the synergistic anti- tumor effects of multiple drugs. However, anti-tumor drug synergy prediction is of importance in improving cancer treatment outcomes. However, identifying effective drug combinations remains a complex and challenging task. This review provides a comprehensive overview of cancer drug synergy therapy and the application of artificial intelligence (AI) techniques in cancer drug synergy prediction. In addition, we discuss the challenges and perspectives associated with deep learning approaches. In conclusion, the review of the AI techniques' application in cancer drug synergy prediction can further advance our understanding of cancer drug synergy and provide more effective treatment plans and reasonable drug use strategies for clinical guidance.

Keywords: Artificial intelligence, anti-cancer drug, prediction model, synergy effect, multi-drug combinations, chemotherapy.

[1]
Siegel, R.L.; Miller, K.D.; Fuchs, H.E.; Jemal, A. Cancer statistics, 2022. CA Cancer J. Clin., 2022, 72(1), 7-33.
[http://dx.doi.org/10.3322/caac.21708] [PMID: 35020204]
[2]
Huang, S.; Yang, J.; Fong, S.; Zhao, Q. Artificial intelligence in the diagnosis of COVID-19: Challenges and perspectives. Int. J. Biol. Sci., 2021, 17(6), 1581-1587.
[http://dx.doi.org/10.7150/ijbs.58855] [PMID: 33907522]
[3]
Huang, S.; Yang, J.; Shen, N.; Xu, Q.; Zhao, Q. Artificial intelligence in lung cancer diagnosis and prognosis: Current application and future perspective. Semin. Cancer Biol., 2023, 89, 30-37.
[http://dx.doi.org/10.1016/j.semcancer.2023.01.006] [PMID: 36682439]
[4]
Yue, H.; Yu, Q.; Liu, C.; Huang, Y.; Jiang, Z.; Shao, C.; Zhang, H.; Ma, B.; Wang, Y.; Xie, G.; Zhang, H.; Li, X.; Kang, N.; Meng, X.; Huang, S.; Xu, D.; Lei, J.; Huang, H.; Yang, J.; Ji, J.; Pan, H.; Zou, S.; Ju, S.; Qi, X. Machine learning-based CT radiomics method for predicting hospital stay in patients with pneumonia associated with SARS-CoV-2 infection: A multicenter study. Ann. Transl. Med., 2020, 8(14), 859.
[http://dx.doi.org/10.21037/atm-20-3026] [PMID: 32793703]
[5]
Zhang, J.; Huang, S.; Xu, Y.; Wu, J. Diagnostic accuracy of artificial intelligence based on imaging data for preoperative prediction of microvascular invasion in hepatocellular carcinoma: A systematic review and meta-analysis. Front. Oncol., 2022, 12, 763842.
[http://dx.doi.org/10.3389/fonc.2022.763842] [PMID: 35280776]
[6]
Huang, S.; Yang, J.; Fong, S.; Zhao, Q. Artificial intelligence in cancer diagnosis and prognosis: Opportunities and challenges. Cancer Lett., 2020, 471, 61-71.
[http://dx.doi.org/10.1016/j.canlet.2019.12.007] [PMID: 31830558]
[7]
Preuer, K.; Lewis, R.P.I.; Hochreiter, S.; Bender, A.; Bulusu, K.C.; Klambauer, G. DeepSynergy: Predicting anti-cancer drug synergy with Deep Learning. Bioinformatics, 2018, 34(9), 1538-1546.
[http://dx.doi.org/10.1093/bioinformatics/btx806] [PMID: 29253077]
[8]
Pein, F.; Pinkerton, R.; Berthaud, P.; Jones, P.K.; Dick, G.; Vassal, G. Dose finding study of oral PSC 833 combined with weekly intravenous etoposide in children with relapsed or refractory solid tumours. Eur. J. Cancer, 2007, 43(14), 2074-2081.
[http://dx.doi.org/10.1016/j.ejca.2007.07.003] [PMID: 17716890]
[9]
Dziadziuszko, R.; Cabanas, G.E.; Rojas, K.; Chelstowska, M.; Blaszkowska, M.; Dudziak, R.; Rzymski, T.; Angelosanto, N.; Littlewood, P.; Nogai, H.; Boni, V.; Lugowska, I. Phase I/II trial of RVU120, a CDK8/CDK19 inhibitor in patients with relapsed/refractory metastatic or advanced solid tumors. Eur. J. Cancer, 2022, 174, S23-S23.
[http://dx.doi.org/10.1016/S0959-8049(22)00865-6]
[10]
Macy, M.; Cash, T.; Pinto, N.; Pressey, J.G.; Szalontay, L.; Furman, W.L.; Bukowinski, A.; Foster, J.H.; Friedman, G.K.; HaDuong, J.; Fox, E.; Weigel, B.J.; Grevel, J.; Huang, F.; Phelps, C.; Childs, B.H.; Chung, J.; Chaturvedi, S.; Schulz, A.; DuBois, S.G. Phase I dose-escalation study of the pan-PI3 K inhibitor copanlisib in children and adolescents with relapsed/refractory solid tumors. Eur. J. Cancer, 2022, 174, S28-S29.
[http://dx.doi.org/10.1016/S0959-8049(22)00878-4]
[11]
Nagao, K.; Maeda, M.; Mañucat, N.B.; Ueda, K. Cyclosporine A and PSC833 inhibit ABCA1 function via direct binding. Biochim. Biophys. Acta Mol. Cell Biol. Lipids, 2013, 1831(2), 398-406.
[http://dx.doi.org/10.1016/j.bbalip.2012.11.002] [PMID: 23153588]
[12]
Awada, A.; Cortés, J.; Martín, M.; Aftimos, P.; Oliveira, M.; Tarruella, L.S.; Espie, M.; Lardelli, P.; Extremera, S.; García, F.E.M.; Delaloge, S. Phase 2 study of trabectedin in patients with hormone receptor–positive, HER-2–negative, advanced breast carcinoma according to expression of xeroderma pigmentosum G gene. Clin. Breast Cancer, 2016, 16(5), 364-371.
[http://dx.doi.org/10.1016/j.clbc.2016.05.005] [PMID: 27266804]
[13]
Liu, Y.Y.; Han, T.Y.; Giuliano, A.E.; Hansen, N.; Cabot, M.C. Uncoupling ceramide glycosylation by transfection of glucosylceramide synthase antisense reverses adriamycin resistance. J. Biol. Chem., 2000, 275(10), 7138-7143.
[http://dx.doi.org/10.1074/jbc.275.10.7138] [PMID: 10702281]
[14]
van Vlerken, L.E.; Duan, Z.; Seiden, M.V.; Amiji, M.M. Modulation of intracellular ceramide using polymeric nanoparticles to overcome multidrug resistance in cancer. Cancer Res., 2007, 67(10), 4843-4850.
[http://dx.doi.org/10.1158/0008-5472.CAN-06-1648] [PMID: 17510414]
[15]
Maheshwari, R.; Tekade, M.; Gondaliya, P.; Kalia, K.; D’Emanuele, A.; Tekade, R.K. Recent advances in exosome-based nanovehicles as RNA interference therapeutic carriers. Nanomedicine, 2017, 12(21), 2653-2675.
[http://dx.doi.org/10.2217/nnm-2017-0210] [PMID: 28960165]
[16]
Mizrahy, S.; Halevy, H.I.; Dammes, N.; Milo, L.D.; Peer, D. Current progress in non-viral RNAi-based delivery strategies to lymphocytes. Mol. Ther., 2017, 25(7), 1491-1500.
[http://dx.doi.org/10.1016/j.ymthe.2017.03.001] [PMID: 28392163]
[17]
Weinstein, S.; Toker, I.A.; Emmanuel, R.; Ramishetti, S.; Hazan-Halevy, I.; Rosenblum, D.; Goldsmith, M.; Abraham, A.; Benjamini, O.; Bairey, O.; Raanani, P.; Nagler, A.; Lieberman, J.; Peer, D. Harnessing RNAi-based nanomedicines for therapeutic gene silencing in B-cell malignancies. Proc. Natl. Acad. Sci., 2016, 113(1), E16-E22.
[http://dx.doi.org/10.1073/pnas.1519273113] [PMID: 26699502]
[18]
Meng, H.; Liong, M.; Xia, T.; Li, Z.; Ji, Z.; Zink, J.I.; Nel, A.E. Engineered design of mesoporous silica nanoparticles to deliver doxorubicin and P-glycoprotein siRNA to overcome drug resistance in a cancer cell line. ACS Nano, 2010, 4(8), 4539-4550.
[http://dx.doi.org/10.1021/nn100690m] [PMID: 20731437]
[19]
Wu, D.D.; Salah, Y.A.; Ngowi, E.E.; Zhang, Y.X.; Khattak, S.; Khan, N.H.; Wang, Y.; Li, T.; Guo, Z.H.; Wang, Y.M.; Ji, X.Y. Nanotechnology prospects in brain therapeutics concerning gene-targeting and nose-to-brain administration. iScience, 2023, 26(8), 107321.
[http://dx.doi.org/10.1016/j.isci.2023.107321] [PMID: 37554468]
[20]
Qiu, C.; Wu, Y.; Guo, Q.; Shi, Q.; Zhang, J.; Meng, Y.; Xia, F.; Wang, J. Preparation and application of calcium phosphate nanocarriers in drug delivery. Mater. Today Bio, 2022, 17, 100501.
[http://dx.doi.org/10.1016/j.mtbio.2022.100501] [PMID: 36466957]
[21]
Wang, Y.; Hou, M.; Duan, S.; Zhao, Z.; Wu, X.; Chen, Y.; Yin, L. Macrophage-targeting gene silencing orchestrates myocardial microenvironment remodeling toward the anti-inflammatory treatment of ischemia-reperfusion (IR) injury. Bioact. Mater., 2022, 17, 320-333.
[http://dx.doi.org/10.1016/j.bioactmat.2022.01.026] [PMID: 35386446]
[22]
Zou, S.; Cao, N.; Cheng, D.; Zheng, R.; Wang, J.; Zhu, K.; Shuai, X. Enhanced apoptosis of ovarian cancer cells via nanocarrier-mediated codelivery of siRNA and doxorubicin. Int. J. Nanomedicine, 2012, 7, 3823-3835.
[PMID: 22888237]
[23]
Liu, W.; Li, S.Y.; Huang, X.E.; Cui, J.J.; Zhao, T.; Zhang, H. Inhibition of tumor growth in vitro by a combination of extracts from Rosa roxburghii Tratt and Fagopyrum cymosum. Asian Pac. J. Cancer Prev., 2012, 13(5), 2409-2414.
[http://dx.doi.org/10.7314/APJCP.2012.13.5.2409] [PMID: 22901230]
[24]
Deng, S.; Hu, B.; An, H.M.; Du, Q.; Xu, L.; Shen, K.P.; Shi, X.F.; Wei, M.M.; Wu, Y. Teng-Long-Bu-Zhong-Tang, a chinese herbal formula, enhances anticancer effects of 5-fluorouracil in CT26 colon carcinoma. BMC Complement. Altern. Med., 2013, 13(1), 128.
[http://dx.doi.org/10.1186/1472-6882-13-128] [PMID: 23758730]
[25]
Gou, H.; Wong, C.C.; Chen, H.; Shang, H.; Su, H.; Zhai, J.; Liu, W.; Liu, W.; Sun, D.; Wang, X.; Yu, J. TRIP6 disrupts tight junctions to promote metastasis and drug resistance and is a therapeutic target in colorectal cancer. Cancer Lett., 2023, 578, 216438.
[http://dx.doi.org/10.1016/j.canlet.2023.216438] [PMID: 37827326]
[26]
Beretta, G.L. Ferroptosis-induced cardiotoxicity and antitumor drugs. Curr. Med. Chem., 2023, 31
[http://dx.doi.org/10.2174/0929867331666230719124453] [PMID: 37469161]
[27]
Chen, L.; Qing, B.L.; Zheng, M.Y. Prediction of effective drug combinations by chemical interaction, protein interaction and target enrichment of KEGG pathways. Biomed Res Int, 2013, 2013, 723780.
[http://dx.doi.org/10.1155/2013/723780]
[28]
Dorman, S.N.; Baranova, K.; Knoll, J.H.M.; Urquhart, B.L.; Mariani, G.; Carcangiu, M.L.; Rogan, P.K. Genomic signatures for paclitaxel and gemcitabine resistance in breast cancer derived by machine learning. Mol. Oncol., 2016, 10(1), 85-100.
[http://dx.doi.org/10.1016/j.molonc.2015.07.006] [PMID: 26372358]
[29]
Ghaisani, F.D.; Wasito, I.; Faturrahman, M.; Mufidah, R. Prognosis cancer prediction model using deep belief network approach. J. Theor. Appl. Inf. Technol., 2017, 95(20), 5369-5378.
[30]
Wang, L.; You, Z.H.; Chen, X.; Xia, S.X.; Liu, F.; Yan, X.; Zhou, Y.; Song, K.J. A computational-based method for predicting drug-target interactions by using stacked autoencoder deep neural network. J. Comput. Biol., 2018, 25(3), 361-373.
[http://dx.doi.org/10.1089/cmb.2017.0135] [PMID: 28891684]
[31]
Gönen, M. Predicting drug–target interactions from chemical and genomic kernels using Bayesian matrix factorization. Bioinformatics, 2012, 28(18), 2304-2310.
[http://dx.doi.org/10.1093/bioinformatics/bts360] [PMID: 22730431]
[32]
Binatlı, O.C.; Gönen, M. MOKPE: Drug–target interaction prediction via manifold optimization based kernel preserving embedding. BMC Bioinformatics, 2023, 24(1), 276.
[http://dx.doi.org/10.1186/s12859-023-05401-1] [PMID: 37407927]
[33]
Kuenzi, B.M.; Park, J.; Fong, S.H.; Sanchez, K.S.; Lee, J.; Kreisberg, J.F.; Ma, J.; Ideker, T. Predicting drug response and synergy using a deep learning model of human cancer cells. Cancer Cell, 2020, 38(5), 672-684.e6.
[http://dx.doi.org/10.1016/j.ccell.2020.09.014] [PMID: 33096023]
[34]
Tsigelny, I.F. Artificial intelligence in drug combination therapy. Brief. Bioinform., 2019, 20(4), 1434-1448.
[http://dx.doi.org/10.1093/bib/bby004] [PMID: 29438494]
[35]
Ding, P.; Luo, J.; Liang, C.; Xiao, Q.; Cao, B.; Li, G. Discovering synergistic drug combination from a computational perspective. Curr. Top. Med. Chem., 2018, 18(12), 965-974.
[http://dx.doi.org/10.2174/1568026618666180330141804] [PMID: 29600766]
[36]
Torkamannia, A.; Omidi, Y.; Ferdousi, R. A review of machine learning approaches for drug synergy prediction in cancer. Brief. Bioinform., 2022, 23(3), bbac075.
[http://dx.doi.org/10.1093/bib/bbac075] [PMID: 35323854]
[37]
Chen, W.; Liu, X.; Zhang, S.; Chen, S. Artificial intelligence for drug discovery: Resources, methods, and applications. Mol. Ther. Nucleic Acids, 2023, 31, 691-702.
[http://dx.doi.org/10.1016/j.omtn.2023.02.019] [PMID: 36923950]
[38]
Sumathi, S.; Suganya, K.; Swathi, K.; Sudha, B.; Poornima, A.; Varghese, C.A.; Aswathy, R. A review on deep learning-driven drug discovery: Strategies, tools and applications. Curr. Pharm. Des., 2023, 29(13), 1013-1025.
[http://dx.doi.org/10.2174/1381612829666230412084137] [PMID: 37055908]
[39]
Wu, L.; Gao, J.; Zhang, Y.; Sui, B.; Wen, Y.; Wu, Q.; Liu, K.; He, S.; Bo, X. A hybrid deep forest-based method for predicting synergistic drug combinations. Cell Rep. Methods, 2023, 3(2), 100411.
[http://dx.doi.org/10.1016/j.crmeth.2023.100411] [PMID: 36936075]
[40]
Murumägi, A.; Ungureanu, D.; Khan, S.; Arjama, M.; Välimäki, K.; Ianevski, A.; Ianevski, P.; Bergström, R.; Dini, A.; Kanerva, A.; Korander, K.R.; Tapper, J.; Lassus, H.; Loukovaara, M.; Mägi, A.; Hirasawa, A.; Aoki, D.; Pietiäinen, V.; Pellinen, T.; Bützow, R.; Aittokallio, T.; Kallioniemi, O. Drug response profiles in patient-derived cancer cells across histological subtypes of ovarian cancer: Real-time therapy tailoring for a patient with low-grade serous carcinoma. Br. J. Cancer, 2023, 128(4), 678-690.
[http://dx.doi.org/10.1038/s41416-022-02067-z] [PMID: 36476658]
[41]
Shah, P.A.; Sambandam, V.; Fernandez, A.M.; Zhao, H.; Mazumdar, T.; Shen, L.; Wang, Q.; Ahmed, K.M.; Ghosh, S.; Frederick, M.J.; Wang, J.; Johnson, F.M. Sustained aurora kinase B expression confers resistance to PI3K inhibition in head and neck squamous cell carcinoma. Cancer Res., 2022, 82(23), 4444-4456.
[http://dx.doi.org/10.1158/0008-5472.CAN-22-1175] [PMID: 36169922]
[42]
Forslund, S.K.; Chakaroun, R.; Zimmermann-Kogadeeva, M.; Markó, L.; Wisnewsky, A.J.; Nielsen, T.; Silva, M.L.; Schmidt, T.S.B.; Falony, G.; Silva, V.S.; Adriouch, S.; Alves, R.J.; Assmann, K.; Bastard, J.P.; Birkner, T.; Caesar, R.; Chilloux, J.; Coelho, L.P.; Fezeu, L.; Galleron, N.; Helft, G.; Isnard, R.; Ji, B.; Kuhn, M.; Le Chatelier, E.; Myridakis, A.; Olsson, L.; Pons, N.; Prifti, E.; Quinquis, B.; Roume, H.; Salem, J.E.; Sokolovska, N.; Tremaroli, V.; Colomer, V.M.; Lewinter, C.; Søndertoft, N.B.; Pedersen, H.K.; Hansen, T.H.; Amouyal, C.; Galijatovic, A.E.A.; Andreelli, F.; Barthelemy, O.; Batisse, J-P.; Belda, E.; Berland, M.; Bittar, R.; Blottière, H.; Bosquet, F.; Boubrit, R.; Bourron, O.; Camus, M.; Cassuto, D.; Ciangura, C.; Collet, J-P.; Dao, M-C.; Djebbar, M.; Doré, A.; Engelbrechtsen, L.; Fellahi, S.; Fromentin, S.; Galan, P.; Gauguier, D.; Giral, P.; Hartemann, A.; Hartmann, B.; Holst, J.J.; Hornbak, M.; Hoyles, L.; Hulot, J-S.; Jaqueminet, S.; Jørgensen, N.R.; Julienne, H.; Justesen, J.; Kammer, J.; Krarup, N.; Kerneis, M.; Khemis, J.; Kozlowski, R.; Lejard, V.; Levenez, F.; Lucas-Martini, L.; Massey, R.; Martinez-Gili, L.; Maziers, N.; Medina-Stamminger, J.; Montalescot, G.; Moute, S.; Neves, A.L.; Olanipekun, M.; Le Pavin, L.P.; Poitou, C.; Pousset, F.; Pouzoulet, L.; Martinez, R.A.; Rouault, C.; Silvain, J.; Svendstrup, M.; Swartz, T.; Vanduyvenboden, T.; Vatier, C.; Walther, S.; Gøtze, J.P.; Køber, L.; Vestergaard, H.; Hansen, T.; Zucker, J-D.; Hercberg, S.; Oppert, J-M.; Letunic, I.; Nielsen, J.; Bäckhed, F.; Ehrlich, S.D.; Dumas, M-E.; Raes, J.; Pedersen, O.; Clément, K.; Stumvoll, M.; Bork, P. Combinatorial, additive and dose-dependent drug– microbiome associations. Nature, 2021, 600(7889), 500-505.
[http://dx.doi.org/10.1038/s41586-021-04177-9] [PMID: 34880489]
[43]
Jin, W.; Stokes, J.M.; Eastman, R.T.; Itkin, Z.; Zakharov, A.V.; Collins, J.J.; Jaakkola, T.S.; Barzilay, R. Deep learning identifies synergistic drug combinations for treating COVID-19. Proc. Natl. Acad. Sci., 2021, 118(39), e2105070118.
[http://dx.doi.org/10.1073/pnas.2105070118] [PMID: 34526388]
[44]
Ding, Y.Y.; Kim, H.; Madden, K.; Loftus, J.P.; Chen, G.M.; Allen, D.H.; Zhang, R.; Xu, J.; Chen, C.H.; Hu, Y.; Tasian, S.K.; Tan, K. Network analysis reveals synergistic genetic dependencies for rational combination therapy in philadelphia chromosome-like acute lymphoblastic leukemia. Clin. Cancer Res., 2021, 27(18), 5109-5122.
[http://dx.doi.org/10.1158/1078-0432.CCR-21-0553] [PMID: 34210682]
[45]
Jacquelot, N.; Seillet, C.; Wang, M.; Pizzolla, A.; Liao, Y.; Hediyeh-zadeh, S.; Grisaru-Tal, S.; Louis, C.; Huang, Q.; Schreuder, J.; Guimaraes, S.F.F.; de Graaf, C.A.; Thia, K.; Macdonald, S.; Camilleri, M.; Luong, K.; Zhang, S.; Chopin, M.; Hauer, M.T.; Nutt, S.L.; Umansky, V.; Ciric, B.; Groom, J.R.; Foster, P.S.; Hansbro, P.M.; McKenzie, A.N.J.; Gray, D.H.D.; Behren, A.; Cebon, J.; Vivier, E.; Wicks, I.P.; Trapani, J.A.; Munitz, A.; Davis, M.J.; Shi, W.; Neeson, P.J.; Belz, G.T. Blockade of the co-inhibitory molecule PD-1 unleashes ILC2-dependent antitumor immunity in melanoma. Nat. Immunol., 2021, 22(7), 851-864.
[http://dx.doi.org/10.1038/s41590-021-00943-z] [PMID: 34099918]
[46]
McConnell, M.J.; Galiano, M.A.J. Designing multi-antigen vaccines against Acinetobacter baumannii using systemic approaches. Front. Immunol., 2021, 12, 666742.
[http://dx.doi.org/10.3389/fimmu.2021.666742] [PMID: 33936107]
[47]
Gomes, A.L.V.; Wee, L.J.K.; Khan, A.M.; Gil, L.H.V.G.; Marques, E.T.A., Jr; Calzavara-Silva, C.E.; Tan, T.W. Classification of dengue fever patients based on gene expression data using support vector machines. PLoS One, 2010, 5(6), e11267.
[http://dx.doi.org/10.1371/journal.pone.0011267] [PMID: 20585645]
[48]
Mudali, D.; Teune, L.K.; Renken, R.J.; Leenders, K.L.; Roerdink, J.B.T.M. Classification of Parkinsonian syndromes from FDG-PET brain data using decision trees with SSM/PCA features. Comput. Math. Methods Med., 2015, 2015, 1-10.
[http://dx.doi.org/10.1155/2015/136921] [PMID: 25918550]
[49]
Su, P.; Wu, X.; Li, C.; Yan, C.; An, Y.; Liu, S. A versatile method for quantitative analysis of total iron content in iron ore using laser-induced breakdown spectroscopy. Appl. Spectrosc., 2023, 77(2), 140-150.
[http://dx.doi.org/10.1177/00037028221141102] [PMID: 36348501]
[50]
Pellisé, F.; Burriel, S.M.; Smith, J.S.; Haddad, S.; Kelly, M.P.; Casademunt, V.A.; Grueso, S.P.F.J.; Bess, S.; Gum, J.L.; Burton, D.C.; Acaroğlu, E.; Kleinstück, F.; Lafage, V.; Obeid, I.; Schwab, F.; Shaffrey, C.I.; Alanay, A.; Ames, C. Development and validation of risk stratification models for adult spinal deformity surgery. J. Neurosurg. Spine, 2019, 1-13.
[http://dx.doi.org/10.3171/2019.3.SPINE181452] [PMID: 31252385]
[51]
Yan, F.J.; Chen, X.H.; Quan, X.Q.; Wang, L.L.; Wei, X.Y.; Zhu, J.L. Development and validation of an interpretable machine learning model-Predicting mild cognitive impairment in a high-risk stroke population. Front. Aging Neurosci., 2023, 15, 1180351.
[http://dx.doi.org/10.3389/fnagi.2023.1180351] [PMID: 37396650]
[52]
Liu, Q.; Zhang, M.; He, Y.; Zhang, L.; Zou, J.; Yan, Y.; Guo, Y. Predicting the risk of incident type 2 diabetes mellitus in chinese elderly using machine learning techniques. J. Pers. Med., 2022, 12(6), 905.
[http://dx.doi.org/10.3390/jpm12060905] [PMID: 35743691]
[53]
Guan, X.; Zhang, B.; Fu, M.; Li, M.; Yuan, X.; Zhu, Y.; Peng, J.; Guo, H.; Lu, Y. Clinical and inflammatory features based machine learning model for fatal risk prediction of hospitalized COVID-19 patients: results from a retrospective cohort study. Ann. Med., 2021, 53(1), 257-266.
[http://dx.doi.org/10.1080/07853890.2020.1868564] [PMID: 33410720]
[54]
Zhang, W.; Jiang, H.; Huang, P.; Wu, G.; Wang, Q.; Luan, X.; Zhang, H.; Yu, D.; Wang, H.; Lu, D.; Wang, H.; An, H.; Liu, S.; Zhang, W. Dracorhodin targeting CMPK2 attenuates inflammation: A novel approach to sepsis therapy. Clin. Transl. Med., 2023, 13(10), e1449.
[http://dx.doi.org/10.1002/ctm2.1449] [PMID: 37859535]
[55]
Loscalzo, J. Molecular interaction networks and drug development: Novel approach to drug target identification and drug repositioning. FASEB J., 2023, 37(1), e22660.
[http://dx.doi.org/10.1096/fj.202201683R] [PMID: 36468661]
[56]
Lu, S.; Sun, X.; Zhou, Z.; Tang, H.; Xiao, R.; Lv, Q.; Wang, B.; Qu, J.; Yu, J.; Sun, F.; Deng, Z.; Tian, Y.; Li, C.; Yang, Z.; Yang, P.; Rao, B. Mechanism of Bazhen decoction in the treatment of colorectal cancer based on network pharmacology, molecular docking, and experimental validation. Front. Immunol., 2023, 14, 1235575.
[http://dx.doi.org/10.3389/fimmu.2023.1235575] [PMID: 37799727]
[57]
Xu, F.; Meng, Q.; Wu, F.; Wang, Y.; Yang, W.; Tong, Y.; Liu, L.; Chen, X. Identification of warning transition points from hepatitis B to hepatocellular carcinoma based on mutation accumulation for the early diagnosis and potential drug treatment of HBV-HCC. Oxid. Med. Cell. Longev., 2022, 2022, 1-29.
[http://dx.doi.org/10.1155/2022/3472179] [PMID: 36105485]
[58]
Du, L.; Du, D.H.; Chen, B.; Ding, Y.; Zhang, T.; Xiao, W. Anti-inflammatory activity of Sanjie Zhentong capsule assessed by network pharmacology analysis of adenomyosis treatment. Drug Des. Devel. Ther., 2020, 14, 697-713.
[http://dx.doi.org/10.2147/DDDT.S228721] [PMID: 32109994]
[59]
Oslin, D.W.; Lynch, K.G.; Shih, M.C.; Ingram, E.P.; Wray, L.O.; Chapman, S.R.; Kranzler, H.R.; Gelernter, J.; Pyne, J.M.; Stone, A.; DuVall, S.L.; Lehmann, L.S.; Thase, M.E.; Aslam, M.; Batki, S.L.; Bjork, J.M.; Blow, F.C.; Brenner, L.A.; Chen, P.; Desai, S.; Dieperink, E.W.; Fears, S.C.; Fuller, M.A.; Goodman, C.S.; Graham, D.P.; Haas, G.L.; Hamner, M.B.; Helstrom, A.W.; Hurley, R.A.; Icardi, M.S.; Jurjus, G.J.; Kilbourne, A.M.; Kreyenbuhl, J.; Lache, D.J.; Lieske, S.P.; Lynch, J.A.; Meyer, L.J.; Montalvo, C.; Muralidhar, S.; Ostacher, M.J.; Paschall, G.Y.; Pfeiffer, P.N.; Prieto, S.; Przygodzki, R.M.; Ranganathan, M.; Rodriguez-Suarez, M.M.; Roggenkamp, H.; Schichman, S.A.; Schneeweis, J.S.; Simonetti, J.A.; Steinhauer, S.R.; Suppes, T.; Umbert, M.A.; Vassy, J.L.; Voora, D.; Wiechers, I.R.; Wood, A.E. Effect of pharmacogenomic testing for drug-gene interactions on medication selection and remission of symptoms in major depressive disorder. JAMA, 2022, 328(2), 151-161.
[http://dx.doi.org/10.1001/jama.2022.9805] [PMID: 35819423]
[60]
Naranbhai, V.; Viard, M.; Dean, M.; Groha, S.; Braun, D.A.; Labaki, C.; Shukla, S.A.; Yuki, Y.; Shah, P.; Chin, K.; Wind-Rotolo, M.; Mu, X.J.; Robbins, P.B.; Gusev, A.; Choueiri, T.K.; Gulley, J.L.; Carrington, M. HLA-A*03 and response to immune checkpoint blockade in cancer: An epidemiological biomarker study. Lancet Oncol., 2022, 23(1), 172-184.
[http://dx.doi.org/10.1016/S1470-2045(21)00582-9] [PMID: 34895481]
[61]
Díaz-Gil, L.; Brasó-Maristany, F.; Locatelli, C.; Centa, A.; Győrffy, B.; Ocaña, A.; Prat, A.; Pandiella, A. Modelling hypersensitivity to trastuzumab defines biomarkers of response in HER2 positive breast cancer. J. Exp. Clin. Cancer Res., 2021, 40(1), 313.
[http://dx.doi.org/10.1186/s13046-021-02098-z] [PMID: 34620206]
[62]
Sun, Y.; Gao, Y.; Chen, J.; Huang, L.; Deng, P.; Chen, J.; Chai, K.X.Y.; Hong, J.H.; Chan, J.Y.; He, H.; Wang, Y.; Cheah, D.; Lim, J.Q.; Chia, B.K.H.; Huang, D.; Liu, L.; Liu, S.; Wang, X.; Teng, Y.; Pang, D.; Grigoropoulos, N.F.; Teh, B.T.; Yu, Q.; Lim, S.T.; Li, W.; Ong, C.K.; Huang, H.; Tan, J. CREBBP cooperates with the cell cycle machinery to attenuate chidamide sensitivity in relapsed/refractory diffuse large B-cell lymphoma. Cancer Lett., 2021, 521, 268-280.
[http://dx.doi.org/10.1016/j.canlet.2021.09.002] [PMID: 34481935]
[63]
Li, H.; Lin, W.P.; Zhang, Z.N.; Sun, Z.J. Tailoring biomaterials for monitoring and evoking tertiary lymphoid structures. Acta Biomater., 2023, 172, 1-15.
[http://dx.doi.org/10.1016/j.actbio.2023.09.028] [PMID: 37739247]
[64]
Nardi, F.; Perurena, N.; Schade, A.E.; Li, Z.H.; Ngo, K.; Ivanova, E.V.; Saldanha, A.; Li, C.; Gokhale, P.C.; Hata, A.N.; Barbie, D.A.; Paweletz, C.P.; Jänne, P.A.; Cichowski, K. Cotargeting a MYC/eIF4A-survival axis improves the efficacy of KRAS inhibitors in lung cancer. J. Clin. Invest., 2023, 133(16), e167651.
[http://dx.doi.org/10.1172/JCI167651] [PMID: 37384411]
[65]
Luo, K.; Qian, Z.; Jiang, Y.; Lv, D.; Zhu, K.; Shao, J.; Hu, Y.; Lv, C.; Huang, Q.; Gao, Y.; Jin, S.; Shang, D. Characterization of the metabolic alteration-modulated tumor microenvironment mediated by TP53 mutation and hypoxia. Comput. Biol. Med., 2023, 163, 107078.
[http://dx.doi.org/10.1016/j.compbiomed.2023.107078] [PMID: 37356294]
[66]
Wang, J.; Yang, H.; Zheng, D.; Sun, Y.; An, L.; Li, G.; Zhao, Z. Integrating network pharmacology and pharmacological evaluation to reveal the therapeutic effects and potential mechanism of S-allylmercapto-N-acetylcysteine on acute respiratory distress syndrome. Int. Immunopharmacol., 2023, 121, 110516.
[http://dx.doi.org/10.1016/j.intimp.2023.110516] [PMID: 37369159]
[67]
Zhang, M.; Zhang, X.; Pei, J.; Guo, B.; Zhang, G.; Li, M.; Huang, L. Identification of phytochemical compounds of Fagopyrum dibotrys and their targets by metabolomics, network pharmacology and molecular docking studies. Heliyon, 2023, 9(3), e14029.
[http://dx.doi.org/10.1016/j.heliyon.2023.e14029] [PMID: 36911881]
[68]
Tang, S.; Chen, S.; Tan, X.; Xu, M.; Xu, X. Network pharmacology prediction and molecular docking-based strategy to explore the pharmacodynamic substances and mechanism of “Mung Bean” against bacterial infection. Drug Dev. Ind. Pharm., 2022, 48(2), 58-68.
[http://dx.doi.org/10.1080/03639045.2022.2094399] [PMID: 35786126]
[69]
Ding, Z.; Zhong, R.; Yang, Y.; Xia, T.; Wang, W.; Wang, Y.; Xing, N.; Luo, Y.; Li, S.; Shang, L.; Shu, Z. Systems pharmacology reveals the mechanism of activity of Ge-Gen-Qin-Lian decoction against LPS-induced acute lung injury: A novel strategy for exploring active components and effective mechanism of TCM formulae. Pharmacol. Res., 2020, 156, 104759.
[http://dx.doi.org/10.1016/j.phrs.2020.104759] [PMID: 32200026]
[70]
Huang, L.; Li, F.; Sheng, J.; Xia, X.; Ma, J.; Zhan, M.; Wong, S.T.C. DrugComboRanker: Drug combination discovery based on target network analysis. Bioinformatics, 2014, 30(12), i228-i236.
[http://dx.doi.org/10.1093/bioinformatics/btu278] [PMID: 24931988]
[71]
Kelvin, J.M.; Chimenti, M.L.; Zhang, D.Y.; Williams, E.K.; Moore, S.G.; Humber, G.M.; Baxter, T.A.; Birnbaum, L.A.; Qui, M.; Zecca, H.; Thapa, A.; Jain, J.; Jui, N.T.; Wang, X.; Fu, H.; Du, Y.; Kemp, M.L.; Lam, W.A.; Graham, D.K.; DeRyckere, D.; Dreaden, E.C. Development of constitutively synergistic nanoformulations to enhance chemosensitivity in T-cell leukemia. J. Control. Release, 2023, 361, 470-482.
[http://dx.doi.org/10.1016/j.jconrel.2023.07.045] [PMID: 37543290]
[72]
Jeon, M.; Kim, S.; Park, S.; Lee, H.; Kang, J. In silico drug combination discovery for personalized cancer therapy. BMC Syst. Biol., 2018, 12(S2), 16.
[http://dx.doi.org/10.1186/s12918-018-0546-1] [PMID: 29560824]
[73]
Esteva, A.; Kuprel, B.; Novoa, R.A.; Ko, J.; Swetter, S.M.; Blau, H.M.; Thrun, S. Dermatologist-level classification of skin cancer with deep neural networks. Nature, 2017, 542(7639), 115-118.
[http://dx.doi.org/10.1038/nature21056] [PMID: 28117445]
[74]
Huang, S.T.; Liu, L.R.; Chiu, H.W.; Huang, M.Y.; Tsai, M.F. Deep convolutional neural network for rib fracture recognition on chest radiographs. Front. Med., 2023, 10, 1178798.
[http://dx.doi.org/10.3389/fmed.2023.1178798] [PMID: 37593404]
[75]
Li, H.; Hou, J.; Adhikari, B.; Lyu, Q.; Cheng, J. Deep learning methods for protein torsion angle prediction. BMC Bioinformatics, 2017, 18(1), 417.
[http://dx.doi.org/10.1186/s12859-017-1834-2] [PMID: 28923002]
[76]
Wang, X.; Cao, K.; Guo, E.; Mao, X.; an, C.; Guo, L.; Zhang, C.; Yang, X.; Sun, J.; Yang, W.; Li, X.; Miao, S. Integrating DOI in T classification improves the predictive performance of laryngeal cancer staging. Cancer Biol. Ther., 2023, 24(1), 2169040.
[http://dx.doi.org/10.1080/15384047.2023.2169040] [PMID: 36729904]
[77]
Cao, R.; Yao, Z.; Lin, Z.; Jiao, P.; Cui, L. The performance of the 2022 ACR/EULAR classification criteria for Takayasu’s arteritis as compared to the 1990 ACR classification criteria in a Chinese population. Clin. Exp. Med., 2023, 23(8), 5291-5297.
[http://dx.doi.org/10.1007/s10238-023-01140-y] [PMID: 37582910]
[78]
van Stigt, M.N.; Camps, C.R.; Coutinho, J.M.; Marquering, H.A.; Doelkahar, B.S.; Potters, W.V. The effect of artifact rejection on the performance of a convolutional neural network based algorithm for binary EEG data classification. Biomed. Signal Process. Control, 2023, 85, 105032.
[http://dx.doi.org/10.1016/j.bspc.2023.105032]
[79]
Mufazzal, S.; Muzakkir, S.M.; Khanam, S. Enhancing the classification performance of machine learning techniques by using hjorth’s and other statistical parameters for precise tracking of naturally evolving faults in ball bearings. Int. J. Acoust. Vib., 2022, 27(2), 138-150.
[http://dx.doi.org/10.20855/ijav.2022.27.21847]
[80]
Al-Mayouf, S.M.; Akbar, L.; Abdwani, R.; Ginesi, G.; Volpi, S.; Gattorno, M.; Bakry, R.; AlHashim, S.; Alsaleem, A. Performance of the EULAR/ACR 2019 classification criteria for systemic lupus erythematous in monogenic lupus. Clin. Rheumatol., 2022, 41(9), 2721-2727.
[http://dx.doi.org/10.1007/s10067-022-06209-9] [PMID: 35590114]
[81]
Ogino, S.; King, E.E.; Beck, A.H.; Sherman, M.E.; Milner, D.A.; Giovannucci, E. Interdisciplinary education to integrate pathology and epidemiology: towards molecular and population-level health science. Am. J. Epidemiol., 2012, 176(8), 659-667.
[http://dx.doi.org/10.1093/aje/kws226] [PMID: 22935517]
[82]
Inamura, K.; Hamada, T.; Bullman, S.; Ugai, T.; Yachida, S.; Ogino, S. Cancer as microenvironmental, systemic and environmental diseases: Opportunity for transdisciplinary microbiomics science. Gut, 2022, 71(10), 2107-2122.
[http://dx.doi.org/10.1136/gutjnl-2022-327209] [PMID: 35820782]
[83]
Ogino, S.; Stampfer, M. Lifestyle factors and microsatellite instability in colorectal cancer: the evolving field of molecular pathological epidemiology. J. Natl. Cancer Inst., 2010, 102(6), 365-367.
[http://dx.doi.org/10.1093/jnci/djq031] [PMID: 20208016]
[84]
Curtin, K.; Samowitz, W.S.; Wolff, R.K.; Herrick, J.; Caan, B.J.; Slattery, M.L. Somatic alterations, metabolizing genes and smoking in rectal cancer. Int. J. Cancer, 2009, 125(1), 158-164.
[http://dx.doi.org/10.1002/ijc.24338] [PMID: 19358278]
[85]
Ogino, S.; Nowak, J.A.; Hamada, T.; Milner, D.A., Jr; Nishihara, R. Insights into pathogenic interactions among environment, host, and tumor at the crossroads of molecular pathology and epidemiology. Annu. Rev. Pathol., 2019, 14(1), 83-103.
[http://dx.doi.org/10.1146/annurev-pathmechdis-012418-012818] [PMID: 30125150]
[86]
Ogino, S.; Chan, A.T.; Fuchs, C.S.; Giovannucci, E. Molecular pathological epidemiology of colorectal neoplasia: An emerging transdisciplinary and interdisciplinary field. Gut, 2011, 60(3), 397-411.
[http://dx.doi.org/10.1136/gut.2010.217182] [PMID: 21036793]
[87]
Haydon, A.M.M.; Macinnis, R.J.; English, D.R.; Giles, G.G. Effect of physical activity and body size on survival after diagnosis with colorectal cancer. Gut, 2006, 55(1), 62-67.
[http://dx.doi.org/10.1136/gut.2005.068189] [PMID: 15972299]
[88]
Meyerhardt, J.A.; Heseltine, D.; Niedzwiecki, D.; Hollis, D.; Saltz, L.B.; Mayer, R.J.; Thomas, J.; Nelson, H.; Whittom, R.; Hantel, A.; Schilsky, R.L.; Fuchs, C.S. Impact of physical activity on cancer recurrence and survival in patients with stage III colon cancer: Findings from CALGB 89803. J. Clin. Oncol., 2006, 24(22), 3535-3541.
[http://dx.doi.org/10.1200/JCO.2006.06.0863] [PMID: 16822843]
[89]
Artificial intelligence predicts drug response. Cancer Discov., 2021, 11(1), 4-5.
[90]
Ratner, B. Statistical and machine-learning data mining. Techniques for better predictive modelling and analysis of big data, 3rd ed; CRC Press Taylor & Francis Group: Boca Raton, FL, 2017.
[91]
Bejani, M.M.; Ghatee, M. A systematic review on overfitting control in shallow and deep neural networks. Artif. Intell. Rev., 2021, 54(8), 6391-6438.
[http://dx.doi.org/10.1007/s10462-021-09975-1]
[92]
Wang, S.; Li, D.; Song, X.; Wei, Y.; Li, H. A feature selection method based on improved fisher’s discriminant ratio for text sentiment classification. Expert Syst. Appl., 2011, 38(7), 8696-8702.
[http://dx.doi.org/10.1016/j.eswa.2011.01.077]
[93]
Shalev-Shwartz, S.; Ben-David, S. Understanding machine learning from theory to algorithms; Cambridge University press: New York, 2014.
[http://dx.doi.org/10.1017/CBO9781107298019]
[94]
James, G.; Witten, D.; Hastie, T.; Tibshirani, R. An introduction to statistical learning: with applications in R; Springer: New York, 2013.
[http://dx.doi.org/10.1007/978-1-4614-7138-7]
[95]
Tzafestas, S.G.; Dalianis, P.J.; Anthopoulos, G. On the overtraining phenomenon of backpropagation neural networks. Math. Comput. Simul., 1996, 40(5-6), 507-521.
[http://dx.doi.org/10.1016/0378-4754(95)00003-8]
[96]
Ng, A.Y. Preventing” overfitting” of cross-validation data. Proceedings of the 14th international conference on machine learning (ICML), 1997, 97, pp. 245-253.
[97]
Camacho, D.M.; Collins, K.M.; Powers, R.K.; Costello, J.C.; Collins, J.J. Next-generation machine learning for biological networks. Cell, 2018, 173(7), 1581-1592.
[http://dx.doi.org/10.1016/j.cell.2018.05.015] [PMID: 29887378]