Acknowledgement
The Ministry of Economy, Trade and Industry's AI-SHIPS Project in Japan was accomplished as a result of collaborative research by all project participants, beginning with Professor Kimito Funatsu (Nara Institute of Science and Technology), who is the team leader. This writing was supported by the Technology Innovation Program (20023658, Development of AI-based toxicity prediction/evaluation technology to support toxicity verification for chemical safety management) funded By the Ministry of Trade, Industry & Energy (MOTIE, Korea).
References
- Uesawa Y (2018) Adverse effect predictions based on computational toxicology techniques and large-scale databases. Yakugaku Zasshi 138:185-190. https://doi.org/10.1248/yakushi.17-00174-4
- Reisfeld B, Mayeno AN (2012) What is computational toxicology? Methods in molecular biology (CliftonNJ). Springer, pp 3-7. https://doi.org/10.1007/978-1-62703-050-2
- Ansari M, Moraiet M, Ahmad S (2014) Insecticides: impact on the environment and human health. In: Malik A, Grohmann E, Akhtar R (eds) Environmental deterioration and human health. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7890-0_6
- Dix DJ, Houck KA, Martin MT, Richard AM, Setzer RW, Kavlock RJ (2007) The ToxCast program for prioritizing toxicity testing of environmental chemicals. Toxicol Sci 95:5-12. https://doi.org/10.1093/toxsci/kf103
- Amari S, Wu S (1999) Improving support vector machine classifiers by modifying kernel functions. Neural Netw 12:783-789. https://doi.org/10.1016/S0893-6080(99)00032-5
- Breiman L (2001) Random forests. Mach Learn 45:5-32. https://doi.org/10.1023/A:1010933404324
- LeCun Y, Bengio Y, Hinton GE (2015) Deep learning. Nature 521:436-444. https://doi.org/10.1038/nature14539
- Tox21 Data Challenge 2014. https://tripod.nih.gov/tox21/challenge/index.jsp. Accessed 15 Nov 2023
- Tox21. https://ntp.niehs.nih.gov/whatwestudy/tox21. Accessed 15 Nov 2023
- The PubChem Project. NCBI. https://pubchem.ncbi.nlm.nih.gov/. Accessed 15 Nov 2023
- Hansch C, Maloney PP, Fujita T, Muir RM (1962) Correlation of biological activity of phenoxyacetic acids with Hammett substituent constants and partition coefficients. Nature 194:178-180. https://doi.org/10.1038/194178b0
- Hansch C, Fujita T (1964) ρ-σ-π Analysis. A method for the correlation of biological activity and chemical structure. J Am Chem Soc 86:1616-1626. https://doi.org/10.1021/ja01062a035
- Fujita T, Iwasa J, Hansch C (1964) A new substituent constant, π, derived from partition coefficients. J Am Chem Soc 86:5175-5180. https://doi.org/10.1021/ja01077a028
- Deeb O, Goodarzi M (2012) In silico quantitative structure toxicity relationship of chemical compounds: some case studies. Curr Drug Saf 7:289-297. https://doi.org/10.2174/157488612804096533
- Final results for blind set prediction. http://www.cadaster.eu/sites/cadaster.eu/files/final_results.html. Accessed 15 Nov 2023
- Tox21. https://www.epa.gov/chemical-research/toxicology-testing-21st-century-tox21. Accessed 15 Nov 2023
- Ettlin RA (2012) Toxicologic pathology in the 21st century. Toxicol Pathol 41(5):689-708. https://doi.org/10.1177/0192623312466192
- Jeong J, Kim D, Choi J (2022) Application of ToxCast/Tox21 data for toxicity mechanism-based evaluation and prioritization of environmental chemicals: perspective and limitations. Toxicol In Vitro 84:105451. https://doi.org/10.1016/j.tiv.2022.105451
- Ankley GT, Bennett RS, Erickson RJ, Hof DJ, Hornung MW, Johnson RD, Mount DR, Nichols JW, Russom CL, Schmieder PK, Serrrano JA, Tietge JE, Villeneuve DL (2010) Adverse outcome pathways: a conceptual framework to support ecotoxicology research and risk assessment. Environ Toxicol Chem 29:730-741. https://doi.org/10.1002/etc.34
- Attene-Ramos MS, Miller N, Huang R, Michael S, Itkin M, Kavlock RJ, Austin CP, Shinn P, Simeonov A, Tice RR, Xia M (2013) The Tox21 robotic platform for the assessment of environmental chemicals-from vision to reality. Drug Discov Today 18:716-723. https://doi.org/10.1016/j.drudis.2013.05.015
- NIH Tox21 Data Challenge 2014. https://tripod.nih.gov/tox21/challenge/. Accessed 15 Nov 2023
- Uesawa Y (2015) Current status of the NIH sponsored competition on toxicity prediction using chemical structure. Farumashia 51:952-956
- Kurosaki K, Wu R, Uesawa Y (2020) A toxicity prediction tool for potential agonist/antagonist activities in molecular initiating events based on chemical structures. Int J Mol Sci 21:7853. https://doi.org/10.3390/ijms21217853
- Huang R, Xia M, Nguyen D-T, Zhao T, Sakamuru S, Zhao J, Shahane SA, Rossoshek A, Simeonov A (2016) Tox21Challenge to build predictive models of nuclear receptor and stress response pathways as mediated by exposure to environmental chemicals and drugs. Front Environ Sci 14:1-9. https://doi.org/10.3389/fenvs.2015.00085
- Uesawa Y (2016) Rigorous selection of random forest models for identifying compounds that activate toxicity-related pathways. Front Environ Sci 4:1-6. https://doi.org/10.3389/fenvs.2016.00009
- Asako Y, Uesawa Y (2017) High-performance prediction of human estrogen receptor agonists based on chemical structures. Molecules 22:1-10. https://doi.org/10.3390/molecules22040675
- Mayr A, Klambauer G, Unterthiner T, Hochreiter S (2016) Deep-Tox: toxicity prediction using deep learning. Front Environ Sci 3:80. https://doi.org/10.3389/fenvs.2015.00080
- Uesawa Y (2018) Quantitative structure-activity relationship analysis using deep learning based on a novel molecular image input technique. Bioorg Med Chem Lett 28:3400-3403. https://doi.org/10.1016/j.bmcl.2018.08.032
- Matsuzaka Y, Uesawa Y (2019) Optimization of a deep-learning method based on the classification of images generated by parameterized deep snap a novel molecular-image-input technique for quantitative structure-activity relationship (QSAR) analysis. Front Bioeng Biotechnol 7:65. https://doi.org/10.3389/fbioe.2019.00065
- Matsuzaka Y, Uesawa Y (2019) Prediction model with high-performance constitutive androstane receptor (CAR) using Deep-Snap-deep learning approach from the Tox21 10K compound library. Int J Mol Sci 20:4855. https://doi.org/10.3390/ijms20194855
- Matsuzaka Y, Uesawa Y (2022) A deep learning-based quantitative structure-activity relationship system construct prediction model of agonist and antagonist with high performance. Int J Mol Sci 23:2141. https://doi.org/10.3390/ijms23042141
- Matsuzaka Y, Uesawa Y (2023) Ensemble learning, deep learning-based and molecular descriptor-based quantitative structure-activity relationships. Molecules 28:2410. https://doi.org/10.3390/molecules28052410
- Kurosaki K, Uesawa Y (2022) Development of in silico prediction models for drug-induced liver malignant tumors based on the activity of molecular initiating events: biologically interpretable features. J Toxicol Sci 47:89-98. https://doi.org/10.2131/jts.47.89
- AI-SHIPS HP. http://www-dsc.naist.jp/ai-ships/. Accessed 15 Nov 2023
- Matsumoto M, Kobayashi K, Takahashi M, Hirata-Koizumi M, Ono A, Hirose A (2015) Summary information of human health hazard assessment of existing chemical substances (I). Kokuritsu Iyakuhin Shokuhin Eisei Kenkyusho Hokoku (133):42-47
- Akahori Y, Yamashita K, Ishida K, Saito F, Nakai M (2020) Transcriptomics-driven evaluation on liver toxicity using adverse outcome pathways (AOP). Yakugaku Zasshi 140:491-498. https://doi.org/10.1248/yakushi.19-00190-3
- The Hazard Evaluation Support System Integrated Platform (HESS). https://integbio.jp/dbcatalog/record/nbdc01319. Accessed 15 Nov 2023
- Lin Z, Chou WC (2022) Machine learning and artificial intelligence in toxicological sciences. Toxicol Sci 189:7-19. https://doi.org/10.1093/toxsci/kfac075