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基于机器学习的纳米材料生物效应研究的科学问题

胡献刚 李佳薇 李佳蔷 靳红叶 于福波

胡献刚, 李佳薇, 李佳蔷, 靳红叶, 于福波. 基于机器学习的纳米材料生物效应研究的科学问题[J]. 环境工程, 2022, 40(6): 171-181. doi: 10.13205/j.hjgc.202206022
引用本文: 胡献刚, 李佳薇, 李佳蔷, 靳红叶, 于福波. 基于机器学习的纳米材料生物效应研究的科学问题[J]. 环境工程, 2022, 40(6): 171-181. doi: 10.13205/j.hjgc.202206022
HU Xiangang, LI Jiawei, LI Jiaqiang, JIN Hongye, YU Fubo. SCIENTIFIC QUESTIONS ON THE BIOLOGICAL EFFECTS OF NANOMATERIALS BASED ON MACHINE LEARNING[J]. ENVIRONMENTAL ENGINEERING , 2022, 40(6): 171-181. doi: 10.13205/j.hjgc.202206022
Citation: HU Xiangang, LI Jiawei, LI Jiaqiang, JIN Hongye, YU Fubo. SCIENTIFIC QUESTIONS ON THE BIOLOGICAL EFFECTS OF NANOMATERIALS BASED ON MACHINE LEARNING[J]. ENVIRONMENTAL ENGINEERING , 2022, 40(6): 171-181. doi: 10.13205/j.hjgc.202206022

基于机器学习的纳米材料生物效应研究的科学问题

doi: 10.13205/j.hjgc.202206022
基金项目: 

国家重点研发计划(2019YFC1804603)

详细信息
    作者简介:

    胡献刚(1983-),男,教授,主要研究方向为机器学习与环境健康交叉。huxiangang@nankai.edu.cn

    通讯作者:

    胡献刚(1983-),男,教授,主要研究方向为机器学习与环境健康交叉。huxiangang@nankai.edu.cn

SCIENTIFIC QUESTIONS ON THE BIOLOGICAL EFFECTS OF NANOMATERIALS BASED ON MACHINE LEARNING

  • 摘要: 纳米材料(nanomaterials,NM)作为一类新型的化学品,认识、控制其引起的不良环境健康风险是推广应用的重要前提。近些年,机器学习(machine learning,ML)作为一种数据驱动的研究方法,在环境、化学和材料等领域引起了广泛关注。从NM引起的细胞毒性、个体效应、蛋白冠与生态冠预测等几方面,介绍了ML的应用,并分析了应用过程中,数据集、描述符、ML方法、模型可解释性等方面存在的问题和解决方法。文章提出,数据提取与挖掘方法、新描述符、新模型、模型解释方法的创新与发展将能够促进ML在NM生物效应领域的应用。同时,随着ML的发展,ML有望能够预测新型的NM和复杂的效应,并揭示了相关原理。以梳理讨论ML在NM生物效应预测中面临的重要科学问题为重点,有助于后续研究者理清思路,解决该领域的难题,促进纳米产业健康可持续发展。
  • [1] WINKLER D A, BURDEN F R, YAN B, et al. Modelling and predicting the biological effects of nanomaterials[J]. Sar and Qsar in Environmental Research, 2014, 25(1/2/3):161-172.
    [2] WINKLER D A. Role of artificial intelligence and machine learning in nanosafety[J]. Small, 2020, 16(36).
    [3] 谢翼飞,李旭东,李福德.生物硫铁纳米材料特性分析及其处理高浓度含铬废水研究[J].环境科学, 2009, 30(4):1060-1065.
    [4] XU P, ZENG G M, HUANG D L, et al. Use of iron oxide nanomaterials in wastewater treatment:a review[J]. Science of the Total Environment, 2012, 424:1-10.
    [5] MAUTER M S, ZUCKER I, PERREAULT F, et al. The role of nanotechnology in tackling global water challenges[J]. Nature Sustainability, 2018, 1(4):166-175.
    [6] HOU X, MU L, CHEN F, et al. Emerging investigator series:design of hydrogel nanocomposites for the detection and removal of pollutants:from nanosheets, network structures, and biocompatibility to machine-learning-assisted design[J]. Environmental Science:Nano, 2018, 5(10):2216-2240.
    [7] 张业.纳米材料的电化学制备及其应用[J].环境工程, 2011, 29(3):128-130

    ,90.
    [8] LIU S, MA C, MA M G, et al. Recent advances in carbon nanomaterials derived from biomass[J]. Science of Advanced Materials, 2019, 11(1):5-17.
    [9] KIM S, KIM K H, BARK C W. Two-dimensional nanomaterials:their structures, synthesis, and applications[J]. Science of Advanced Materials, 2017, 9(9):1441-1457.
    [10] FAN Z X, HUANG X, CHEN Y, et al. Facile synthesis of gold nanomaterials with unusual crystal structures[J]. Nature Protocols, 2017, 12(11):2367-2376.
    [11] 韩伟,于艳军,李宁涛,等.纳米复合材料在食品包装中的应用及其安全评价[J].科学通报, 2011, 56(3):198-209.
    [12] 郑明彬,赵鹏飞,罗震宇,等.纳米技术在癌症诊疗一体化中的应用[J].科学通报, 2014, 59(31):3009-3024.
    [13] POON W, KINGSTON B R, OUYANG B, et al. A framework for designing delivery systems[J]. Nature Nanotechnology, 2020, 15(10):819-829.
    [14] BENFENATI F, LANZANI G. Clinical translation of nanoparticles for neural stimulation[J]. Nature Reviews Materials, 2021, 6(1):1-4.
    [15] 闻雷,宋仁升,石颖,等.炭材料在锂离子电池中的应用及前景[J].科学通报, 2013, 58(31):3157-3171.
    [16] KAH M, TUFENKJI N, WHITE J C. Nano-enabled strategies to enhance crop nutrition and protection[J]. Nature Nanotechnology, 2019, 14(6):532-540.
    [17] GILBERTSON L M, POURZAHEDI L, LAUGHTON S, et al. Guiding the design space for nanotechnology to advance sustainable crop production[J]. Nature Nanotechnology, 2020, 15(9):801-,.
    [18] YANAMALA N, ORANDLE M S, KODALI V K, et al. Supervised machine learning approaches predict and characterize nanomaterial exposures:MWCNT markers in lung lavage fluid[C]//Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics (ACM-BCB), Boston, MA, F 2017.
    [19] 张学治,孙红文,张稚妍.鲤鱼对纳米二氧化钛的生物富集[J].环境科学, 2006,27(8):1631-1635.
    [20] YU F B, WEI C H, DENG P, et al. Deep exploration of random forest model boosts the interpretability of machine learning studies of complicated immune responses and lung burden of nanoparticles[J]. Science Advances, 2021, 7(22):14.
    [21] DEV A, SRIVASTAVA A K, KARMAKAR S. Nanomaterial toxicity for plants[J]. Environmental Chemistry Letters, 2018, 16(1):85-100.
    [22] LUAN F, TANG L L, ZHANG L H, et al. A further development of the QNAR model to predict the cellular uptake of nanoparticles by pancreatic cancer cells[J]. Food and Chemical Toxicology, 2018, 112:571-580.
    [23] BAN Z, YUAN P, YU F B, et al. Machine learning predicts the functional composition of the protein corona and the cellular recognition of nanoparticles[J]. Proceedings of the National Academy of Sciences of the United States of America, 2020, 117(19):10492-10499.
    [24] YU H J, ZHAO Z L, CHENG F. Predicting and investigating cytotoxicity of nanoparticles by translucent machine learning[J]. Chemosphere, 2021, 276:130164.
    [25] FURXHI I, MURPHY F, MULLINS M, et al. Nanotoxicology data for in silico tools:a literature review[J]. Nanotoxicology, 2020, 14(5):612-637.
    [26] WANG M, WANG T, CAI P Q, et al. Nanomaterials discovery and design through machine learning[J]. Small Methods, 2019, 3(5).
    [27] TO K T, TRUONG L, EDWARDS S, et al. Multivariate modeling of engineered nanomaterial features associated with developmental toxicity[J]. Nanoimpact, 2019, 16:100185.
    [28] PENG T, WEI C H, YU F B, et al. Predicting nanotoxicity by an integrated machine learning and metabolomics approach[J]. Environmental Pollution, 2020, 267:115434.
    [29] MARCHWIANY M E, BIROWSKA M, POPIELSKI M, et al. Surface-related features responsible for cytotoxic behavior of mXenes layered materials predicted with machine learning approach[J]. Materials, 2020, 13(14).
    [30] KOTZABASAKI M I, SOTIROPOULOS I, SARIMVEIS H. QSAR modeling of the toxicity classification of superparamagnetic iron oxide nanoparticles (SPIONs) in stem-cell monitoring applications:an integrated study from data curation to model development[J]. RSC Advances, 2020, 10(9):5385-5391.
    [31] HAN Z W, SALAWU O A, ZENOBIO J E, et al. Emerging investigator series:immobilization of arsenic in soil by nanoscale zerovalent iron:role of sulfidation and application of machine learning[J]. Environmental Science-Nano, 2021, 8(3):619-633.
    [32] GUL G, YILDIRIM R, ILERI-ERCAN N. Cytotoxicity analysis of nanoparticles by association rule mining[J]. Environmental Science:Nano, 2021, 8(4):937-949.
    [33] VARSOU D D, ELLIS L J A, AFANTITIS A, et al. Ecotoxicological read-across models for predicting acute toxicity of freshly dispersed versus medium-aged NMs to Daphnia magna[J]. Chemosphere, 2021, 285:131452.
    [34] SUBRAMANIAN N A, PALANIAPPAN A. NanoTox:development of a parsimonious in silico model for toxicity assessment of metal-oxide nanoparticles using physicochemical features[J]. ACS Omega, 2021, 6(17):11729-11739.
    [35] SIZOCHENKO N, SYZOCHENKO M, FJODOROVA N, et al. Evaluating genotoxicity of metal oxide nanoparticles:application of advanced supervised and unsupervised machine learning techniques[J]. Ecotoxicology and Environmental Safety, 2019, 185:109733.
    [36] SIZOCHENKO N, MIKOLAJCZYK A, JAGIELLO K, et al. How the toxicity of nanomaterials towards different species could be simultaneously evaluated:a novel multi-nano-read-across approach[J]. Nanoscale, 2018, 10(2):582-591.
    [37] SINGH A V, MAHARJAN R-S, KANASE A, et al. Machine-learning-based approach to decode the influence of nanomaterial properties on their interaction with cells[J]. Acs Applied Materials&Interfaces, 2021, 13(1):1943-1955.
    [38] PAPADIAMANTIS A G, JANES J, VOYIATZIS E, et al. Predicting cytotoxicity of metal oxide nanoparticles using isalos analytics platform[J]. Nanomaterials, 2020, 10(10):2017.
    [39] KOTZABASAKI M, SOTIROPOULOS I, CHARITIDIS C, et al. Machine learning methods for multi-walled carbon nanotubes (MWCNT) genotoxicity prediction[J]. Nanoscale Advances, 2021, 3(11):3167-3176.
    [40] KAR S, PATHAKOTI K, TCHOUNWOU P B, et al. Evaluating the cytotoxicity of a large pool of metal oxide nanoparticles to Escherichia coli:mechanistic understanding through In Vitro and In Silico studies[J]. Chemosphere, 2021, 264:128428.
    [41] HALDER A K, MELO A, CORDEIRO M N D S. A unified in silico model based on perturbation theory for assessing the genotoxicity of metal oxide nanoparticles[J]. Chemosphere, 2020, 244:125489.
    [42] FURXHI I, MURPHY F, MULLINS M, et al. Machine learning prediction of nanoparticle in vitro toxicity:a comparative study of classifiers and ensemble-classifiers using the Copeland Index[J]. Toxicology Letters, 2019, 312:157-166.
    [43] CHOI J S, TRINH T X, YOON T H, et al. Quasi-QSAR for predicting the cell viability of human lung and skin cells exposed to different metal oxide nanomaterials[J]. Chemosphere, 2019, 217:243-249.
    [44] CHAU Y T, YAP C W. Quantitative Nanostructure-Activity Relationship modelling of nanoparticles[J]. Rsc Advances, 2012, 2(22):8489-8496.
    [45] CONCU R, KLEANDROVA V V, SPECK-PLANCHE A, et al. Probing the toxicity of nanoparticles:a unified in silico machine learning model based on perturbation theory[J]. Nanotoxicology, 2017, 11(7):891-906.
    [46] FINDLAY M R, FREITAS D N, MOBED-MIREMADI M, et al. Machine learning provides predictive analysis into silver nanoparticle protein corona formation from physicochemical properties[J]. Environmental Science:Nano, 2018, 5(1):64-71.
    [47] LIM G P, SOON C F, MA N L, et al. Cytotoxicity of MXene-based nanomaterials for biomedical applications:a mini review[J]. Environmental Research, 2021, 201:111592.
    [48] SIMEONE F C, COSTA A L. Assessment of cytotoxicity of metal oxide nanoparticles on the basis of fundamental physical-chemical parameters:a robust approach to grouping[J]. Environmental Science:Nano, 2019, 6(10):3102-3112.
    [49] CHEN G C, VIJVER M G, XIAO Y L, et al. A review of recent advances towards the development of (quantitative) structure-activity relationships for metallic nanomaterials[J]. Materials, 2017, 10(9):1013.
    [50] SASON H, SHAMAY Y. Nanoinformatics in drug delivery[J]. Israel Journal of Chemistry, 2020, 60(12):1108-1117.
    [51] MA Y, WANG J L, WU J Y, et al. Meta-analysis of cellular toxicity for graphene via data-mining the literature and machine learning[J]. Science of the Total Environment, 2021, 793:148532.
    [52] HAYAT H, NUKALA A, NYAMIRA A, et al. A concise review:the synergy between artificial intelligence and biomedical nanomaterials that empowers nanomedicine[J]. Biomedical Materials, 2021, 16(5).
    [53] SHEEHAN B, MURPHY F, MULLINS M, et al. Hazard screening methods for nanomaterials:a comparative study[J]. International Journal of Molecular Sciences, 2018, 19(3):649.
    [54] KARATZAS P, MELAGRAKI G, ELLIS L J A, et al. Development of deep learning models for predicting the effects of exposure to engineered nanomaterials on Daphnia magna[J]. Small, 2020, 16(36).
    [55] GOMES S I L, AMORIM M J B, POKHREL S, et al. Machine learning and materials modelling interpretation of in vivo toxicological response to TiO2 nanoparticles library (UV and non-UV exposure)[J]. Nanoscale, 2021, 13(35):14666-14678.
    [56] GOUSIADOU C, ROBINSON R L M, KOTZABASAKI M, et al. Machine learning predictions of concentration-specific aggregate hazard scores of inorganic nanomaterials in embryonic zebrafish[J]. Nanotoxicology, 2021, 15(4):446-476.
    [57] BAN Z, ZHOU Q X, SUN A Q, et al. Screening priority factors determining and predicting the reproductive toxicity of various nanoparticles[J]. Environmental Science&Technology, 2018, 52(17):9666-9676.
    [58] YANAMALA N, DESAI I C, MILLER W, et al. Grouping of carbonaceous nanomaterials based on association of patterns of inflammatory markers in BAL fluid with adverse outcomes in lungs[J]. Nanotoxicology, 2019, 13(8):1102-1016.
    [59] PAPA E, DOUCET J P, SANGION A, et al. Investigation of the influence of protein corona composition on gold nanoparticle bioactivity using machine learning approaches[J]. Sar and Qsar in Environmental Research, 2016, 27(7):521-538.
    [60] HELMA C, RAUTENBERG M, GEBELE D. Nano-Lazar:read across predictions for nanoparticle toxicities with calculated and measured properties[J]. Frontiers in Pharmacology, 2017, 8.
    [61] WEI L F, ZHANG Q, HOU X W, et al. Species-dependent eco-corona dictates the aggregation of black phosphorus nanosheets:the role of protein and calcium[J]. Environmental Science:Nano, 2021, 8(11):3098-30109.
    [62] CHAKRABORTY D, ETHIRAJ K R, CHANDRASEKARAN N, et al. Mitigating the toxic effects of CdSe quantum dots towards freshwater alga Scenedesmus obliquus:role of eco-corona[J]. Environmental Pollution, 2021, 270:116049.
    [63] FADARE O O, WAN B, LIU K Y, et al. Eco-corona vs protein corona:effects of humic substances on corona formation and nanoplastic particle toxicity in Daphnia magna[J]. Environmental Science&Technology, 2020, 54(13):8001-8019.
    [64] JIA Y Y, HOU X, WANG Z W, et al. Machine learning boosts the design and discovery of nanomaterials[J]. ACS Sustainable Chemistry&Engineering, 2021, 9(18):6130-6147.
    [65] TAO H C, WU T Y, ALDEGHI M, et al. Nanoparticle synthesis assisted by machine learning[J]. Nature Reviews Materials, 2021, 6(8):701-716.
    [66] KARAKUS C O, WINKLER D A. Overcoming roadblocks in computational roadmaps to the future for safe nanotechnology[J]. Nano Futures, 2021, 5(2).
    [67] LI Y, PU Q, LI S, et al. Machine learning methods for research highlight prediction in biomedical effects of nanomaterial application[J]. Pattern Recognition Letters, 2019, 117:111-118.
    [68] BASEI G, HRISTOZOV D, LAMON L, et al. Making use of available and emerging data to predict the hazards of engineered nanomaterials by means of in silico tools:a critical review[J]. Nanoimpact, 2019, 13:76-99.
    [69] YAN X, ZHANG J, RUSSO D P, et al. Prediction of nano-bio interactions through convolutional neural network analysis of nanostructure images[J]. ACS Sustainable Chemistry&Engineering, 2020, 8(51):19096-19104.
    [70] TO K T, TRUONG L, EDWARDS S, et al. Multivariate modeling of engineered nanomaterial features associated with developmental toxicity (vol 16C, 100185, 2019)[J]. Nanoimpact, 2021, 21.
    [71] YAN X L, SEDYKH A, WANG W Y, et al. Construction of a web-based nanomaterial database by big data curation and modeling friendly nanostructure annotations[J]. Nature Communications, 2020, 11(1):2519.
    [72] SUN S, DENG P, MU L, et al. Bionanoscale recognition underlies cell fate and therapy[J]. Advanced Healthcare Materials, 2021, 10(22).
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  • 收稿日期:  2021-12-16
  • 网络出版日期:  2022-09-01
  • 刊出日期:  2022-09-01

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