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基于主体的模型 Agent-based model (查看源代码)

2020年11月13日 (五) 18:08的版本

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基于主体建模已被广泛用于生物学,包括流行病的传播的分析<ref>{{cite arxiv |eprint=nlin/0403035 |last1=Situngkir |first1=Hokky |title=Epidemiology Through Cellular Automata: Case of Study Avian Influenza in Indonesia |year=2004}}</ref>和细菌战的威胁,生物用途包括种群动力学<ref>{{cite journal |last=Caplat |first=Paul |author2=Anand, Madhur |author3=Bauch, Chris |title=Symmetric competition causes population oscillations in an individual-based model of forest dynamics |journal=Ecological Modelling |date=March 10, 2008 |volume=211 |issue=3–4 |pages=491–500 |doi=10.1016/j.ecolmodel.2007.10.002}}</ref>、随机基因表达<ref>{{Cite journal|last=Thomas|first=Philipp|date=December 2019|title=Intrinsic and extrinsic noise of gene expression in lineage trees|journal=Scientific Reports|volume=9|issue=1|pages=474|doi=10.1038/s41598-018-35927-x|issn=2045-2322|pmc=6345792|pmid=30679440|bibcode=2019NatSR...9..474T}}</ref> 、动植物交互<ref>Fedriani JM, T Wiegand, D Ayllón, F Palomares, A Suárez-Esteban and V. Grimm.  2018. Assisting seed dispersers to restore old-fields: an individual-based model of the interactions among badgers, foxes, and Iberian pear trees. Journal of Applied Ecology 55: 600–611.</ref>、植被生态学 <ref name="Ch'ng, E. (2009)">Ch'ng, E. (2009) An Artificial Life-Based Vegetation Modelling Approach for Biodiversity Research, in Nature-Inspired informatics for Intelligent Applications and Knowledge Discovery: Implications in Business, Science and Engineering, R. Chiong, Editor. 2009, IGI Global: Hershey, PA. http://complexity.io/Publications/NII-alifeVeg-eCHNG.pdf {{Webarchive|url=https://web.archive.org/web/20131113173223/http://complexity.io/Publications/NII-alifeVeg-eCHNG.pdf |date=November 13, 2013 }}</ref> 、景观多样性<ref>{{Cite journal |last1=Wirth |first1=E. |last2=Szabó |first2=Gy. |last3=Czinkóczky |first3=A. |date=2016-06-07 |journal=ISPRS Annals of the Photogrammetry, Remote Sensing and Spatial Information Sciences |volume=III-8 |pages=145–151 |doi=10.5194/isprs-annals-iii-8-145-2016 |bibcode=2016ISPAnIII8..145W|title=Measure of Landscape Heterogeneity by Agent-Based Methodology |doi-access=free }}</ref> 、古代文明的兴衰,民族中心主义的进化行为<ref>{{cite journal |last1=Lima |first1=Francisco W. S. |last2=Hadzibeganovic |first2=Tarik |last3=Stauffer |first3=Dietrich |year=2009 |title=Evolution of ethnocentrism on undirected and directed Barabási–Albert networks |journal=Physica A |volume=388 |issue=24 |pages=4999–5004 |doi=10.1016/j.physa.2009.08.029 |bibcode=2009PhyA..388.4999L |arxiv=0905.2672 |s2cid=18233740 }}</ref> ,强迫位移/迁移<ref>{{cite book |title=The Chaos of Forced Migration: A Modeling Means to an Humanitarian End |first=Scott |last=Edwards |date=June 9, 2009 |publisher=[[VDM Verlag]] |pages=168 |isbn=978-3-639-16516-6}}</ref> ,语言选择动力学<ref>{{cite journal |last1=Hadzibeganovic |first1=Tarik |last2=Stauffer |first2=Dietrich |last3=Schulze |first3=Christian |year=2009 |title=Agent-based computer simulations of language choice dynamics |url=|journal=Annals of the New York Academy of Sciences |volume=1167 |issue=1|pages=221–229 |doi=10.1111/j.1749-6632.2009.04507.x |pmid=19580569 |bibcode=2009NYASA1167..221H |s2cid=32790067 }}</ref>,认知建模,生物医学应用包括三维乳腺组织形态形成建模<ref>{{cite journal |last1=Tang |first1=Jonathan |last2=Enderling |first2=Heiko |last3=Becker-Weimann |first3=Sabine |last4=Pham |first4=Christopher |last5=Polyzos |first5=Aris |last6=Chen |first6=Charlie |last7=Costes |first7=Sylvain |year=2011 |title=Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling |url=|journal=Integrative Biology |volume=3 |issue=4 |pages=408–21 |doi=10.1039/c0ib00092b |pmid=21373705 |pmc=4009383 }}</ref>，电离辐射对乳房干细胞亚群动力学<ref>{{cite journal |last1=Tang |first1=Jonathan |last2=Fernando-Garcia |first2=Ignacio |last3=Vijayakumar |first3=Sangeetha |last4=Martinez-Ruis |first4=Haydeliz |last5=Illa-Bochaca |first5=Irineu |last6=Nguyen |first6=David |last7=Mao |first7=Jian-Hua |last8=Costes |first8=Sylvain |last9=Barcellos-Hoff |first9=Mary Helen |year=2014 |title=Irradiation of juvenile, but not adult, mammary gland increases stem cell self-renewal and estrogen receptor negative tumors |url=|journal=Stem Cells |volume=32 |issue=3 |pages=649–61 |doi=10.1002/stem.1533 |pmid=24038768  |s2cid=32979016 }}</ref>、炎症<ref>{{cite journal |last1=Tang |first1=Jonathan |last2=Ley |first2=Klaus |last3=Hunt |first3=C. Anthony |year=2007 |title=Dynamics of in silico leukocyte rolling, activation, and adhesion |url=|journal=BMC Systems Biology |volume=1 |issue=14 |pages=14 |doi=10.1186/1752-0509-1-14 |pmid=17408504 |pmc=1839892 }}</ref>
 
基于主体建模已被广泛用于生物学,包括流行病的传播的分析<ref>{{cite arxiv |eprint=nlin/0403035 |last1=Situngkir |first1=Hokky |title=Epidemiology Through Cellular Automata: Case of Study Avian Influenza in Indonesia |year=2004}}</ref>和细菌战的威胁,生物用途包括种群动力学<ref>{{cite journal |last=Caplat |first=Paul |author2=Anand, Madhur |author3=Bauch, Chris |title=Symmetric competition causes population oscillations in an individual-based model of forest dynamics |journal=Ecological Modelling |date=March 10, 2008 |volume=211 |issue=3–4 |pages=491–500 |doi=10.1016/j.ecolmodel.2007.10.002}}</ref>、随机基因表达<ref>{{Cite journal|last=Thomas|first=Philipp|date=December 2019|title=Intrinsic and extrinsic noise of gene expression in lineage trees|journal=Scientific Reports|volume=9|issue=1|pages=474|doi=10.1038/s41598-018-35927-x|issn=2045-2322|pmc=6345792|pmid=30679440|bibcode=2019NatSR...9..474T}}</ref> 、动植物交互<ref>Fedriani JM, T Wiegand, D Ayllón, F Palomares, A Suárez-Esteban and V. Grimm.  2018. Assisting seed dispersers to restore old-fields: an individual-based model of the interactions among badgers, foxes, and Iberian pear trees. Journal of Applied Ecology 55: 600–611.</ref>、植被生态学 <ref name="Ch'ng, E. (2009)">Ch'ng, E. (2009) An Artificial Life-Based Vegetation Modelling Approach for Biodiversity Research, in Nature-Inspired informatics for Intelligent Applications and Knowledge Discovery: Implications in Business, Science and Engineering, R. Chiong, Editor. 2009, IGI Global: Hershey, PA. http://complexity.io/Publications/NII-alifeVeg-eCHNG.pdf {{Webarchive|url=https://web.archive.org/web/20131113173223/http://complexity.io/Publications/NII-alifeVeg-eCHNG.pdf |date=November 13, 2013 }}</ref> 、景观多样性<ref>{{Cite journal |last1=Wirth |first1=E. |last2=Szabó |first2=Gy. |last3=Czinkóczky |first3=A. |date=2016-06-07 |journal=ISPRS Annals of the Photogrammetry, Remote Sensing and Spatial Information Sciences |volume=III-8 |pages=145–151 |doi=10.5194/isprs-annals-iii-8-145-2016 |bibcode=2016ISPAnIII8..145W|title=Measure of Landscape Heterogeneity by Agent-Based Methodology |doi-access=free }}</ref> 、古代文明的兴衰,民族中心主义的进化行为<ref>{{cite journal |last1=Lima |first1=Francisco W. S. |last2=Hadzibeganovic |first2=Tarik |last3=Stauffer |first3=Dietrich |year=2009 |title=Evolution of ethnocentrism on undirected and directed Barabási–Albert networks |journal=Physica A |volume=388 |issue=24 |pages=4999–5004 |doi=10.1016/j.physa.2009.08.029 |bibcode=2009PhyA..388.4999L |arxiv=0905.2672 |s2cid=18233740 }}</ref> ,强迫位移/迁移<ref>{{cite book |title=The Chaos of Forced Migration: A Modeling Means to an Humanitarian End |first=Scott |last=Edwards |date=June 9, 2009 |publisher=[[VDM Verlag]] |pages=168 |isbn=978-3-639-16516-6}}</ref> ,语言选择动力学<ref>{{cite journal |last1=Hadzibeganovic |first1=Tarik |last2=Stauffer |first2=Dietrich |last3=Schulze |first3=Christian |year=2009 |title=Agent-based computer simulations of language choice dynamics |url=|journal=Annals of the New York Academy of Sciences |volume=1167 |issue=1|pages=221–229 |doi=10.1111/j.1749-6632.2009.04507.x |pmid=19580569 |bibcode=2009NYASA1167..221H |s2cid=32790067 }}</ref>,认知建模,生物医学应用包括三维乳腺组织形态形成建模<ref>{{cite journal |last1=Tang |first1=Jonathan |last2=Enderling |first2=Heiko |last3=Becker-Weimann |first3=Sabine |last4=Pham |first4=Christopher |last5=Polyzos |first5=Aris |last6=Chen |first6=Charlie |last7=Costes |first7=Sylvain |year=2011 |title=Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling |url=|journal=Integrative Biology |volume=3 |issue=4 |pages=408–21 |doi=10.1039/c0ib00092b |pmid=21373705 |pmc=4009383 }}</ref>，电离辐射对乳房干细胞亚群动力学<ref>{{cite journal |last1=Tang |first1=Jonathan |last2=Fernando-Garcia |first2=Ignacio |last3=Vijayakumar |first3=Sangeetha |last4=Martinez-Ruis |first4=Haydeliz |last5=Illa-Bochaca |first5=Irineu |last6=Nguyen |first6=David |last7=Mao |first7=Jian-Hua |last8=Costes |first8=Sylvain |last9=Barcellos-Hoff |first9=Mary Helen |year=2014 |title=Irradiation of juvenile, but not adult, mammary gland increases stem cell self-renewal and estrogen receptor negative tumors |url=|journal=Stem Cells |volume=32 |issue=3 |pages=649–61 |doi=10.1002/stem.1533 |pmid=24038768  |s2cid=32979016 }}</ref>、炎症<ref>{{cite journal |last1=Tang |first1=Jonathan |last2=Ley |first2=Klaus |last3=Hunt |first3=C. Anthony |year=2007 |title=Dynamics of in silico leukocyte rolling, activation, and adhesion |url=|journal=BMC Systems Biology |volume=1 |issue=14 |pages=14 |doi=10.1186/1752-0509-1-14 |pmid=17408504 |pmc=1839892 }}</ref>
 
<ref>{{cite journal |last1=Tang |first1=Jonathan |last2=Hunt |first2=C. Anthony |year=2010 |title=Identifying the rules of engagement enabling leukocyte rolling, activation, and adhesion |url=|journal=PLOS Computational Biology |volume=6 |issue=2 |pages=e1000681 |doi=10.1371/journal.pcbi.1000681 |pmid=20174606 |pmc=2824748 |bibcode=2010PLSCB...6E0681T }}</ref> 和人类免疫系统<ref>{{cite book |last1=Castiglione |first1=Filippo |first2=Franco |last2=Celada |url=http://www.crcpress.com/product/isbn/9781466597488 |title=Immune System Modeling and Simulation |publisher=CRC Press, Boca Raton |year=2015 |pages=274 |isbn=978-1-4665-9748-8}}
 
<ref>{{cite journal |last1=Tang |first1=Jonathan |last2=Hunt |first2=C. Anthony |year=2010 |title=Identifying the rules of engagement enabling leukocyte rolling, activation, and adhesion |url=|journal=PLOS Computational Biology |volume=6 |issue=2 |pages=e1000681 |doi=10.1371/journal.pcbi.1000681 |pmid=20174606 |pmc=2824748 |bibcode=2010PLSCB...6E0681T }}</ref> 和人类免疫系统<ref>{{cite book |last1=Castiglione |first1=Filippo |first2=Franco |last2=Celada |url=http://www.crcpress.com/product/isbn/9781466597488 |title=Immune System Modeling and Simulation |publisher=CRC Press, Boca Raton |year=2015 |pages=274 |isbn=978-1-4665-9748-8}}
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</ref>的影响。基于主体的模型也被用于开发决策支持系统，如乳腺癌<ref>{{Cite book |doi=10.1109/ICICT.2009.5267202 |chapter-url=http://www.cs.stir.ac.uk/~man/papers/ICICT_Cameraready_June20_09.pdf |url-status=dead |archiveurl=https://web.archive.org/web/20110614051810/http://www.cs.stir.ac.uk/~man/papers/ICICT_Cameraready_June20_09.pdf |archivedate=June 14, 2011 |df=mdy-all |chapter=A new hybrid agent-based modeling & simulation decision support system for breast cancer data analysis |title=2009 International Conference on Information and Communication Technologies |pages=134–139 |year=2009 |last1=Siddiqa |first1=Amnah |last2=Niazi |first2=Muaz |last3=Mustafa |first3=Farah |last4=Bokhari |first4=Habib |last5=Hussain |first5=Amir |last6=Akram |first6=Noreen |last7=Shaheen |first7=Shabnum |last8=Ahmed |first8=Fouzia |last9=Iqbal |first9=Sarah |isbn=978-1-4244-4608-7 |s2cid=14433449 }} (Breast Cancer DSS)</ref> 。基于主体的模型越来越多地被用于在早期阶段和临床前研究中为药理学系统建模，以帮助药物开发，并获得对生物系统的洞见<ref name=CPT>{{cite journal |last1=Butler |first1=James |last2=Cosgrove |first2=Jason |last3=Alden |first3=Kieran |last4=Read |first4=Mark |last5=Kumar |first5=Vipin |last6=Cucurull‐Sanchez |first6=Lourdes |last7=Timmis |first7=Jon |last8=Coles |first8=Mark |title=Agent‐Based Modeling in Systems Pharmacology |journal=CPT: Pharmacometrics & Systems Pharmacology |date=2015 |volume=4 |issue=11 |pages=615–629 |doi=10.1002/psp4.12018 |pmid = 26783498|pmc=4716580 }}</ref> Military applications have also been evaluated.<ref>{{cite book |title=Engineering Principles of Combat Modeling and Distributed Simulation |first1=Gnana |last1=Barathy |first2=Levent |last2=Yilmaz |first3=Andreas |last3=Tolk |location=Hoboken, NJ |publisher=[[John Wiley & Sons|Wiley]] |pages=669–714 |date=March 2012 |doi=10.1002/9781118180310.ch27 |chapter=Agent Directed Simulation for Combat Modeling and Distributed Simulation |isbn=9781118180310}}</ref> 。此外，基于主体的模型最近被用于研究分子水平的生物系统。<ref>{{Cite journal |last1=Azimi |first1=Mohammad |last2=Jamali |first2=Yousef |last3=Mofrad |first3=Mohammad R. K. |title=Accounting for Diffusion in Agent Based Models of Reaction-Diffusion Systems with Application to Cytoskeletal Diffusion |journal=PLOS ONE |volume=6 |issue=9 |pages=e25306 |doi=10.1371/journal.pone.0025306 |pmc=3179499 |pmid=21966493 |year=2011 |bibcode=2011PLoSO...625306A}}</ref><ref>{{Cite journal |last1=Azimi |first1=Mohammad |last2=Mofrad |first2=Mohammad R. K. |title=Higher Nucleoporin-Importinβ Affinity at the Nuclear Basket Increases Nucleocytoplasmic Import |journal=PLOS ONE |volume=8 |issue=11 |pages=e81741 |doi=10.1371/journal.pone.0081741 |pmc=3840022 |pmid=24282617 |year=2013 |bibcode=2013PLoSO...881741A}}</ref><ref>{{Cite journal |last1=Azimi |first1=Mohammad |last2=Bulat |first2=Evgeny |last3=Weis |first3=Karsten |last4=Mofrad |first4=Mohammad R. K. |date=2014-11-05 |title=An agent-based model for mRNA export through the nuclear pore complex |journal=Molecular Biology of the Cell |volume=25 |issue=22 |pages=3643–3653 |doi=10.1091/mbc.E14-06-1065 |pmc=4230623 |pmid=25253717}}</ref>
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</ref>的影响。基于主体的模型也被用于开发决策支持系统，如乳腺癌<ref>{{Cite book |doi=10.1109/ICICT.2009.5267202 |chapter-url=http://www.cs.stir.ac.uk/~man/papers/ICICT_Cameraready_June20_09.pdf |url-status=dead |archiveurl=https://web.archive.org/web/20110614051810/http://www.cs.stir.ac.uk/~man/papers/ICICT_Cameraready_June20_09.pdf |archivedate=June 14, 2011 |df=mdy-all |chapter=A new hybrid agent-based modeling & simulation decision support system for breast cancer data analysis |title=2009 International Conference on Information and Communication Technologies |pages=134–139 |year=2009 |last1=Siddiqa |first1=Amnah |last2=Niazi |first2=Muaz |last3=Mustafa |first3=Farah |last4=Bokhari |first4=Habib |last5=Hussain |first5=Amir |last6=Akram |first6=Noreen |last7=Shaheen |first7=Shabnum |last8=Ahmed |first8=Fouzia |last9=Iqbal |first9=Sarah |isbn=978-1-4244-4608-7 |s2cid=14433449 }} (Breast Cancer DSS)</ref> 。基于主体的模型越来越多地被用于在早期阶段和临床前研究中为药理学系统建模，以帮助药物开发，并获得对生物系统的洞见<ref name=CPT>{{cite journal |last1=Butler |first1=James |last2=Cosgrove |first2=Jason |last3=Alden |first3=Kieran |last4=Read |first4=Mark |last5=Kumar |first5=Vipin |last6=Cucurull‐Sanchez |first6=Lourdes |last7=Timmis |first7=Jon |last8=Coles |first8=Mark |title=Agent‐Based Modeling in Systems Pharmacology |journal=CPT: Pharmacometrics & Systems Pharmacology |date=2015 |volume=4 |issue=11 |pages=615–629 |doi=10.1002/psp4.12018 |pmid = 26783498|pmc=4716580 }}</ref> <ref>{{cite book |title=Engineering Principles of Combat Modeling and Distributed Simulation |first1=Gnana |last1=Barathy |first2=Levent |last2=Yilmaz |first3=Andreas |last3=Tolk |location=Hoboken, NJ |publisher=[[John Wiley & Sons|Wiley]] |pages=669–714 |date=March 2012 |doi=10.1002/9781118180310.ch27 |chapter=Agent Directed Simulation for Combat Modeling and Distributed Simulation |isbn=9781118180310}}</ref> 。此外，基于主体的模型最近被用于研究分子水平的生物系统。<ref>{{Cite journal |last1=Azimi |first1=Mohammad |last2=Jamali |first2=Yousef |last3=Mofrad |first3=Mohammad R. K. |title=Accounting for Diffusion in Agent Based Models of Reaction-Diffusion Systems with Application to Cytoskeletal Diffusion |journal=PLOS ONE |volume=6 |issue=9 |pages=e25306 |doi=10.1371/journal.pone.0025306 |pmc=3179499 |pmid=21966493 |year=2011 |bibcode=2011PLoSO...625306A}}</ref><ref>{{Cite journal |last1=Azimi |first1=Mohammad |last2=Mofrad |first2=Mohammad R. K. |title=Higher Nucleoporin-Importinβ Affinity at the Nuclear Basket Increases Nucleocytoplasmic Import |journal=PLOS ONE |volume=8 |issue=11 |pages=e81741 |doi=10.1371/journal.pone.0081741 |pmc=3840022 |pmid=24282617 |year=2013 |bibcode=2013PLoSO...881741A}}</ref><ref>{{Cite journal |last1=Azimi |first1=Mohammad |last2=Bulat |first2=Evgeny |last3=Weis |first3=Karsten |last4=Mofrad |first4=Mohammad R. K. |date=2014-11-05 |title=An agent-based model for mRNA export through the nuclear pore complex |journal=Molecular Biology of the Cell |volume=25 |issue=22 |pages=3643–3653 |doi=10.1091/mbc.E14-06-1065 |pmc=4230623 |pmid=25253717}}</ref>
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=== 在流行病学中 ===
 
=== 在流行病学中 ===
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