exclusion criteria : 1026 Selected studies for evaluation : 106 Number of discarding duplicates : 18 Final Sample : 88

Individual-based model (IBM) has been used to simulate and to design control strategies for dynamic systems that are subject to stochasticity and heterogeneity, such as infectious diseases. In the IBM, an individual is represented by a set of specific characteristics that may change dynamically over time. This feature allows a more realistic analysis of the spread of an epidemic. This paper presents a literature survey of IBM applied to biomedical and epidemiology research. The main goal is to present existing techniques, advantages and future perspectives in the development of the model. We evaluated 89 articles, which mostly analyze interventions aimed at endemic infections. In addition to the review, an overview of IBM is presented as an alternative to complement or replace compartmental models, such as the SIR (Susceptible-Infected-Recovered) model. Numerical simulations also illustrate the capabilities of IBM, as well as some limitations regarding the effects of discretization. We show that similar side-effects of discretization scheme for compartmental models may also occur in IBM, which requires careful attention.

[1]  James L Regens,et al.  An individual-based model of Plasmodium falciparum malaria transmission on the coast of Kenya. , 2003, Transactions of the Royal Society of Tropical Medicine and Hygiene.

[2]  M. Saravanan,et al.  Mobile Agent-Based approach for modeling the epidemics of communicable diseases , 2013, 2013 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM 2013).

[3]  Ricardo H. C. Takahashi,et al.  Multiobjective synthesis of robust vaccination policies , 2017, Appl. Soft Comput..

[4]  S. K. Jha,et al.  Quantifying Uncertainty in Epidemiological Models , 2012, 2012 ASE/IEEE International Conference on BioMedical Computing (BioMedCom).

[5]  Shah Jamal Alam,et al.  Detectable signals of episodic risk effects on acute HIV transmission: strategies for analyzing transmission systems using genetic data. , 2013, Epidemics.

[6]  S. Omer,et al.  Vaccine Refusal, Mandatory Immunization, and the Risks of Vaccine-Preventable Diseases , 2010 .

[7]  Xiaolong Zheng,et al.  Heterogeneous and Stochastic Agent-Based Models for Analyzing Infectious Diseases' Super Spreaders , 2013, IEEE Intelligent Systems.

[8]  S. Galea,et al.  Evaluating HIV prevention strategies for populations in key affected groups: the example of Cabo Verde , 2015, International Journal of Public Health.

[9]  V. Tran,et al.  Hepatitis C treatment as prevention of viral transmission and liver‐related morbidity in persons who inject drugs , 2016, Hepatology.

[10]  V. Grimm Ten years of individual-based modelling in ecology: what have we learned and what could we learn in the future? , 1999 .

[11]  T. Cullen,et al.  Global existence of solutions for the relativistic Boltzmann equation on the flat Robertson-Walker space-time for arbitrarily large intial data , 2005, gr-qc/0507035.

[12]  Pierre-Yves Boëlle,et al.  Modelling the Effects of Population Structure on Childhood Disease: The Case of Varicella , 2011, PLoS Comput. Biol..

[13]  N. Geard,et al.  Determining the Best Strategies for Maternally Targeted Pertussis Vaccination Using an Individual-Based Model , 2017, American journal of epidemiology.

[14]  David L. Buckeridge,et al.  Predictive Validation of an Influenza Spread Model , 2013, PloS one.

[15]  E. McBryde,et al.  Can Australia eliminate TB? Modelling immigration strategies for reaching MDG targets in a low‐transmission setting , 2014, Australian and New Zealand journal of public health.

[16]  Boris V. Schmid,et al.  Transmission of Chlamydia trachomatis through sexual partnerships: a comparison between three individual-based models and empirical data , 2012, Journal of The Royal Society Interface.

[17]  J. Valls,et al.  Individual-Based Modeling of Tuberculosis in a User-Friendly Interface: Understanding the Epidemiological Role of Population Heterogeneity in a City , 2016, Front. Microbiol..

[18]  Jacques Demongeot,et al.  Random Modelling of Contagious (Social and Infectious) Diseases: Examples of Obesity and HIV and Perspectives Using Social Networks , 2012, 2012 26th International Conference on Advanced Information Networking and Applications Workshops.

[19]  Effectiveness assessment of countermeasures against bioterrorist smallpox attacks in Japan using an individual-based model , 2010, Environmental health and preventive medicine.

[20]  M. Harry,et al.  Simulating Population Genetics of Pathogen Vectors in Changing Landscapes: Guidelines and Application with Triatoma brasiliensis , 2014, PLoS Neglected Tropical Diseases.

[21]  S. Merler,et al.  Evaluating vaccination strategies for reducing infant respiratory syncytial virus infection in low-income settings , 2015, BMC Medicine.

[22]  Steven F. Railsback,et al.  Individual-based modeling and ecology , 2005 .

[23]  F. Rubel,et al.  Cross-scale modeling of a vector-borne disease, from the individual to the metapopulation: The seasonal dynamics of sylvatic plague in Kazakhstan , 2016 .

[24]  Connie Celum,et al.  Cost-effectiveness of community-based strategies to strengthen the continuum of HIV care in rural South Africa: a health economic modelling analysis , 2015, The lancet. HIV.

[25]  M. Halloran,et al.  The Effects of Vector Movement and Distribution in a Mathematical Model of Dengue Transmission , 2013, PloS one.

[26]  Y. Sakurai,et al.  The Contribution of Residents Who Cooperate With Ring-Vaccination Measures Against Smallpox Epidemic , 2012, Disaster Medicine and Public Health Preparedness.

[27]  K. Thompson,et al.  Modeling Measles Transmission in the North American Amish and Options for Outbreak Response , 2016, Risk analysis : an official publication of the Society for Risk Analysis.

[28]  O. Bjørnstad,et al.  Dynamics of measles epidemics: Estimating scaling of transmission rates using a time series sir model , 2002 .

[29]  N. Hens,et al.  Integrating between-host transmission and within-host immunity to analyze the impact of varicella vaccination on zoster , 2015, eLife.

[30]  Richard T. Gray,et al.  Increased HIV Testing Will Modestly Reduce HIV Incidence among Gay Men in NSW and Would Be Acceptable if HIV Testing Becomes Convenient , 2013, PloS one.

[31]  W. O. Kermack,et al.  A contribution to the mathematical theory of epidemics , 1927 .

[32]  A. Hatzakis,et al.  Treatment and primary prevention in people who inject drugs for chronic hepatitis C infection: is elimination possible in a high‐prevalence setting? , 2017, Addiction.

[33]  T. Tian,et al.  Stochastic dynamics of a Hepatitis B virus transmission model , 2011, 2011 IEEE International Symposium on IT in Medicine and Education.

[34]  S. D. de Vlas,et al.  Global elimination of leprosy by 2020: are we , 2015, Parasites & Vectors.

[35]  L. Stone,et al.  Seasonal dynamics of recurrent epidemics , 2007, Nature.

[36]  B. Dervaux,et al.  Extending the Human Papillomavirus Vaccination Programme to Include Males in High-Income Countries: A Systematic Review of the Cost-Effectiveness Studies , 2015, Clinical Drug Investigation.

[37]  David A. Rolls,et al.  Hepatitis C Transmission and Treatment in Contact Networks of People Who Inject Drugs , 2013, PloS one.

[38]  S. Merler,et al.  School closure policies at municipality level for mitigating influenza spread: a model-based evaluation , 2016, BMC Infectious Diseases.

[39]  V. Tran,et al.  Dynamic modelling of hepatitis C virus transmission among people who inject drugs: a methodological review , 2013, Journal of viral hepatitis.

[40]  C. Dorso,et al.  Modeling dengue outbreaks. , 2010, Mathematical biosciences.

[41]  Jianhua Gong,et al.  Human Daily Behavior Based Simulation for Epidemic Transmission: A Case Study of SARS , 2006, 16th International Conference on Artificial Reality and Telexistence--Workshops (ICAT'06).

[42]  R. Lowe,et al.  An agent-based model driven by tropical rainfall to understand the spatio-temporal heterogeneity of a chikungunya outbreak , 2013, Acta Tropica.

[43]  Li Yang,et al.  Emerging Infectious Disease: A Computational Multi-agent Model , 2012, 2012 ASE/IEEE International Conference on BioMedical Computing (BioMedCom).

[44]  L. Allen Some discrete-time SI, SIR, and SIS epidemic models. , 1994, Mathematical biosciences.

[45]  A. Hill,et al.  Comparing Drivers and Dynamics of Tuberculosis in California, Florida, New York, and Texas , 2017, American journal of respiratory and critical care medicine.

[46]  S. Galea,et al.  Understanding the effects of different HIV transmission models in individual-based microsimulation of HIV epidemic dynamics in people who inject drugs , 2016, Epidemiology and Infection.

[47]  Cláudia Torres Codeço,et al.  DengueME: A Tool for the Modeling and Simulation of Dengue Spatiotemporal Dynamics † , 2016, International journal of environmental research and public health.

[48]  H. Ishikawa,et al.  Assessment of intervention strategies against a novel influenza epidemic using an individual-based model , 2009, Environmental health and preventive medicine.

[49]  Takao Terano,et al.  A Health Policy Simulation Model of Smallpox and Ebola Haemorrhagic Fever , 2015, KES-AMSTA.

[50]  Nadra Guizani,et al.  Modeling and evaluation of disease spread behaviors , 2014, 2014 International Wireless Communications and Mobile Computing Conference (IWCMC).

[51]  Zhidong Teng,et al.  Stability and bifurcation analysis in a discrete SIR epidemic model , 2014, Math. Comput. Simul..

[52]  Chris Beyrer,et al.  The Impact of Pre-Exposure Prophylaxis Among Men Who Have Sex With Men: An Individual-Based Model. , 2017, Journal of acquired immune deficiency syndromes.

[53]  Nikolai V. Pertsev,et al.  Using High Performance Algorithms for the Hybrid Simulation of Disease Dynamics on CPU and GPU , 2015, ICCS.

[54]  W. David Kelton,et al.  Estimating the proportion of tuberculosis recent transmission via simulation , 2014, Proceedings of the Winter Simulation Conference 2014.

[55]  Maleq Khan,et al.  An integrated agent-based approach for modeling disease spread in large populations to support health informatics , 2016, 2016 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI).

[56]  I. Andrianakis,et al.  History matching of a complex epidemiological model of human immunodeficiency virus transmission by using variance emulation , 2016, Journal of the Royal Statistical Society. Series C, Applied statistics.

[57]  William W. L. Wong,et al.  A Parallel Sliding Region Algorithm to Make Agent-Based Modeling Possible for a Large-Scale Simulation: Modeling Hepatitis C Epidemics in Canada , 2016, IEEE Journal of Biomedical and Health Informatics.

[58]  Investigation of Prediction and Establishment of SIR Model for H1N1 Epidemic Disease , 2010, 2010 4th International Conference on Bioinformatics and Biomedical Engineering.

[59]  M. Law,et al.  Identifying factors that lead to the persistence of imported gonorrhoeae strains: a modelling study , 2016, Sexually Transmitted Infections.

[60]  G. Milne,et al.  A Small Community Model for the Transmission of Infectious Diseases: Comparison of School Closure as an Intervention in Individual-Based Models of an Influenza Pandemic , 2008, PloS one.

[61]  J. Gareth Polhill,et al.  The ODD protocol: A review and first update , 2010, Ecological Modelling.

[62]  Bin Chen,et al.  A synthetic computational environment: To control the spread of respiratory infections in a virtual university , 2018 .

[63]  C. Viboud,et al.  Using phenomenological models for forecasting the 2015 Ebola challenge. , 2016, Epidemics.

[64]  M. Jit,et al.  Potential overestimation of HPV vaccine impact due to unmasking of non-vaccine types: quantification using a multi-type mathematical model. , 2012, Vaccine.

[65]  R. Riolo,et al.  HIV Transmission by Stage of Infection and Pattern of Sexual Partnerships , 2010, Epidemiology.

[66]  Segev Wasserkrug,et al.  Utilizing model characteristics to obtain efficient parallelization in the context of agent based epidemiological models , 2007, 2007 Winter Simulation Conference.

[67]  Pejman Rohani,et al.  An Agent-Based Model to study the epidemiological and evolutionary dynamics of Influenza viruses , 2011, BMC Bioinformatics.

[68]  P. Kaye Infectious diseases of humans: Dynamics and control , 1993 .

[69]  D. DeAngelis,et al.  Individual-based models in ecology after four decades , 2014, F1000prime reports.

[70]  Stefano Merler,et al.  An individual-based model of hepatitis A transmission. , 2009, Journal of theoretical biology.

[71]  M. Pallansch,et al.  Individual-based modeling of potential poliovirus transmission in connected religious communities in North America with low uptake of vaccination. , 2014, Journal of Infectious Diseases.

[72]  Susan M. Sanchez,et al.  A scalable discrete event stochastic agent-based model of infectious disease propagation , 2015, 2015 Winter Simulation Conference (WSC).

[73]  A. Fauci,et al.  The challenge of emerging and re-emerging infectious diseases , 2004, Nature.

[74]  Robert C. Spear,et al.  Exploring the contribution of host susceptibility to epidemiological patterns of Schistosoma japonicum infection using an individual-based model. , 2015, The American journal of tropical medicine and hygiene.

[75]  Nilimesh Halder,et al.  Analysis of the effectiveness of interventions used during the 2009 A/H1N1 influenza pandemic , 2010, BMC public health.

[76]  D. Donnell,et al.  High Incidence Is Not High Exposure: What Proportion of Prevention Trial Participants Are Exposed to HIV? , 2015, PloS one.

[77]  Steven F. Railsback,et al.  Agent-Based and Individual-Based Modeling: A Practical Introduction , 2011 .

[78]  Cesare Furlanello,et al.  Modeling socio-demography to capture tuberculosis transmission dynamics in a low burden setting. , 2011, Journal of theoretical biology.

[79]  Su Yan The model of Ebola disease control and optimization algorithm of pharmaceutical logistics path , 2015, 2015 8th International Conference on Biomedical Engineering and Informatics (BMEI).

[80]  R. Legood,et al.  Economic modelling assessment of the HPV quadrivalent vaccine in Brazil: a dynamic individual-based approach. , 2012, Vaccine.

[81]  Wayne M. Getz,et al.  Using Nova to construct agent-based models for epidemiological teaching and research , 2015, 2015 Winter Simulation Conference (WSC).

[82]  John C. Carlson,et al.  A simulation model of African Anopheles ecology and population dynamics for the analysis of malaria transmission , 2004, Malaria Journal.

[83]  Jong-Hoon Kim,et al.  Transmission dynamics of oral polio vaccine viruses and vaccine-derived polioviruses on networks. , 2015, Journal of theoretical biology.

[84]  Charly Favier,et al.  Influence of spatial heterogeneity on an emerging infectious disease: the case of dengue epidemics , 2005, Proceedings of the Royal Society B: Biological Sciences.

[85]  S. D. de Vlas,et al.  Leprosy New Case Detection Trends and the Future Effect of Preventive Interventions in Pará State, Brazil: A Modelling Study , 2016, PLoS neglected tropical diseases.

[86]  A. Ramanathan,et al.  Verification of Compartmental Epidemiological Models Using Metamorphic Testing, Model Checking and Visual Analytics , 2012, 2012 ASE/IEEE International Conference on BioMedical Computing (BioMedCom).

[87]  S. Tisue NetLogo : Design and Implementation of a Multi-Agent Modeling Environment , 2004 .

[88]  R M May,et al.  AIDS pathogenesis: mathematical models of HIV and SIV infections. , 1992 .

[89]  Jane Labadin,et al.  An epidemic aggregate and individual-based model in a patchy environment , 2013, 2013 8th International Conference on Information Technology in Asia (CITA).

[90]  Xiuju FU,et al.  A multi-agent model for adaptive vaccination during infectious disease outbreaks , 2016, 2016 International Conference on Computing Technologies and Intelligent Data Engineering (ICCTIDE'16).

[91]  Ricardo H. C. Takahashi,et al.  Reducing vaccination level to eradicate a disease by means of a mixed control with isolation , 2018, Biomed. Signal Process. Control..

[92]  S. D. de Vlas,et al.  Mathematical modelling of leprosy and its control. , 2015, Advances in parasitology.

[93]  H. Ward,et al.  How Many HIV Infections May Be Averted by Targeting Primary Infection in Men Who Have Sex With Men? Quantification of Changes in Transmission-Risk Behavior, Using an Individual-Based Model , 2014, The Journal of infectious diseases.

[94]  J. Baeten,et al.  Could misreporting of condom use explain the observed association between injectable hormonal contraceptives and HIV acquisition risk?☆☆☆★ , 2017, Contraception.

[95]  W. Kelton,et al.  A Novel Tool Improves Existing Estimates of Recent Tuberculosis Transmission in Settings of Sparse Data Collection , 2015, PloS one.

[96]  M. Kretzschmar,et al.  Cost-Effectiveness of Hepatitis C Treatment for People Who Inject Drugs and the Impact of the Type of Epidemic; Extrapolating from Amsterdam, the Netherlands , 2016, PloS one.

[97]  A. McKane,et al.  Stochastic formulation of ecological models and their applications. , 2012, Trends in ecology & evolution.

[98]  Benoit Gaudou,et al.  O.D.D.: A Promising but Incomplete Formalism for Individual-Based Model Specification , 2010, 2010 IEEE RIVF International Conference on Computing & Communication Technologies, Research, Innovation, and Vision for the Future (RIVF).

[99]  Birgit Müller,et al.  A standard protocol for describing individual-based and agent-based models , 2006 .

[100]  Nathan H. Schumaker,et al.  HexSim: a modeling environment for ecology and conservation , 2018, Landscape Ecology.

[101]  James O Lloyd-Smith,et al.  Potential impact of vaccination on the hepatitis C virus epidemic in injection drug users. , 2009, Epidemics.

[102]  Jan Broeckhove,et al.  Social Contact Patterns in an Individual-based Simulator for the Transmission of Infectious Diseases (Stride) , 2017, ICCS.

[103]  Niel Hens,et al.  Lessons from a decade of individual-based models for infectious disease transmission: a systematic review (2006-2015) , 2017, BMC Infectious Diseases.

[104]  C. Furlanello,et al.  Mitigation Measures for Pandemic Influenza in Italy: An Individual Based Model Considering Different Scenarios , 2008, PloS one.

[105]  I B Schwartz,et al.  Seasonality and period-doubling bifurcations in an epidemic model. , 1984, Journal of theoretical biology.

[106]  K. Axhausen,et al.  Reconstructing the 2003/2004 H3N2 influenza epidemic in Switzerland with a spatially explicit, individual-based model , 2011, BMC infectious diseases.

[107]  J. J. Nutaro,et al.  Agent-Based vs. Equation-Based Epidemiological Models: A Model Selection Case Study , 2012, 2012 ASE/IEEE International Conference on BioMedical Computing (BioMedCom).

[108]  Ricardo H. C. Takahashi,et al.  INDIVIDUAL-BASED MODEL (IBM): AN ALTERNATIVE FRAMEWORK FOR EPIDEMIOLOGICAL COMPARTMENT MODELS , 2016 .