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The COVID-19 pandemic has highlighted the importance of in-silico epidemiological modelling in predicting the dynamics of infectious diseases to inform health policy and decision makers about suitable prevention and containment strategies.
MCMC using Hamiltonian dynamics
Radford M. Neal · 1901
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Etalumis: Bringing Probabilistic Programming to Scientific Simulators at Scale
Atılım Güneş Baydin, Lei Shao, Wahid Bhimji, Lukas Heinrich, Lawrence Meadows, Jialin Liu, Andreas Munk, Saeid Naderiparizi, Bradley Gram-Hansen, Gilles Louppe, Mingfei Ma, Xiaohui Zhao, Philip Torr, Victor Lee, Kyle Cranmer, Prabhat, and Frank Wood · 1907
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Deep Probabilistic Surrogate Networks for Universal Simulator Approximation
Andreas Munk, Adam Ścibior, Atılım Güneş Baydin, Andrew Stewart, Goran Fernlund, Anoush Poursartip, and Frank Wood · 1910
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The frontier of simulation-based inference
Kyle Cranmer, Johann Brehmer, and Gilles Louppe · 1911
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A contribution to the mathematical theory of epidemics
William Ogilvy Kermack and Anderson G McKendrick · 1927
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Some discrete-time SI, SIR, and SIS epidemic models
Linda JS Allen · 1994
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Bayesian calibration of computer models
Marc C. Kennedy and Anthony O’Hagan · 2001
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Approximate Bayesian computation in population genetics
Mark A Beaumont, Wenyang Zhang, and David J Balding · 2002
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Systematic review of the use and value of computer simulation modelling in population health and health care delivery
David Fone, Sandra Hollinghurst, Mark Temple, Alison Round, Nathan Lester, Alison Weightman, Katherine Roberts, Edward Coyle, Gwyn Bevan, and Stephen Palmer · 2003
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Planning as Inference in Epidemiological Models
Frank Wood, Andrew Warrington, Saeid Naderiparizi, Christian Weilbach, Vaden Masrani, William Harvey, Adam Scibior, Boyan Beronov, and Ali Nasseri · 2003
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Probabilistic sensitivity analysis of complex models: a Bayesian approach
Jeremy E Oakley and Anthony O’Hagan · 2004
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Strategies for mitigating an influenza pandemic
Neil M. Ferguson, Derek A. T. Cummings, Christophe Fraser, James C. Cajka, Philip C. Cooley, and Donald S. Burke · 2006
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Cooking up an open source EMR for developing countries: OpenMRS–a recipe for successful collaboration
Burke W Mamlin, Paul G Biondich, Ben A Wolfe, Hamish Fraser, Darius Jazayeri, Christian Allen, Justin Miranda, and William M Tierney · 2006
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Mathematical modeling of the impact of malaria vaccines on the clinical epidemiology and natural history of plasmodium falciparum malaria: Overview
Thomas Smith, Gerry F Killeen, Nicolas Maire, Amanda Ross, Louis Molineaux, Fabrizio Tediosi, Guy Hutton, Jürg Utzinger, Klaus Dietz, and Marcel Tanner · 2006
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Compartmental models in epidemiology
Fred Brauer · 2008
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A tutorial on particle filtering and smoothing: Fifteen years later
Arnaud Doucet and Adam M Johansen · 2009
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Calibration methods used in cancer simulation models and suggested reporting guidelines
Natasha K Stout, Amy B Knudsen, Chung Yin Kong, Pamela M McMahon, and G Scott Gazelle · 2009
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Approximate Bayesian computation (ABC) in practice
Katalin Csilléry, Michael GB Blum, Oscar E Gaggiotti, and Olivier François · 2010
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Application of a system dynamics model to inform investment in smoking cessation services in New Zealand
Martin I Tobias, Robert Y Cavana, and Ashley Bloomfield · 2010
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Handbook of Markov Chain Monte Carlo
Steve Brooks, Andrew Gelman, Galin Jones, and Xiao-Li Meng · 2011
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Using discrete event simulation to compare the performance of family health unit and primary health care centre organizational models in Portugal
André S Fialho, Mónica D Oliveira, and Armando B Sá · 2011
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Mathematical models for the study of HIV spread and control amongst men who have sex with men
Narat Punyacharoensin, William John Edmunds, Daniela De Angelis, and Richard Guy White · 2011
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Church: a language for generative models
Noah Goodman, Vikash Mansinghka, Daniel M Roy, Keith Bonawitz, and Joshua B Tenenbaum · 2012
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Ensemble Modeling of the Likely Public Health Impact of a Pre-Erythrocytic Malaria Vaccine
Thomas Smith, Amanda Ross, Nicolas Maire, Nakul Chitnis, Alain Studer, Diggory Hardy, Alan Brooks, Melissa Penny, and Marcel Tanner · 2012
High-quality health systems in the sustainable development goals era: time for a revolution
Margaret E Kruk, Anna D Gage, Catherine Arsenault, Keely Jordan, Hannah H Leslie, Sanam Roder-DeWan, Olusoji Adeyi, Pierre Barker, Bernadette Daelmans, Svetlana V Doubova, et al · 2018
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Reinforcement Learning and Control as Probabilistic Inference: Tutorial and Review
Sergey Levine · 2018
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Artificial intelligence, machine learning and health systems
Trishan Panch, Peter Szolovits, and Rifat Atun · 2018
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Simple, distributed, and accelerated probabilistic programming
Dustin Tran, Matthew D. Hoffman, Dave Moore, Christopher Suter, Srinivas Vasudevan, Alexey Radul, Matthew Johnson, and Rif A. Saurous · 2018
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An introduction to probabilistic programming
Jan-Willem van de Meent, Brooks Paige, Hongseok Yang, and Frank Wood · 2018
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Rethinking health systems strengthening: key systems thinking tools and strategies for transformational change
R Chad Swanson, Adriano Cattaneo, Elizabeth Bradley, Somsak Chunharas, Rifat Atun, Kaja M Abbas, Korina Katsaliaki, Navonil Mustafee, Benjamin Mason Meier, and Allan Best · 2012
Cited alongside, same era.
Learning about physical parameters: The importance of model discrepancy
Jennỳ Brynjarsdóttir and Anthony O’Hagan · 2014
Cited alongside, same era.
Global, regional, and national incidence and mortality for HIV, tuberculosis, and malaria during 1990–2013: a systematic analysis for the global burden of disease study 2013
Christopher JL Murray, Katrina F Ortblad, Caterina Guinovart, Stephen S Lim, Timothy M Wolock, D Allen Roberts, Emily A Dansereau, Nicholas Graetz, Ryan M Barber, Jonathan C Brown, et al · 2014
Cited alongside, same era.
Impact of different policies on unhealthy dietary behaviors in an urban adult population: an agent-based simulation model
Donglan Zhang, Philippe J Giabbanelli, Onyebuchi A Arah, and Frederick J Zimmerman · 2014
Cited alongside, same era.
Mobile Health: A Technology Road Map , volume 5
Sasan Adibi · 2015
Cited alongside, same era.
Bayesian History Matching of Complex Infectious Disease Models Using Emulation: A Tutorial and a Case Study on HIV in Uganda
Ioannis Andrianakis, Ian R. Vernon, Nicky McCreesh, Trevelyan J. McKinley, Jeremy E. Oakley, Rebecca N. Nsubuga, Michael Goldstein, and Richard G. White · 2015
Cited alongside, same era.
Probabilistic programming in Python using PyMC3
John Salvatier, Thomas V Wiecki, and Christopher Fonnesbeck · 2016
Cited alongside, same era.
Later among the works it cites.
Artificial intelligence (AI) and global health: how can AI contribute to health in resource-poor settings?
Brian Wahl, Aline Cossy-Gantner, Stefan Germann, and Nina R Schwalbe · 2018
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Mean Field Multi-Agent Reinforcement Learning
Yaodong Yang, Rui Luo, Minne Li, Ming Zhou, Weinan Zhang, and Jun Wang · 2018
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Systems modelling as an approach for understanding and building consensus on non-communicable diseases (NCD) management in Cambodia
John P Ansah, Amina Mahmood Islam, Victoria Koh, Vanthy Ly, Hero Kol, David B Matchar, Chhun Loun, and Mondol Loun · 2019
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Pyro: Deep universal probabilistic programming
Eli Bingham, Jonathan P Chen, Martin Jankowiak, Fritz Obermeyer, Neeraj Pradhan, Theofanis Karaletsos, Rohit Singh, Paul Szerlip, Paul Horsfall, and Noah D Goodman · 2019
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The role of modelling in the policy decision making process for cancer screening: example of prostate specific antigen screening
Abraham M Getaneh, Eveline Heijnsdijk, and Harry de Koning · 2019
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Efficient Bayesian inference for nested simulators
Bradley Gram-Hansen, Christian Schroeder de Witt, Robert Zinkov, Saeid Naderiparizi, Adam Scibior, Andreas Munk, Frank Wood, Mehrdad Ghadiri, Philip Torr, Yee Whye Te, Atılım Güneş Baydin, and Tom Rainforth · 2019
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Hijacking malaria simulators with probabilistic programming
Bradley Gram-Hansen, Christian Schroeder, Philip H.S. Torr, Yee Whye Teh, Tom Rainforth, and Atılım Güneş Baydin · 2019
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Multitask soft option learning
Maximilian Igl, Andrew Gambardella, Jinke He, Nantas Nardelli, N Siddharth, Wendelin Böhmer, and Shimon Whiteson · 2019
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Amortized rejection sampling in universal probabilistic programming
Saeid Naderiparizi, Adam Ścibior, Andreas Munk, Mehrdad Ghadiri, Atılım Güneş Baydin, Bradley Gram-Hansen, Christian Schroeder de Witt de Witt, Robert Zinkov, Philip H.S. Torr, Tom Rainforth, Yee Whye Teh, and Frank Wood · 2019
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Agent-Based and Individual-Based Modeling: A Practical Introduction
Steven F Railsback and Volker Grimm · 2019
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Coronavirus, 2020
WHO · 2019
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Commentary on Ferguson, et al., “Impact of Non-pharmaceutical Interventions (NPIs) to Reduce COVID-19 Mortality and Healthcare Demand”
S. Eubank, I. Eckstrand, B. Lewis, S. Venkatramanan, M. Marathe, and C. L. Barrett · 2020
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Report 9: Impact of non-pharmaceutical interventions (NPIs) to reduce COVID19 mortality and healthcare demand
Neil Ferguson, Daniel Laydon, Gemma Nedjati Gilani, Natsuko Imai, Kylie Ainslie, Marc Baguelin, Sangeeta Bhatia, Adhiratha Boonyasiri, ZULMA Cucunuba Perez, Gina Cuomo-Dannenburg, et al · 2020
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Covid-19: public health experts demand evidence behind UK’s short self-isolation advice
Elisabeth Mahase · 2020
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