Publications

Swapnil Mishra, Seth Flaxman, Tresnia Berah, Harrison Zhu, Mikko Pakkanen, Samir Bhatt (2022). π VAE: a stochastic process prior for Bayesian deep learning with MCMC. Statistics and Computing.

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Matthew J Penn, Daniel J Laydon, Joseph Penn, Charles Whittaker, Christian Morgenstern, Oliver Ratmann, Swapnil Mishra, Mikko S Pakkanen, Christl A Donnelly, Samir Bhatt (2022). The uncertainty of infectious disease outbreaks is underestimated. arXiv preprint arXiv:2210.14221.

Andrea Brizzi, Charles Whittaker, Luciana Servo, Iwona Hawryluk, Carlos A Prete, William M de Souza, Renato S Aguiar, Leonardo JT Araujo, Leonardo S Bastos, Alexandra Blenkinsop, others (2022). Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals. Nature medicine.

Elizaveta Semenova, Yidan Xu, Adam Howes, Theo Rashid, Samir Bhatt, Swapnil Mishra, Seth Flaxman (2022). PriorVAE: encoding spatial priors with variational autoencoders for small-area estimation. Journal of the Royal Society Interface.

Nicholas F Brazeau, Robert Verity, Sara Jenks, Han Fu, Charles Whittaker, Peter Winskill, Ilaria Dorigatti, Patrick GT Walker, Steven Riley, Ricardo P Schnekenberg, others (2022). Estimating the COVID-19 infection fatality ratio accounting for seroreversion using statistical modelling. Communications medicine.

Xenia Miscouridou, Samir Bhatt, George Mohler, Seth Flaxman, Swapnil Mishra (2022). Cox-Hawkes: doubly stochastic spatiotemporal Poisson processes. arXiv preprint arXiv:2210.11844.

Seth Flaxman, Charles Whittaker, Elizaveta Semenova, Theo Rashid, Robbie Parks, Alexandra Blenkinsop, H Juliette T Unwin, Swapnil Mishra, Samir Bhatt, Deepti Gurdasani, others (2022). Covid-19 is a leading cause of death in children and young people ages 0-19 years in the United States. medRxiv.

George Altman, Janvi Ahuja, Joshua Teperowski Monrad, Gurpreet Dhaliwal, Charlie Rogers-Smith, Gavin Leech, Benedict Snodin, Jonas B Sandbrink, Lukas Finnveden, Alexander John Norman, others (2022). A dataset of non-pharmaceutical interventions on SARS-CoV-2 in Europe. Scientific Data.

Petra Mlcochova, Steven A Kemp, Mahesh Shanker Dhar, others, Swapnil Mishra, Charles Whittaker, Thomas Mellan, others, Samir Bhatt, Seth Flaxman, Leo C James, Davide Corti, Luca Piccoli, Wendy S Barclay, Partha Rakshit, Anurag Agrawal, Ravindra K Gupta (2021). SARS-CoV-2 B. 1.617. 2 Delta variant replication and immune evasion. Nature (2021).

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Mahesh S. Dhar, Robin Marwal, Radhakrishnan VS, Kalaiarasan Ponnusamy, Bani Jolly, Rahul C. Bhoyar, Viren Sardana, Salwa Naushin, Mercy Rophina, Thomas A. Mellan, Swapnil Mishra, Charles Whittaker, others, Seth Flaxman, Samir Bhatt, Rajesh Pandey, Debasis Dash, Mohammed Faruq, Hemlata Lall, Hema Gogia, Preeti Madan, Sanket Kulkarni, Himanshu Chauhan, Shantanu Sengupta, Sandhya Kabra, INSACOG, Ravindra K. Gupta, Sujeet K. Singh, Anurag Agrawal, Partha Rakshit (2021). Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science (2021).

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Mrinank Sharma*, Sören Mindermann*, Charlie Rogers-Smith, Gavin Leech, Benedict Snodin, Janvi Ahuja, Jonas B. Sandbrink, Joshua Teperowski Monrad, George Altman, Gurpreet Dhaliwal, Lukas Finnveden, Alexander John Norman, Sebastian B. Oehm, Julia Fabienne Sandkühler, Laurence Aitchison, Tomáš Gavenčiak, Thomas Mellan, Jan Kulveit, Leonid Chindelevitch, Seth Flaxman, Yarin Gal, Swapnil Mishra**, Samir Bhatt**, Jan Markus Brauner** (2021). Understanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe. Nat. Commun..

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Swapnil Mishra*, Sören Mindermann*, Mrinank Sharma*, Charles Whittaker*, Thomas A Mellan, Thomas Wilton, Dimitra Klapsa, Ryan Mate, Martin Fritzsche, Maria Zambon, Janvi Ahuja, Adam Howes, Xenia Miscouridou, Guy P Nason, Oliver Ratmann, Elizaveta Semenova, Gavin Leech, Julia Fabienne Sandkühler, Charlie Rogers-Smith, Michaela Vollmer, H Juliette T Unwin, Yarin Gal, Meera Chand, Axel Gandy, COG-UK, Javier Martin, Erik Volz, Neil M Ferguson, Samir Bhatt*, Jan M Brauner*, Seth Flaxman* (2021). Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England. EClinicalMedicine.

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Gideon Meyerowitz-Katz, Samir Bhatt, Oliver Ratmann, Jan Markus Brauner, Seth Flaxman, Swapnil Mishra, Mrinank Sharma, Sören Mindermann, Valerie Bradley, Michaela Vollmer, Lea Merone, Gavin Yamey (2021). Is the cure really worse than the disease? The health impacts of lockdowns during COVID-19. BMJ Global Health.

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Swapnil Mishra*, James A Scott*, Daniel J Laydon*, Seth Flaxman*, Axel Gandy, Thomas A Mellan, H Juliette T Unwin, Michaela Vollmer, Helen Coupland, Oliver Ratmann, Melodie Monod, Harrison H Zhu, Anne Cori, Katy AM Gaythorpe, Lilith K Whittles, Charles Whittaker, Christl A Donnelly, Neil M Ferguson*, Samir Bhatt* (2021). Comparing the responses of the UK, Sweden and Denmark to COVID-19 using counterfactual modelling. Scientific Reports.

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Soumik Purkayastha, Rupam Bhattacharyya, Ritwik Bhaduri, Ritoban Kundu, Xuelin Gu, Maxwell Salvatore, Debashree Ray, Swapnil Mishra, Bhramar Mukherjee (2021). A comparison of five epidemiological models for transmission of SARS-CoV-2 in India. BMC infectious diseases.

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Konrad Krawczyk, Tadeusz Chelkowski, Daniel J Laydon, Swapnil Mishra, Denise Xifara, Seth Flaxman, Thomas Mellan, Veit Schwämmle, Richard Röttger, Johannes T Hadsund, Samir Bhatt (2021). Quantifying Online News Media Coverage of the COVID-19 Pandemic: Text Mining Study and Resource.

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Swapnil Mishra*, Nuno R. Faria*, Thomas A. Mellan*, Charles Whittaker*, Ingra M. Claro*, Darlan da S. Candido*, others, Oliver G. Pybus‡, Seth Flaxman‡, Samir Bhatt‡, Ester C. Sabino‡ (2021). Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science (2021).

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Daniel J Laydon, Swapnil Mishra, Wes R Hinsley, Pantelis Samartsidis, Seth Flaxman, Axel Gandy, Neil M Ferguson, Samir Bhatt (2021). Modelling the impact of the tier system on SARS-CoV-2 transmission in the UK between the first and second national lockdowns. BMJ open.

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Swapnil Mishra*, Erik Volz*, Meera Chand*, Jeffrey C. Barrett*, Robert Johnson*, Lily Geidelberg, Wes R. Hinsley, Daniel J. Laydon, Gavin Dabrera, Áine O’Toole, Roberto Amato, Manon Ragonnet-Cronin, Ian Harrison, Ben Jackson, Cristina V. Ariani, Olivia Boyd, Nicholas J. Loman, John T. McCrone, Sónia Gonçalves, David Jorgensen, Richard Myers, Verity Hill, David K. Jackson, Katy Gaythorpe, Natalie Groves, John Sillitoe, Dominic P. Kwiatkowski, The COVID-19 Genomics UK (COG-UK) consortium, Seth Flaxman, Oliver Ratmann, Samir Bhatt, Susan Hopkins, Axel Gandy*, Andrew Rambaut*, Neil M. Ferguson* (2021). Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature (2021).

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Mélodie Monod, Alexandra Blenkinsop, Xiaoyue Xi, Daniel Hebert, Sivan Bershan, Simon Tietze, Marc Baguelin, Valerie C. Bradley, Yu Chen, Helen Coupland, Sarah Filippi, Jonathan Ish-Horowicz, Martin McManus, Thomas Mellan, Axel Gandy, Michael Hutchinson, H. Juliette T Unwin, Sabine L. van Elsland, Michaela A. C. Vollmer, Sebastian Weber, Harrison Zhu, Anne Bezancon, Neil M. Ferguson, Swapnil Mishra, Seth Flaxman, Samir Bhatt, Oliver Ratmann, on behalf of the Imperial College COVID-9 Response Team (2021). Age groups that sustain resurging COVID-9 epidemics in the United States. Science (2021).

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H Juliette T Unwin, Isobel Routledge, Seth Flaxman, Marian-Andrei Rizoiu, Shengjie Lai, Justin Cohen, Daniel J Weiss, Swapnil Mishra, Samir Bhatt (2021). Using Hawkes Processes to model imported and local malaria cases in near-elimination settings. PLoS computational biology.

Amelia Bertozzi-Villa, Caitlin A Bever, Hannah Koenker, Daniel J Weiss, Camilo Vargas-Ruiz, Anita K Nandi, Harry S Gibson, Joseph Harris, Katherine E Battle, Susan F Rumisha, others (2021). Maps and metrics of insecticide-treated net access, use, and nets-per-capita in Africa from 2000-2020. Nature communications.

Oliver J Watson, Mervat Alhaffar, Zaki Mehchy, Charles Whittaker, Zack Akil, Nicholas F Brazeau, Gina Cuomo-Dannenburg, Arran Hamlet, Hayley A Thompson, Marc Baguelin, others (2021). Leveraging community mortality indicators to infer COVID-19 mortality and transmission dynamics in Damascus, Syria. Nature communications.

Manon Ragonnet-Cronin, Olivia Boyd, Lily Geidelberg, David Jorgensen, Fabricia F Nascimento, Igor Siveroni, Robert A Johnson, Marc Baguelin, Zulma M Cucunubá, Elita Jauneikaite, others (2021). Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions. Nature communications.

Iwona Hawryluk, Henrique Hoeltgebaum, Swapnil Mishra, Xenia Miscouridou, Ricardo P Schnekenberg, Charles Whittaker, Michaela Vollmer, Seth Flaxman, Samir Bhatt, Thomas A Mellan (2021). Gaussian process nowcasting: application to COVID-19 mortality reporting. Uncertainty in Artificial Intelligence.

James A Scott, Axel Gandy, Swapnil Mishra, Samir Bhatt, Seth Flaxman, H Juliette T Unwin, Jonathan Ish-Horowicz (2021). Epidemia: An R Package for Semi-Mechanistic Bayesian Modelling of Infectious Diseases using Point Processes. arXiv preprint arXiv:2110.12461.

Michaela AC Vollmer, Ben Glampson, Thomas Mellan, Swapnil Mishra, Luca Mercuri, Ceire Costello, Robert Klaber, Graham Cooke, Seth Flaxman, Samir Bhatt (2021). A unified machine learning approach to time series forecasting applied to demand at emergency departments. BMC Emergency Medicine.

G Mohler, S Mishra, B Ray, L Magee, P Huynh, M Canada, D O’Donnell, S Flaxman (2021). A modified two-process Knox test for investigating the relationship between law enforcement opioid seizures and overdoses. Proceedings of the Royal Society A.

Iwona Hawryluk, Thomas A. Mellan, Henrique Hoeltgebaum, Swapnil Mishra, Ricardo P. Schnekenberg, Charles Whittaker, Harrison Zhu, Axel Gandy, Christl A. Donnelly, Seth Flaxman, Samir Bhatt (2020). Inference of COVID-19 epidemiological distributions from Brazilian hospital data. J. R. Soc. Interface.

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Swapnil Mishra*, H. Juliette T. Unwin*, Valerie C Bradley*, Axel Gandy*, Michaela A. C. Vollmer, Thomas A. Mellan, Helen Coupland, Charles Whittaker, Harrison Zhu, Imperial College COVID-19 Response Team, Azra C. Ghani, Neil M. Ferguson, Steven M. Riley, Christl A. Donnelly, Samir Bhatt*, Seth Flaxman* (2020). State-level tracking of COVID-19 in the United States.. Nat. Commun..

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Patrick G. T. Walker, Charles Whittaker, Oliver J. Watson, Swapnil Mishra, Imperial College COVID-19 Response Team, Neil M. Ferguson, Azra C. Ghani (2020). The impact of COVID-19 and strategies for mitigation and suppression in low- and middle-income countries. Science (2020).

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Darlan S. Candido, Ingra M. Claro, Jaqueline G. de Jesus, William M. Souza, Filipe R. R. Moreira, Simon Dellicour, Thomas A. Mellan, others, Swapnil Mishra, Oliver G. Pybus, Ester C. Sabino, Nuno Rodrigues Faria (2020). Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science (2020).

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Enrico Lavezzo, Elisa Franchin, Constanze Ciavarella, others, Swapnil Mishra, Imperial College COVID-19 Response Team, Christl A. Donnelly, Neil M. Ferguson, Ilaria Dorigatti, Andrea Crisanti (2020). Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo’. Nature (2020).

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Lucy C Okell, Robert Verity, Oliver J Watson, Swapnil Mishra, Patrick Walker, Charlie Whittaker, Aris Katzourakis, Christl A Donnelly, Steven Riley, Azra C Ghani, Axel Gandy, Seth Flaxman, Neil M Ferguson, Samir Bhatt (2020). Have deaths from COVID-19 in Europe plateaued due to herd immunity?. The Lancet.

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Swapnil Mishra*, Seth Flaxman*, Axel Gandy*, H. Juliette T. Unwin, Thomas A. Mellan, Helen Coupland, Charles Whittaker, Harrison Zhu, Tresnia Berah, Jeffrey W. Eaton, Mélodie Monod, Imperial College COVID-19 Response Team, Azra C. Ghani, Christl A. Donnelly, Steven M. Riley, Michaela A. C. Vollmer, Neil M. Ferguson, Lucy C. Okell, Samir Bhatt* (2020). Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe.. Nature (2020).

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Swapnil Mishra*, Thomas A. Mellan*, Henrique H Hoeltgebaum*, Swapnil Mishra*, Charles Whittaker*, RicardoPSchnekenberg*, Axel Gandy*, H. Juliette T. Unwin, Michaela A C Vollmer, Helen Coupland, Harrison Zhu, Imperial College COVID-19 Response Team, Azra C. Ghani, Neil M. Ferguson, Steven M. Riley, Christl A. Donnelly, Seth Flaxman*, Samir Bhatt* (2020). Estimating COVID-19 cases and reproduction number in Brazil.. .

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Swapnil Mishra∗, Michaela A.C. Vollmer∗, H Juliette T Unwin∗, Axel Gandy∗, Thomas A. Mellan, Valerie Bradley, Helen Coupland, Harrison Zhu, Imperial College COVID-19 Response Team, Azra C. Ghani, Neil M. Ferguson, Steven M. Riley, Christl A. Donnelly, Ilaria Dorigatti, Seth Flaxman*, Samir Bhatt* (2020). A sub-national analysis of the rate of transmission of COVID-19 in Italy.. .

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Swapnil Mishra (2019). Linking Models for Collective Attention in Social Media. ANU.

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Swapnil Mishra (2019). Bridging Models for Popularity Prediction on Social Media. WSDM.

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Swapnil Mishra, Marian-Andrei Rizoiu, Lexing Xie (2018). Modeling Popularity in Asynchronous Social Media Streams with Recurrent Neural Networks. ICWSM.

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Marian-Andrei Rizoiu, Young Lee, Swapnil Mishra, Lexing Xie (2018). Hawkes Processes for Events in Social Media. Frontiers of Multimedia Research.

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Marian-Andrei Rizoiu, Swapnil Mishra, Quyu Kong, Mark Carman, Lexing Xie (2017). SIR-Hawkes: Linking Epidemic Models and Hawkes Processes to Model Diffusions in Finite Populations. WWW.

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Swapnil Mishra, Marian-Andrei Rizoiu, Lexing Xie (2016). Feature Driven and Point Process Approaches for Popularity Prediction. CIKM.

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Wray L. Buntine, Swapnil Mishra (2014). Experiments with non-parametric topic models. KDD.

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