Publications

Yanlong Zhao, Xiaoyuan Cheng, Huihang Liu, Baihua He, Xinyu Zhang, Harrison Bo Hua Zhu, Wenlong Chen, Li Zeng, Zhuo Sun (2026). When Lower Reconstruction Loss Hurts: Distributionally Robust Refinement for Low-Bit LLM Quantization. arXiv.

Alessandro Micheli, Andrea Zerio, Samir Bhatt (2026). Discrete Wasserstein Flows for One-Step Generative Modeling. arXiv.

Rachel J. Kavanagh, Laura D. Bertola, Sascha Dreyer Nielsen, Harrison Bo Hua Zhu, Rasmus Heller, Samir Bhatt, David Alejandro Duchêne (2026). Multiple drivers of genomic novelty across ruminants. iScience.

Andrea Zerio, Yighua Yao, Alessandro Micheli, Roland G. Huber, Mile Šikić, Samir Bhatt, Andrés R. Masegosa, Yuangang Pan (2026). Sequence-Informed Geometric Evaluation of RNA 3D Structures. arXiv.

Johan Skov Bundgaard, Jonas Skjold Raaschou-Pedersen, Kasper Karmark Iversen, Henning Bundgaard, Mark Khurana, Daniel Raaschou‐Oddershede (2026). Quantifying the inclusion of cardiovascular research into clinical guidelines. Clinical Research in Cardiology.

Zhuo Sun, Entong Li, Yanlong Zhao, Xiaoyuan Cheng, Wenxuan Yuan, Kaiyu Li, Che Liu, Huihang Liu, Baihua He, Xinyu Zhang, Harrison Bo Hua Zhu, Li Zeng (2026). SR-OPSD: Self-Referenced On-Policy Self-Distillation. arXiv.

Cecilie Christensen, David Alejandro Duchêne, Mark Khurana, Samir Bhatt, Alexandros Katsiferis (2026). Definitions and Metrics of Interdisciplinarity: A PRISMA-ScR Scoping Review Protocol.

Caroline Klint Johannesen, Neil Scheidwasser, Theis Lange, Tyra Grove Krause, Thea K Fischer (2026). Changed frequency of enterovirus hospitalisations after change of polio vaccination scheme: a nation-wide cohort study from Denmark. BMJ Public Health.

Alessandro Micheli, Yueqi Cao, Anthea Monod, Samir Bhatt (2026). Generative Modeling on Metric Graphs via Neural Optimal Transport. arXiv.

Christian Morgenstern, Mark Khurana, Tristan M. Naidoo, Thomas Rawson, Anne Cori, David Alejandro Duchêne, Neil M. Ferguson, Moritz U. G. Kraemer, Samir Bhatt (2026). Federated analysis of incubation period distributions using individual-level observed data and heterogeneous summary statistics. medRxiv.

Prince Ravi Leow, Neil Scheidwasser, Rebecca Oscarsson, P. Jensen, Samir Bhatt, David Alejandro Duchêne (2026). PlayClass: Automated Play Behaviour Classification in Poultry. arXiv.

Naoki Kiyohara, Harrison Bo Hua Zhu, Riccardo El Hassanin, Zhuo Sun, Wenlong Chen, Samir Bhatt, Yingzhen Li (2026). Interdomain Attention: Beyond Token-Level Key-Value Memory. arXiv.

Mark Khurana, Johan Skov Bundgaard, Kidola Jeremiah, Cody Cichowitz, Godfrey Kisigo, Grace Ruselu, Lily Yan, Maja Valentin Kragh, Rasmus Bo Hasselbalch, Borja Ibáñez, George PrayGod, Daniel Faurholt‐Jepsen, Henning Bundgaard, Robert N. Peck (2026). Ischemic heart disease burden and healthcare system readiness across sub-Saharan Africa. Nature Cardiovascular Research.

Yanlong Zhao, Xiaoyuan Cheng, Huihang Liu, Baihua He, Xinyu Zhang, Harrison Bo Hua Zhu, Wenlong Chen, Li Zeng, Zhuo Sun (2026). Saliency-Aware Regularized Quantization Calibration for Large Language Models. arXiv.

Alessandro Micheli, Silvia Sapora, Anthea Monod, Samir Bhatt (2026). Entropic Riemannian Neural Optimal Transport. arXiv.

Johannes Hruza, Arvid Sjölander, Erin E. Gabriel, Samir Bhatt, Michael Charles Sachs (2026). Evaluation of clinical utility in emulated clinical trials. European Journal of Epidemiology.

Mark Khurana, Joseph L.-H. Tsui, Bernardo Gutierrez, Ayush Chopra, Neil Scheidwasser, Harrison Bo Hua Zhu, Serina Y. Chang, David Alejandro Duchêne, Cathal L. Mills, Rhys P. D. Inward, Benjamin Reddy, John Brittain, Abhishek Dasgupta, James Sheldon, George Githinji, John S. Brownstein, Mélodie Monod, Luca Ferretti A, Sivan Bershan, Simon Tietze, Leo Ferres, Silvia Argimón, Timothy J. Dallman, Etien Koua, Oliver Ratmann, Simon Cauchemez, Lauren Ancel Meyers, Lili Su, Alessandro Vespignani, Paul Pronyk, Aine Niamh O’Toole, Andrew Rambaut, Nicholas James Loman, Edward Charles Holmes, Seth Flaxman, Nicola Mulder, Oliver W Morgan, Houriiyah Tegally, Manuel Gomez-Rodriguez, Nigel Shadbolt, Christian Tientcha Happi, Meera a Chand, Sofonias Kifle Tessema, Placide Mbala Kingebeni, Marc A. Suchard, Oliver George Pybus, Samuel v. Scarpino, Samir Bhatt, Moritz U. G. Kraemer (2026). Global approaches to infectious disease surveillance and modeling. Nature Medicine.

Alfred Ferrer Florensa, José Juan Almagro Armenteros, Rolf Sommer Kaas, Philip T. L. C. Clausen, Henrik Vedel Nielsen, Burkhard Rost, Frank M. Aarestrup (2026). Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models with PathogenFinder2. Bioinformatics.

Alessandro Micheli, Yueqi Cao, Anthea Monod, Samir Bhatt (2026). Riemannian Neural Optimal Transport. arXiv.

Rupa Banerjee, Nalini Raghunathan, Vineeth Mellacheruvu, Pravalika Pantham, S Reddy, S Sriramoj, H Reddy, Partha Pal, Rajendra Patel, Dhanush Mekala, Alice Fracchia, Tine Jess, S Bhatt, Kaustubh Chakradeo, Aleksejs Sazonovs (2026). P1293 Rapid Urbanisation and IBD Prevalence in Rural India: Insights from a Satellite Based Deep Learning Index. Journal of Crohn s and Colitis.

Alexandros Katsiferis, Andrea Joensen, Liselotte Vogdrup Petersen, Claus Thorn Ekstrøm, Else Marie Olsen, Samir Bhatt, Tri‐Long Nguyen, Katrine Strandberg‐Larsen (2025). “Developing machine learning models of self-reported and register-based data to predict eating disorders in adolescence”. npj Mental Health Research.

Victoria A. Cox, Katie Tiley, Roberto Rosà, Andrea Pugliese, Paola Angelini, Marco Carrieri, Samir Bhatt, Marco Tamba, Giovanni Marini, Mattia Calzolari, Ilaria Dorigatti (2025). Meteorological and environmental drivers of West Nile virus prevalence in Culex pipiens mosquitoes in Emilia-Romagna, Italy in 2013 to 2022. PLoS Pathogens.

Neil Scheidwasser, Ayush Nag, Matthew J. Penn, Anthony M.V. Jakob, Frederik Mølkjær Andersen, Mark Khurana, Landung Setiawan, David Alejandro Duchêne, Samir Bhatt (2025). phylo2vec: a library for vector-based phylogenetic tree manipulation. The Journal of Open Source Software.

Bin Zhu, Liutong Chen, Yifei He, Ning Zhang, Hao Xue, Samir Bhatt, Minghui Ren, Ying Mao (2025). Beyond distance: integrating economic burden into large-scale primary healthcare accessibility analysis. Global Health Research and Policy.

Alexandros Katsiferis, Neil Scheidwasser, Tri‐Long Nguyen, Theis Lange, Mark Khurana, Pernille Brok Nielsen, Kasper Karmark Iversen, Christian Sylvest Meyhoff, Eske Kvanner Aasvang, Jesper Mølgaard, Adrian G. Zucco, Tibor v. Varga, Samir Bhatt (2025). Development and validation of early warning scores predicting 24-hour mortality addressing intercurrent medical interventions: a multi-centre retrospective cohort study of 2·08 million hospital encounters. medRxiv.

Neil Scheidwasser, Louise Ladefoged Poulsen, Prince Ravi Leow, Mark Khurana, Maider Iglesias‐Carrasco, Daniel J. Laydon, Christl Ann Donnelly, Anders Miki Bojesen, Samir Bhatt, David Alejandro Duchêne (2025). Deep learning from videography as a tool for measuring E. coli infection in poultry. Royal Society Open Science.

Penn, Matthew J., Christl Ann Donnelly, Samir Bhatt (2025). Continuous football player tracking from discrete broadcast data. Royal Society Open Science.

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Adrian G. Zucco, Henning Johannes Drews, Jeroen F. Uleman, Samir Bhatt, Naja Hulvej Rod (2025). Exploring nationwide patterns of sleep problems from late adolescence to adulthood using machine learning. Science Advances.

Mikkel Malham, Christoffer Sejling, Megan Davies, Vibeke Wewer, Samir Bhatt, Matthew P. Fox, Naja Hulvej Rod (2025). How early-life adversity affects the risk of pediatric-onset immune-mediated inflammatory disease. Journal of Autoimmunity.

Amanda Marie Egeskov-Cavling, C. Hansen, Caroline Klint Johannesen, Birgitte Lindegaard, Samir Bhatt, Cecile G. Viboud, Thea Kølsen Fischer (2025). Excess mortality and hospitalisations associated with respiratory syncytial virus, influenza, and COVID-19 among adults in Denmark (2015–2024): a modelling study. The Lancet Regional Health - Europe.

Robert Verity, Anne Cori, Swapnil Mishra, Seth Flaxman, Samir Bhatt (2025). Robert Verity, Samir Bhatt, Anne Cori, Seth Flaxman, and Swapnil Mishra’s contribution to the Discussion of ‘Some statistical aspects of the Covid-19 response’ by Wood et al.. Journal of the Royal Statistical Society Series A (Statistics in Society).

John‐Stuart Brittain, Joseph L.-H. Tsui, Rhys P. D. Inward, Bernardo Gutiérrez, Gaspary Mwanyika, Houriiyah Tegally, Tuyen Huynh, George Githinji, Sofonias Kifle Tessema, John T. McCrone, Samir Bhatt, Abhishek Dasgupta, Stephen Ratcliffe, Moritz U. G. Kraemer (2025). GRAPEVNE - Graphical Analytical Pipeline Development Environment for Infectious Diseases. Wellcome Open Research.

Christian Morgenstern, Thomas Rawson, Wes R. Hinsley, Pablo N. Perez‐Guzman, Samir Bhatt, Neil M. Ferguson (2025). Socioeconomic and temporal heterogeneity in SARS-CoV-2 exposure and disease in England from May 2020 to February 2023. Science Advances.

Kaustubh Chakradeo, Alexandros Katsiferis, Neil Scheidwasser, Iwona Hawryluk, Katherine E. Battle, Swapnil Mishra, David Lawson Smith, Seth Flaxman, David Alejandro Duchêne, Samir Bhatt (2025). Estimating the worst-case scenario for malaria parasite rate in sub-Saharan Africa. medRxiv.

Helen Coupland, Neil Scheidwasser, Alexandros Katsiferis, Megan Davies, Seth Flaxman, Naja Hulvej Rod, Swapnil Mishra, Samir Bhatt, H. Juliette T. Unwin (2025). Exploring the potential and limitations of deep learning and explainable AI for longitudinal life course analysis. BMC Public Health.

Rusul Al-Kaisy, Samir Bhatt, David Alejandro Duchêne (2025). Distinct evolutionary regimes across domains of the Plasmodium falciparum CSP gene. Scientific Reports.

Rama Cont A, Alessandro Micheli, Eyal Neuman (2025). Fast and Slow Optimal Trading with Exogenous Information. Finance and Stochastics.

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David Alejandro Duchêne, Al-Aabid Chowdhury, Jingyi Yang, Maider Iglesias‐Carrasco, Josefin Stiller, Shaohong Feng, Samir Bhatt, Marcus Thomas P. Gilbert, Guojie Zhang, Joseph A. Tobias, Simon Y. W. Ho (2025). Drivers of avian genomic change revealed by evolutionary rate decomposition. Nature.

Mathilde Marie Brünnich Sloth, Johannes Hruza, Laust Hvas Mortensen, Samir Bhatt, Alexandros Katsiferis (2025). Cause-specific mortality after spousal bereavement in a Danish register-based cohort. Scientific Reports.

Moritz U. G. Kraemer, Joseph L.-H. Tsui, Serina Y. Chang, Spyros Lytras, Mark Khurana, Samantha Vanderslott, Sumali Bajaj, Neil Scheidwasser, Jacob Liam Curran-Sebastian, Elizaveta Semenova, Mengyan Zhang, H. Juliette T. Unwin, Oliver John Watson, Cathal L. Mills, Abhishek Dasgupta, Luca Ferretti A, Samuel v. Scarpino, Etien Koua, Oliver W Morgan, Houriiyah Tegally, Ulrich Paquet, Loukas Moutsianas, Christophe Fraser, Neil M. Ferguson, Eric J. Topol, David Alejandro Duchêne, Tanja Stadler, Patricia Kingori, Michael James Parker, Francesca Dominici, Nigel Shadbolt, Marc A. Suchard, Oliver Ratmann, Seth Flaxman, Edward Charles Holmes, Manuel Gomez-Rodriguez, Bernhard Schölkopf, Christl Ann Donnelly, Oliver George Pybus, Simon Cauchemez, Samir Bhatt (2025). Artificial intelligence for modelling infectious disease epidemics. Nature.

Penn, Matthew J., Neil Scheidwasser, Mark Khurana, Christl Ann Donnelly, David Alejandro Duchêne, Samir Bhatt (2025). Generalised Bayesian distance-based phylogenetics for the genomics era. arXiv.

Matthew J. Penn, Neil Scheidwasser, Christl Ann Donnelly, David Alejandro Duchêne, Samir Bhatt (2025). Bayesian Inference of Phylogenetic Distances: Revisiting the Eigenvalue Approach. Bulletin of Mathematical Biology.

Wenlong Chen, Naoki Kiyohara, Harrison Bo Hua Zhu, Jacob Curran-Sebastian, Samir Bhatt, Yingzhen Li (2025). Recurrent Memory for Online Interdomain Gaussian Processes. Advances in Neural Information Processing Systems (NeurIPS).

Jacob Liam Curran-Sebastian, Frederik Mølkjær Andersen, Samir Bhatt (2025). Modelling the Stochastic Importation Dynamics and Establishment of Novel Pathogenic Strains Using a General Branching Processes Framework. Mathematical Biosciences.

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Lucy S. Tusting, Swapnil Mishra, Harry S. Gibson, Steve W. Lindsay, Daniel J. Weiss, Seth Flaxman, Samir Bhatt (2024). Ethnicity and anthropometric deficits in children: A cross-sectional analysis of national survey data from 18 countries in sub-Saharan Africa. PLOS Global Public Health.

Kinley Wangdi, H. Juliette T. Unwin, Kinley Penjor, Tsheten Tsheten, Tobgyal, Archie C. A. Clements, Darren James Gray, Manas Kotepui, Samir Bhatt, Peter W. Gething (2024). Estimating the impact of imported malaria on local transmission in a near elimination setting: a case study from Bhutan. The Lancet Regional Health - Southeast Asia.

Azeem Majeed, Jennifer Kathleen Quint, Samir Bhatt, Firoza Davies, Nazrul Islam (2024). Non-pharmaceutical interventions: evaluating challenges and priorities for future health shocks. BMJ.

Harrison Bo Hua Zhu, Ivan Fung, Yingke Zhu, Lahiru Samarakoon (2024). Configurable Multilingual ASR with Speech Summary Representations. arXiv.

Daniel J. Laydon, David L. Smith, Kaustubh Chakradeo, Mark Khurana, Jaffer Okiring, David Alejandro Duchêne, Samir Bhatt (2024). Climate Change and Malaria: A Call for Robust Analytics. medRxiv.

Nieves Derqui, Swapnil Mishra, Wes R. Hinsley, Samir Bhatt, Daniel J. Laydon (2024). Modelling the impact of vaccination on SARS-CoV-2 transmission in England. medRxiv.

Mark Khurana, Jacob Liam Curran-Sebastian, Samir Bhatt, Gwenan M. Knight (2024). Modelling the implementation of narrow versus broader spectrum antibiotics in the empiric treatment of E. coli bacteraemia. Scientific Reports.

Alfred Ferrer Florensa, José Juan Almagro Armenteros, Henrik Nielsen, Frank M. Aarestrup, Philip T. L. C. Clausen (2024). SpanSeq: similarity-based sequence data splitting method for improved development and assessment of deep learning projects. NAR Genomics and Bioinformatics.

Matthew J Penn, Neil Scheidwasser, Mark Khurana, David Alejandro Duchêne, Christl Ann Donnelly, Samir Bhatt (2024). Phylo2Vec: A Vector Representation for Binary Trees. Systematic Biology.

Christian Morgenstern, Daniel J. Laydon, Charles A. Whittaker, Swapnil Mishra, David Haw, Samir Bhatt, Neil M. Ferguson (2024). The interaction of disease transmission, mortality, and economic output over the first 2 years of the COVID-19 pandemic. PLoS ONE.

Ela Iwaszkiewicz-Eggebrecht, Vera Marie Alida Zizka, Christina Islas Lynggaard (2024). Three steps towards comparability and standardization among molecular methods for characterizing insect communities. Philosophical Transactions of the Royal Society B Biological Sciences.

Kåre Mølbak, Thorkild I. A. Sørensen, Samir Bhatt, Frederik Plesner Lyngse, Lone Simonsen, Peter Aaby (2024). Severity of respiratory tract infections depends on the infectious dose. Perspectives for the next pandemic. Frontiers in Public Health.

Judith A. Bouman, Anthony Hauser, Simon L. Grimm, Martin Wohlfender, Samir Bhatt, Elizaveta Semenova, Andrew Gelman, Christian Lorenz Althaus, Julien Riou (2024). Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models. PLOS Computational Biology.

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Pernille Yde, Majken K. Jensen, Namiko Mitarai, Samir Bhatt (2024). The Gompertz Law emerges naturally from the inter-dependencies between sub-components in complex organisms. Scientific Reports.

Elizaveta Semenova, Swapnil Mishra, Samir Bhatt, Seth Flaxman, H. Juliette T. Unwin (2024). Deep learning and MCMC with aggVAE for shifting administrative boundaries: mapping malaria prevalence in Kenya. Epistemic Uncertainty in Artificial Intelligence (Lecture Notes in Computer Science).

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Mark Khurana, Neil Scheidwasser, Matthew J Penn, Samir Bhatt, David Alejandro Duchêne (2023). The Limits of the Constant-rate Birth–Death Prior for Phylogenetic Tree Topology Inference. Systematic Biology.

Matthew J Penn, Neil Scheidwasser, Joseph Penn, Christl Ann Donnelly, David Alejandro Duchêne, Samir Bhatt (2023). Leaping through Tree Space: Continuous Phylogenetic Inference for Rooted and Unrooted Trees. Genome Biology and Evolution.

Rebecca K. Nash, Samir Bhatt, Anne Cori, Pierre Nouvellet (2023). Estimating the epidemic reproduction number from temporally aggregated incidence data: A statistical modelling approach and software tool. PLoS Computational Biology.

Caitriona Murphy, Wey Wen Lim, Cathal L. Mills, Jessica Y. Wong, Dongxuan Chen, Yanmy Xie, Mingwei Li, Susan Gould, Hualei Xin, Justin K. Cheung, Samir Bhatt, Benjamin John Cowling, Christl Ann Donnelly (2023). Effectiveness of social distancing measures and lockdowns for reducing transmission of COVID-19 in non-healthcare, community-based settings. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences.

Iwona Hawryluk, Swapnil Mishra, Seth Flaxman, Samir Bhatt, Thomas A. Mellan (2023). Application of referenced thermodynamic integration to Bayesian model selection. PLoS ONE.

Alexandros Katsiferis, Samir Bhatt, Laust Hvas Mortensen, Swapnil Mishra, Majken K. Jensen, Rudi G. J. Westendorp (2023). Machine learning models of healthcare expenditures predicting mortality: A cohort study of spousal bereaved Danish individuals. PLoS ONE.

Christina Islas Lynggaard, Sébastien Calvignac‐Spencer, Colin A. Chapman, Urs Kalbitzer, Fabian Hubertus Leendertz, Patrick A. Omeja, Emmanuel A. Opito, Dipto Sarkar, Kristine Bohmann, Jan F. Gogarten (2023). Vertebrate environmental DNA from leaf swabs. Current Biology.

Mikko S. Pakkanen, Xenia Miscouridou, Penn, Matthew J., Charles A. Whittaker, Tresnia Berah, Swapnil Mishra, Thomas A. Mellan, Samir Bhatt (2023). Unifying incidence and prevalence under a time-varying general branching process. Journal of Mathematical Biology.

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Zihan Wu, Neil Scheidwasser, Karl El Hajal, Miloš Cerňak (2023). Speaker Embeddings as Individuality Proxy for Voice Stress Detection. Interspeech.

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Alexandros Katsiferis, Laust Hvas Mortensen, Mark Khurana, Swapnil Mishra, Majken K. Jensen, Samir Bhatt (2023). Predicting mortality risk after a fall in older adults using health care spending patterns: a population-based cohort study. Age and Ageing.

Christina Islas Lynggaard, Tobias Guldberg Frøslev, Matthew Stanley Johnson, Morten Tange Olsen, Kristine Bohmann (2023). Airborne environmental DNA captures terrestrial vertebrate diversity in nature. Molecular Ecology Resources.

Alessandro Micheli, Johannes Muhle‐Karbe, Eyal Neuman (2023). Closed‐loop Nash competition for liquidity. Mathematical Finance.

Pernille Yde, Majken K. Jensen, Namiko Mitarai, Samir Bhatt (2023). A Systems Level Explanation for Gompertzian Mortality Patterns is provided by the “Multiple and Inter-dependent Component Cause Model”. bioRxiv.

Shozen Dan, Yu Chen, Yining Chen, Mélodie Monod, Veronika K. Jaeger, Samir Bhatt, André Karch, Oliver Ratmann, On Behalf of the Machine Learning & Global Health Network (2023). Estimating fine age structure and time trends in human contact patterns from coarse contact data: The Bayesian rate consistency model. PLoS Computational Biology.

Kimberly Fornace, Hillary Mariko Topazian, Isobel Routledge, Syafie Asyraf, Jenarun Jelip, Kim A. Lindblade, Mohammad Saffree Jeffree, Pablo Ruiz Cuenca, Samir Bhatt, Kamruddin Ahmed, Azra C. Ghani, CHRIS J. DRAKELEY (2023). No evidence of sustained nonzoonotic Plasmodium knowlesi transmission in Malaysia from modelling malaria case data. Nature Communications.

Matthew J. Penn, Daniel J. Laydon, Penn, Joseph, Charles A. Whittaker, Morgenstern, Christian, Oliver Ratmann, Swapnil Mishra, Mikko S. Pakkanen, Christl Ann Donnelly, Samir Bhatt (2023). Intrinsic Randomness in Epidemic Modelling Beyond Statistical Uncertainty. Communications Physics.

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Karl El Hajal, Zihan Wu, Neil Scheidwasser, Gasser Elbanna, Miloš Cerňak (2023). Efficient Speech Quality Assessment using Self-supervised Framewise Embeddings. IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).

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Kaiyu Li, Yiming Yang, Xiaoyuan Cheng, Yi He, Zhuo Sun (2023). Multilevel Control Functional. arXiv.

Adrienne Epstein, Jane Frances Namuganga, Isaiah Nabende, Emmanuel Victor Kamya, Moses Robert Kamya, Grant Dorsey, Hugh J. W. Sturrock, Samir Bhatt, Isabel Rodríguez-Barraquer, Bryan Greenhouse (2023). Mapping malaria incidence using routine health facility surveillance data in Uganda. BMJ Global Health.

Nicolas Banholzer, Thomas A. Mellan, H. Juliette T. Unwin, Stefan Feuerriegel, Swapnil Mishra, Samir Bhatt (2023). A comparison of short-term probabilistic forecasts for the incidence of COVID-19 using mechanistic and statistical time series models. arXiv.

Amelia Bertozzi-Villa, Caitlin A. Bever, Jaline Gerardin, Joshua L. Proctor, Meikang Wu, Dennis Harding, T. Déirdre Hollingsworth, Samir Bhatt, Peter W. Gething (2023). An archetypes approach to malaria intervention impact mapping: a new framework and example application. Malaria Journal.

Daniel J. Laydon, Simon Cauchemez, Wes R. Hinsley, Samir Bhatt, Neil M. Ferguson (2023). Impact of proactive and reactive vaccination strategies for health-care workers against MERS-CoV: a mathematical modelling study. The Lancet Global Health.

Pernille Yde, Andreas Bartholdy, Lise Mette Rahbek Gjerdrum, Rudi G. J. Westendorp, Laust Hvas Mortensen, Samir Bhatt, Majken K. Jensen (2023). Danish Pathology Life Course (PATHOLIFE) cohort: a register based cohort extending upon a national tissue biobank. BMJ Open.

Junyao Zheng, Ning Zhang, Guoquan Shen, Fengchao Liang, Yang William Zhao, Xiaochen He, Ying Wang, Rongxin He, Wenna Chen, Hao Xue, Yue Shen, Yang Fu, Wei‐Hong Zhang, Lei Zhang, Samir Bhatt, Ying Mao, Bin Zhu (2023). Spatiotemporal and Seasonal Trends of Class A and B Notifiable Infectious Diseases in China: Retrospective Analysis. JMIR Public Health and Surveillance.

Adrian Lison, Nicolas Banholzer, Mrinank Sharma, Sören Mindermann, H. Juliette T. Unwin, Swapnil Mishra, Tanja Stadler, Samir Bhatt, Neil M. Ferguson, Jan Brauner, Werner Vach (2023). Effectiveness assessment of non-pharmaceutical interventions: lessons learned from the COVID-19 pandemic. The Lancet Public Health.

Alexandros Katsiferis, Samir Bhatt, Laust Hvas Mortensen, Swapnil Mishra, Rudi G. J. Westendorp (2023). Sex differences in health care expenditures and mortality after spousal bereavement: A register-based Danish cohort study. PLoS ONE.

Samir Bhatt, Neil M. Ferguson, Seth Flaxman, Axel Gandy, Swapnil Mishra, James a Scott (2023). Semi-mechanistic Bayesian modelling of COVID-19 with renewal processes. Journal of the Royal Statistical Society Series A (Statistics in Society).

Charles Whittaker, Arran Hamlet, Ellie Sherrard-Smith, Peter Winskill, Gina Cuomo-Dannenburg, Patrick G. T. Walker, Marianne E Sinka, Samuel Pironon, Ashwani Kumar, Azra C. Ghani, Samir Bhatt, Thomas S. Churcher (2023). Seasonal dynamics of Anopheles stephensi and its implications for mosquito detection and emergent malaria control in the Horn of Africa. Proceedings of the National Academy of Sciences.

Naja Hulvej Rod, Jessica Bengtsson, Leonie K. Elsenburg, Megan Davies, David Carlton Taylor-Robinson, Samir Bhatt, Andreas Rieckmann (2023). Cancer burden among adolescents and young adults in relation to childhood adversity: a nationwide life-course cohort study of 1.2 million individuals. The Lancet Regional Health - Europe.

Peter Bager, Jens Ole Nielsen, Samir Bhatt, Lise Birk Nielsen, Tyra Grove Krause, Lasse Skafte Vestergaard (2023). Conflicting COVID-19 excess mortality estimates. The Lancet.

Seth Flaxman, Charles A. Whittaker, Elizaveta Semenova, Theo Rashid, Robbie M. Parks, Alexandra Blenkinsop, H. Juliette T. Unwin, Swapnil Mishra, Samir Bhatt, Deepti Gurdasani, Oliver Ratmann (2023). Assessment of COVID-19 as the Underlying Cause of Death Among Children and Young People Aged 0 to 19 Years in the US. JAMA Network Open.

Arash Mehrjou, Ashkan Soleymani, Amin Abyaneh, Samir Bhatt, Bernhard Schölkopf, Stefan Bauer (2023). Pyfectious: An individual-level simulator to discover optimal containment policies for epidemic diseases. PLoS Computational Biology.

Zhuo Sun, Alessandro Barp, François-Xavier Briol (2023). Vector-Valued Control Variates. Proceedings of Machine Learning Research.

Mark Khurana (2023). The Trajectory of Discovery:What Determines the Rate and Direction of Medical Progress?.

Giovanni Charles, Timothy M. Wolock, Peter Winskill, Azra Ghani, Samir Bhatt, Seth Flaxman (2023). Seq2Seq Surrogates of Epidemic Models to Facilitate Bayesian Inference. AAAI Conference on Artificial Intelligence (AAAI).

Zhuo Sun, Chris J. Oates, François-Xavier Briol (2023). Meta-learning Control Variates: Variance Reduction with Limited Data. Proceedings of Machine Learning Research.

Harrison Bo Hua Zhu, Carles Balsells Rodas, Yingzhen Li (2023). Markovian Gaussian Process Variational Autoencoders. International Conference on Machine Learning.

Mark Khurana, Emil Bargmann Madsen (2022). Perspectives on the narrowing and clustering of research trajectories: an epistemic threat to medical progress?. Science and Public Policy.

Kristine Bohmann, Christina Islas Lynggaard (2022). Transforming terrestrial biodiversity surveys using airborne eDNA. Trends in Ecology & Evolution.

Anderson Fernandes Brito, Elizaveta Semenova, Gytis Dudas, Gabriel W. Hassler, Chaney C. Kalinich, Moritz U. G. Kraemer, Joses Ho, Houriiyah Tegally, George Githinji, Charles N. Agoti, Lucy E. Matkin, Charles Whittaker, COVID-19 Impact Project, Network for Genomic Surveillance in South Africa (NGS-SA), GISAID Core Curation Team, Benjamin P. Howden, Vitali Sintchenko, Neta S. Zuckerman, Orna Mor, Heather M. Blankenship, Túlio De Oliveira, Raymond Tzer Pin Lin, Marilda Mendonça Siqueira, Paola Cristina Resende, Ana Tereza Ribeiro De Vasconcelos, Fernando Rosado Spilki, Renato Santana Aguiar, Ivailo Alexiev, Ivan N. Ivanov, Ivva Philipova, Christine v. F. Carrington, Nikita S. D. Sahadeo, Céline Gurry, Sebastian Maurer‐Stroh, Dhamari Naidoo, Karin Jasmijn Von Eije, Mark D. Perkins, Maria D. Van Kerkhove, Sarah Catherine Hill, Éster Cerdeira Sabino, Oliver George Pybus, Christopher Dye, Samir Bhatt, Seth Flaxman, Marc A. Suchard, Nathan D. Grubaugh, Guy Baele, Nuno R. Faria (2022). Global disparities in SARS-CoV-2 genomic surveillance. Nature Communications.

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Mita Eva Sengupta, Christina Islas Lynggaard, Samson Mukaratirwa, Birgitte Jyding Vennervald, Anna‐Sofie Stensgaard (2022). Environmental DNA in human and veterinary parasitology - Current applications and future prospects for monitoring and control. Food and Waterborne Parasitology.

Swapnil Mishra, James A. Scott, Daniel J. Laydon, Harrison Bo Hua Zhu, Neil M. Ferguson, Samir Bhatt, Seth Flaxman, Axel Gandy (2022). Authors’ Reply to the Discussion of ‘A COVID-19 Model for Local Authorities of the United Kingdom’ by Mishra et al. in Session 2 of the Royal Statistical Society’s Special Topic Meeting on COVID-19 Transmission: 11 June 2021. Journal of the Royal Statistical Society Series A (Statistics in Society).

Swapnil Mishra, James A. Scott, Daniel J. Laydon, Harrison Bo Hua Zhu, Neil M. Ferguson, Samir Bhatt, Seth Flaxman, Axel Gandy (2022). A COVID-19 Model for Local Authorities of the United Kingdom. Journal of the Royal Statistical Society Series A (Statistics in Society).

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

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

Mélodie Monod, Alexandra Blenkinsop, Andrea Brizzi, Yu Chen, Carlos Cardoso Correia Perello, Vidoushee Jogarah, Yuanrong Wang, Seth Flaxman, Samir Bhatt, Oliver Ratmann (2022). Regularised B-splines Projected Gaussian Process Priors to Estimate Time-trends in Age-specific COVID-19 Deaths. Bayesian Analysis.

Bente Christensen, Daniel J. Laydon, Tadeusz Chełkowski, Dariusz Jemielniak, Michaela Vollmer, Samir Bhatt, Konrad Krawczyk (2022). Quantifying Changes in Vaccine Coverage in Mainstream Media as a Result of the COVID-19 Outbreak: Text Mining Study. JMIR Infodemiology.

Adrienne Epstein, Catherine Maiteki‐Sebuguzi, Jane Frances Namuganga, Joaniter Immaculate Nankabirwa, Samuel Gonahasa, Jimmy Opigo, Sarah G. Staedke, Damian Rutazaana, Emmanuel Arinaitwe, Moses Robert Kamya, Samir Bhatt, Isabel Rodríguez-Barraquer, Bryan Greenhouse, Martin J. Donnelly, Grant Dorsey (2022). Resurgence of malaria in Uganda despite sustained indoor residual spraying and repeated long lasting insecticidal net distributions. PLOS Global Public Health.

David Haw, Christian Morgenstern, Giovanni Forchini, Johnson, Robert, Patrick Doohan, PETER C. SMITH, Katharina Hauck (2022). Data needs for integrated economic-epidemiological models of pandemic mitigation policies. RePEc: Research Papers in Economics.

Tommy Nyberg, Neil M. Ferguson, Joshua Blake, Wes R. Hinsley, Samir Bhatt, Daniela De Angelis, Simon Thelwall, Anne Margaret Presanis (2022). Misclassification bias in estimating clinical severity of SARS-CoV-2 variants – Authors' reply. The Lancet.

Tomáš Gavenčiak, Joshua Teperowski Monrad, Gavin Leech, Mrinank Sharma, Sören Mindermann, Jan Brauner, Samir Bhatt, Jan Kulveit (2022). Seasonal variation in SARS-CoV-2 transmission in temperate climates: A Bayesian modelling study in 143 European regions. PLoS Computational Biology.

Maxwell Salvatore, Rupam Bhattacharyya, Soumik Purkayastha, Lauren Zimmermann, Debashree Ray, Aditi Hazra, Michael Kleinsasser, Thomas Mellan, C Whittaker, Seth Flaxman, Samir Bhatt, Swapnil Mishra, Bhramar Mukherjee (2022). Lessons from SARS-CoV-2 in India: A data-driven framework for pandemic resilience. Science Advances.

Janet R. Saul, Caroline Cooney, Parviez Rana Hosseini, Ta’Adhmeeka Beamon, Nora Toiv, Samir Bhatt, Irum F. Zaidi, Deborah L. Birx (2022). Modeling DREAMS impact: trends in new HIV diagnoses among women attending antenatal care clinics in DREAMS countries. AIDS.

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.

Gavin Leech, Darren Smith, Joshua Teperowski Monrad, Jonas B. Sandbrink, Benedict Snodin, Robert Zinkov, Benjamin M. Rader, John S. Brownstein, Yarin Gal, Samir Bhatt, Mrinank Sharma, Sören Mindermann, Jan Brauner, Laurence Aitchison (2022). Mask wearing in community settings reduces SARS-CoV-2 transmission. Proceedings of the National Academy of Sciences.

Alexander Pondaven, Märt Bakler, Donghu Guo, Hamzah Hashim, Martin Ignatov, Harrison Bo Hua Zhu (2022). Convolutional Neural Processes for Inpainting Satellite Images. arXiv.

Andrea Brizzi, Charles Whittaker, Luciana Mendes Santos Servo, Iwona Hawryluk, Carlos Augusto Prete Junior, William Marciel De Souza, Renato Santana Aguiar, Leonardo José Tadeu De Araújo, Leonardo Soares Bastos, Alexandra Blenkinsop, Lewis Buss, Darlan Da Silva Cândido, Márcia C. Castro, Sílvia Figueiredo Costa, Júlio Croda, Andreza Aruska De Souza Santos, Christopher Dye, Seth Flaxman, Paula Luize Camargos Fonseca, Victor Emmanuel Viana Geddes, Bernardo Gutiérrez, Philippe Lemey, Anna Sara Levin, Thomas A. Mellan, Diego Menezes, Xenia Miscouridou, Swapnil Mishra, Mélodie Monod, Filipe Romero Rebello Moreira, Bruce Nelson, Rafael H. M. Pereira, Otavio Ranzani, Ricardo Parolin Schnekenberg, Elizaveta Semenova, Raphael Sonabend, Renan Pedra De Souza, Xiaoyue Xi, Éster Cerdeira Sabino, Nuno R. Faria, Samir Bhatt, Oliver Ratmann (2022). Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals. Nature Medicine.

Peter Bager, Jan Wohlfahrt, Samir Bhatt, Marc Stegger, Rebecca A. Legarth, Camilla Holten Møller, Robert Leo Skov, Palle Valentiner‐Branth, Marianne Voldstedlund, Thea Kølsen Fischer, Lone Simonsen, Nikolai Soren Kirkby, Marianne Kragh Thomsen, Katja Spieß, Ellinor Lindberg Marving, Nicolai Balle Larsen, Troels Lillebæk, Henrik Ullum, Kåre Mølbak, Tyra Grove Krause, Sofie Marie Edslev, Raphael Niklaus Sieber, Anna Cäcilia Ingham, Maria Overvad, Mie Agermose Gram, Frederikke Kristensen Lomholt, Louise Hallundbæk, Caroline Hjorth Espensen, Sophie Madeleine Gubbels, Marianne Karakis, Karina Lauenborg Møller, Stefan Schytte Olsen, Zitta Barrella Harboe, Caroline Klint Johannesen, Maarten Van Wijhe, Jon Gitz Holler, Ram Benny Dessau, Martin Friis, David Fuglsang-Damgaard, Mette Pinholt, Thomas Vognbjerg Sydenham, John Eugenio Coia, Ea Sofie Marmolin, Anders Fomsgaard, Jannik Fonager, Morten Rasmussen, Arieh Sierra Cohen (2022). Risk of hospitalisation associated with infection with SARS-CoV-2 omicron variant versus delta variant in Denmark: an observational cohort study. The Lancet Infectious Diseases.

Charles Whittaker, Peter Winskill, Marianne E Sinka, Samuel Pironon, Claire Massey, Daniel J. Weiss, Huong Lan Thi Nguyen, Peter W. Gething, Ashwani Kumar, Azra C. Ghani, Samir Bhatt (2022). A novel statistical framework for exploring the population dynamics and seasonality of mosquito populations. Proceedings of the Royal Society B Biological Sciences.

Christina Islas Lynggaard, Joanne E. Littlefair, Kristine Bohmann, Elizabeth L. Clare (2022). Shunning the scoop: Sidestepping the race to publish. iScience.

Mark Khurana, Daniel Emil Tadeusz Raaschou-Pedersen, Jørgen A. L. Kurtzhals, Jakob E. Bardram, Sisse Rye Ostrowski, Johan Skov Bundgaard (2022). Digital health competencies in medical school education: a scoping review and Delphi method study. BMC Medical Education.

Mahan Ghafari, Louis Du Plessis, Jayna Raghwani, Samir Bhatt, Bo Xu, Oliver George Pybus, Aris Katzourakis (2022). Purifying selection determines the short-term time dependency of evolutionary rates in SARS-CoV-2 and pH1N1 influenza. Molecular Biology and Evolution.

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Alfred Ferrer Florensa, Rolf Sommer Kaas, Philip T. L. C. Clausen, Derya Aytan-Aktug, Frank M. Aarestrup (2022). ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microbial Genomics.

Rhys Kingston, Isobel Routledge, Samir Bhatt, Leigh Bowman (2022). Novel Epidemic Metrics to Communicate Outbreak Risk at the Municipality Level: Dengue and Zika in the Dominican Republic. Viruses.

Christina Islas Lynggaard, Mads F. Bertelsen, Casper Vindahl Jensen, Matthew Stanley Johnson, Tobias Guldberg Frøslev, Morten Tange Olsen, Kristine Bohmann (2022). Airborne environmental DNA for terrestrial vertebrate community monitoring. Current Biology.

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

Xing Liu, Harrison Bo Hua Zhu, Jean-François Ton, Wynne, George, Andrew Duncan (2022). Grassmann Stein Variational Gradient Descent. International Conference on Artificial Intelligence and Statistics (AISTATS).

Lesley Erica Scott, Marvin Hsiao, Sikhuline Moyo, Lavanya Singh, Houriiyah Tegally, Graeme Dor, Piet Maes, Oliver George Pybus, Moritz U. G. Kraemer, Elizaveta Semenova, Samir Bhatt, Seth Flaxman, Nuno Rodrigues Faria, Túlio De Oliveira (2021). Track Omicron’s spread with molecular data. Science.

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

Elizaveta Semenova, Yidan Xu, Adam Howes, Theo Rashid, Samir Bhatt, Swapnil Mishra, Seth Flaxman (2021). PriorVAE: Encoding spatial priors with VAEs for small-area estimation. arXiv.

Harrison Wilde, Thomas A. Mellan, Iwona Hawryluk, John Dennis, Spiros Denaxas, Christina Pagel, A. Duncan, Samir Bhatt, Seth Flaxman, Bilal Akhter Mateen, Sebastian J. Vollmer (2021). The association between mechanical ventilator compatible bed occupancy and mortality risk in intensive care patients with COVID-19: a national retrospective cohort study. BMC Medicine.

Christina Islas Lynggaard, Alejandro Francisco Oceguera-Figueroa, Sebastian Kvist, Marcus Thomas P. Gilbert, Kristine Bohmann (2021). The potential of aquatic bloodfeeding and nonbloodfeeding leeches as a tool for iDNA characterisation. Molecular Ecology Resources.

Gideon Meyerowitz‐Katz, Samir Bhatt, Oliver Ratmann, Jan 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.

Isobel Routledge, H. Juliette T. Unwin, Samir Bhatt (2021). Inference of malaria reproduction numbers in three elimination settings by combining temporal data and distance metrics. Scientific Reports.

Konrad Krawczyk, Tadeusz Chełkowski, S. Mishra, D. Xifara, B. Gibert, D.J. Laydon, Seth Flaxman, Thomas A. Mellan, Veit Schwämmle, Richard Röttger, Johannes Thorling Hadsund, Samir Bhatt (2021). Quantifying Online News Media Coverage of the COVID-19 Pandemic: Text Mining Study and Resource. Journal of Medical Internet Research.

Kristine Bohmann, Physilia Chua, Luke E. Holman, Christina Islas Lynggaard (2021). DNAqua‐Net conference unites participants from around the world with the quest to standardize and implement DNA‐based aquatic biomonitoring. Environmental DNA.

Harrison Bo Hua Zhu, Adam Howes, Owen Van Eer, Maxime Rischard, Yingzhen Li, Dino Sejdinović, Seth Flaxman (2021). Aggregated Gaussian Processes with Multiresolution Earth Observation Covariates. arXiv.

Brian Li Han Wong, Mark Khurana, Robert Dean Smith, Omnia El Omrani, Ave Põld, Amine Lotfi, Charlotte O’Leary, Diah Satyani Saminarsih (2021). Harnessing the digital potential of the next generation of health professionals. Human Resources for Health.

H. Juliette T. Unwin, Isobel Routledge, Seth Flaxman, Marian-Andrei Rizoiu, Shengjie Lai, Justin M 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.

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.

Oliver Ratmann, Samir Bhatt, Seth Flaxman (2021). Implications of a highly transmissible variant of SARS-CoV-2 for children. Archives of Disease in Childhood.

Christina Islas Lynggaard, Luis García‐Prieto, Carmen Guzmán‐Cornejo, Martín García‐Varela (2021). Description of a new species of Moniliformis (Acanthocephala: Moniliformidae) from Peromyscus hylocetes (Rodentia: Cricetidae) in Mexico. Parasitology International.

Esra Süel, Samir Bhatt, Michael D Brauer, Seth Flaxman, Majid Ezzati (2021). Multimodal deep learning from satellite and street-level imagery for measuring income, overcrowding, and environmental deprivation in urban areas. Remote Sensing of Environment.

Michaela Vollmer, Ben Glampson, Thomas A. Mellan, Swapnil Mishra, Luca Mercuri, Ceire Costello, Robert Edward 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.

Xiaoxu Li, Jijie Wu, Zhuo Sun, Zhanyu Ma, Jie Cao, Jing-Hao Xue (2021). BSNet: Bi-Similarity Network for Few-shot Fine-grained Image Classification. IEEE Transactions on Image Processing.

Iwona Hawryluk, Swapnil Mishra, Seth Flaxman, Samir Bhatt, Thomas A. Mellan (2020). Referenced Thermodynamic Integration for Bayesian Model Selection: Application to COVID-19 Model Selection. arXiv.