Publications and Presentations

Our team has been busy supporting the challenges of real-time epidemic science, particularly pertaining to the COVID-19 pandemic

52 Publications and Preprints

Optimal, near-optimal, and robust epidemic control. Communication PhysicsAccepted. Morris D, Rossine F, Plotkin J, Levin S (2021)

Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes. Science. Mar 9, 10.1126/science.abg8663. Saad-Roy C, Morris S, Metcalf CJ, Mina M, Baker R, Farrar J, Holmes E, Pybus O, Graham A, Levin S, Grenfell B, Wagner C (2021)

Prioritizing allocation of COVID-19 vaccines based on social contacts increases vaccination effectiveness. medRxiv. Feb 15. Chen J, Hoops S, Marathe A, Mortveit H, Lewis B, Venkatramanan S, Haddadan A, Bhattacharya P, Adiga A, Vullikanti A, Srinivasan A, Wilson ML, Ehrlich G, Fenster M, Eubank S, Barrett C, Marathe M (2021)

Persistence of anti-vaccine sentiment in social networks through strategic interactions. Proceedings of the Thirty-Fifth AAAI Conference on Artificial IntelligenceFeb 9. Haque ASM, Thakur M, Bielskas M, Marathe A, Vullikanti A (2021)

DeepCOVID: An Operational Deep Learning-driven Framework for Explainable Real-time COVID-19 Forecasting. Proceedings of the Thirty-Fifth AAAI Conference on Artificial IntelligenceFeb 9. Rodríguez A, Tabassum A, Cui J, Xie J, Ho J, Agarwal P, Adhikari B, Prakash BA (2021)

Steering a Historical Disease Forecasting Model Under a Pandemic: Case of Flu and COVID-19. Proceedings of the Thirty-Fifth AAAI Conference on Artificial IntelligenceFeb 9. Rodriguez A, Muralidhar N, Adhikari B, Tabassum A, Ramakrishnan N, Prakash BA (2021)

Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US. medRxiv. Feb 5. Cramer EY, et al (2021)

Trajectory of individual immunity and vaccination required for SARS-CoV-2 community immunity: a conceptual investigation. Journal of the Royal Society Interface. Feb 3, 18(175):20200683. Saad-Roy CM, Levin SA, Metcalf CJ, Grenfell BT (2021)

Supporting COVID-19 policy response with large-scale mobility-based modeling. Proceedings of the 27th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), Applied Data Science Track. Submitted. Chang S, Wilson ML, Lewis B, Mehrab Z, Dudakiya K, Pierson E, Koh PW, Gerardin J, Redbird B, Grusky D, Marathe M, Leskovec J (2021)

All Models are Useful: Bayesian Ensembling for Robust High Resolution COVID-19 Forecasting. Proceedings of the 27th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), Applied Data Science Track. Submitted. Adiga A, Wang L, Hurt B, Peddireddy A, Porebski P, Venkatramanan S, Lewis B, Marathe M (2021)

Adaptive human behavior in epidemics: the impact of risk misperception on the spread of epidemics. Submitted. Espinoza B, Marathe M, Swarup S, Thakur M (2021)

Superinfection and the evolution of an initial asymptomatic stage. Royal Society Open Science. Jan 27, 8(1):202212. Saad-Roy CM, Grenfell BT, Levin SA, Pellis L, Stage HB, van den Driessche P, Wingreen NS (2021)

Cross-country evidence on the association between contact tracing and COVID-19 case fatality rates. Scientific Reports, Jan 25, 11(1):1-6. Yalaman A, Basbug G, Elgin C, Galvani AP (2021)

Optimal COVID-19 quarantine and testing strategies. Nature Communications, Jan 7, 12(1):1-9. Wells CR, Townsend JP, Pandey A, Moghadas SM, Krieger G, Singer B, McDonald RH, Fitzpatrick MC, Galvani AP (2021)

Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes. medRxiv. Jan 1. Saad-Roy CM, Morris SE, Metcalf CJ, Mina MJ, Baker RE, Farrar J, Holmes EC, Pybus O, Graham AL, Levin SA, Grenfell BT (2021)

Incorporating Expert Guidance in Epidemic Forecasting. arXiv:2101.10247, Dec 24. Rodríguez A, Adhikari B, Ramakrishnan N, Prakash BA (2020).

Cohorting to isolate asymptomatic spreaders: An agent-based simulation study on the Mumbai Suburban Railway. arXiv:2012.12839. Dec 23. Talekar A, Shriram S, Vaidhiyan N, Aggarwal G, Chen J, Venkatramanan S, Wang L, Adiga A, Sadilek A, Tendulkar A, Marathe M (2020)

Economic and behavioral influencers of vaccination and antimicrobial use. Frontiers in Public Health, Dec 21, 8: 614113. Wagner CE, Prentice JA, Saad-Roy CM, Yang L, Grenfell BT, Levin SA, Laxminarayan R (2020)

Using Mobility Data to Understand and Forecast COVID19 Dynamics. medRxiv, Dec 15. Wang L, Ben X, Adiga A, Sadilek A, Tendulkar A, Venkatramanan S, Vullikanti A, Aggarwal G, Talekar A, Chen J, Lewis B, Swarup S, Kapoor A, Tambe M, Marathe M (2020)

Mapping network states using connectivity queries. Proceedings of IEEE International Conference on Big Data 2020, Dec 10. Rodríguez A, Adhikari B, González AD, Nicholson C, Vullikanti A, Prakash BA (2020)

Evolution of similar configurations in graph dynamical systems. International Conference on Complex Networks and Their Applications. Dec 1, 544-555. Priest J, Marathe M, Ravi SS, Rosenkrantz D, Stearns R (2020)

Blocking the Propagation of Two Simultaneous Contagions over Networks. International Conference on Complex Networks and Their Applications. Dec 1, 455-468. Carscadden H, Kuhlman C, Marathe M, Ravi SS, Rosenkrantz D (2020)

Epidemiological and Economic Impact of COVID-19 in the US. medRxiv. Nov 30. Chen J, Vullikanti A, Santos J, Venkatramanan S, Hoops S, Mortveit H, Lewis B, You W, Eubank S, Marathe M, Barrett C (2020)

High resolution proximity statistics as early warning for US universities reopening during COVID-19. medRxivMehrab Z, Ranga A, Sarkar D, Venkatramanan S, Baek Y, Swarup S, Marathe M (2020)

Data-driven modeling for different stages of pandemic response. Journal of the Indian Institute of Science, Nov 16, 100:901-915. Adiga A, Chen J, Marathe M, Mortveit H, Venkatramanan S, Vullikanti A (2020)

Immune life history, vaccination, and the dynamics of SARS-CoV-2 over the next 5 years. Science, Nov 13, 370(6518):811-8. Saad-Roy CM, Wagner CE, Baker RE, Morris SE, Farrar J, Graham AL, Levin SA, Mina MJ, Metcalf CJ, Grenfell BT (2020)

Wisdom of the Ensemble: Improving Consistency of Deep Learning Models. arXiv, Nov 13. Wang L, Ghosh D, Gonzalez Diaz M, Farahat A, Alam M, Gupta C, Chen J, Marathe M (2020)

Mobility network models of COVID-19 explain inequities and inform reopening. Nature, Nov 10, 1-6. Chang S, Pierson E, Koh PW, Gerardin J, Redbird B, Grusky D, Leskovec J (2020)

PREEMPT: Scalable Epidemic Interventions Using Sub-Modular Optimization on Multi-GPU Systems. Proceedings of SC20: International Conference for High Performance Computing, Networking, Storage, and Analysis (IEEE), Nov 9, 765-779. Minutoli M, Sambaturu P, Halappanavar M, Tumeo A, Kalyanaraman A, Vullikanti A (2020)

Epidemiology and transmission dynamics of COVID-19 in two Indian states. Science, Nov 6, 370(6517):691-697. Laxminarayan R, Wahl B, Reddy Dudala S, Gopal K, Mohan C, Neelima S, Jawahar Reddy KS, Radhakrishnan J, Lewnard J (2020)

Medical costs of keeping the US economy open during COVID-19. Scientific Reports. Oct 28, 10(1):1-0. Chen J, Vullikanti A, Hoops S, Mortveit H, Lewis B, Venkatramanan S, You W, Eubank S, Marathe M, Barrett C, Marathe A (2020)

Mathematical Models for COVID-19 Pandemic: A Comparative Analysis. Journal of the Indian Institute of Science, Oct 30, 100:793-807. Adiga A, Dubhashi D, Lewis B, Marathe M, Venkatramanan S, Vullikanti A (2020)

Examining Deep Learning Models with Multiple Data Sources for COVID-19 Forecasting. arXiv, Oct 27. Wang L, Adiga A, Venkatramanan S, Chen J, Lewis B, Marathe M (2020)

AICov: An Integrative Deep Learning Framework for COVID-19 Forecasting with Population Covariates. arXiv:2010.03757, Oct 8. Fox GC, von Laszewski G, Wang F, Pyne S (2020)

Commentary on Ferguson, et al, "Impact of Non-pharmaceutical Interventions (NPIs) to Reduce COVID-19 Mortality and Healthcare Demand. Bulletin of Mathematical Biology 82, Oct 7. Eubank S, Eckstrand I, Lewis B, Venkatramanan S, Marathe M, Barrett C (2020)

Broadcasting on two-dimensional regular grids. arXiv:2010.01390, Oct 3. Makur A, Mossel E, Polyanskiy Y (2020)

Steering a Historical Disease Forecasting Model Under a Pandemic: Case of Flu and COVID-19. arXiv:2009.11407, Sep 23. Rodriguez A, Muralidhar N, Adhikari B, Tabassum A, Ramakrishnan N, Prakash BA (2020)

Distance Encoding--Design Provably More Powerful GNNs for Structural Representation Learning. arXiv:2009.00142, Aug 31. Li P, Wang Y, Wang H, Leskovec J (2020)

OCEAN: Online Task Inference for Compositional Tasks with Context Adaptation. Conference on Uncertainty in Artificial Intelligence, Aug 27:1378-1387. PMLR. Ren H, Zhu Y, Leskovec J, Anandkumar A, Garg A (2020)

Interplay of global multi-scale human mobility, social distancing, government interventions, and COVID-19 dynamics. medRxiv, Aug 24. Adiga A, Wang L, Sadilek A, Tendulkar A, Venkatramanan S, Vullikanti A, Aggarwal G, Talekar A, Ben X, Chen J, Lewis B, Swarup S, Tambe M, Marathe M (2020)

Ensemble Forecasts of Coronavirus Disease 2019 (COVID-19) in the US. medRxiv, Aug 22. Ray EL, et al (2020)

Mobility network modeling explains higher SARS-CoV-2 infection rates among disadvantaged groups and informs reopening strategies. medRxiv. Aug 14. Chang S, Pierson E, Koh PW, Gerardin J, Redbird B, Grusky D, Leskovec J (2020)

Approximation Algorithms for Radius-Based, Two-Stage Stochastic Clustering Problems with Budget Constraints. arXiv:2008.03325, Aug 7. Brubach B, Grammel N, Harris DG, Srinivasan A, Tsepenekas L, Vullikanti A (2020)

Cut-n-Reveal: Time Series Segmentations with Explanations. ACM Transactions on Intelligent Systems and Technology (TIST), Jul 28, 11(5):1-26. Muralidhar N, Tabassum A, Chen L, Chinthavali S, Ramakrishnan N, Prakash BA (2020)

The implications of silent transmission for the control of COVID-19 outbreaks. Proceedings of the National Academy of Sciences, Jul 28, 117(30):17513-17515. Moghadas SM, Fitzpatrick MC, Sah P, Pandey A, Shoukat A, Singer BH, Galvani AP (2020)

Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans. PLoS Computational Biology. Jun 25; 16(6):e1007892. Saad-Roy CM, Arinaminpathy N, Wingreen NS, Levin SA, Akey JM, Grenfell BT (2020)

Networked epidemiology for COVID-19. SIAM News, Jun 1Chen J, Eubank S, Levin S, Mortveit H, Venkataramanan S, Vullikanti A, Marathe M (2020)

Staggered Release Policies for COVID-19 Control: Costs and Benefits of Sequentially Relaxing Restrictions by Age. arXiv, May 12. Zhao H, Feng Z, Castillo-Chavez C, Levin S (2020)

COVID-19: Regression Approaches of Survival Data in the Presence of Competing Risks: an Application to COVID-19. Letters in Biomathematics, May. Ghosh S, Samanta GP, Mubayi A (2020)

Explaining the "bomb-like" dynamics of COVID-19 with modeling and implications for policy. CDC MinD-Healthcare Program. To be submitted. Lin G, Strauss AT, Pinz M, Martinez DA, Tseng KT, Schueller E, Gatalo O, Yang Y, Levin S, Klein EY (2020)

Computational challenges and opportunities for forecasting epidemic dynamics using network models. Submitted. Marathe M, Vullikanti A, Rosenkrantz D, Ravi SS, Stearns R, Levin S (2020)

Modeling and analysis of the spread of COVID-19 under a multiple-strain model with mutations. Harvard Data Science Review. Submitted. Osman Y, Sridhar A, Eletreby R, Levin SA, Plotkin JB, Poor HV (2020)

 

Presentations

Representation Learning for Logical Reasoning in Knowledge Graphs. Automated Knowledge Base Construction. Leskovec J (June 2020)

A Lab of One's Own: One Woman's Personal Journey Through Sexism in Science. Harvard Science Book Talk. Colwell R (Sept 2020)

Real-Time Computational Science for COVID-19 Pandemic Planning and Response. ACM BCB 2020. Marathe M (Sept 2020)

Projecting hospital utilization and assessing implications of silent transmission during the COVID-19 outbreak in the United States. COVID-19 Consortium Colloquium Speaker Series, UT Austin. Galvani A and Pandey A (Sept 2020)

Robustness meets Algorithms. Trustworthy and Robust AI Collaboration (TRAC) Workshop. Moitra A (June 2020)

Graph Structure of Neural Networks: Good Neural Networks Are Alike. MLG20. Leskovec J (Aug 2020)

Predicting and Analyzing Pandemics. Technology, Culture and Society in the Age of COVID-19 Continuing Studies Course, Rice University. Marathe M (Oct 2020)

Graph Neural Networks for Reasoning over Multimodal Content. ML4MD at ICML2020. Leskovec J (July 2020)

Towards real-time computational epidemiology. Workshop on Knowledge Guided Machine Learning (KGML). Marathe M (Aug 2020)

Uncertainty & Precision in Math Modeling to Mitigate the Threat of COVID-19. Mathematical Models on Epidemiology in Connection with COVID-19, Dept of Mathematics, Vellore Institute of Technology, TN, India. Mubayi A (June 2020)

Underreporting, Preparedness, and Silent Typhoid Marys: A Cautionary Tale of Modeling COVID Dynamics. COVID-19 Modeling Webinar Series, Indian Institute of Public Health, Gandhinagar, India. Mubayi A (June 2020)

Responding to the COVID-19 Pandemic: Role of Computing and Data Science. IIT Madras Leadership Lecture Series. Marathe M (May 2020)

Tackling the COVID-19 Crisis. UVA Research virtual panel. Marathe M (May 2020)

Computational and Statistical Tools to Control a Pandemic. Theoretically Speaking Series, Simons Institute for the Theory of Computing. Team members on the virtual panel: Moitra A, Marathe M, Vullikanti A (May 2020)

Computational Science for Real-time COVID-19 Response. ACM India Industry Webinar. Marathe M (Apr 2020)

Recommendations for Improving Science During Crisis. AAAS Annual Meeting. Colwell R (Feb 2020)