Ye (Lennon) Li

Biostatistician | Data Scientist | Public Health Researcher

Ye (Lennon) Li

Portrait of Ye (Lennon) Li

Ye (Lennon) Li PhD, P.Stat.

Human-centered Agentic Data Science Architect

Designing human-centered multi-agent systems to uncover truth from data.

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20+
years applied public health statistics

45+
publications and scholarly outputs

16
graduate trainees supervised

P.Stat.
Statistical Society of Canada

I work at the intersection of biostatistics, data science, AI, and human judgment. My goal is to use data not simply to produce models, but to uncover truth, support better decisions, and make complex evidence understandable. I also have a background in computer science, which shapes how I think about systems, automation, and practical implementation.

I see statistics as both a scientific discipline and a way of thinking: every model is a simplified view of reality, useful only when its assumptions, limitations, and uncertainty are made clear. My work philosophy is to build practical, transparent systems that connect analysis, validation, interpretation, and real-world use.

As AI agents become part of this process, I am interested in designing human-centered workflows where machines assist with execution and scale, while humans remain responsible for meaning, ethics, judgment, and direction.

My formal training is in biostatistics and computer science: I earned a PhD and an MSc in Biostatistics from the University of Toronto, along with an Honours BSc in Computer Science and Statistics from the University of Toronto Mississauga. That background shapes how I move between statistical reasoning, software, and applied problem solving.

Areas of Focus

  • Human-centered agentic systems for data science
  • Multi-agent analytical workflows and orchestration
  • Statistical modelling, surveillance, and decision support
  • Reproducible reporting, automation, and tool building
  • Applied experimentation in public health and academic settings

Career Highlights

  • More than 20 years of applied statistical work in public health, surveillance, and operational analytics.
  • Building R Shiny applications since 2014, with a portfolio of over 100+ project-specific and general-purpose apps.
  • Built analytical workflows and interactive applications that support recurring reporting, model interpretation, and expert decision making.
  • Graduate-level teaching and supervision across epidemiology, biostatistics, and applied public health.
  • Strong applied R background, with additional experience in SAS, Python, LaTeX, knitr, and R Markdown.

Biostats.ai

Statistical Consultant
June 2010 to present

Courses

  • CHL5201: Biostatistics for Epidemiologists I
  • CHL7001: Applied Spatial Statistics for Public Health Data
  • CHL5207/5208: Laboratory in Statistical Design and Analysis

Graduate Supervision

  • Harieswar Sundaram, MSc, and Hunter Pozzebon, MSc. Phylodynamics: inferring infectious disease epidemiological and evolutionary behavior from pathogen genomic sequences. 2023-2024
  • Marija Pajdakovska, MSc. Short-term forecasting of respiratory virus transmission and severe disease risk for public health planning in Ontario. 2023-2024
  • Yushu Zou, MSc. Comparison of statistical and machine learning models in forecasting COVID-19 burden in Ontario, Canada. 2022-2023
  • Fatima Shire, MSc. Temporal tracking of SARS-CoV-2 main protease mutations on nirmatrelvir/ritonavir (paxlovid) resistance. 2022-2023
  • Hana Fu, MSc. Places, populations and health: simulating alcohol policies in Ontario. 2021-2022
  • Wei Zhuo, MSc. Applications to estimate future burden of nutrition-related cardiovascular disease and evaluate nutrition policy options for maximizing population health benefit in Canada. 2019-2020
  • Shuting Luo, MSc. R Shiny interactive web app for diabetes risk using the Diabetes Population Risk Tool (DPoRT) model. 2019-2020
  • Hana Dampf, MSc. The burden of Group A and B Streptococci in Ontario. 2018-2019
  • Ling Lin, MSc. Cardiovascular disease attributable to nutrition-related causes: estimating future burden and evaluating nutrition policy options for maximizing population health benefit in Canada. 2018-2019
  • Yue Wang, MSc. Un-immunized children in Ontario: how many, where, and why? 2017-2018
  • Sudipta Saha, PhD. Impact of an on-shelf nutrition labeling system on processed foods purchased in supermarkets in Canada. 2016-2017
  • Reuben Pereira, MSc. Building spatial surveillance systems for infectious disease data in Ontario. 2015-2016
  • Wenqi Fan, MSc. Statistical methods for temporal aberration event detection. 2014-2015
  • Osvaldo Espin-Garcia, PhD. Bootstrap methods in longitudinal survey data. 2013-2014
  • Konstantin Shestopaloff, PhD. Statistical methods in syndromic surveillance. 2012-2013

Methods and Core Contributions

  • Erjia Ge, Chengchun Yu, Eric Lavigne, Paul J Villeneuve, Xin Liu, Nicholas Grubic, Wendy Lou, Jeffrey Brook, Zihang Lu, Ye Lennon Li, Teresa To. Early-life greenness and childhood asthma and allergic rhinitis: An Ontario birth cohort study. European Respiratory Journal. 2026. doi:10.1183/13993003.02272-2025
  • Paul LA, Li Y, Leece P, Gomes T, Bayoumi MA, Herring J, Murray R, Brown P. Identifying the changing age distribution of opioid-related mortality with high-frequency data. PLoS One. 2022;17(4):e0265509
  • Li Y, Whelan M, Hobbs L, Fan WQ, Fung C, Wong K, Marchand-Austin A, Badiani T, Johnson I. Data Driven Approach of CUSUM Algorithm in Temporal Aberrant Event Detection Using Interactive Web Applications. Canadian Journal of Public Health. 2016;107(1):e9-e15
  • Li Y, Brown P, Rue H and Gesink D. Log Gaussian Cox processes and spatially aggregated disease incidence data. Statistical Methods in Medical Research. 2012;21(5):479-507
  • Li Y, Brown P and Rue H. Spatial modelling of lupus incidence over 40 years with changes in census areas. Journal of the Royal Statistical Society Series C (Applied Statistics). 2012;61(1):99-115

Applications and Collaborations

  • Butt DA, Li Y, Moineddin R, O’Neill B, Train AD, Gronsbell J, Gershon AS, Tu K. Healthcare use in individuals with and without attention-deficit/hyperactivity disorder: A population-based longitudinal matched cohort study. PLOS Mental Health. 2025;2(7):e0000342
  • Peci A, Zhang P, Sullivan A, Li Y, Bi Y, Murphy A, Leibson K, Gubbay JB, Majury A. Impact of COVID-19 pandemic on Legionella testing and infection rates in Ontario. BMC Public Health. 2025;25(1):1-10
  • Duvvuri V, Shire F, Isabel S, Braukmann T, Clark S, Marchand-Austin A, Eshaghi A, Bandukwala H, Varghese N, Li Y, et al. Large scale analysis of the SARS-CoV-2 main protease reveals marginal presence of nirmatrelvir-resistant SARS-CoV-2 Omicron mutants in Ontario, Canada, December 2021-September 2023. Canada Communicable Disease Report. 2024;50(10):365
  • Weerasinghe A, Thielman J, Li Y, Doguparty VB, Medeiros A, Keller-Olaman S, Carsley S, Richmond SA. Trends in falls among older adults before and during the COVID-19 pandemic in Ontario, Canada: A retrospective observational study. BMC Geriatrics. 2024;24(418)
  • Medeiros A, Li Y, Smith BT, Carsley S, Zheng A, Pike I, Macpherson AK, Thielman J, Weerasinghe A, Karmali S, Saunders N, Richmond RA. Inflicted violence-related injuries among children and youth in Ontario during the COVID-19 pandemic. Child Protection and Practice. 2024;2(1):100020
  • Bolotin S, Osman S, Hughes SL, Ariyarajah A, Tricco AC, Khan S, Li Y, Johnson C, Friedman L, Gul N, Jardine R, Faulkner M, Hahne SJM, Heffernan JM, Dabbagh A, Rota PA, Severini A, Jit M, Durrheim DN, Orenstein WA, Moss WJ, Funk S, Turner N, Schluter W, Jawad JS, Crowcroft NS. In Elimination Settings, Measles Antibodies Wane After Vaccination but Not After Infection: A Systematic Review and Meta-Analysis. Journal of Infect Diseases. 2022;226(7):1127-1139
  • Nelder MP, Russell CB, Johnson S, Li Y, Cronin K, Cawston T, Patel SN. American dog ticks along their expanding range edge in Ontario, Canada. Scientific Report. 2022;12(1):11063
  • Abdulnoor M, Eshaghi A, Perusini S, Broukhanski G, Corbeil A, Cronin K, Fittipaldi N, Forbes J, Guthrie J, Kus J, Li Y, Majury A, Mallo G, Mazzulli T, Melano R, Olsha R, Sullivan A, Tran V, Patel S, Allen V, and Gubbay J. Real-time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with Variants of Concern. Microbiology Spectrum. 2022;10(1):e0068121
  • Warren C, Hobin E, Manuel DG, Anderson LN, Hammond D, Jessri M, Arcand J, L’Abbe J, Li Y, Rosella LC, Manson H, Smith BT. Socioeconomic Position and Consumption of Sugary Drinks, Sugar-Sweetened Beverages and 100% Juice among Canadians: A Cross-Sectional Analysis of the 2015 Canadian Community Health Survey-Nutrition. Can J Public Health. 2022;113(3):341-362
  • Myran DT, Smith BT, Cantor N, Li Y, Saha S, Paradis C, Jesseman R, Tanuseputro P, Hobin E. Changes in the dollar value of per capita alcohol, essential, and non-essential retail sales in Canada during COVID-19. BMC Public Health. 2021;21(2162)
  • Crowcroft NS, Bolotin S, Li Y, Campbell H, Amirthalingam G. Infant pertussis and maternal immunity: The curious case of Canada. Vaccine. 2021;39(14):1977-1981
  • Wilson SE, Bunko A, Johnson S, Murray J, Wang Y, Deeks SL, Crowcroft NS, Friedman L, Loh LC, MacLeod M, Taylor C, Li Y. The geographic distribution of un-immunized children in Ontario, Canada: Hotspot detection using Bayesian spatial analysis. Vaccine. 2021;39(8):1349-1357
  • Hughes SL, Kwong JC, Schwartz KL, Chen C, Johnson C, Li Y, Marchand-Austin A, Bolotin S, Jamieson FB, Drews SJ, Russell ML, Svenson LW, Mahmud SM, Crowcroft NS. Exploring the reasons for low pertussis vaccine effectiveness in Ontario, Canada - 2006-2008: A Canadian Immunization Research Network study. Can J Public Health. 2021. PMID: 34424508. DOI: 10.17269/s41997-021-00536-1
  • Peci A, Tran V, Guthrie JL, Li Y, Nelson P, Schwartz KL, Eshaghi A, Buchan SA, Gubbay JB. Prevalence of Co-Infections with Respiratory Viruses in Individuals Investigated for SARS-CoV-2 in Ontario, Canada. Viruses. 2021;13(1)
  • Crowcroft NS, Schwartz KL, Savage RD, Chen C, Johnson C, Li Y, Marchand-Austin A, Bolotin S, Deeks SL, Jamieson FB, Drews SJ, Russell ML, Svenson LW, Simmonds K, Righolt CH, Bell C, Mahmud SM, Kwong JC. A call for caution in use of pertussis vaccine effectiveness studies to estimate waning immunity: A Canadian Immunization Research Network Study. Clin Infect Dis. 2020;ciaa518
  • Ling R, Achonu C, Li Y, Katz KC, Garber G, Johnstone J. Investigating the relationship between vancomycin-resistant Enterococcus control practices and the incidence of health care-associated Clostridioides difficile infections in Ontario. Am J Infect Control. 2020;48(3):324-326
  • Nelder MP, Russell CB, Johnson S, Li Y, Cronin K, Warshawsky B, Brandon N, Patel SN. Assessing human exposure to spotted fever and typhus group rickettsiae in Ontario, Canada (2013-2018): a retrospective, cross-sectional study. BMC Infect Dis. 2020;20(1):523
  • Johnstone J, Shing E, Saedi A, Adomako K, Li Y, Brown KA, Garber G. Discontinuing Contact Precautions for Vancomycin-Resistant Enterococcus (VRE) Is Associated With Rising VRE Bloodstream Infection Rates in Ontario Hospitals, 2009-2018: A Quasi-experimental Study. Clin Infect Dis. 2020;71(7):1756-1759
  • Hughes SL, Bolotin S, Khan S, Li Y, Johnson C, Friedman L, Tricco AC, Hahne SJM, Heffernan JM, Dabbagh A, Durrheim DN, Orenstein WA, Moss WJ, Jit M, Crowcroft NS. The effect of time since measles vaccination and age at first dose on measles vaccine effectiveness: A systematic review. Vaccine. 2020;38(3):460-469
  • Peci A, Winter AL, Li Y, Gnaneshan S, Liu J, Mubareka S, Gubbay JB. Effect of absolute and relative humidity, temperature and wind speed on influenza activity in Toronto, Canada. Applied and Environmental Microbiology. 2019;85(6):e02426-18
  • Hartley J, Li Y, Kunkel L, Crowcroft NS. The burden of infant group B streptococcal infections in Ontario: Analysis of administrative data to estimate the potential benefits of new vaccines. Human Vaccines & Immunotherapeutics. 2019;15(1):193-202
  • Allison KR, Philipneri AN, Vu-Nguyen K, Manson HE, Dwyer JJM, Hobin E, Ng B, Li Y. School and classroom effects on Daily Physical Activity policy implementation fidelity in Ontario classrooms: a multi-level analysis. BMC Public Health. 2018;18(1):802
  • Johnson K, Nelder MP, Li Y, Badiani T, Sander B, Sider D, Patel SN. Clinical manifestations of reported Lyme disease cases in Ontario, Canada: 2005-2014. PLoS ONE. 2018;13(6):e0198509
  • Crowcroft NS, Johnson C, Chen C, Li Y, Marchand-Austin A, Bolotin S, et al. Underreporting of pertussis in Ontario: A Canadian Immunization Research Network study using capture-recapture. PLoS ONE. 2018;13(5):e0195984
  • Prematunge C, Policarpio M, Johnstone J, Adomako K, Nadolny E, Lam F, Li Y, Brown K, Garber G. Impact of an independent quarterly audit on publicly reported vancomycin-resistant enterocococi bacteremia data in Ontario, Canada. American Journal of Infection Control. 2018;46:1036-1040
  • Drudge C, Johnson J, MacIntyre E, Li Y, Copes R, Johnson S, Varughese S, Chen H. Exploring Nighttime Road Traffic Noise: A Comprehensive Predictive Surface for Toronto, Canada. Journal of Occupational & Environmental Hygiene. 2018;15(5):389-398
  • Khan Y, Leung GJ, Belanger P, Gournis E, Buckeridge D, Liu L, Li Y, Johnson I. Comparing Twitter data to routine data sources in public health surveillance for the 2015 Pan/Parapan American Games: An ecological study. Canadian Journal of Public Health. 2018;109(3):419-426
  • Lebenbaum M, Espin-Garcia O, Li Y, Rosella LC. Development and validation of a population based risk algorithm for obesity: The Obesity Population Risk Tool (OPoRT). PLoS ONE. 2017;13(1):e0191169
  • Guerra FM, Bolotin S, Lim G, Heffernan, Deeks L, Li Y, Crowcroft NS. The basic reproduction number (\(R_0\)) of measles: a systematic review. The Lancet Infectious Diseases. 2017;17(12):e420-e428
  • Johnstone J, Policarpio ME, Lam F, Adomako K, Prematunge C, Nadolny E, Li Y, Brown K, Kerr E, Garber G. Rates of blood cultures positive for vancomycin-resistant Enterococcus in Ontario: a quasi-experimental study. CMAJ Open. 2017;5(2):e273-e280
  • Rivera L, Li Y, Savage RD, Crowcroft NS, Bolotin S, Rosella LC, Lou W, Hopkins J, Gemmill I, Johnson I. Evaluation of the ability of standardized supports to improve public health response to syndromic surveillance for respiratory disease. BMC Public Health. 2017;17:199
  • Li L, Pereira R, Johnson S, Johnson I. Integrated spatiotemporal surveillance system: Data, Analysis and Visualization. Online Journal of Public Health Informatics. 2017;9(1):e062
  • Minnery JGW, Marras TK, Andrews ER, Burnett C, Jagt K, Johnson JE, Johnson S, Li L, MacIntyre E, Marchand-Austin A, et al. Drinking Water Quality Attributes And Nontuberculous Mycobacterial Pulmonary Disease. American Journal of Respiratory and Critical Care Medicine. 2017;195
  • Peterson E, Shapiro H, Li Y, Minnery JG, Copes R. Arsenic from community water fluoridation: Quantifying the effect. Journal of Water and Health. 2016;14(2):236-242
  • Parpia AS, Li Y, Chen C, Dhar D, Crowcroft NS. Encephalitis in Ontario. Emerging Infectious Diseases. 2016;22(3):426-432
  • Rajaram H, Hohenadel K, Gattoni L, Khan Y, Birk-Urovitz E, Li Y, Schwartz B. Assessing health impacts of the December 2013 Ice Storm in Ontario, Canada. BMC Public Health. 2016;16:544
  • Nelder M, Russel CB, Sheehan NJ, Sander B, Moore S, Li Y, Johnson S, Patel SN, Sider D. Human pathogens associated with the blacklegged tick Ixodes scapularis: a systematic review. Parasites & Vectors. 2016;9:265
  • Gesink D, Li Y. What can we infer about incarceration and STDs? Sexually Transmitted Infections. 2015;42(7):402
  • Stoltey JE, Li Y, Bernstein KT, Philip SS. Ecological analysis examining the association between census tract-level incarceration and reported chlamydia incidence among female adolescents and young adults in San Francisco. Sexually Transmitted Infections. 2015;91(5):370-374
  • Sahai D, Peterson E, Li Y. Microbiological assessment of utensils cleaned by domestic dishwashers in Ontario small establishments. Food Protection Trends. 2015;35(3):185-195
  • Nelder M, Russell C, Lindsay LR, Dhar B, Patel SN, Johnson S, Moore S, Kristjanson E, Li Y, Ralevski F. Population-based passive tick surveillance and detection of expanding foci of blacklegged ticks Ixodes scapularis and the Lyme disease agent Borrelia burgdorferi in Ontario, Canada. PLoS ONE. 2014;9(8):e105358
  • Zuo F, Li Y, Johnson S, Johnson J, Varughese S, Liu F, Wu H, Hou R, Copes R, Chen H. Temporal and spatial variability of traffic-related noise in the City of Toronto, Canada. Science of the Total Environment. 2014;472:1100-1107
  • Rosella L, Lebenbaum M, Li Y, Wang J, Manuel DG. Risk distribution and its influence on the population targets for diabetes prevention. Preventive Medicine. 2014;58:17-21
  • Kim E, Hoetmer SE, Li Y, Vandenberg JE. Relationship between intention to supplement with infant formula and breastfeeding duration. Canadian Journal of Public Health. 2013;104(5):388-393
  • Nelder M, Russel C, Williams D, Johnson K, Li Y, Baker SL, Marshall S, Bhanich-Supapol W, Pillai DR, Ralevski F. Spatiotemporal dynamics and demographic profiles of imported Plasmodium falciparum and Plasmodium vivax infections in Ontario, Canada (1990-2009). PLoS ONE. 2013;8(9):e76208
  • Hobin E, Hammond D, White C, Li Y, Chiu M, O’Brien MF. Nutritional quality of fast food items on “Kids’ Menus”: comparisons across countries and companies. Public Health Nutrition. 2014;17(10):2263-2269
  • Peterson E, Aker A, Kim JH, Li Y, Brand K, Copes R. Lung-cancer risk from radon in Ontario, Canada: How many lung cancers can we prevent. Cancer Causes & Control. 2013;24(11):2013-2020
  • Al-Maini M, Jeyalingam Y, Brown P, Lee J, Li Y, Su J, Gladman DD, Fortin PR. A hot spot for systemic lupus erythematosus, but not for psoriatic arthritis, identified by spatial analysis suggests an interaction between ethnicity and place of residence. Arthritis and Rheumatism. 2013;65(6):1579-1585
  • Hawker G, Gignac M, Badley E, Davis A, French M, Li Y, Perruccio A, Power JD, Sale J, Lou W. A longitudinal study to explain the pain depression link in older adults with osteoarthritis. Arthritis Care and Research. 2011;63(10):1381-1380
  • Li Y, Qi Y. Effects of Genetic Variation on the Relationship between Diet and Cardiovascular Disease Risk. Liaison. 2008;22(3)
  • Gale GD, Rothbart PJ, Li Y. Infrared Therapy for Chronic Low Back Pain, A Randomized Controlled Trial. Pain Research & Management. 2005;11(3):193-196

These are my public links and profile pages. I will add app links here over time.

About Me

Apps

  • R Copilot
  • More app links will be added here later.