Sean L. Wu, PhD

Research Scientist at Merck slwood89 (at) gmail (dot) com (he/him) Google Scholar GitHub (and GitHub Gists) ResearchGate (seldom updated) CV LinkedIn Notes website twitter (mostly nonsense) mastodon (awaiting nonsense)

Table of Contents Research Interests Introduction Publications Software Personal Projects Rogues' Gallery Miscellany

Research Interests

Major Interests:

• Mechanistic stochastic modelling, especially non-Markovian or delayed systems
• Graphical methods to specify conceptual models (Petri Nets, compartmental model diagrams, DAGs)
• Software design patterns and architecture for infectious disease modeling software

Minor Interests:

• Probabilistic risk assessment for rare events
  
  I am very interested in thinking about what we can learn from earthquake forecasting here.
• Epistemic uncertainty in stochastic models
  
  I haven't thought about it very deeply, but I like Keith Beven's work on this, from hydrology.
• Variance reduction for Monte Carlo simulation and uncertainty quantification for computationally expensive models
  I'm fascinated by Quasi-Monte Carlo techniques, that is, when you can do better than random.

Introduction

I attended the University of California (UC), Irvine from 2008 to 2013 where I studied International Studies & Statistics. I received my MPH in Epidemiology & Biostatistics in 2016, and my PhD in Epidemiology with a designated emphasis in Computational Biology in 2020, both under John M. Marshall at UC Berkeley.

My main research interest is the process of going from a whiteboard description of a complex system to a verifiable simulation program. This process tends to proceed from observation about a real system to a conceptual model, usually expressed with some kind of graphical formalism, which is often a unique minimal representation of that system (such that anything simpler isn't that system). The conceptual model may then be turned into a mathematical model, which respects all the assumptions and simplifications made at the conceptual stage. From there, often times scientific code must be written to simulate solutions of the mathematical model. I am interested in developing methods and software to help scientists better navigate this process while respecting the complexity of the processes under study.

I have been involved in various research projects, including a research internship at Microsoft Research where I worked on detailed stochastic models of mosquito ecology under Simon D.W. Frost. I have also been at the Malaria Elimination Initiative at UC San Francisco, and spent a summer in Sichuan Province, China studying possible genetic biomarkers of susceptibility to schistosomiasis infection at the Berkeley Schistosomiasis Group, under Robert C. Spear. During the first year of my PhD I attended the Complex Systems Summer School (2017) at the Santa Fe Institute and found it life changing.

My middle name is Lawrence. My Chinese name is 吳瑞華 (wú ruì huá). My father is Cantonese Chinese from Hong Kong and my mother is Scandinavian & Oglala Sioux from San Diego, California and am proud of my mixed heritage. I grew up in and around San Diego, California. Before coming to Berkeley I worked as a computer hardware repairperson for a cardiology group, office assistant at UC Irvine, waiter at a Taiwanese beef noodle soup restaurant, clinical care assistant at a large hospital, and medical assistant at a pediatric office. My favorite TV show is Battlestar Galactica. I like to read books; some recent favorites are the Area X trilogy by Jeff VanderMeer and the Three Body Problem by Liu Cixin. I have recently been playing a lot of Disco Elysium. My favorite philosopher is the criminally underrated Plotinus.

In addition to English I speak fluent Mandarin Chinese and conversational Cantonese Chinese.

Languages I can speak to computers are R (native), C++ (fluent), Julia (fluent), C (conversational).

Publications

Journal Articles

1. Health inequities in SARS-CoV-2 infection, seroprevalence, and COVID-19 vaccination: Results from the East Bay COVID-19 study.
   Adams C, Horton M, Solomon O, Wong M, Wu SL, Fuller S, Shao X, Fedrigo I, Quach HL, Quach DL, Meas M, Lopez L, Broughton A, Barcellos AL, Shim J, Seymens Y, Hernandez S, Montoya M, Johnson DM, Beckman KB, Busch MP, Coloma J, Lewnard JA, Harris E, Barcellos LF.
   PLOS Global Public Health 2(8): e0000647.
2. Comparison of entomological impacts of two methods of intervention designed to control Anopheles gambiae s.l. via swarm killing in Western Burkina Faso.
   Sawadogo SP, Niang A, Wu SL, Millogo AA, Bonds J, Latham M, Dabiré RK, Tatarsky A, Tripet F, Diabaté A.
   Scientific Reports 12.1 (2022): 1-11.
3. Association between indoor residual spraying and pregnancy outcomes: a quasi-experimental study from Uganda.
   Roh ME, Mpimbaza A, Oundo B, Irish A, Murphy M, Wu SL, White JS, Shiboski Stephen, Glymour MM, Gosling R, Dorsey G, Sturrock H.
   International Journal of Epidemiology, 2022.
4. individual: An R package for individual-based epidemiological models.
   Charles GD, Wu SL.
   Journal of Open Source Software, 6(66), 3539.
5. Measuring the accuracy of gridded human population density surfaces: A case study in Bioko Island, Equatorial Guinea.
   Fries B, Guerra CA, García GA, Wu SL, Smith JM, Oyono JN, Donfack OT, Nfumu JO, Smith DL, Dolgert AJ.
   PLoS one. 2021 Sep 1;16(8):e0248646.
6. Quantifying malaria acquired during travel and its role in malaria elimination on Bioko Island.
   Citron DT, Guerra CA, Garcia GA, Wu SL, Battle KE, Gibson HS, Smith DL.
   Malaria Journal. 2021 Aug 31: 20,359.
7. MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics.
   Wu SL, Bennett JB, Sánchez HC, Dolgert AJ, León TM, Marshall JM.
   PLoS computational biology. 2021 May 21;17(5):e1009030.
8. Comparing metapopulation dynamics of infectious diseases under different models of human movement.
   Citron DT, Smith DL, Wu SL, Sánchez HC, Dolgert AJ, Henry JM, Guerra CA.
   PNAS May 4, 2021 118 (18) e2007488118.
9. School closures reduced social mixing of children during COVID-19 with implications for transmission risk and school reopening policies.
   Head JR, Andrejko K, Cheng Q, Collender PA, Phillips S, Boser A, Heaney AK, Hoover CM, Wu SL, Northrup GR, Click K, Harrison R, Lewnard JA, Remais JV.
   J. R. Soc. Interface 18: 20200970.
10. New genotype invasion of dengue virus serotype 1 drove massive outbreak in Guangzhou, China.
    Ma MM, Wu SL, He ZJ, Yuan LH, Bai ZJ, Marshall JM, Lu JH, Yang ZC, Jing QL.
    Parasites & Vectors 14.1 (2021): 1-12.
11. Pregnancy does not modify the risk of MS in genetically susceptible women.
    Adams CJ, Wu SL, Shao XR, Bradshaw PT, Gonzales E, Smith JB, Xiang AH, Bellesis KH, Chinn T, Bos SD, Wendel-Haga MW, Olsson T, Kockum I, Langer-Gould AM, Schaefer C, Alfredsson L, Barcellos LF.
    Neurol Neuroimmunol Neuroinflamm Nov 2020, 7 (6).
12. Substantial underestimation of SARS-CoV-2 infection in the United States.
    Wu SL, Mertens A, Crider YS, Nguyen A, Pokpongkiat NN, Djajadi S, Seth A, Hsiang MS, Colford JM, Reingold A, Arnold BF, Hubbard A, Benjamin-Chung J.
    Nature Communications. 11, 4507 (2020).
13. Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology.
    Wu SL, Sánchez HC, Henry JM, Citron DT, Zhang Q, Compton K, Liang B, Verma A, Cummings DA, Le Menach A, Scott TW, Wilson AL, Lindsay SW, Moyes CL, Hancock PA, Russell TL, Burkot TR, Marshall JM, Kiware S, Reiner RC, Smith DL.
    PLoS computational biology. 2020 Apr 22;16(4):e1007446.
14. Modeling confinement and reversibility of threshold-dependent gene drive systems in spatially-explicit Aedes aegypti populations.
    Sánchez HC, Bennett JB, Wu SL, Rašić G, Akbari OS, Marshall JM.
    BMC biology. 2020 Dec;18:1-4.
15. MGDrivE: A modular simulation framework for the spread of gene drives through spatially explicit mosquito populations.
    Sánchez HC, Wu SL, Bennett JB, Marshall JM.
    Methods in Ecology and Evolution. 2020 Feb;11(2):229-39.
16. An example of augmenting regional sensitivity analysis using machine learning software.
    Spear RC, Cheng Q, Wu SL.
    Water Resources Research. 2020 Apr;56(4):e2019WR026379.
17. Transforming insect population control with precision guided sterile males with demonstration in flies.
    Kandul NP, Liu J, Sánchez HC, Wu SL, Marshall JM, Akbari OS.
    Nature communications. 2019 Jan 8;10(1):1-2.
18. Mathematical models of human mobility of relevance to malaria transmission in Africa.
    Marshall JM, Wu SL, Sánchez HC, Kiware SS, Ndhlovu M, Ouédraogo AL, Touré MB, Sturrock HJ, Ghani AC, Ferguson NM.
    Scientific Reports. 2018 May 16;8(1):1-2.
19. Attacking the mosquito on multiple fronts: Insights from the Vector Control Optimization Model (VCOM) for malaria elimination.
    Kiware S, Chitnis N, Tatarsky A, Wu SL, Sánchez HC, Gosling R, Smith DL, Marshall JM.
    PLoS one. 2017 Dec 1;12(12):e0187680.

Preprints

1. Spatial Dynamics of Malaria Transmission.
   Wu SL, Henry JM, Citron DT, Ssebuliba DM, Nsumba JN, Sánchez HC, Brady OJ, Guerra CA, García GA, Carter AR, Ferguson HM, Afolabi BE, Hay SI, Reiner RC., Kiware S, Smith DL.
   medRxiv. 2022 Nov 15.
2. Report 48 - The value of vaccine booster doses to mitigate the global impact of the Omicron SARS-CoV-2 variant.
   Hogan AB, Wu SL, Doohan P, Watson OJ, Winskill P, Charles GD, Barnesley G, Riley EM, Khoury DS, Ferguson NM, Ghani AC.
   Imperial College London (15-12-2021), doi: https://doi.org/10.25561/93034.
3. Eliminating Aedes aegypti from its southern margin in Australia: insights from genomic data and simulation modeling.
   Rašić G, Filipović I, Wu SL, León TM, Bennett JB, Sánchez HC, Marshall JM, Trewin B.
   bioRxiv. 2021 Aug 22.
4. Principled simulation of agent-based models in epidemiology.
   Wu SL, Dolgert AJ, Lewnard JA, Marshall JM, Smith DL.
   bioRxiv. 2020 Dec 21.
5. Effects of Spatial Heterogeneity on Transmission Potential in Vectorial-Contact Networks: A Comparison of Three Aedes aegypti Control Strategies.
   Sánchez HC, Marshall JM, Wu SL, Vallejo EE.
   bioRxiv. 2017 Oct 28.

Miscellaneous

1. Individual.jl: Rewriting individual-based models for epidemiology using graph rewriting.
   Wu SL, Libkind S, Brown K, Patterson E, Fairbanks J.
   Applied Category Theory 2022
2. Organic Urban Boundaries and Clusters - Analyzing Singapore as an Example.
   Zhou Y, Park D, Wu SL.
   Sante Fe Institute Complex Systems Summer School 2017 Proceedings
3. Quantifying and comparing 'memory' in biological, ecological, physical, and socio-economic systems
   Jurgens A, Kraay A, Weissman J, Dong J, Pangallo M, Wu SL, Stopnitzky S, Zhan SH, Gurevich Y, Liu Y
   Sante Fe Institute Complex Systems Summer School 2017 Proceedings

Software

1. exDE (Extensible Differential Equations for mosquito-borne pathogen modeling)
   R package available on CRAN and GitHub
   Wu SL, Smith SL (2022).
2. Population.jl: a dynamically-structured matrix population model
   Julia package available on the Julia general repository and GitHub
   Erguler K, Wu SL (2022).
3. Micro-MoB: Microsimulation for mosquito-borne pathogens
   R package available on CRAN and GitHub
   Wu SL, Smith DL (2022).
4. Individual.jl: an individual-based modeling framework based on applied category theory
   Julia package available on the Julia general repository and GitHub
   Wu SL (2022).
5. individual: Framework for Specifying and Simulating Individual Based Models
   R package available on CRAN and GitHub
   Charles GD, Wu SL, Winskill P (2021).
6. MGDrivE2: Mosquito Gene Drive Explorer 2
   R package available on CRAN
   Wu SL, Bennett JB, Sánchez HC, León TM, Dolgert AJ, Marshall JM (2020).
7. MGDrivE: Mosquito Gene Drive Explorer
   R package available on CRAN
   Sánchez HC, Bennett JB, Wu SL, Marshall JM (2019).

Personal Projects

Inspiration for collecting these notes and scraps is largely from Cosma Shalizi's excellent and voluminous collection of notebooks on everything under the sun.
I am trying to move all of my notes and examples to a dedicated website, which is very slowly taking form at https://slwu89.github.io/Categorical-Idiot//

Notebooks and miscellanea

Notebooks, to keep things around I want to remember in the future. These are personal and thus have strange allusions, (not funny) humor, and misspellings. There may even be errors.

• Notes on the single jump approximation: this short and unfinished document describes one way to approximate continuous time Markov chains. It's what the pomp package calls an Euler-Multinomial scheme. I call it single jump for reasons that I hope the document explains. My literature search has led me to believe the first time it was expressed was here A Software Reliability Model with Multiple-Error Introduction & Removal but I have not checked the probability literature thoroughly.
• Notes on stochastic simulation: notes on various papers regarding simulation stochastic topics.
• Notes on "Bayesian Melding", a probabilistic move to do something that's technically not allowed but very very useful in practice.
• A short tutorial with R code to help people understand the relationship between the Poisson process, gamma, and exponential distributions.
• Math Notes: an Overleaf document with various notes on purely mathematical topics. Right now just has a bit of number theory, from when I was trying to learn how random number generators actually spit out their "random" numbers.
• Stochastic Process Notes: A large (and growing) set of notes on what consumes most of my mental energy, discrete state continuous time stochastic processes.
• Notes on Simon Wood's GAM book: I am slowly trying to do many of the examples from the excellent book Generalized Additive Models: An Introduction with R.
• Probabilistic Reasoning for Epidemiology: one night I couldn't sleep and typed up a hypothetical syllabus for a course I'd like to teach one day. It probably wouldn't make sense to anyone but myself, but I'm working on that.
• Short Guide to Competing Hazards: I typed up a set of slides for my lab to describe how Exponential competing hazards models are used with an eye towards simulation. I may someday extend this to generic (semi-Markov) competing hazards models and include classic discrete event simulation algorithms.
• Profiling R packages with C++: this is an absolute bare-bones guide on how to use Google's C++ profiler to profile R code that calls compiled code and produce a nice graph. I am putting it here so I don't forget how to deal with various small annoyances that occur when using it.

Notes on books

• Notes on Simon Wood's GAM book: I am slowly trying to do many of the examples from the excellent book Generalized Additive Models: An Introduction with R.
• Notes on Network Science by Albert-László Barabási: Notes on the book "Network Science"..

Rogues' Gallery

Friends, Mentors, Acquaintances

• My friend & colleage Drew Dolgert with whom I design software to simulate malaria at IHME. Physicist #1.
• A colleague turned friend: Daniel T. Citron. Physicist #2.
• A friend I met at the Santa Fe Institute who works on Very Interesting Things, Alex Jurgens. Physicist #3.
• Friend since age 5, now a scientist at Lawrence Berkeley National Laboratory, Tess Smidt. Physicist #4.
• My friend and one-time classmate, now in digital health, Maria Ma. Not a physicist (Infectious Disease).
• Long time friend and colleague, Héctor Sánchez Manuel Castellanos. Not a physicist (Computer Science).
• A very very old friend, Don Paul Whigan. Not a physicist (journalism, creative services, photography).

People with Interesting Web Pages, and other internet oddities

• Chaos, statistics, stochastics, economics, other: Cosma Shalizi.
• Statistician: Radford Neal.
• Random numbers, probability: Luc Devroye.
• Cybernetics: Paul Pangaro.
• Mathematics, Category theory: Tai-Danae Bradley.
• Art, Bay Area housing and transportation policy advocate: Alfred Twu.
• Nuclear secrecy: Alex Wellerstein.
• Zompist: a little bit of linguistics, sci-fi, liberalism, etc.
• Computer software design, mathematics: Eli Bendersky.
• Copius amounts of book reviews on everything under the sun: Danny Yee.
• Pictures of cats in Tokyo. Updated very regularly. Cats cats cats.
• Software, also spiders: Melissa McEwen.
• Random numbers, software design, other topics: Agner Fog.
• C++ & software development: Scott Meyers.
• Statistics, computing, statistical computing: John Myles White.
• This person wrote a C library to do statistics. That in itself is shocking, but more shocking is his very fascinating research at the Census Bureau.
• Dan Luu blogs about many interesting things.
• Jeff Suzuki, history of mathematics, SCA, other things. "A Legend in His Own Mind".
• Ben Lynn, many interesting topics in theoretical computer science. Notably binary decision diagrams, and zero-suppressed decision diagram.
  • More on ZDDs from another blogger.
• Keith Schwarz has many code implementations of various data structures and algorithms but perhaps most interesting is this extended piece about the alias method to sample discrete distributions.
• Anthropologist David Jordan has a wealth of interesting articles about culture, language, and other topics.
• Craig Reynolds, the person who made boids, has a fantastic page on individual based models in a variety of disciplines.
• There is another Sean Wu also from San Diego who runs a lab at Stanford. I am not him.

Other

• ORBIS: your google maps direction routing for travel in the Pax Romana.
• The Recompiler: a feminist technology magazine from Portland, OR.
• Logic: technology with a social bent.
• Alice and Kev: a Sims 3 awareness project of playing a homeless family.
• The Norbert Wiener Learning Center: a collection of video, audio, and textual media devoted to learning more about the life and work of the founder of Cybernetics.
• How the most unique programming language actually works: Raw R.

Miscellany

This website benefitted substantially from Dave Raggett's guides to HTML.

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