Sean L. Wu, PhD
- 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
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.
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.
I will soon be starting a postdoc with Nicole Mideo in the department of Ecology and Evolutionary Biology at the University of Toronto.
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, oftentimes 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.
In addition to English I speak fluent Mandarin Chinese. I am trying to learn Cantonese and Taiwanese.
Languages I can speak to computers are R (native), C++ (fluent), C (conversational), and Julia (conversational).
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.
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.
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.
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.
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).
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).
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.
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.
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.
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.
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.
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.
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.
(Submitted to Malaria Journal) 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.
medRxiv. 2021 Apr 22.
Principled simulation of agent-based models in epidemiology.
Wu SL, Dolgert AJ, Lewnard JA, Marshall JM, Smith DL.
bioRxiv. 2020 Dec 21.
(Under review at PLoS ONE)
Measuring the accuracy of gridded human population density surfaces: a case study in Bioko Island, Equatorial Guinea.
Fries B, Smith DL, Wu SL, Dolgert AJ, Guerra CA, Hay SI, García GA, Smith JM, Oyono JN, Donfack OT, Nfumu JO.
bioRxiv. 2020 Jun 20.
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.
individual: Framework for Specifying and Simulating Individual Based Models
R package available on CRAN
Charles G, Wu SL, Winskill P (2021).
MGDrivE2: Mosquito Gene Drive Explorer 2
R package available on CRAN
Wu SL, Bennett JB, Sánchez HC, León TM, Dolgert AJ, Marshall JM (2020).
MGDrivE: Mosquito Gene Drive Explorer
R package available on CRAN
Sánchez HC, Bennett JB, Wu SL, Marshall JM (2019).
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
and comparing 'memory' in biological, ecological, physical, and
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
Inspiration for collecting these notes and scraps is largely from Cosma Shalizi's excellent and voluminous collection of notebooks
on everything under the sun.
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.
Writing too disorganized to even be called notes.
- 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
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.
- 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.
- 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.
This website benefitted substantially from Dave Raggett's guides to HTML.
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