CS:4980 Topics in Computer Science II: Computational Epidemiology

Spring 2020, 9:30-10:45 TTh 221 MLH (MacLean Hall)

Instructors:
Sriram V. Pemmaraju
101G MLH, sriram-pemmaraju@uiowa.edu, 319-353-2956
Office Hours: 1:30-2:30 M, 10:30-11:30 W, 2:00-3:00 F.
Alberto M. Segre
14G MLH, alberto-segre@uiowa.edu, 319-335-1713
Office: TBA.

Our office hours are "walk-in" hours and you don't need to make an appointment to see us during office hours. We are also happy to meet with students outside office hours by prior appointment.

Course webpage: homepage.cs.uiowa.edu/~sriram/4980/spring20/
Department website: http://www.cs.uiowa.edu/

This is a graduate-level Computer Science (CS) course on computational epidemiology, which is the study and development of computational techniques and tools for modeling, simulating, predicting, forecasting, surveilling, mitigating, and visualizing the spread of disease. In this course, we will use techniques from different areas of CS including algorithms, data mining, discrete-event simulations, machine learning, and network science. The course is organized into four parts: (i) Disease-spread models and analysis of disease dynamics, (ii) Inference, prediction, and forecasting problems related to disease-spread, (iii) Infection control and disease surveillance problems, (iv) Additional topics including a discussion of disease-related datasets and the use of technology for gathering contact data. A more detailed list of topics and readings appears further below.

No prior background in epidemiology or biology is assumed. However, a solid background in discrete mathematics, especially graph theory and discrete probability, and a solid background in programming and data structures will be assumed. Background in linear algebra and statistics is not required, but mathematical maturity in these areas will likely be helpful. A substantial portion of student evaluation will be via a group project, that will include an end-of-term technical paper and presentation. Additional modes of evaluation will include solving homework problems, writing short technical pieces, participating in classroom and online discussions, and scribing lecture notes. There will be no exams in this course.

Syllabus document, Announcements, Assignments, Weekly Topics

Announcements

For your use, sample latex source files for scribe notes are available in this directory.
Updates on the 2019 coronavirus (COVID-19), from UI and from the CDC.
COVID-19 resources for projects:
1. COVID tracking project
2. COVID-19 reports from the Imperial College, London
3. COVID-19 social distancing scoreboard
4. Slate article on social distancing as measured by NYC metro turnstile deta
5. R package for COVID-19 modeling and visualization, with links to mostly Chinese data sources
6. Coronavirus (Covid-19) Data in the United States from the New York Times.
7. NYT analysis of social distancing based on cell phone data from a company called Cuebiq that provides "COVID-19 mobility insights".
8. Google mobility reports.

Assignments

Reading Response 1. Due in class Tue, 1/28.
Reading Response 2. Due in class Thu, 2/20.
Project Plans.
Links to external datasets and presentation describing the UIHC datasets.
Reading Response 3. Due before class Thu, 4/2.

Weekly Topics

1/20-1/24

Introduction. What is epidemiology? What is computational epidemiology? Brief history of epidemiology and computational epidemiology. Bernoulli's math model for smallpox from 1760s. John Snow and the Broad Street Cholera outbreak. Main themes of the course. slides
Recent research on C.diff infections (CDI) at the University of Iowa Hospitals and Clinics (UIHC). slides
Readings:

The next plague is coming: Is America ready? by Ed Yong, The Atlantic, July/Aug 2018.
1/27-1/31
- Recent research on statistical tests that show spatio-temporal clustering of C.diff infections (CDI) at the University of Iowa Hospitals and Clinics (UIHC). slides
- Introduction to compartmental models. Analysis of the compartmental SIR model. Other related models such as SIS and SEIR. Definition of the basic reproductive number and its implications to disease-spread.
  Lecture notes for Jan 28, 30.
Readings:
1. Writeup on the Knox test.
2. SpatioTemporal Clustering of in-Hospital Clostridioides difficile Infection (CDI), Pai et al. Draft of paper to appear in ICHE 2020.
3. The next plague is coming: Is America ready? by Ed Yong, The Atlantic, July/Aug 2018.
4. Sections 1 and 2 from Mathematical Approaches to Infectious Disease Prediction and Control, Dimitrov and Meyers. INFORMS: Tutorials in Operations Research, 2010.
5. Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions, 27 Jan 2020, Read et al.
2/3-2/7
- Variants of the SIR model: SEIR, SIS, MSIR, SIRS, etc., limitations of compartmental models and motivation for contact network modeling of disease spread, the cascades model for disease-spread on contact networks, the definition and role of R0, connections to percolation, implications for computation.
Readings:
1. Sections 4 and 5.1 (including the introductory portion of Section 5) from Mathematical Approaches to Infectious Disease Prediction and Control, Dimitrov and Meyers. INFORMS: Tutorials in Operations Research, 2010.
2. Sections 21.1, 21.2, and 21.3 from Networks, Crowds, and Markets: Reasoning about a Highly Connected World by Easley and Kleinberg.
2/10-2/14
- Case study of a contact network of healthcare workers from the University of Iowa Hospitals and Clinics (UIHC), generated from data.
- Features of contact network that are typically modeled. Degree distributions and configuration model graphs. Power-law degree distributions.
- Small-world networks and implications for disease-spread.
Readings:
1. Healthcare Worker Contact Networks and the Prevention of Hospital-Acquired Infections, Curtis et al., PLOS One, December 2013.
2. Collective dynamics of "small-world" networks, Watts and Strogatz, Nature, June 1998.
3. Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study, Wu, Leung, and Leung, The Lancet, Jan 31 2020.
2/24-2/28
- Introduction to inference problems for disease models, Markov chain Monte Carlo (MCMC) methods for inferring disease parameters in compartmental models.
- Inferring infection sources in contact network models.
Readings:
1. Model fitting and inference for infectious disease dynamics, by Funk et al. We will focus on the first two sections: "Introduction" and "MCMC." Most of the material covered in class will be from the lecture slides for these sections.
2. Detecting sources of computer viruses in networks: theory and experiment, by Shah and Zaman, SIGMETRICS 2010.
3/9-3/13
- Inferring the role of in-hospital spread of C.diff infection using simple logistic regression models.
- Inferring the role of asymptomatic spreaders in contact network models.
Readings:
1. Evaluation of Clostridium difficile-Associated Disease Pressure as a Risk Factor for C difficile Associated Disease, by Dubberke et al., Archives of Internal Medicine, 2007.
2. Learning the Probability of Activation in the Presence of Latent Spreaders, by Makar, Guttag and Wiens, AAAI 2018.
3/30-4/3
- Introduction to the design and evaluation of disease control policies.
- Report on the impact of non-pharmaceutical interventions (NPIs) to reduce COVID-19 mortality and healthcare demand. This is a report published on March 16th by modelers and epidemiologists from the Imperial College, London.
Slides and videos:
1. Tue 3/31 slides, video, and discussion questions.
Readings:
1. Start reading from (and including) the subsection "Design of effective vaccination policies" from Healthcare Worker Contact Networks and the Prevention of Hospital-Acquired Infections, Curtis et al., PLOS One, December 2013. Focus on Figures 4, 5, and 6.
2. Section 6 from Mathematical Approaches to Infectious Disease Prediction and Control, Dimitrov and Meyers. INFORMS: Tutorials in Operations Research, 2010.
3. Report 9: Impact of non-pharmaceutical interventions (NPIs) to reduce COVID-19 mortality and healthcare demand by Neil M. Ferguson et al, March 16th 2020.
4/6-4/10
- This week's focus will be on the vaccine allocation problem and we will study two very different ways of modeling this problem and solving it.
- An algorithmic perspective of the vaccine allocation problem. Modeling the vaccine allocation on a contact network as the Minimum Sum-of-Squares graph partition (MSSP) problem. Approximation algorithms for MSSP.
- Optimizing Vaccine influenza vaccine distribution using compartmental modeling with age cohorts.
Slides and videos:
1. Tue 4/7 slides
2. Tue 4/9 slides
Readings:
1. Optimizing Influenza Vaccine Distribution, Medlock and Galvani, Science 2009.
2. Slides on the above paper.
4/13-4/17
- This week's focus will be on the disease surveillance problem.
- We will overview a wide varity of disease surveillance methods including geographically locating an optimal set of sentinal surveillance sites, locating "senors" in networks, using online search history (e.g., Google Flu trends), and social media analysis (e.g., the twitter metwork).
- We will then dig deeper into the datasets and the optimization problems driving the results in the two papers below (in Readings) on geographic surveillance.
Slides and videos:
1. Tue 4/14 slides
Readings:
1. Primary Stroke Centers Should Be Located Using Maximal Coverage Models for Optimal Access, Enrique C. Leira, Geoffrey Fairchild, Alberto M. Segre, Gerard Rushton, Michael T. Froehler, and Philip M. Polgreen, Stroke 2012;43:2417–2422.
2. How many suffice? A computational framework for sizing sentinel surveillance networks, Geoffrey Fairchild, Philip M. Polgreen, Eric Foster, Gerard Rushton, and Alberto M. Segre, Int J Health Geogr. 2013; 12: 56.
4/20-4/24
- This week's focus will continue to be be on the disease surveillance problem.
- We will study the problem of optimally locating sensors for disease-spread on a social network, given very limited knowledge of the network. The approach in the Christakis-Fowler paper below relies on the so called "friendship paradox" in social networks.
- We will study an approach to surveillance of healthcare associated infections (HAIs) in the paper by Adhikari et al.
Slides and videos:
1. Tue 4/21 slides with questions and lecture slides.
2. Tue 4/23 slides.
Readings:
1. Social Network Sensors for Early Detection of Contagious Outbreaks, Christakis and Fowler, Sep 2010, PLOS One.
2. Fast and near-optimal monitoring for healthcare acquired infection outbreaks, Bijaya Adhikari, Bryan Lewis, Anil Vullikanti, José Mauricio Jiménez, B. Aditya Prakash, PLOS Comp. Bio., Sep 2019.
5/4-5/8
- This week, to finish up the semester, we will focus on 3 relatively short and light readings on COVID-19.
- The first reading takes a "micro" view of the spread of COVID-19 by studying the temporal dynamics of viral shedding of COVID-19 patients.
- The second reading takes a "macro" view of pandemic, does some "crystal ball" gazing, and forecasts different possible pandemic scenarios over the next 2 years.
- The third reading (which is non-technical) is by Ed Yong, whose article "The next plague is coming: Is America ready?" started us off at the beginning of the semester.
Readings:
1. Temporal dynamics in viral shedding and transmissibility of COVID-19, Xi He at al, Nature Medicine, April 15 2010, Nature Medicine.
2. Part 1: The Future of the COVID-19 Pandemic: Lessons Learned from Pandemic Influenza, Kristine A. Moore, Marc Lipsitch, John M. Barry, and Michael T. Osterholm, April 30 2020, COVID-19: The CIDRAP Viewpoint.
3. Why the Coronavirus Is So Confusing, Ed Yong, April 29 2020.