Here are a slew of interesting things for computer scientists interested in global health, from the UW CSE Industrial Affiliates Program. This came my from the UW Change mailing list.
Category Archives: global health
Global Health Metrics and Evaluation (GHME) Conference 2011
The Global Health Metrics and Evaluation (GHME) Conference 2011 is something that might interest you. It’s in Seattle, from March 14-16, 2011. More from the conference website:
The Global Health Metrics & Evaluation (GHME) conference aims to bring together all the different disciplines involved in global health measurement and evaluation under one roof to share innovative tools and methods to get a better understanding of what the possibilities are in approaching population health measurement.
Who should come? People who are interested in cutting edge science, who want to learn from others in their fields and in other fields. Specifically, researchers, academic leaders, students, policymakers, non-governmental organizations, foundations, country offices of health statistics, and national and multi-national health organizations.
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Speaking of graphics…
I got this email the other day:
the open data kit team is in dire need of a logo and we need your help. if you know a designer (or are a designer) looking to contribute to a growing open source project, now is your chance!
before you get started, we have three rules.
- go big! although the core team works on healthcare in africa, odk is a much broader project. try to stay away from global development or health themes, but feel free to play off the words and ideas in the project name.
- think unified! we build a lot of tools (collect, aggregate, build, voice, clinic, etc), so a brand that could be used across all of them would be great. for example, most of the adobe creative suite applications use the same basic theme. see them at http://goo.gl/1HYP.
- be inspired! if you’ve never designed a logo, http://goo.gl/2KBy has some great ideas to help you get started. that site also has links to an amazing array of examples.
our goal is to have a couple of logos that we can pick from, so spread the word and send in a few! the deadline for the competition is november 1 at midnight. send your attempts to yano…@gmail.com.
thanks for helping make odk a more visually pleasing project,
yaw
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Global Congress on Verbal Autopsy in 2011 open for abstract submission
Have you heard me say that Verbal Autopsy is a exemplary machine learning challenge? I think I say it about once a week.
Now there’s going to be a great forum for saying it. Read more here.
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MCMC in Python: How to stick a statistical model on a system dynamics model in PyMC
A recent question on the PyMC mailing list inspired me. How can you estimate transition parameters in a compartmental model? I did a lit search for just this when I started up my generic disease modeling project two years ago. Much information, I did not find. I turned up one paper which said basically that using a Bayesian approach was a great idea and someone should try it (and I can’t even find that now!).
Part of the problem was language. I’ve since learned that micro-simulators call it “calibration” when you estimate parameter values, and there is a whole community of researchers working on “black-box modeling plug-and-play inference” that do something similar as well. These magic phrases are incantations to the search engines that help find some relevant prior work.
But I started blazing my own path before I learned any of the right words; with PyMC, it is relatively simple. Consider the classic SIR model from mathematical epidemology. It’s a great place to start, and it’s what Jason Andrews started with on the PyMC list. I’ll show you how to formulate it for Bayesian parameter estimation in PyMC, and how to make sure your MCMC has run for long enough. Continue reading
Filed under global health, MCMC, statistics
IHME and a Gates Foundation Critique
I was forwarded a recent article about the Gates Foundation and how it has partnered with news organizations like ABC News and The Guardian. And guess what? IHME makes an appearance in the second half of the second page! I wouldn’t say that it’s positive about my work, but I am delighted to see the technical appendix mentioned in print.
During my recent education in medicine, I’ve learned that an appendix is something that people think you don’t need. Also, if something goes wrong with it, it can kill you. And it’s true that the “webpendix” is 219 pages, but the bulk of that is pictures. The first 19 pages are a pretty decent stats paper about how we used Gaussian Processes to model really noisy time-series data.
Yearly percentage decline in mortality in children younger than 5 years between 1990 and 2010
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Applied Approximate Counting: Malaria
My first first-authored global health paper came out today (I consider it my first “first-authored” paper ever, since the mathematicians I’ve worked with deviantly list authorship in alphabetical order regardless of seniority and contribution). It’s a bit of a mouthful by title: Rapid Scaling Up of Insecticide-Treated Bed Net Coverage in Africa and Its Relationship with Development Assistance for Health: A Systematic Synthesis of Supply, Distribution, and Household Survey Data.
What I find really pleasing about this research paper is the way it continues research I worked on in graduate school, but in a completely different and unexpected direction. Approximate counting is something that my advisor specialized in, and he won a big award for the random polynomial time algorithm for approximating the volume of convex bodies. I followed in his footsteps when I was a student, and I’m still doing approximate counting, it’s just that now, instead of approximating the amount of high-dimensional sand that will fit in an oddly shaped high-dimensional box, I’ve been approximating the number of insecticide-treated bednets that have made it from manufacturers through the distribution supply-chain and into the households of malaria-endemic regions of the world. I’m even using the same technique, Markov-chain Monte Carlo.
I’ve been itching to write about the computational details of this research for a while, and now that the paper’s out, I will have my chance. But for today, I refer you to the PLoS Med paper, and the technical appendix, and the PyMC code on github.
Filed under global health, MCMC
Guest post from “the field”
One cool program here at IHME is the field placements for our Post-Bachelors Fellows. This is a roughly 6 week stint during the summer of their second year here where they travel from Seattle to some distant place, to see where the numbers we’ve been crunching come from. Kyle Foreman is in Sri Lanka doing this now, and here is a guest post he’s written about an ICT4D challenge he’s seeing that he wants your ideas on:
I’m spending this summer in Sri Lanka working with the Ministry of Health and the community health department of the University of Peradeniya, observing how Sri Lanka’s medical record keeping and vital statistics system works. They’d like for me to make some suggestions on how it could be improved, so I was hoping to get some feedback on how to make this work.
Here’s the problem: keeping track of something as simple as the number of people who die each year is very difficult here. Patient records are kept at each hospital, then they are tabulated and sent to a regional office, then tabulated at a district office, ad nauseam, until they finally reach the national level. It takes literally years (they just finished the 2006 returns), is full of errors (because they do it all by hand), and is very incomplete (because every step along the way there’s further tabulation which strips away valuable data). They thus have difficulty identifying problems (especially outbreaks), targeting resources, and assessing the outcomes of their efforts. Continue reading
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The GBD 2010 Health Measurement Survey is here
Have you got 15 minutes for science? Take this strange survey that I’ve been excited about for the last two years. I’ve been calling it the Disability Weights Survey, but now that it’s all professionally implemented and communications-department approved, it is officially the GBD 2010 Health Measurement Survey.
The survey is part of the Global Burden of Diseases, Injuries, and Risk Factors Study 2010 led by the Institute for Health Metrics and Evaluation (IHME) at the University of Washington, in collaboration with four other leading institutions: Harvard University, Johns Hopkins University, the University of Queensland, and the World Health Organization.
Our goal is to collect responses from at least 50,000 people worldwide. Please consider sharing this and encouraging participation within your organization. In addition, we would ask you to consider forwarding information about this survey to colleagues and contacts outside your organization who might be interested in participating.
The survey takes about 15 minutes to complete. Participation is completely voluntary and anonymous. In the near future, we hope to translate the survey into additional languages.
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Child Mortality Paper
Check it out, my first published research in global health: Neonatal, postneonatal, childhood, and under-5 mortality for 187 countries, 1970—2010: a systematic analysis of progress towards Millennium Development Goal 4. I’m the ‘t’ in et al, and my contribution was talking them into using the really fun Gaussian Process in their model (and helping do it).
I’ve long wanted to write a how-to style tutorial about using Gaussian Processes in PyMC, but time continues to be on someone else’s side. Instead of waiting for that day, you can enjoy the GP Users Guide now.
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Healthy Algorithms 