August 2014 - Darpa-chikun-challenge

Re: [Darpa-chikun-challenge] CHIKV Challenge Submission #1
by Alessandro Vespignani 25 Aug '14

25 Aug '14

Hello Prithwish, No problem for the air travel dataset. Can we talk on monday (tomorrow) to define format, time scale etc.? Regards Alex Vespignani On Sat, Aug 23, 2014 at 2:50 AM, Prithwish Chakraborty <prithwi(a)vt.edu> wrote: > Hi All, > > As you may recall, the first submission is due on Sep 1 (in a weeks time). > For that, we have to send 6 months-ahead predictions for 55 > countries/regions (weekly case count). As was discussed during the first > meeting of the group, Elaine , James and I met today and here's what we > thought of doing. Please chime in with your thoughts. > > To summarize, we are going with country specific compartmental SEIR model > for baseline estimates. We can add inter-country transmission effects to the > same. However we would need airline data to do so (details in P.S.). Prof. > Vespignani, I was wondering whether your group can help in organizing this > dataset or perhaps this is already setup? > > For Textual sources we need some keyword list to filter for. Am attaching > the ones Elaine came up with very quickly (also added to wiki at > Data-Sources#keywords-for-textual-sources). It would be of great help, if > you all can add more. > > Thanks > Prithwish > > > <P.S> > Wiki/Repo Access > ============== > Just a reminder that the wiki for this challenge can be found at > https://github.com/prithwi/dac_chik/wiki. It has several pages already being > setup describing the project details (with link outs to folder in the repo > which contains the submission templates), models and data sources. If you > don't have access to it, please send me a mail with your github username so > that I can add you to the collaborators list. > > Baseline Model > ============= > 1. @Elaine will produce ODE based compartmental SEIR simulations to > generate forecasts. ETA Tuesday Aug 26. > > Salient points : > a) @Prithiwsh will provide population estimates. Baseline data already > setup. > b) Won't include transmission factors between countries. > > 2. @James and @Prithwish: Will try to get transmission factors between > countries based on the Nowcasting paper. > > Salient Points: **NEED AIRLINE TRAVEL DATA to create the transmission map** > > Data Sources > ========== > Data Sources | Assigned | Status > 1) Weather | James | may get ready before submission #1 > 2) Healthmap | Prithwish | ETA Monday Aug 25. > 3) Twitter | Prithwish | ETA Monday Aug 25. > 4) GST | Prithwish | ETA Tuesday Aug 26. > 5) Mosquito | Elaine | Has data for Dominican Republic. > 6) Air Travel | TBD | TBD > > Prithwish Chak > raborty > Graduate Resea > rch Assistant > Dept. of Compu > ter Science > Discovery Anal > ytics Center > Virginia Polyte > chnic Institute and State University > email: prithwi(a)vt.edu > web: http://people.cs.vt.edu/~prithwi/ > > _______________________________________________ > Darpa-chikun-challenge mailing list > Darpa-chikun-challenge(a)cs.vt.edu > https://mailman.cs.vt.edu/mailman/listinfo/darpa-chikun-challenge > -- --------------------------------------------- Sternberg Distinguished University Professor, Department of Physics College of Computer and Information Sciences Bouve' College of Health Sciences Northeastern University, Boston MA

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Weather Bleed Started
by James Schlitt 23 Aug '14

23 Aug '14

Hi All, Hope all is going well. I just set up a weather scraper to pull some quick forecasts and historic data for us. For each country listed on the challenge, I am pulling data once every three days via forecast.io from Jan 1, 2014 to March 1, 2015 from the 2 most populated cities of the given country. This should take about 3 days to complete with cities being pulled in order of decreasing country population. If you need access to this data as it pulls, please send a gmail account and I'll share the file. The cities used as well as city metro area and country population data may be found here: https://docs.google.com/spreadsheets/d/1xvqgAF17Av7NuDLZ3PaZoaKV7fvdQ_VLfaY… Cheers, James Schlitt

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Action items from today's meeting
by Naren Ramakrishnan 21 Aug '14

21 Aug '14

Folks, Great to get started on this challenge. Some action items: 1. Prithwish will setup a Github/Wiki page and share with all. 2. Prithwish and Elaine to coordinate to generate forecasts with a baseline model for the first prediction to be delivered. 3. Alex and Elaine/John - pl consult with your colleague(s) if they would like to join the team, and I will add them to the list. 4. John to share some recent relevant papers on CHIKV. More coming soon, Best, Naren -- Naren Ramakrishnan Thomas L. Phillips Professor of Engineering Department of Computer Science http://www.cs.vt.edu/~naren Director, Discovery Analytics Center, Virginia Tech http://dac.cs.vt.edu

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