Follow the Data

A data driven blog

Archive for the category “Events”

Online analysis contests and animal testing

I’d like to draw your attention to two online data analysis challenges that both, in their way, address drug testing on animals and how results of such testing translate to human physiology.

CAMDA 2013 (12th international conference on critical assessment of massive data analysis) is a conference that focuses on massive data sets in the life sciences. This year, it has two associated analysis challenges, one of which is “prediction of drug compatibility from an extremely large toxicogenomic data set.” The data set used in this challenge contains over dataset contains over 20,000 genome expression microarrays, each measuring perhaps about 20,000 genes in the liver of rats treated with mainly human drugs. There are two questions that the organizers want to address:

  • Question 1: Can we replace animal studies with in vitro assays? ["in vitro" literally means "in glass", for instance in a test tube]
  • Question 2: Can we predict liver injury in humans using toxicogenomics data from animals?

Meanwhile, the SBV (systems biology verification) Improver project, which ran a prediction contest last year that was covered in this blog, is starting its new Species Translation Challenge,  which also aims to address how “translatable” biological events in rats or mice are to humans. This challenge, which has four sub-challenges, aims to answer the following questions:

  • Can the perturbations of signaling pathways in one species predict the response to a given stimulus in another species?
  • Which biological pathways, functions and gene expression profiles are most robustly translated?
  • Which gene expression profiles and associated biological pathways / functions are most robustly translated?
  • Does translation depend on the nature of the stimulus or data type collected such as protein phosphorylation and cytokine responses?
  • Which computational methods are most effective for inferring gene, phosphorylation and pathway response from one species to another?

I think it will be very interesting to see how these challenges play out and to compare their respective outcomes.

BigData.SG and The human face of big data

By an amazing coincidence, I was able to attend a session of the Singapore big data meetup group, BigData.SG, after having attended the NGS Asia 2012 conference here in the Lion City. This group was started earlier this year and tries to meet once a month (a more ambitious schedule than the Stockholm group.) Today, about 40 people were in attendance, and I had a nice time chatting to some of them. The invited speaker was Michael Howard, VP of marketing at Greenplum. He had one nice quip – “big data means so little to so many” and talked a little bit about Chorus, a collaborative data science platform from Greenplum which I hadn’t heard about. He hinted that Chorus and Kaggle have something big going on together – something that will revolutionize the whole crowdsourced prediction “business.” It will be interesting to see what it is.
Earlier today, Howard had announced the Human Face of Big Data project, which has been / will be launched in several cities all over the world today (probably still hasn’t launched in the US).  The project, which “lets people compare themselves to each other”, uses a downloadable app (for Android; the iOS version wasn’t working yet) that you can use to collect data about yourself with. There is “passive data collection”: how far and at what speed you’ve moved, how many Bluetooth hot spots you’ve passed, and so on, and active collection through questions that the app asks you; either “serious” questions such as whether you would modify the genes of your unborn infant if given the opportunity (and if so, what would you improve – immune system, intelligence, …) – apparently men and women answered this very differently – or more open-ended “fantasy” questions.

The app also lets you find your “data doppelganger”, which is of course the user who is most similar to you in terms of the collected data. Howard said that despite the short time since the launch, the app has already yielded interesting information about gender differences and topics of interest.

Stockholm Big Data Meetup

The first meetup of the Stockholm Big Data group was organized yesterday (Sep 6 2012) by Mikael Hussain at the Klarna headquarters. The audience was packed, with close to a 100 people attending and others unfortunately left out (due to fire regulations.) Apparently a lot of people (including us) had been thirsting for this sort of event.

The format was 1.5h of rapid talks (supposed to be 10 min each but probably a bit longer in practice) on widely different topics – we will refer to Marina Santini’s excellent writeup for details on the talks – followed by socializing in the pub around the corner. Follow the Data was represented by me (Mikael) as I gave a short talk about the benefits of competing in (and organizing) online prediction contests.

During the course of the event, I learned about three companies that I didn’t know about and who are all actively looking for analytics and big data talent:

  • Campanja - online advertising, heavily into Erlang and AI. Looking to fill several positions of different kinds
  • Svensk Lånemarknad (~Swedish Loan Exchange?) – help customers find the best banks and loans for them – looking to fill a predictive analytics position
  • Tink – not quite sure what they are doing (the home page is a bit cryptic) – looking for developers

I’m sure there were other companies as well looking to recruit – I only had time to talk to a small fraction of the participants, obviously!

All in all, I think the meetup was a lot of fun and I am looking forward to more meetups in Stockholm soon.

Meetup groups for Big Data & Predictive Modeling and Quantified Self in Stockholm

Two interesting new meetup groups have formed in Stockholm (well, there are other interesting ones but for the purposes of this blog these two are the most exciting):

Fun!

Health Hack Day ’12: Day 1 impressions

So as mentioned in the previous post, Health Hack Day ’12 in Stockholm is underway right now; it started with a number of lectures and a party yesterday and the actual hacking will start today, with the winning apps to be presented tomorrow. You can follow the #hhd12 hashtag on Twitter or go to the link above to see the recorded lectures.

I thought the arrangements and speaker line-up yesterday were surprisingly good, which bodes well for the survival of the Health Hack Day concept, in fact I’m sure they will be back next year. The lectures (which were recorded and can be viewed online at the link above) were given in a smallish space (part of a fin de siècle apartment complex now used as an office hotel for creative types, located near Stureplan in central Stockholm) decorated with thousands of yellow strips of paper hanging down from the ceiling – a nice-looking installation which also provided some relief from the heat in the room when the wind occasionally blew in through the window and turned the paper strips into a giant ceiling fan. Meanwhile, visitors could sip some excellent free coffee (from Stockholm roast).

Hoa Ly is a young, enterprising fellow who works for Psykologifabriken (“The Psychology Factory”) and his own sister company Hoa’s Tool Shop (both of these companies were involved in arranging the event), as well as doing clinical psychology research at Linköping university and being a successful DJ. He talked about behavior change through digital tools, exemplifying with the Viary mobile & web app which has been used successfully for depression treatment but, as I understand it, is quite general in nature so you could track any kind of behavior & goals (incidentally, the statistics interface looks a lot like the WordPress interface where I look at access statistics for this blog!) Hoa also talked about correlating data from different sources like Viary, the Zeo sleep tracker and exercise data from heiaheia.com. Integrating data from different sources is of course very interesting but I didn’t feel we quite got any really solid concrete examples here, just a general sense that it should be useful. Anyway. The most intriguing part of Hoa’s talk was when he described the launch of a new project to “disrupt the whole dance music industry” (or words to that effect). The idea is to treat DJ performances as scientific experiments and “gather data from the audience”, for instance by measuring adrenaline levels in response to song selections. Hoa and his partners have created a new  country called Yamarill (link in Swedish) to construct a narrative around which this project will be built. The inauguration of the new country will apparently be celebrated on June 1 at the Hoa’s Tool Shop office spaces. The Yamarill “delegation” has already played several DJ gigs “combining electronic dance music, technology and psychology” as they say in the linked interview (I might also add “quirky clothes”).

Pernilla Rydmark from .SE talked about different forms of crowdfunding and presented five Swedish platforms for it. .SE is also introducing an interesting form of funding called “guaranteed funding” where they pick projects that are already popular on crowdfunding platforms and promise to fund them up to their stated goal in case they don’t succeed in reaching it through the crowdfunding platform. Thus, the goal of the funding is rather paradoxically that no one should get it (because .SE is hoping that the projects will get fully funded by the crowd.)

Bill Day from Runkeeper talked about the need for an open, global health platform and presented HealthGraph, a free platform with tens or millions of users initiated by the RunKeeper team but which is expanding far beyond that community.

Mathias Karlsson from Calmark presented his company’s approach to rapid blood biomarker testing, which is making consumable platforms for colorimetric assays (the measurement of interest is transformed into a color) which can be analyzed on the spot using, for example, a smartphone camera. He brought a developer team who will attempt to build a new test (for bilirubin) into the platform in 24 hours during the hackathon part of the event.

Linus Bengtsson from FlowMinder described intriguing reality mining (or in less spectacular terms, call log analysis) work where data from mobile phone providers was used to track the movements of people during and after the Haiti earthquake, and the subsequent cholera outbreak. Linus and his team tracked 1.9 million SIM cards from Port-Au-Prince residents to obtain their estimates on migration patterns. FlowMinder is a non-profit and provides free analysis of the same kind during any kind of global disaster (in collaboration with mobile telephony providers, naturally.)

Sara Eriksson and Johan Nilsson from United Minds talked about the “new health”, including a lot of topics that have been frequently mentioned on this blog, like 23andme, PatientsLikeMe, and even the MinION sequencer from Oxford Nanopore. I had heard / thought about most of it before but what I took away from it was the concept of “biosociality” as coined by Paul Rabinow, and also that only 37% of surveyed Stockholm smart phone users did *not* want to collect data on themselves through the phone; a whopping 59% wanted not only to collect the data but to analyze it themselves.

Megan Miller from Bonnier (a Swedish media company which has an enormous influence in the media here; however Megan was working for its US branch) described Teemo, a platform for “digital wellness”, with components of collaborative adventuring and social exercise (you try to accomplish “quests” together with your friends by exercising.) Teemo looks like it has a pretty nifty design, inspired by paper cuts and Nordic (=Helsinki?) design style. As Megan put it, Teemo wants to “put fun first and track behavior in the background.)

We will see whether Follow the Data has the energy to visit again tomorrow and see what apps have come out of the hackathon, which should be starting in a few hours from now!

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