Thursday, 10 November 2011

Biovis/Visweek recap

Finally time to write something about the biovis/visweek conference I attended about a week ago in Providence (RI)... And I must say: they'll see me again next year. (Hopefully @infosthetics will be able to join me then). Meanwhile, several blog posts are popping up discussing it (see here and here, for example).

This was the first time that biovis (aka the IEEE Symposium on Biological Data Visualization) was organized. It's similar to the 2-year old vizbi, but has an agenda that is more focused on research in visualization rather than application of visualization in the biological sciences. Really interesting talks, posters and people.

The biovis contest
This first installment of biovis included a data visualization contest, focusing on "specific biological problem domains, and based on realistic domain data and domain questions". The topic this year was on eQTL (expression quantitative trait loci) data, and I'm really happy that Ryo Sakai -  now a PhD student in my lab - won the "biologists' favourite" award!! The biologist jury was impressed with the ease in which his visualizations of the eQTL data highlighted and confirmed prior knowledge, and how it suggested directions for further experiments. It was interesting to see that there was a huge variation in the submissions, going from just showing the raw data in an interesting way (which Sakai-san did) to advanced statistical and algorithmic munging of the input data and visualizing the end result (which the winner of the "dataviz professionals' favourite" award did). See how this relates to my previous post on humanizing bioinformatics?

Interesting talks - amazing (good & bad) talks
As this was the first time that I attended visweek, I was really looking forward to the high quality presentations/papers and posters. Overall, I got what I wanted. But there were some examples of papers and posters that I have major doubts about (taking into account that I have to be humble here in talking about people working in the field for far longer than I do).
One example that seemed pretty counterintuitive was a presentation by Basak Alper from Microsoft about a new set visualization technique that they baptized LineSets. The main issue that they want to solve is the visualization of intersections of >3 sets (up to 3 you'd just use Venn diagrams). Their approach is to connect the different elements from a set by a line; hence: linesets. However, I (and many others with me) felt that this approach has some very serious drawbacks. Most of all, it suggests that there is an implicit ordering of the elements, which there isn't. In the image below, for example, line sets were used to connect Italian restaurants (in orange) and Mexican restaurants (in purple). That's the only thing this visualization wants to do: tell me which of the restaurants are Italian and which are Mexican. But give this picture to 10 people, and every single one of them will think that the lines are actually paths or routes between these restaurants. Which they're not... The example below shows data that has specific positions on a map, but they demonstrate this approach on social networks as well.
Another example comes from the biovis conference: TIALA or Time Series Alignment Analysis. Suppose you have the time-dependent gene expression values for a single gene, which you'd plot using a line plot. Now what would you do if you have that type of data for 100 genes? Would you put those plots into 3D? I know I wouldn't... And better still: would you then connect these plots so you end up with some sort of 3D-landscape? That's like connecting the tops of a barchart displaying categorical data with a line...

TIALA - Time Series Alignment Analysis

But of course there were plenty really good talks as well. Some of the talks I really enjoyed are those about HiTSEE (by Bertini et al) on the analysis of high-throughput screening experiments, EVEVis (Miller et al) on multi-scale visualization for dense evolutionary data, arc length-based aspect ratio selection (Talbot et al) which is an alternative to banking to 45 degrees, drawing road networks with focus regions (Haunert et al), and especially DICON which showed an amazing application of visual analysis of multidimensional clusters using healthcare data.


Road networks with focus regions
DICON - interactive visual analysis of multidimensional clusters

Meeting interesting people
But of course this was very much about meeting interesting people as well. It was really nice to exchange ideas again with the biovis crowd (Nils Gehlenborg, Cydney, Tamara, Will Ray, ...), and I finally had the chance to have a chat with @filwd Enrico. All those discussions with Thorri from Icelandic DataMarket were both useful and fun (as was our day hanging out in town, chatting to the Occupy Providence woman (forgot her name, I'm afraid) and trying to find a good hat).
At the airport on my way back, as I was trying to find out how to get to Brussels (as our flights were cancelled due to the weather), a chap comes to me and introduces himself as someone from Belgium. From Leuven. From our very own faculty. So together with @infosthetics Andrew that now makes three of us :-)

Anyway: I'll definitely be back next year (have to play some more official role anyway) and already looking forward to it.