Razib Khan One-stop-shopping for all of my content

January 26, 2011

Visualizing variation, input → output

I have noted a few times that one thing you have to be careful about in two dimensional plots which show genetic variance is that the dimensions in which the data are projected upon are often generated from the data itself. So adding more data can change the spatial relationships of previous data points. Additionally, in 23andMe’s global similarity advanced plot you are projected onto the dimensions generated from the HGDP data set. There are some practical reasons for this. First, it’s computationally intensive to recalculate components of variance every time someone is added to the data set. Second, it isn’t as if the ethnic identity of any given individual is validated. What would you do if an alien sent in a kit and spuriously put “French” as their ancestry?

So, in reply to this comment: “Let me rephrase: is there any difference when you switch to the world-wide plot? I imagine not, or you would’ve mentioned it.” Actually, there is a slight difference. Below on the right you have a “world view,” with my position being marked with green, and on the left a “zoom in” for Central/South Asia in the HGDP data set.

December 9, 2010

How close are scientific disciplines?

Filed under: Data Visualization,science — Razib Khan @ 3:08 am

Chemistry likes to think of itself as the “central science.” Is that true? Intuitively it makes sense. But how can we measure that more rigorously? In comes the Stanford Dissertation Browser:

The Stanford Dissertation Browser is an experimental interface for document collections that enables richer interaction than search. Stanford’s PhD dissertation abstracts from 1993-2008 are presented through the lens of a text model that distills high-level similarity and word usage patterns in the data. You’ll see each Stanford department as a circle, colored by school and sized by the number of PhD students graduating from that department.

When you click a department, it becomes the focus of the browser and every other department moves to show its relative similarity to the centered department. The similarity scores are computed using a supervised mixture model based on Labeled LDA: every dissertation is taken as a weighted mixture of a unigram language model associated with every Stanford department. This lets us infer, that, say, dissertation X is 60% computer science, 20% physics, and so on. These scores are averaged within a department to compute department-level statistics (the similarities shown), and need not be symmetric. For instance, Economics dissertations at Stanford use more words from Political Science than vice versa. Essentially, the visualization shows word overlap between departments measured by letting the dissertations in one department borrow words from another department. Which departments borrow the most words from which others? The statistics are computed for each year in the data.

You can play around with the browser here. I’m assuming at some point in the near future this sort of analysis is going to get much, much, easier, because of the sea of data which powerful software can extract and visualize patterns out of. Below are the fold are five screen shots I thought were of interest. Genetics, biology, and chemistry dissertations in 2008. And Anthropology in 2007 and 1998.

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