Posts from March 2013 (75)

The Herald has an interesting set of displays of the latest DigiPoll political opinion survey.  According to the internets it was even worse earlier in the day, but we can pass over that and only point out that corrections in news stories shouldn’t happen silently (except perhaps for typos).

We can start with the standard complaint: the margin of error for the poll itself is 3.6%, so the margin of error for change since the last poll is 1.4 times higher, or a little over 5%. None of the changes is larger than 5%, and only one comes close.

Secondly, there is a big table for the minor parties. I would normally not quote the whole table, but in this case it’s already changed once today.

The total reported for the minor parties is 6.1%, and since there were 750 people sampled, 46 of them indicated support for one of these parties. That’s not really enough to split up over 7 parties. These 46 then get split up further, by age and gender. At this point, some of the sample proportions are zero, displayed as “-” for some reason.

[Updated to add: and why does the one male 40-64 yr old Aucklander who supported ACT not show up in the New Zealand total?]

Approximately 1 in 7 New Zealanders is 65+, so that should be about 6 or 7 minor-party supporters in the sample.  That’s really not enough to estimate a split over 7 parties. Actually, the poll appears to have been lucky in recruiting older folks: it looks like 6 NZ First, 2 Conservative, 1 Mana.

That’s all pretty standard overtabulating, but the interesting and creative problems happen at the bottom of the page.  There’s an interactive graph, done with the Tableau data exploration software.  From what I’ve heard, Tableau is really popular in business statistics: it gives a nice clear interface to selecting groups of cells for comparison, dropping dimensions, and other worthwhile data exploration activities, and helps analysts present this sort of thing to non-technical managers.

However, the setup that the Herald have used appears to be intended for counts or totals, not for proportions.  For example, if you click on April 2012, and select View Data, you get

which is unlikely to improve anyone’s understanding of the poll.

I like interactive graphics.  I’ve put a lot of time and effort into making interactive graphics.  I’ve linked to a lot of good interactive graphics on this blog. The Herald has the opportunity to show the usefulness of interactive graphics to a much wider community that I’ll ever manage. But not this way.

From Bradley Voytek, apparently from Reddit, but unfortunately not further sourced there either

I think the legend at the bottom right just makes this perfect.

From the Grantland blog at ESPN

New technology and statistics will change the way we understand basketball, even if they also create friction between coaches and front-office personnel trying to integrate new concepts into on-court play. The most important innovation in the NBA in recent years is a camera-tracking system, known as SportVU, that records every movement on the floor and spits it back at its front-office keepers as a byzantine series of geometric coordinates. Fifteen NBA teams have purchased the cameras, which cost about $100,000 per year, from STATS LLC; turning those X-Y coordinates into useful data is the main challenge those teams face.

Some teams are just starting with the cameras, while others that bought them right away are far ahead and asking very interesting questions. Those 15 teams have been very secretive in revealing how they’ve used the data, but one team that has made serious progress — the Toronto Raptors — opened up the black box in a series of meetings this month with Grantland.

The Raptors do have a current record of 26-41, so there seem to be limits to what the analytics can achieve…

There’s a good piece in one of the New Yorker‘s blogs  about the Human Connectome Project and the proposed Brain Activity Map.  The Connectome project has produced two terabytes of functional and structural data on the brains of 68 volunteers, and the Brain Activity Map is more or less what it says on the tin.

Almost certainly people will be able to do something useful with all this data, but some of the claims for what it means to our understanding of the brain are a bit much. As the RealClearScience blog points out (in a slightly different context), we know the complete nervous system of the nematode C. elegans.  We know every cell and all its connnections to other cells.  We still can’t use this knowledge to reliably predict the nematode’s behaviour even by brute-force simulation, let alone by sophisticated analysis.

Simply using Big Data to work out how a complex system functions requires a lot of simplifying assumptions to be true.  This isn’t because we’re not smart enough to build more complex models (though we’re not), and it isn’t because the computation is beyond us (though it is), it’s a fundamental limitation on learning without an underlying theory to help you.

The way Amazon or Netflix does prediction with all its data is to look for a large group of people who are similar to you, in relevant ways, and see what they bought or watched. That sounds easy, but the weasel words are ‘in relevant ways’.  If you have a moderately large number of variables, there are far too many ways in which people, or nerve signals, or protein concentrations could be similar, and you need to decide which ones are relevant.   This is critical, because finding the true relationships in large numbers of associations is only possible if nearly all the associations are zero; in current jargon, the model is ‘sparse’.

In order to see sparseness, you need to know how to look.    Consider the economy: if you just look at associations between measurements, everything is correlated: you see inflation, you see population growth,  you see seasonal variation.  These patterns need to be removed to get a sparse model where you’ve got some hope of disentangling cause and effect.

In really complex fields like brain activity, we don’t know enough about how to pose the problem so that Big Data will have a hope of solving it.

Team Ratings for Round 3

Here are the team ratings prior to Round 3, along with the ratings at the start of the season. I have created a brief description of the method I use for predicting rugby games. Go to my Department home page to see this.

Performance So Far

So far there have been 16 matches played, 12 of which were correctly predicted, a success rate of 75%.

Here are the predictions for last week’s games.

Predictions for Round 3

Here are the predictions for Round 3. The prediction is my estimated expected points difference with a positive margin being a win to the home team, and a negative margin a win to the away team.

Team Ratings for Round 6

This year the predictions have been slightly changed with the help of a student, Joshua Dale. The home ground advantage now is different when both teams are from the same country to when the teams are from different countries. The basic method is described on my Department home page.

Here are the team ratings prior to Round 6, along with the ratings at the start of the season.

Performance So Far

So far there have been 28 matches played, 19 of which were correctly predicted, a success rate of 67.9%.

Here are the predictions for last week’s games.

Predictions for Round 6

Here are the predictions for Round 6. The prediction is my estimated expected points difference with a positive margin being a win to the home team, and a negative margin a win to the away team.

The NIWA soil moisture maps from March 10 and yesterday show how much difference a single storm doesn’t make:

It’s a good thing there are date labels to distinguish them.

There’s a new research paper out that sequences the genome of one of the most important cancer cell lines, HeLa.  It shows the fascinating genomic mess that can arise when a cell is freed from the normal constraints against genetic damage, and it gives valuable information about a vital research resource.

However, the discussion on Twitter (or at least the parts I frequent) has been dominated by another fact about the paper.  The researchers apparently didn’t consult at all with the family of Henrietta Lacks, the person whose tumour this originally was.  There are two reasons this is bad.

Firstly, publishing a genome of  an ancestor of yours allows people to learn a lot about your genome. The high levels of mutation in the cancer cell line reduces this information a bit, but there’s still a lot there. As a trivial example, even without worrying about genetic disease risks, you could use the data to tell if someone who thought they were a descendant of Ms Lacks actually was or wasn’t. Publishing a genome without consent from, or consultation with, anyone is at best rude.

And secondly: come on, guys, didn’t you read the book? From the author’s summary

In 1950, Henrietta Lacks, a young mother of five children, entered the colored ward of The Johns Hopkins Hospital to begin treatment for an extremely aggressive strain of cervical cancer. As she lay on the operating table, a sample of her cancerous cervical tissue was taken without her knowledge or consent and given to Dr. George Gey, the head of tissue research. Gey was conducting experiments in an attempt to create an immortal line of human cells that could be used in medical research. Those cells, he hoped, would allow scientists to unlock the mysteries of cancer, and eventually lead to a cure for the disease. Until this point, all of Gey’s attempts to grow a human cell line had ended in failure, but Henrietta’s cells were different: they never died.

Less than a year after her initial diagnosis, Henrietta succumbed to the ravages of cancer and was buried in an unmarked grave on her family’s land. She was just thirty-one years old. Her family had no idea that part of her was still alive, growing vigorously in laboratories—first at Johns Hopkins, and eventually all over the world.

That’s how they did things back then.  It’s not how we do things now. If there was a symbolically worse genome to sequence without some sort of consultation, I’d have a hard time thinking of it.

I don’t think anyone’s saying laws or regulations were violated, and I’m not saying that the family should have had veto power, but they should at least have been talked to.

We’ve encountered Karl Broman before, for his list of the top ten worst graphs in the scientific literature.  He also has some nice examples of interactive scientific graphics, both stand-alone and embedded in slides for talks.

One example: 500 boxplots of gene expression ratios (no, you don’t need to know or care what these are).  The top panel shows minimum, maximum, median, quartiles, and as you move the mouse along, the bottom panel shows the whole distribution.  Click, and the distribution stays in the bottom panel for comparison with others.

Karl, on Twitter, has also recommended a column on visualisation in the journal Nature Methods, but it’s not open-access, sadly.

Promoted from comments: Steve Black

In the Wall St Journal article there is a graphic which does an excellent example of showing why you have to be careful. 

So what we’re looking at is that 2011 and 2012 are real. All the rest are made up. And it looks like they made up the trend for 2014-2016 from the pattern of 2011-2013 (two about the same, next two higher) even though 2013 itself is not yet a quarter over. Less than a concrete example?

Yup. I should have noticed that one.

Standard practice is to use a different colour or shading for imaginary numbers: