Mailund on the Internet

Some more news coverage of the orangutan genome paper:

• Orangutan DNA boosts survival chances: study
• Researchers perform genomic analysis of orangutans
• Scientists determine what makes an orangutan an orangutan
• Tiny orangutan populations are surprisingly diverse
• Genome analysis outlines variations in orangutans of Borneo, Sumatra
• Orangutan genome full of surprises

The paper mentioned at the bottom of the last one is this one, and there’s a press release for that one as well:

• Genetic archaeology finds parts of our genome more closely related to orangutans than chimps

I was just told over email that the orangutan genome paper is out at Nature. Right now, I cannot connect to Nature, though, so I cannot really tell.

Anyway, I found posts about it here and here.

We’ve been involved in the analysis here in Aarhus, applying our CoalHMM methods, and we will have two companion papers out. The first in Genome Research – any minute now, really, it is supposed to come out today – and the second in PLoS Genetics – not sure when, it is in the pipeline but I haven’t received a release date yet.

We’ve received a lot of questions to the Genome Research paper the last couple of days, and I’m busy answering emails right now, but I’ll be back and commenting on it here as soon as I have the time.

Update: Ah, Nature is up again, and you can start reading here.

On Monday I start teaching my Machine Learning course again. I’m looking at the material for the first week right now, and I want to change it from last year.

Typically, my students will have had classes on mathematical modeling, a bit of probability theory and a bit of statistics, but experience tells me that they only have a very superficial knowledge about it. They don’t need much more for this class, but I still want to get some key points out regarding the statistics that we will be using in the class, and the last few years I don’t think I managed that well.

I don’t want to focus on modeling so much, and I certainly don’t want to discuss experiment design since the data we look at generally is just collected data that we need to make some kind of sense of, not collected to decide one theory against another.

It really is about a few points: Given the data and some generic model, say a neural network, why do we estimate the parameters in the way we do? What can we say about the accuracy of predictions? That kind of stuff.

I usually go a little bit into Bayesian statistics for model selection, but most of what they see in the class are different generic models that they estimate parameters for through maximum likelihood.

The thing is, while they generally remember how they estimate the parameters in different models when we get to the exam, they focus on the details of a particular model and rarely remember that they are essentially doing the same thing for all the models: maximizing a likelihood in a probabilistic model.

The first couple of years I taught this class, I definitely focused too much on the mathematical details in this. Going through derivations of the math, explaining how you got various posteriors from conjugate priors and such. Major fail.

I tried changing that last year, focusing more on examples, but it didn’t help much once we got to the exam.

Do any of you have experience with teaching statistics core concepts, preferably with some good examples? Care to share?

If you don’t teach this stuff, but have had classes like it, what worked for you as a student and what definitely didn’t work?

I got an iPad a few weeks ago, and I was a bit disappointed to find out that the notes application there doesn’t automatically synchronize over an IMAP mail box. Notes in Mail can be synchronized that way.

Some sort of “Cloud” is a must for me when it comes to most files, and especially to notes. I have a stationary computer at work and at home, a laptop when I’m traveling, and now an iPad that I plan to use when at meetings and such. If I have to manually synchronize these machines, it is a show stopper.

So, since it seems I cannot add iPad to the machines where I can just use Mail, I looked around after alternatives.

First, I tried SimpleNote.  There’s a website interface, apps for both iPad and iPhone, and several options for desktop applications (JustNotes, shown below, is the one I liked the most).

It’s a pretty simple service. Just text notes with some labels and such for categorizing notes. As far as I can see there aren’t any ways of formatting notes or adding files and such to them, but on the other hand, simple is sometimes just the right thing. Fewer things can go wrong, and there is really no learning curve.

I’m also trying out Evernote, though. Again, there are apps for iPad and iPhone and a desktop application for the Macs. I’m not sure about a web interface, but I don’t really need that if I have useful apps on every platform I’m on.

Evernote is in the complete opposite end of the feature scale. It looks like you can put just about anything in there as a note. There is rich formatting of notes and different ways of organizing them.

I doubt that I will ever use all the features of Evernote, but if I use enough of them to compensate for the more complex interface — and it doesn’t get much simpler than SimpleNote’s — then I am probably still going for that.

Haven’t quite decided yet, though.

Are there other note taking tools I should consider?

With the whole RSI stuff, I’ve been away from the blog since August. So long, really, that I hardly think about blogging any more. So I figure that if I don’t get started again soon, I probably never will. So here’s the first post in a long while.

It’s also the first post I’ve written on an iPad, so let’s see how that goes.

So much has happened while I’ve been away from the blog that I would have loved to write about, but by now it would just seem silly to rehash old news. But I am sure that there will soon be interesting news to write about.

I expect a slow start now that I try to get back. I’m still in physiotherapy and far from recovered, so I have to keep my computer time pretty short, but let’s see how it goes.