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kxs | 5 years ago | on: AlphaFold: a solution to a 50-year-old grand challenge in biology

They trained on 170k sequences/ structures/ proteins, each sequence has 10s to 100s or even 1000s amino acids. Structure is much more conserved than sequence. Out of the 100 targets, roughly 1/4th have no similarity to known structures, so there shouldn't be an overlap for those with the training set. They did very well on those targets.

kxs | 5 years ago | on: AlphaFold: a solution to a 50-year-old grand challenge in biology

There are different categories of samples, namely FM and TBM targets. FM targets don't have any similarity to known structures. Roughly a quarter were FM targets. I think the more interesting thing to look at is the size of the multiple sequence alignments (MSAs) which is the basis of this and essentially all methods. They seem to do very well with few MSAs, which bodes well for other targets, although there are families of proteins with few MSAs.

kxs | 7 years ago | on: AlphaFold: Using AI for scientific discovery

The targets are completely unknown. They were experimentally solved, but not submitted to the Protein Data Bank. You basically get a target every day (meaning sequence of amino acids) and then depending on the category, you have three days to predict it (I think upto two weeks for "human" servers). In the modeling category they participated in, you can submit 5 models. A model is a fully predicted 3d structure of the protein. The targets are mostly independent. Some targets were split over a few days. But in principle, a target on day X has no connection to a target on day Y. The targets have varying difficulty. There are two categories: TBM (templated based) and FM (free modeling). You don't know which protein corresponds to which category, you can just guess by looking at the available template data. They focused on FM targets. Meaning there are no homologous available. It's hard to say how good of an indicator the results are. Looking at the contact prediction results, many methods are getting very good at constructing MSAs (gathering similar sequences). We already saw this at CASP12 - I think the FM targets are getting "easier" in that sense. There is basically zero feedback throughout the whole competition. Some targets are released after the deadline (because of publications), but in general, you don't know anything until the CASP meeting, which currently takes place. The competition ended in August.

kxs | 7 years ago | on: Probiotics labelled 'quite useless'

Did the supplement contain pepper? AFAIK you need to consume turmeric together with black pepper to make it effective (blocks something in the liver IIRC). Maybe that was the reason?

kxs | 8 years ago | on: Who the Hell Uses Onion Juice?

I used to get a lot of sinus infections, to remedy this, I drank for an extended period of my life cooled "onion juice" (onion + water + honey, cooked for ~1h). My whole family was disgusted by it, but I somehow enjoyed it.

kxs | 11 years ago | on: Everyday hassles in Go

You should look into Debug.Trace for quick printf-like debugging. Usage: trace ("error occurs here") (f x)

kxs | 13 years ago | on: Light Table 0.4 released

It seems to be possible to use the Chrome PDF Viewer. This could be nice for LaTeX development.

kxs | 13 years ago | on: The amount of crap Windows users have to put up with is incredible

Although I haven't tried Windows 8 yet, I had the same experience using Windows 7.

It's interesting that only 7 years ago you probably wouldn't have be able to sit me in front of a Windows machine without resistance or at least some complaining. Since then I turned out to be a frequent defender of Microsoft in my surroundings and I'm considering ditching my Apple ecosystem for Windows 8 (esp. because of Surface and Windows Phone 8).

But the real problem, as have stated other, is OEM software and 3rd-party-apps. It takes effort to maintain your system (although not much, at least in my opinion, but you have to pay attention to, for example, what is installed along the way). I usually have none of the problems my peers or friends have (with Windows) and if you look at their machine, you'll see why. Almost every time I visit my father, there is a new (worthless) toolbar installed.

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