Much of my research in machine learning is aimed at small-sample, high-dimensional bioinformatics data sets. For instance, here is a paper of mine on the topic.
A large number of papers proposing new machine-learning methods that target high-dimensional data use the same two data sets and consider few others. These data sets are the 1) Alon colon cancer...
My coworkers at Fred Hutchinson regularly use
the development version of R (i.e., R-devel) and have urged me to do the same.
This post details how I have set up the development version of R on our Linux server,
which I use remotely because it is much faster than my Mac.
First, I downloaded the R-devel source into ~/local/, which...
As I have mentioned previously, I have begun reading Statistical Methods in Bioinformatics by Ewens and Grant and working selected problems for each chapter. In this post, I will give my solution to two problems. The first problem is pretty straightforward.
Suppose that a parent of genetic type Mm has three children. Then the parent transmits...
As part of my effort to acquaint myself more with biology, bioinformatics, and statistical genetics, I am trying to find as many resources as I can that provide a solid foundation. For instance, I am wading through Molecular Biology of the Cell at a pa...
It has been just a few weeks since my wife, my son, and I moved to Seattle so that I could begin my postdoc at The Hutch. Now that we have been here a short time and are settled, we intend to start exploring Seattle, doing typical touristy things as we...
One of my goals for 2012 has been to blog more. Much more. When I first set this goal, I had great aspirations of posting frequently. However, I had a Ph.D. to complete, and quite frankly, it demanded much higher priority. Now that I have submitted my ...
I have never been one to set New Year’s resolutions. Personally, they instill a dangerous personal freedom that often yield naive, subconscious mentalities, such as I can do anything I want until December 31, and I will change abruptly the next day. ...
Today was my 29th birthday, and I kept things simple: I ate with my wife and my newborn son at a local eatery. Later, my wife cooked steaks for dinner. For the most part, I took the day off in that I did not work on my dissertation. But I did spent muc...
Given that there are almost 13 million views of Steve Jobs’ commencement address, I am certain that I missed this video when it went viral. I am glad that I did not see it until now because I may not have appreciated his words of wisdom. And although...
Earlier, I found an interesting post from Bo Allen on pseudo-random vs random numbers, where the author uses a simple bitmap (heat map) to show that the rand function in PHP has a systematic pattern and compares these to truly random numbers obtained from random.org. The post’s results suggest that pseudo-randomness in
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
