Articles by John Ramey

MLB Rankings Using the Bradley-Terry Model

August 31, 2013 |

Today, I take my first shots at ranking Major League Baseball (MLB) teams. I see my efforts at prediction and ranking an ongoing process so that my models improve, the data I incorporate are more meaningful, and ultimately my predictions are largely accurate. For the first attempt, let’s rank ... [Read more...]

A Brief Look at Mixture Discriminant Analysis

July 2, 2013 |

Lately, I have been working with finite mixture models for my postdoctoral work on data-driven automated gating. Given that I had barely scratched the surface with mixture models in the classroom, I am becoming increasingly comfortable with them. With this in mind, I wanted to explore their application to classification ... [Read more...]

High-Dimensional Microarray Data Sets in R for Machine Learning

December 29, 2012 |

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 ... [Read more...]

Setting Up the Development Version of R

August 28, 2012 |

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 ... [Read more...]

Chapter 2 Solutions – Statistical Methods in Bioinformatics

August 14, 2012 |

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. Problem 2.20 Suppose that a parent of genetic type Mm ... [Read more...]

Textbook – Statistical Methods in Bioinformatics

August 14, 2012 |

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... [Read more...]

Now That We Live in Seattle

August 11, 2012 |

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 ... [Read more...]

And Now I Blog Again

August 4, 2012 |

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 ... [Read more...]

Goals for 2012

January 9, 2012 |

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. ... [Read more...]

When I was 29…

January 8, 2012 |

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 ... [Read more...]

Steve Jobs’ 2005 Stanford Commencement Address

December 4, 2011 |

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... [Read more...]

Pseudo-Random vs. Random Numbers in R

November 25, 2011 |

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 ... [Read more...]

Listing of Statistics and Machine Learning Conferences

June 12, 2011 |

Occasionally, I will query Google with “statistics conferences”, “machine learning conferences” or “pattern recognition conferences” and the like. But often, it is difficult to obtain anything meaningful other than the conferences of which ... [Read more...]

Conway’s Game of Life in R with ggplot2 and animation

June 5, 2011 |

In undergrad I had a computer science professor that piqued my interest in applied mathematics, beginning with Conway’s Game of Life. At first, the Game of Life (not the board game) appears to be quite simple — perhaps, too simple — but it has been widely explored and is useful for ... [Read more...]

Getting Started with Some Baseball Data

May 24, 2011 |

With all of the discussions (hype?) regarding applied statistics, machine learning, and data science, I have been looking for a go-to source of data unrelated to my day-to-day work. I loved baseball as a kid. I love baseball now. I love baseball stats.... [Read more...]