Tag Archives: random forests

The sleeping beauty in the random forest: T-Trees

A sleeping beauty refers to an article that is undervalued and is not cited very often and then awakens later and is recognised as important. The most famous one is the work of Mendel that were published in 1865 and rediscovered 34 years later. To learn more about this concept, you can read this or that.

Today, I want to talk about a paper that is a bit too young to be a sleeping beauty but that seems undervalued :

Exploiting SNP Correlations within Random Forest for Genome-Wide Association Studies (2014) by Vincent Botta, Gilles Louppe, Pierre Geurts, Louis Wehenkel

The four authors are from Liège in Belgium. Their team is known to work on Random forest (if you do not know what that is, you can read my earlier blogpost on the subject). Geurts and Wehenkel have proposed a variant of random forest called extremely randomized trees. Gilles Louppe is the one who implemented random forest for the scikit-learn package for python (which I use. Thanks!). The first author Vincent Botta left academia after his PhD and went to work for a company (a start-up in newspeak).

Motivation

The idea of the paper is to use biological structure in order to increase prediction accuracy. The additional structure used here is chromosomal distance. A SNP is located on a chromosome and it has neighbours. This information can be useful in several ways: Continue reading

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Everything is not linear: the example of Random Forest

Linear regression is great. But unfortunately, not everything in nature is linear. If you drink alcohol, you get drunk. If you take your prescribed drugs, you are healthy. But if you do both at the same time, you will not be drunk and healthy, you will probably get very sick. This is an interaction. In general, we talk about interaction when there is a departure from linearity. There are many ways to try and capture interaction using statistical learning but today, I will focus on Random Forest. But before, I explain what a forest is I have to explain what a decision tree is.

“Erik – Prunus sp 02” by Zeynel Cebeci – Own work. Licensed under CC BY-SA 4.0 via Wikimedia Commons – https://commons.wikimedia.org/wiki/File:Erik_-_Prunus_sp_02.JPG#/media/File:Erik_-_Prunus_sp_02.JPG

The good people at www.r2d3.us did a great job of explaining what a decision tree is in a very visual way. So click here and go look at it. Also, subtle Star Wars reference. Continue reading

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