Ancestry Determination via Genetic Variant Analysis Part 2

In this post, the techniques outlined in an earlier blog post are employed to predict the ancestry of the author. Two approaches are considered: an approach using a classification model and one using similarity functions. Finally, scatter plots depicting low dimensional projections of the data are shown, plotting the genome of the author alongside samples from the IGSR dataset.

Read more

Ancestry Determination via Genetic Variant Analysis

Introduction

Sequencing of the human genome began in 1990 as part of the Human Genome Project. With the technology available at the time, the project was a substantial undertaking. The human genome contains two sets of 23 chromosomes each with roughly 3.2 billion base pairs. A number of institutions, in countries around the world, participated in the project. Thirteen years later the project was complete at a cost of roughly three billion US dollars. The result was the first reference human genome.

Rapid advances in the field of genomics have dramatically lowered the cost of genetic sequencing and have ushered in the age of the once fabled “$1000 genome.” Now, a growing list of companies offer whole genome sequencing for hundreds of dollars with turn around time measured in weeks. This technology enables introspection into the sequences of nucleobases that comprise DNA and thus the genes of anyone curious enough to take the plunge.

Read more

Applying Correlation as a Criterion in Hierarchical Decision Trees

Decision trees are a simple yet powerful method of machine learning. A binary tree is constructed in which the leaf nodes represent predictions. The internal nodes are decision points. Thus, paths from the root to the leafs represent sequences of decisions that result in an ultimate prediction.

Decision trees can also be used in hierarchical models. For instance, the leafs can instead represent subordinate models. Thus, a path from the root to a leaf node is a sequence of decisions that result in a prediction made by a subordinate model. The subordinate model is only responsible for predicting samples that fall within the leaf.

This post presents an approach for a hierarchical decision tree model with subordinate linear regression models.

Read more

A Method for Addressing Nonhomogeneous Data using an Implicit Hierarchical Linear Model

Datasets containing nonhomogenous groups of samples present a challenge to linear models. In particular, such datasets violate the assumption that there is a linear relationship between the independent and dependent variables. If the data is grouped into distinct clusters, linear models may predict responses that fall in between the clusters. These predictions can be quite far from the targets depending on how the data is structured. In this post, a method is presented for automatically handling nonhomogenous datasets using linear models.

Read more