Statistical Espresso for Biologists
Can’t stop the signal: machine learning, big data & summarizing variation
BIOL{6750{07 | Fall 2017
Instructor: William D. Pearse
1 Course description and learning objectives
There are two kinds of \problem” in statistics that everyone wishes they had: so many observations that you
don’t know what’s going on (many rows), and so many variables you don’t know what’s important (many
columns). In both cases it can be difficult to even see what’s going on in your data, let alone statistically model
it. By the end of this course, you will:
 Understand the basic principles of machine learning and management of `big data’
 Be able to use principal components analysis, ordination, and cluster analysis to identify groups and associations
among variables
 Be able to use regression trees and least angle regressions to summarize complex datasets
 Be able to manipulate, visualize, and perform regressions on large (>10Gb) datasets in R (e.g., all known
global observations of plants)
The class emphasizes both theoretical concepts and practical applications equally: students are encouraged to
`follow-along’ with the examples given in the lecture in the R statistical environment. This will give you the
practical skills you need to make use of the statistical approaches covered in the class in your own work.
As a graduate student, much of your grade will be determined by a written project, using the skills you develop
in the class to investigate a dataset of your choosing. Through one-on-one meetings with the instructor during
and after the class, you will learn to apply the concepts you practiced in the classroom in an entirely novel
setting. This is an excellent opportunity to get help with your thesis…
2 Course materials
No text-books are required for this course, but a laptop computer (Windows, Mac, or Linux) with RStudio
version  1.0.143 (using R version  3.4.0) and SQLite version  3.19.3. Advice and help getting these tools
installed will be provided ahead of the start of class.
3 Requirements
Basic statistical classes (i.e., knowledge of how to perform a t-test and simple linear regression) are required for
this class. No prior experience with R whatsoever is required, as the class will focus entirely on how to interpret
R output and students will have no need to perform any programming in the class. Students who are concerned
about their level of R experience are encouraged to study the USU baseR website (,
which covers more detail than is required for this course. The starting statistical requirements for this course
are very low, but, nevertheless, students who are concerned are encouraged to contact Dr Pearse directly
4 Attendance & participation
Attendance of all lectures is compulsory; we are covering a lot of ground in a compressed period of time and students
who miss one session may not be able to catch back up. Students who miss more than one session may be dropped
from the course, unless they can give a good reason (with evidence if necessary) for missing that session.
5 Assessment
You will be assessed through a combination of coursework and a short exam delivered a few weeks after the
end of the class. Coursework will be started in the classroom, and will consist of completing an analysis of one
or more datasets on which the instructor will give guidance, and then analyzing and interpreting additional
dataset(s) in a similar vein. The exam will be short, and test the retention of key statistical concepts|it will not
require detailed calculations or rote memorization of arcane statistical facts. Example questions (and answers)
will be given to the students ahead of the exam.
In addition to this, graduate students will be required to complete a short paper describing the use of the
statistical techniques developed within this class in a novel dataset. Graduate students are strongly encouraged to
use this as an opportunity to develop one of their thesis chapters. The marking breakdown for the undergraduate
4XXX series, and graduate 6XXX series, classes are given below:
Section 4XXX % 6XXX %
Coursework 55 27.5
Exam 35 17.5
Paper 0 45
Participation 10 10
The \Honor System” of Utah State University applies to the coursework and paper. I strongly advise you not
to copy-paste answers to exercises from the Internet or from the work of other students. Not only are solutions
from outside sources (and other students) often wrong, they are also quite simple for me to detect and those
who cheat will be punished in accordance with Utah State University regulations.
6 Schedule
The course is split into three main sections. In the first (weeks 1{2), you will learn the classical concepts of data
summary and basic commands in the R statistical language, and in the second (weeks 3{4) we will learn about the
most common kinds ofmodernmachine learning tools. In the third and final section (week 5), we will reviewmodern
data manipulation and storage techniques, and learn about best-practices with data. No coursework will be due
until the end of the class, but students are strongly encouraged to complete exercises as the class proceeds.
Week Title 1st session 2nd session
1 Classical tools PCA factor analysis
2 Clustering hierarchical k-means
3 Machine Learning 1 regression trees least angle regression
4 Machine Learning 2 support vectors artificial neural networks
5 Data & synthesis sql(ite) pipelines
Each week follows the same format: two sessions, each comprised of one 40-minute lecture and a 40-minute session
to work on coursework and practical examples. Each lecture will give equal weight to core theoretical concepts
and practical demonstrations of those within R: this is not a theoretical class, it is a practical class where you
will pick up skills and experience. It is likely that students will want to have whatever they use for note-taking
to hand and their laptops to try things with the instructor in real-time in R. The coursework practicals will
be an opportunity for students to continue working through the examples given in the preceding lectures, and
also to begin work on their coursework exercises and receive feedback and help with those exercises.
7 Miscellanea
 ADA compliance: Students with physical, sensory, emotional or medical impairments may be eligible for
reasonable accommodations in accordance with the Americans with Disabilities Act and Section 504 of the
Rehabilitation Act of 1973. All accommodations are coordinated through the Disability Resource Center in
Room 101 of the University Inn, 797-2444 voice, 797-0740 TTY, or toll free at 1-800-259-2966. Please contact
the DRC as early in the semester as possible. Alternate format materials (Braille, large print or digital) are
available with advance notice.
 Sexual harassment is defined by the Affirmative Action/Equal Employment Opportunity Commission as any
\unwelcome sexual advances, requests for sexual favors, and other verbal or physical conduct of a sexual nature.”
If you feel you are a victim of sexual harassment, you may talk to or file a complaint with the Affirmative
Action/Equal Employment Opportunity Office located in Old Main, Room 161, or call the AA/EEO Office
at 797-1266.
 Students whose religious activities conflict with the class schedule should contact me at the beginning of the
semester to make alternative arrangements.
 Course scheduling and structure may change at short notice with no warning.