through the looking-glass of data sciencepages.stat.wisc.edu/~claudia/talk-women-stem.pdf ·...
TRANSCRIPT
Through the looking-glass of Data Science
Claudia Solís-Lemus, PhDEmory University
April 5, 2019
Math &Stats Coding
SkillsField
Expertise
DataScience
Slide courtesy of D. Pimentel-Alarcon
Which one has Alzheimer?Slide courtesy of D. Pimentel-Alarcon
Slide courtesy of D. Pimentel-Alarcon
Slide courtesy of D. Pimentel-Alarcon
Expertise: Lizards are longer!Slide courtesy of D. Pimentel-Alarcon
?
Expertise: Lizards are longer!Slide courtesy of D. Pimentel-Alarcon
Length
Wei
ght
?
Slide courtesy of D. Pimentel-Alarcon
Length
Wei
ght
?
Slide courtesy of D. Pimentel-Alarcon
Length
Wei
ght
?
(x,y)
Slide courtesy of D. Pimentel-Alarcon
Length
Wei
ght
?
(x,y)
Slide courtesy of D. Pimentel-Alarcon
Length
Wei
ght
?
(x,y)
Slide courtesy of D. Pimentel-Alarcon
Length
Wei
ght
?
(x,y)
Slide courtesy of D. Pimentel-Alarcon
Length
Wei
ght
?
(x,y)
Slide courtesy of D. Pimentel-Alarcon
Length
Wei
ght
?
(x,y)
Math & Stats: Find the Line.
Slide courtesy of D. Pimentel-Alarcon
Length
Wei
ght
y = ax+b
b
a
?
Math & Stats: Find the Line.
Slide courtesy of D. Pimentel-Alarcon
Length
Wei
ght
y = ax+b
?
?
Slide courtesy of D. Pimentel-Alarcon
Length
Wei
ght
y = ax+b
?
?
Coding Skills:
Slide courtesy of D. Pimentel-Alarcon
So, what did we do?
Field Expertise y = ax+b
Math & StatsCoding Skills
Slide courtesy of D. Pimentel-Alarcon
Pseudomonas aeruginosa
Joint work with Sam Brown (GaTech) and Daniel Pimentel-Alarcon (GSU)https://lungdiseasenews.com/2015/07/21/antibiotic-treatments-found-reduce-not-eliminate-pseudomonas-aeruginosa-colonization-cystic-fibrosis/
Joint work with Sam Brown (GaTech) and Daniel Pimentel-Alarcon (GSU)
Pseudomonas aeruginosaData
https://lungdiseasenews.com/2015/07/21/antibiotic-treatments-found-reduce-not-eliminate-pseudomonas-aeruginosa-colonization-cystic-fibrosis/
https://lungdiseasenews.com/2015/07/21/antibiotic-treatments-found-reduce-not-eliminate-pseudomonas-aeruginosa-colonization-cystic-fibrosis/
Joint work with Sam Brown (GaTech) and Daniel Pimentel-Alarcon (GSU)
Pseudomonas aeruginosaData
Outcome of interest: Drug resistance
Joint work with Sam Brown (GaTech) and Daniel Pimentel-Alarcon (GSU)
Pseudomonas aeruginosaData
Predicting drug resistance
Methods
�
=np
XY
r
Joint work with Sam Brown (GaTech) and Daniel Pimentel-Alarcon (GSU)
Pseudomonas aeruginosaData
Predicting drug resistance
Methods
�
=np
XY
r
Penalized regression
Neural Networks
Genetic InformationGeneticInformation
A A A T C G G T T A C T
Understanding Humans: Introduction to Physical Anthropology and Archeology 10th Ed., p. 45
Bacterium 1 A A A T C G G T T A C T Bacterium 2 A A A T C G G T T A C T Bacterium 3 A A A T C G G T T A C T Bacterium 4 A A A T C G G A T A C T Bacterium 5 A A A T C G G A T A C T
Gene
Bacterium 1 A A A T C G G T T A C T Bacterium 2 A A A T C G G T T A C T Bacterium 3 A A A T C G G T T A C T Bacterium 4 A A A T C G G A T A C T Bacterium 5 A A A T C G G A T A C T
Gene
Bacterium 1 A A A T C G G T T A C T Bacterium 2 A A A T C G G T T A C T Bacterium 3 A A A T C G G T T A C T Bacterium 4 A A A T C G G A T A C T Bacterium 5 A A A T C G G A T A C T
Gene
Genetic variant SNP = Single Nucleotide Polymorphism
Bacterium 1 A A A T C G G T T A C T Bacterium 2 A A A T C G G T T A C T Bacterium 3 A A A T C G G T T A C T Bacterium 4 A A A T C G G A T A C T Bacterium 5 A A A T C G G A T A C T
Gene
Bacterium 1 A A A T C G G T T A C T Bacterium 2 A A A T C G G T T A C T Bacterium 3 A A A T C G G T T A C T Bacterium 4 A A A T C G G A T A C T Bacterium 5 A A A T C G G A T A C T
Genedrug susceptible drug susceptible drug susceptible
drug resistant drug resistant
Bacterium 1 A A A T C G G T T A C T Bacterium 2 A A A T C G G T T A C T Bacterium 3 A A A T C G G T T A C T Bacterium 4 A A A T C G G A T A C T Bacterium 5 A A A T C G G A T A C T
Gene
Could this be due to random chance?
drug susceptible drug susceptible drug susceptible
drug resistant drug resistant
healthy A A A T C G G T T A C T healthy A A A T C G G T T A C T healthy A A A T C G G T T A C T sick A A A T C G G A T A C T sick A A A T C G G A T A C T
Gene
healthy healthy healthy
sick sick
The left panels (top and bottom) show the eye of a normal fly. The
right panels (top and bottom) show
the eye of a fly genetically
engineered to produce human
tau protein. Image Source:
Photo courtesy of J. Paul Taylor,
M.D., Ph.D., St. Jude Children's
Research Hospital.
Math &Stats Coding
SkillsField
Expertise
DataScience
My experience
Math &Stats Coding
SkillsField
Expertise
DataScience
Collaborations
FieldExpertise
My experience
Math &Stats Coding
SkillsField
Expertise
DataScience
Collaborations
Formal training: PhD Stat, MA Math
FieldExpertise
Math &Stats
My experience
Math &Stats Coding
SkillsField
Expertise
DataScience
Collaborations
Formal training: PhD Stat, MA Math
Informal training: C++, julia, R, git
FieldExpertise
Math &Stats Coding
Skills
My experience
Thank you!Cécile Ané (UW) Paul Bastide (KU-Leuven) Bret Larget (UW) Douglas Bates (UW) David Baum (UW)
Michael Epstein (Emory) Daniel Pimentel-Alarcon (GSU) Timothy Read (Emory) Samuel Brown (GaTech) Elizabeth Allman (Alaska) James Degnan (New Mexico) Megan Owen (CUNY)
http://crsl4.github.io/[email protected]
Students: Mengyao Yang John Malloy John Spaw Noah Stenz Nan Ji Jordan Vonderwell Josh McGrath Michelle Su