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Understanding cancer behaviour with F#
Evelina Gabasova
F# eXchange 2015
Traditional medicine
Precision medicine
Integrative clusteringBreastcancer
Gene expression
microRNA expression
Methylation data
Reverse-phase protein array
Integrative clusteringBreastcancer
Data
Data Data
Data
Scientific programming
Scripting languages fast prototyping, easy to use
R, Python, Matlab
Why F#?
Why F#?
Vector? Matrix? List? Array? Data frame?
Why F#?
Case studyRewrite an algorithm from Matlab into F#
adaptive rejection sampling
Case study
Matlab
Pattern matching
Matlab
F#
Pattern matching
Matlab
F#
Legibility
Legibility
Legibility
Breastcancer
Gene expression
microRNA expression
Methylation data
Reverse-phase protein array
Typical workflow
Problem
Typical workflow
Problem
Model
Typical workflow
Problem
Model Evaluation
Typical workflow
Problem Data
Model Evaluation
Typical workflow
Problem Data
Model Evaluation
Usually takes much more time
than it should
Dealing with real-world data
Type providers
F# Data - typed access to external data sources
Csv files
JSON, XML, HTML
RProvider
Results
Results
So… why F#?• The best of both worlds: fast scripting & type system
• Easy access to data of different types
• Using R only for what it is good at
• Provide types for all the things!