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!

Thank you

@evelgab

evelinag.com

evelina@evelinag.com