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91 Pages·2014·14.38 MB·English

Data Mining in the Life Sciences
The Path to Personalized Medicine
Karsten Borgwardt
Machine Learning and Computational Biology Research Group
Max Planck Institute for Intelligent Systems &
Max Planck Institute for Developmental Biology, Tu¨bingen
Eberhard Karls Universit¨at Tu¨bingen
Machine Learning for Personalized Medicine
ITN Summer School
September 23-27, 2013
Karsten Borgwardt Data Mining in the Life Sciences September 2013 1
Our FP7 Marie Curie Initial Training Network: MLPM
Karsten Borgwardt Data Mining in the Life Sciences September 2013 2
Our Initial Training Network: In Numbers
◮ 6 countries: Belgium, France, Germany, Spain, United Kingdom,
United States
◮ 13 ESRs + 1 ER
◮ 12 labs at 10 nodes, 8 academic partners and 2 industrial nodes
(Siemens, Pharmatics)
◮ Duration: 4 years, January 2013 — December 2016
◮ Funding: Up to 3.75 million EUR
◮ 3 years of funding per student
◮ 2 three-month secondments per student
◮ 4 annual summer schools (Tu¨bingen, UK, France, Spain)
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Our Initial Training Network: As a Map
◮ Pharmatics, Edinburgh
◮ University of Sheffield
◮ University of Li`ege
◮ INSERM and ARMINES,
Paris
◮ MPI for Intelligent Systems,
Tu¨bingen
◮ MPI for Psychiatry,
& Siemens Munich
◮ Universidad Carlos III de
Madrid
◮ Prince Felipe Research
Centre (CIPF) in Valencia
◮ MSKCC New York
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Our Initial Training Network: Who is Who? The PIs
◮ Belgium: University of Li`ege (Prof. Kristel Van Steen)
◮ France: ARMINES (Prof. Jean-Philippe Vert), INSERM (Prof.
Florence Demenais)
◮ Spain: UC3 Madrid (Prof. Fernando Perez-Cruz), CIPF Valencia
(Prof. Joaquin Dopazo)
◮ United Kingdom: University of Sheffield (Prof. Neil Lawrence, Prof.
Magnus Rattray - now Manchester), Pharmatics (Dr. Felix Agakov)
◮ United States: MSKCC (Prof. Gunnar R¨atsch)
◮ Germany: Siemens (Prof. Volker Tresp), Max-Planck-Society (Prof.
Bertram Mu¨ller-Myhsok, Prof. Bernhard Scho¨lkopf and Prof. Karsten
Borgwardt)
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Our Initial Training Network: Who is Who? The ESRs
MPG (Borgwardt) Mr Felipe Llinares-Lo´pez
MPG (Borgwardt) Mr Carl-Johann Simon-Gabriel
MPG (Scho¨lkopf) Mr James McMurray
MPG (Mu¨ller-Myhsok) Ms Meiwen Jia
Siemens Mr Cristo´bal Esteban
U Sheffield Mr Max Zwießele
U Li`ege Ms Ramouna Fouladi
ARMINES Paris Mr Yunlong Jiao
INSERM Paris Mr Yuanlong Liu
UC3 Madrid Ms M´elanie Fern´andez Pradier
CIPF Valencia Mr Cancut Cubuk
MSKCC Mr Yi Zhong
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Our Initial Training Network: Our Topics
◮ Research Goal A.1: Biomarker discovery
◮ Research Goal A.2: Data Integration
◮ Research Goal B.1: Causal Mechanisms of Disease
◮ Research Goal B.2: Gene- Environment Interactions
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The Need for Machine Learning in Computational Biology
High-throughput technologies:
◮ Genome and RNA sequencing
◮ Compound screening
◮ Genotyping chips
◮ Bioimaging
BGI Hong Kong, Tai Po Industrial Estate, Hong Kong
Molecular databases are growing much faster than our knowledge of
biological processes.
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The Evolution of Bioinformatics
◮ Classic Bioinformatics: Focus on Molecules
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Classic Bioinformatics: Focus on Molecules
◮ Large collections of molecular data
◮ Gene and protein sequences
◮ Genome sequence
◮ Protein structures
◮ Chemical compounds
◮ Focus: Inferring properties of molecules
◮ Predict the function of a gene given its sequence
◮ Predict the structure of a protein given its sequence
◮ Predict the boundaries of a gene given a genome segment
◮ Predict the function of a chemical compound given its molecular
structure
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