Proteomic mass spectra classification using decision tree based ensemble methods.
BACKGROUND
Modern mass spectrometry allows the determination of proteomic fingerprints of body fluids like serum, saliva or urine. These measurements can be used in many medical applications in order to diagnose the current state or predict the evolution of a disease. Recent developments in machine learning allow one to exploit such datasets, characterized by small numbers of very high-dimensional samples.


RESULTS
We propose a systematic approach based on decision tree ensemble methods, which is used to automatically determine proteomic biomarkers and predictive models. The approach is validated on two datasets of surface-enhanced laser desorption/ionization time of flight measurements, for the diagnosis of rheumatoid arthritis and inflammatory bowel diseases. The results suggest that the methodology can handle a broad class of similar problems.
Geurts
Pierre
P
Department of Electrical Engineering and Computer Science, University of Liège 4000 Liège, Belgium. p.geurts@ulg.ac.be
Fillet
Marianne
M
de Seny
Dominique
D
Meuwis
Marie-Alice
MA
Malaise
Michel
M
Merville
Marie-Paule
MP
Wehenkel
Louis
L
D000465:Algorithms; D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D030562:Databases, Protein; D003663:Decision Trees; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D010449:Peptide Mapping / Q000379:methods*; D020543:Proteome / Q000032:analysis / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
D020543:Proteome