a kernel based framework for predicting interactions between methanotrophs and heterotrophs
TRANSCRIPT
A Kernel-Based Model to Predict Interaction Between Methanotrophic
and Heterotrophic BacteriaMichiel Stock
KERMIT
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A general network:
Some biological applications...
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zondag, 13 mei 2012
Enzyme function
prediction
Food pairing
Protein-ligand interaction
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Learning relations
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7.663.415.019.763.78
SVMRLS
K-PCA...
LigandsProteins
Learning algorithm based on kernel matrices
Microbial interactions
How do heterotrophic microorganisms influence the growth of methanotrophs?
METHANOTROPHS HETEROTROPHS
METHANE
CARBONCOMPOUNDS
VITAMINS?ANTIBIOTICS?
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Experimental setup
• 270 interactions
• 10 methanotrophs
• 27 heterotrophs
• Methane as sole carbon source
• Measurement of OD every 2 days for two weeks 6
Optical density time series
• Three types of labels• maximal optical density• maximal increase in optical density• time of maximal increase in optical density
0 5 10 15
0.00
0.05
0.10
0.15
0.20
0.25
0.30
Meth_5 and Hetero_2
Time (days)
OD
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max OD
max increasment OD
0 5 10 15
0.00
0.05
0.10
0.15
0.20
Meth_7 and Hetero_10
Time (days)O
D
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max OD
max increasment OD
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Quantification of interaction
M 4
M 8
M 2
M 7
M 6
M 3
M 9
M 1
M 5
H 15H 13H 10H 3H 8H 1H 25H 12H 19H 23H 22H 2H 14H 24H 20H 17H 21H 16H 18H 5H 11H 4H 7H 9H 6
Heat map of the log_2 of the relative max. OD
−4 −2 0 2Value
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Color Keyand Histogram
Cou
nt
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Matrix completion
• Key idea:• remove a subset
of interactions• predict missing
values• Using kernel
methods or probabilistic PCA
Measuredinteractions
Completed interaction
matrix
Learningalgorithm
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Results matrix completion
False positive rate
Aver
age
true
posi
tive
rate
0.0 0.2 0.4 0.6 0.8 1.0
0.0
0.2
0.4
0.6
0.8
1.0
ROC curve for max. increase density missing values inference
10 % missing (AUC = 0.7482)25 % missing (AUC = 0.7315)50 % missing (AUC = 0.7253)
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Take-home messages• Many biological
problems are about relations
• Data mining as a useful tool for analyzing experiments
• Predictive models to aid wet-lab experiments 11
Acknowledgments
• KERMIT• Willem Waegeman• Bernard De Baets
• LM UGent• Sven De Groeve• Kim Heylen
• Labmet• Frederiek-Maarten Kerckhof• Nico Boon
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