Supplementary web site for
Kevin Y. Yip, Philip M. Kim, Drew McDermott and Mark Gerstein,
Multi-level Learning: Improving the Prediction of Protein, Domain and Residue Interactions by Allowing Information Flow between Levels
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Prediction accuracies (AUC) at various inclusion thresholds. At an inclusion threshold of x, pairs with a predicted probability of interaction less than x will be treated as auxiliary negative examples, while pairs with a predicted probability of interaction more than 1-x will be treated as auxiliary positive examples.
Inclusion threshold = 0.20
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Independent levels |
Unidirectional flow |
Bidirectional flow |
Level |
|
PD |
PR |
DR |
PD |
PR |
DR |
PDR |
Proteins |
0.6538 |
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0.6604 |
0.6953 |
|
0.6890 |
Domains |
0.5300 |
0.5497 |
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0.6715 |
|
0.6845 |
0.6828 |
Residues |
0.5825 |
|
0.5195 |
0.5227 |
|
0.6676 |
0.6540 |
0.7857 |
Inclusion threshold = 0.25
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Independent levels |
Unidirectional flow |
Bidirectional flow |
Level |
|
PD |
PR |
DR |
PD |
PR |
DR |
PDR |
Proteins |
0.6855 |
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|
0.6840 |
0.7176 |
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0.7175 |
Domains |
0.5136 |
0.6156 |
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0.7304 |
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0.7242 |
0.7323 |
Residues |
0.5875 |
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0.5178 |
0.5307 |
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0.6701 |
0.7109 |
0.8203 |
Inclusion threshold = 0.30 (reported in main text)
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Independent levels |
Unidirectional flow |
Bidirectional flow |
Level |
|
PD |
PR |
DR |
PD |
PR |
DR |
PDR |
Proteins |
0.7153 |
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0.7205 |
0.7227 |
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0.7257 |
Domains |
0.5214 |
0.5854 |
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0.7015 |
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0.6796 |
0.6986 |
Residues |
0.5675 |
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0.5296 |
0.5128 |
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0.6581 |
0.6182 |
0.7361 |
Inclusion threshold = 0.35
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Independent levels |
Unidirectional flow |
Bidirectional flow |
Level |
|
PD |
PR |
DR |
PD |
PR |
DR |
PDR |
Proteins |
0.7245 |
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0.7253 |
0.7269 |
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0.7281 |
Domains |
0.5279 |
0.5744 |
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0.6878 |
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0.6638 |
0.6818 |
Residues |
0.5826 |
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0.5207 |
0.5165 |
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0.6666 |
0.6119 |
0.6634 |
Inclusion threshold = 0.40
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Independent levels |
Unidirectional flow |
Bidirectional flow |
Level |
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PD |
PR |
DR |
PD |
PR |
DR |
PDR |
Proteins |
0.7261 |
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0.7265 |
0.7331 |
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0.7329 |
Domains |
0.5269 |
0.6033 |
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0.6318 |
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0.6471 |
0.6634 |
Residues |
0.5733 |
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0.5205 |
0.5280 |
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0.6594 |
0.5754 |
0.6290 |
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