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

Download software:
With data: mllwithdata.jar (168MB, 473MB after decompression)
Without data: mll.jar (1.9MB, 2.2MB after decompression)

Readme file
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
  Independent levels Unidirectional flow Bidirectional flow
Level   PD PR DR PD PR DR PDR
Proteins 0.6538       0.6604 0.6953   0.6890
Domains 0.5300 0.5497     0.6715   0.6845 0.6828
Residues 0.5825   0.5195 0.5227   0.6676 0.6540 0.7857


Inclusion threshold = 0.25
  Independent levels Unidirectional flow Bidirectional flow
Level   PD PR DR PD PR DR PDR
Proteins 0.6855       0.6840 0.7176   0.7175
Domains 0.5136 0.6156     0.7304   0.7242 0.7323
Residues 0.5875   0.5178 0.5307   0.6701 0.7109 0.8203


Inclusion threshold = 0.30 (reported in main text)
  Independent levels Unidirectional flow Bidirectional flow
Level   PD PR DR PD PR DR PDR
Proteins 0.7153       0.7205 0.7227   0.7257
Domains 0.5214 0.5854     0.7015   0.6796 0.6986
Residues 0.5675   0.5296 0.5128   0.6581 0.6182 0.7361


Inclusion threshold = 0.35
  Independent levels Unidirectional flow Bidirectional flow
Level   PD PR DR PD PR DR PDR
Proteins 0.7245       0.7253 0.7269   0.7281
Domains 0.5279 0.5744     0.6878   0.6638 0.6818
Residues 0.5826   0.5207 0.5165   0.6666 0.6119 0.6634


Inclusion threshold = 0.40
  Independent levels Unidirectional flow Bidirectional flow
Level   PD PR DR PD PR DR PDR
Proteins 0.7261       0.7265 0.7331   0.7329
Domains 0.5269 0.6033     0.6318   0.6471 0.6634
Residues 0.5733   0.5205 0.5280   0.6594 0.5754 0.6290