Table 4

Comparative results for interaction pair extraction

Compared models

Whole collection

SwissProt only article collection


Precision

Recall

F1 score

Precision

Recall

F1 score


Mean

0.1062

0.1858

0.1035

0.1160

0.2000

0.1127

Standard deviation

0.0945

0.1001

0.0761

0.1035

0.1062

0.0836

Median

0.0755

0.1961

0.0788

0.0808

0.2156

0.0842

Best reported in terms of F1 score [8]

0.3908

0.2970

0.2849

0.3893

0.3073

0.2885


Template-based method (threshold = 0.0)

0.1373

0.2905

0.1578

0.1566

0.3189

0.1784

Template-based method (threshold = 80.0)

0.2177

0.2651

0.2038

0.2434

0.2828

0.2247

Profile-based method

0.3096

0.2935

0.2623

0.3695

0.3268

0.3042


'Whole collection' means that all of the articles have been considered. 'SwissProt only article collection' include articles containing interaction pairs that can be normalized to SwissProt entries. The table shows the comparative results for the extraction of interaction pairs.

Huang et al. Genome Biology 2008 9(Suppl 2):S12   doi:10.1186/gb-2008-9-s2-s12

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