Table 3 The overlap of the pairs that are the most difficult and the easiest to classify correctly by the collection of kernels using cross-validation (CV) and cross-learning (CL) settings
From: A detailed error analysis of 13 kernel methods for protein-protein interaction extraction
Difficulty class | Corpus | Total | |||||||
|---|---|---|---|---|---|---|---|---|---|
Difficulty | GT | Class/setting | AIMed | BioInfer | HPRD50 | IEPA | LLL | # | % |
difficult | unknown | D CV | 537 | 1 077 | 41 | 82 | 39 | 1776 | 10.4 |
D CL | 628 | 1 003 | 35 | 99 | 37 | 1802 | 10.6 | ||
D =DCV∩DCL | 105 | 530 | 8 | 28 | 0 | 671 | 3.9 | ||
p-value | 10−10 | 10−281 | 1 0−2 | 10−8 | 1.0 | ||||
positive | PD CV | 162 | 281 | 20 | 32 | 17 | 512 | 12.2 | |
PD CL | 142 | 319 | 15 | 26 | 16 | 518 | 12.3 | ||
PD =PDCV∩PDCL | 61 | 111 | 2 | 9 | 7 | 190 | 4.5 | ||
p-value | 10−60 | 10−95 | 1 0−1 | 10−7 | 10−6 | ||||
negative | ND CV | 463 | 610 | 37 | 50 | 39 | 1199 | 9.3 | |
ND CV | 557 | 644 | 32 | 37 | 28 | 1298 | 10.1 | ||
ND =NDCV∩NDCL | 184 | 295 | 12 | 19 | 11 | 521 | 4.0 | ||
p-value | 10−76 | 10−204 | 10−6 | 10−15 | 10−4 | ||||
easy | unknown | E CV | 2137 | 1870 | 85 | 83 | 36 | 4211 | 24.7 |
E CL | 777 | 2563 | 45 | 95 | 73 | 3558 | 20.8 | ||
E =ECV∩ECL | 464 | 1017 | 23 | 20 | 4 | 1528 | 8.9 | ||
p-value | 10−45 | 10−184 | 10−7 | 10−3 | 1.0 | ||||
positive | PE CV | 104 | 301 | 26 | 48 | 36 | 515 | 12.3 | |
PE CL | 115 | 364 | 29 | 27 | 22 | 557 | 13.3 | ||
PE =PECV∩PECL | 49 | 147 | 6 | 10 | 7 | 219 | 5.2 | ||
p-value | 10−59 | 10−136 | 1 0−3 | 10−7 | 1 0−2 | ||||
negative | NE CV | 2105 | 1752 | 59 | 94 | 23 | 4033 | 31.3 | |
NE CL | 593 | 2548 | 32 | 87 | 21 | 3281 | 25.5 | ||
NE =NECV∩NECL | 440 | 1014 | 21 | 27 | 8 | 1510 | 11.7 | ||
p-value | 10−88 | 10−215 | 10−12 | 10−7 | 10−5 | ||||