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Table 4 Performance of the two-tier extraction system: our rule-based system in the first tier

From: On the efficacy of per-relation basis performance evaluation for PPI extraction and a high-precision rule-based approach

Min #Inst. per Relation #Uniq. Relation #Instances Methods Per-Relation Per-Instance
  Pos Neg Pos Neg   TP FP Precision Recall F-Score TP FP Precision Recall F-Score
      ours 132 7 0.950 0.214 0.349 153 10 0.939 0.153 0.263
      +hybrid 477 326 0.594 0.772 0.671 701 555 0.558 0.701 0.621
      +SST-PT 231 112 0.673 0.374 0.481 287 167 0.632 0.287 0.395
1 618 2,312 1,000 4,834 +SVM 152 44 0.776 0.246 0.374 172 67 0.720 0.172 0.278
      +NB 247 254 0.493 0.400 0.442 285 410 0.410 0.285 0.336
      +DT 155 40 0.795 0.251 0.382 180 67 0.729 0.180 0.289
      +kNN 215 226 0.488 0.348 0.406 242 310 0.438 0.242 0.312
      ours 80 3 0.964 0.406 0.571 101 5 0.953 0.174 0.294
      +hybrid 183 151 0.548 0.929 0.689 395 310 0.560 0.682 0.615
      +SST-PT 127 62 0.672 0.645 0.658 186 102 0.646 0.321 0.429
2 197 695 579 2,827 +SVM 94 36 0.723 0.477 0.575 116 63 0.648 0.200 0.306
      +NB 113 110 0.507 0.574 0.538 151 196 0.435 0.261 0.326
      +DT 90 21 0.811 0.457 0.585 112 45 0.713 0.193 0.304
      +kNN 129 138 0.483 0.655 0.556 163 235 0.410 0.282 0.334
      ours 51 2 0.962 0.573 0.718 67 3 0.957 0.185 0.310
      +hybrid 88 94 0.484 0.989 0.650 257 222 0.537 0.708 0.611
      +SST-PT 70 38 0.648 0.787 0.711 129 58 0.690 0.355 0.469
3 89 314 363 1,835 +SVM 58 22 0.725 0.652 0.687 78 32 0.709 0.215 0.330
      +NB 59 54 0.522 0.663 0.584 86 89 0.491 0.237 0.320
      +DT 53 5 0.914 0.596 0.722 70 8 0.897 0.193 0.318
      +kNN 66 85 0.437 0.742 0.550 97 153 0.388 0.267 0.316
      ours 35 2 0.946 0.686 0.795 50 3 0.943 0.201 0.331
      +hybrid 51 63 0.447 1 0.618 171 150 0.533 0.687 0.600
      +SST-PT 45 27 0.625 0.882 0.732 92 43 0.681 0.369 0.479
4 51 181 249 1,349 +SVM 38 15 0.717 0.745 0.731 55 25 0.688 0.221 0.335
      +NB 42 43 0.494 0.824 0.618 67 86 0.438 0.269 0.333
      +DT 36 5 0.878 0.706 0.783 54 8 0.871 0.217 0.347
      +kNN 44 56 0.440 0.863 0.583 74 104 0.416 0.297 0.347
      ours 23 1 0.958 0.821 0.884 37 1 0.974 0.236 0.380
      +hybrid 28 40 0.412 1 0.584 108 88 0.551 0.688 0.612
      +SST-PT 25 14 0.641 0.893 0.746 57 22 0.722 0.363 0.483
5 28 107 157 984 +SVM 25 12 0.676 0.893 0.769 40 18 0.690 0.255 0.372
      +NB 24 21 0.533 0.857 0.657 40 40 0.500 0.255 0.338
      +DT 23 4 0.852 0.821 0.836 37 8 0.822 0.236 0.367
      +kNN 26 31 0.456 0.929 0.612 45 51 0.469 0.287 0.356