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Table 6 Performance of the two-tier extraction system: our rule-based system in the second 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   Neg   TP FP Precision Recall F-Score TP FP Precision Recall F-Score
1 618 2,312 1,000 4,834 ours 132 7 0.950 0.214 0.349 153 10 0.939 0.153 0.263
      hybrid+ 479 344 0.582 0.775 0.665 705 584 0.547 0.705 0.616
      SST-PT+ 257 108 0.704 0.416 0.523 322 178 0.644 0.322 0.429
      SVM+ 131 57 0.697 0.212 0.325 140 84 0.625 0.140 0.229
      NB+ 235 247 0.488 0.380 0.427 261 410 0.389 0.261 0.312
      DT+ 157 73 0.683 0.254 0.370 169 120 0.585 0.169 0.262
      kNN+ 219 260 0.457 0.354 0.399 237 366 0.393 0.237 0.296
2 197 695 579 2,827 ours 80 3 0.964 0.406 0.571 101 5 0.953 0.174 0.294
      hybrid+ 183 164 0.527 0.929 0.673 399 327 0.550 0.689 0.612
      SST-PT+ 132 73 0.644 0.670 0.657 203 118 0.632 0.351 0.451
      SVM+ 88 48 0.647 0.447 0.529 106 78 0.576 0.183 0.278
      NB+ 107 113 0.486 0.543 0.513 140 230 0.378 0.242 0.295
      DT+ 88 41 0.682 0.447 0.540 104 85 0.550 0.180 0.271
      kNN+ 125 151 0.453 0.635 0.529 152 250 0.378 0.263 0.310
3 89 314 363 1,835 ours 51 2 0.962 0.573 0.718 67 3 0.957 0.185 0.310
      hybrid+ 88 98 0.473 0.989 0.640 262 236 0.526 0.722 0.609
      SST-PT+ 71 48 0.597 0.798 0.683 136 82 0.624 0.375 0.468
      SVM+ 43 28 0.606 0.483 0.538 59 40 0.596 0.163 0.256
      NB+ 59 69 0.461 0.663 0.544 82 113 0.421 0.226 0.294
      DT+ 49 17 0.742 0.551 0.632 61 26 0.701 0.168 0.271
      kNN+ 59 86 0.407 0.663 0.504 84 151 0.357 0.231 0.281
4 51 181 249 1,349 ours 35 2 0.946 0.686 0.795 50 3 0.943 0.201 0.331
      hybrid+ 50 67 0.427 0.980 0.595 171 171 0.500 0.687 0.579
      SST-PT+ 45 32 0.584 0.882 0.703 98 57 0.632 0.394 0.485
      SVM+ 33 19 0.635 0.647 0.641 47 35 0.573 0.189 0.284
      NB+ 41 53 0.436 0.804 0.565 64 116 0.356 0.257 0.299
      DT+ 32 7 0.821 0.627 0.711 43 11 0.796 0.173 0.284
      kNN+ 39 61 0.390 0.765 0.517 59 118 0.333 0.237 0.277
5 28 107 157 984 ours 23 1 0.958 0.821 0.884 37 1 0.974 0.236 0.380
      hybrid+ 28 44 0.389 1 0.560 114 105 0.521 0.726 0.607
      SST-PT+ 25 16 0.610 0.893 0.725 66 31 0.680 0.420 0.519
      SVM+ 21 14 0.600 0.750 0.667 29 22 0.569 0.185 0.279
      NB+ 23 41 0.359 0.821 0.500 35 73 0.324 0.223 0.264
      DT+ 18 3 0.857 0.643 0.735 26 4 0.867 0.166 0.279
      kNN+ 24 38 0.387 0.857 0.533 35 68 0.340 0.223 0.269