neuralbioinfo
/

prokbert-mini

@@ -152,6 +152,50 @@ except ImportError:
 *Promoter prediction performance metrics on a diverse test set. A comparative analysis of various promoter prediction tools, showcasing their performance across key metrics including accuracy, F1 score, MCC, sensitivity, and specificity.*
 ### Ethical Considerations and Limitations

 *Promoter prediction performance metrics on a diverse test set. A comparative analysis of various promoter prediction tools, showcasing their performance across key metrics including accuracy, F1 score, MCC, sensitivity, and specificity.*
+### Evaluation on phage recognitation benchmark
+| method        |    L |   auc_class1 |      acc |       f1 |      mcc |   recall |   sensitivity |   specificity |   tn |   fp |   fn |   tp |    Np |    Nn |   eval_time |
+|:--------------|-----:|-------------:|---------:|---------:|---------:|---------:|--------------:|--------------:|-----:|-----:|-----:|-----:|------:|------:|------------:|
+| DeepVirFinder |  256 |     0.734914 | 0.627163 | 0.481213 | 0.309049 | 0.345317 |      0.345317 |      0.909856 | 4542 |  450 | 3278 | 1729 |  5007 |  4992 |  7580       |
+| DeepVirFinder |  512 |     0.791423 | 0.708    | 0.637717 | 0.443065 | 0.521192 |      0.521192 |      0.889722 | 4510 |  559 | 2361 | 2570 |  4931 |  5069 |  2637       |
+| DeepVirFinder | 1024 |     0.826255 | 0.7424   | 0.702678 | 0.505333 | 0.605651 |      0.605651 |      0.880579 | 4380 |  594 | 1982 | 3044 |  5026 |  4974 |  1294       |
+| DeepVirFinder | 2048 |     0.853098 | 0.7717   | 0.743339 | 0.557177 | 0.6612   |      0.6612   |      0.8822   | 4411 |  589 | 1694 | 3306 |  5000 |  5000 |  1351       |
+| INHERIT       |  256 |     0.75982  | 0.6943   | 0.67012  | 0.393179 | 0.620008 |      0.620008 |      0.76883  | 3838 | 1154 | 1903 | 3105 |  5008 |  4992 |  2131       |
+| INHERIT       |  512 |     0.816326 | 0.7228   | 0.651408 | 0.479323 | 0.525248 |      0.525248 |      0.914973 | 4638 |  431 | 2341 | 2590 |  4931 |  5069 |  2920       |
+| INHERIT       | 1024 |     0.846547 | 0.7264   | 0.659447 | 0.495935 | 0.527059 |      0.527059 |      0.927825 | 4615 |  359 | 2377 | 2649 |  5026 |  4974 |  3055       |
+| INHERIT       | 2048 |     0.864122 | 0.7365   | 0.668595 | 0.518541 | 0.5316   |      0.5316   |      0.9414   | 4707 |  293 | 2342 | 2658 |  5000 |  5000 |  3225       |
+| MINI          |  256 |     0.846745 | 0.7755   | 0.766462 | 0.552855 | 0.735623 |      0.735623 |      0.815505 | 4071 |  921 | 1324 | 3684 |  5008 |  4992 |     6.68888 |
+| MINI          |  512 |     0.924973 | 0.8657   | 0.859121 | 0.732696 | 0.83046  |      0.83046  |      0.89998  | 4562 |  507 |  836 | 4095 |  4931 |  5069 |    16.3681  |
+| MINI          | 1024 |     0.956432 | 0.9138   | 0.911189 | 0.829645 | 0.879825 |      0.879825 |      0.94813  | 4716 |  258 |  604 | 4422 |  5026 |  4974 |    51.3319  |
+| MINI-C        |  256 |     0.827635 | 0.7512   | 0.7207   | 0.51538  | 0.640974 |      0.640974 |      0.861779 | 4302 |  690 | 1798 | 3210 |  5008 |  4992 |     7.33697 |
+| MINI-C        |  512 |     0.913378 | 0.8466   | 0.834876 | 0.69725  | 0.786453 |      0.786453 |      0.905109 | 4588 |  481 | 1053 | 3878 |  4931 |  5069 |    17.6749  |
+| MINI-C        | 1024 |     0.94644  | 0.8937   | 0.891564 | 0.788427 | 0.869479 |      0.869479 |      0.918175 | 4567 |  407 |  656 | 4370 |  5026 |  4974 |    54.204   |
+| MINI-LONG     |  256 |     0.777697 | 0.71495  | 0.686224 | 0.437727 | 0.622404 |      0.622404 |      0.807792 | 8065 | 1919 | 3782 | 6234 | 10016 |  9984 |     6.10304 |
+| MINI-LONG     |  512 |     0.880831 | 0.81405  | 0.798001 | 0.632855 | 0.744879 |      0.744879 |      0.881338 | 8935 | 1203 | 2516 | 7346 |  9862 | 10138 |    12.1307  |
+| MINI-LONG     | 1024 |     0.9413   | 0.88925  | 0.884917 | 0.781465 | 0.847195 |      0.847195 |      0.931745 | 9269 |  679 | 1536 | 8516 | 10052 |  9948 |    30.5088  |
+| MINI-LONG     | 2048 |     0.964551 | 0.929    | 0.927455 | 0.85878  | 0.9077   |      0.9077   |      0.9503   | 9503 |  497 |  923 | 9077 | 10000 | 10000 |    94.404   |
+| Virsorter2    |  512 |     0.620782 | 0.6259   | 0.394954 | 0.364831 | 0.247617 |      0.247617 |      0.993884 | 5038 |   31 | 3710 | 1221 |  4931 |  5069 |  2057       |
+| Virsorter2    | 1024 |     0.719898 | 0.7178   | 0.621919 | 0.51036  | 0.461799 |      0.461799 |      0.976478 | 4857 |  117 | 2705 | 2321 |  5026 |  4974 |  3258       |
+| Virsorter2    | 2048 |     0.816142 | 0.8103   | 0.778724 | 0.647532 | 0.6676   |      0.6676   |      0.953    | 4765 |  235 | 1662 | 3338 |  5000 |  5000 |  5737       |
+### Column Descriptions
+- **method**: The algorithm or method used for prediction (e.g., DeepVirFinder, INHERIT).
+- **L**: Length of the genomic segment.
+- **auc_class1**: Area under the ROC curve for class 1, indicating the model's ability to distinguish between classes.
+- **acc**: Accuracy of the prediction, representing the proportion of true results (both true positives and true negatives) among the total number of cases examined.
+- **f1**: The F1 score, a measure of a test's accuracy that considers both the precision and the recall.
+- **mcc**: Matthews correlation coefficient, a quality measure for binary (two-class) classifications.
+- **recall**: The recall, or true positive rate, measures the proportion of actual positives that are correctly identified.
+- **sensitivity**: Sensitivity or true positive rate; identical to recall.
+- **specificity**: The specificity, or true negative rate, measures the proportion of actual negatives that are correctly identified.
+- **fp**: The number of false positives, indicating how many negative class samples were incorrectly identified as positive.
+- **tp**: The number of true positives, indicating how many positive class samples were correctly identified.
+- **eval_time**: The time taken to evaluate the model or method, usually in seconds.
 ### Ethical Considerations and Limitations