A look back at the quality of Protein Function Prediction tools in CAFA

A look back at the quality of Protein Function Prediction tools in CAFA. Pourreza Shahri, M., Srinivasan, M., Bimczok, D., Kanewala, U., & Kahanda, I. PeerJ Preprints, 6:e27161v1, August, 2018.

Paper doi abstract bibtex

The Critical Assessment of protein Function Annotation algorithms (CAFA) is a large-scale experiment for assessing the computational models for automated function prediction (AFP). The models presented in CAFA have shown excellent promise in terms of prediction accuracy, but quality assurance has been paid relatively less attention. The main challenge associated with conducting systematic testing on AFP software is the lack of a test oracle, which determines passing or failing of a test case; unfortunately, the exact expected outcomes are not well defined for the AFP task. Thus, AFP tools face the oracle problem. Metamorphic testing (MT) is a technique used to test programs that face the oracle problem using metamorphic relations (MRs). A MR determines whether a test has passed or failed by specifying how the output should change according to a specific change made to the input. In this work, we use MT to test nine CAFA2 AFP tools by defining a set of MRs that apply input transformations at the protein-level. According to our initial testing, we observe that several tools fail all the test cases and two tools pass all the test cases on different GO ontologies.

@Article{ALookBack2018,
  author   = {Pourreza Shahri, Morteza and Srinivasan, Madhusudan and Bimczok, Diane and Kanewala, Upulee and Kahanda, Indika},
  title    = {A look back at the quality of Protein Function Prediction tools in CAFA},
  doi      = {10.7287/peerj.preprints.27161v1},
  issn     = {2167-9843},
  pages    = {e27161v1},
  url      = {https://doi.org/10.7287/peerj.preprints.27161v1},
  volume   = {6},
  abstract = {The Critical Assessment of protein Function Annotation algorithms (CAFA) is a large-scale experiment for assessing the computational models for automated function prediction (AFP). The models presented in CAFA have shown excellent promise in terms of prediction accuracy, but quality assurance has been paid relatively less attention. The main challenge associated with conducting systematic testing on AFP software is the lack of a test oracle, which determines passing or failing of a test case; unfortunately, the exact expected outcomes are not well defined for the AFP task. Thus, AFP tools face the oracle problem. Metamorphic testing (MT) is a technique used to test programs that face the oracle problem using metamorphic relations (MRs). A MR determines whether a test has passed or failed by specifying how the output should change according to a specific change made to the input. In this work, we use MT to test nine CAFA2 AFP tools by defining a set of MRs that apply input transformations at the protein-level. According to our initial testing, we observe that several tools fail all the test cases and two tools pass all the test cases on different GO ontologies.},
  journal  = {PeerJ Preprints},
  keywords = {Metamorphic Testing, Automated Protein Function Prediction, AFP Tools},
  month    = aug,
  year     = {2018},
}

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