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

Background: Most previous Protein Protein Interaction (PPI) studies evaluated their algorithms' performance based on «per-instance» precision and recall, in which the instances of an interaction relation were evaluated independently. However, we argue that this standard evaluation method should be revisited. In a large corpus, the same relation can be described in various different forms and, in practice, correctly identifying not all but a small subset of them would often suffice to detect the given interaction. Methods. In this regard, we propose a more pragmatic «per-relation» basis performance evaluation method instead of the conventional per-instance basis method. In the per-relation basis method, only a subset of a relation's instances needs to be correctly identified to make the relation positive. In this work, we also introduce a new high-precision rule-based PPI extraction algorithm. While virtually all current PPI extraction studies focus on improving F-score, aiming to balance the performance on both precision and recall, in many realistic scenarios involving large corpora, one can benefit more from a high-precision algorithm than a high-recall counterpart. Results: We show that our algorithm not only achieves better per-relation performance than previous solutions but also serves as a good complement to the existing PPI extraction tools. Our algorithm improves the performance of the existing tools through simple pipelining. Conclusion: The significance of this research can be found in that this research brought new perspective to the performance evaluation of PPI extraction studies, which we believe is more important in practice than existing evaluation criteria. Given the new evaluation perspective, we also showed the importance of a high-precision extraction tool and validated the efficacy of our rule-based system as the high-precision tool candidate.