CoCoScore: Context-aware co-occurrence scoring for text mining applications using distant supervision

Motivation: Information extraction by mining the scientific literature is key to uncovering relations between biomedical entities. Most existing approaches based on natural language processing extract relations from single sentence-level co-mentions, ignoring co-occurrence statistics over the whole corpus. Existing approaches counting entity co-occurrences ignore the textual context of each co-occurrence. Results: We propose a novel corpus-wide co-occurrence scoring approach to relation extraction that takes the textual context of each co-mention into account. Our method, called CoCoScore, scores the certainty of stating an association for each sentence that co-mentions two entities. CoCoScore is trained using distant supervision based on a gold-standard set of associations between entities of interest. Instead of requiring a manually annotated training corpus, co-mentions are labeled as positives/negatives according to their presence/absence in the gold standard. We show that CoCoScore outperforms previous approaches in identifying human disease-gene and tissue-gene associations as well as in identifying physical and functional protein-protein associations in different species. CoCoScore is a versatile text mining tool to uncover pairwise associations via co-occurrence mining, within and beyond biomedical applications.