Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT

• Published in: BMC bioinformatics Vol. 23; no. 1; pp. 4 - 23
• Main Authors: Elangovan, Aparna, Li, Yuan, Pires, Douglas E. V., Davis, Melissa J., Verspoor, Karin
• Format: Journal Article
• Language: English
• Published: London BioMed Central 04.01.2022; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Analysis; Annotations; Automation; BioBERT; Bioinformatics; Biomedical and Life Sciences; Calibration; Computational Biology/Bioinformatics; Computational linguistics; Computer Appl. in Life Sciences; Data Mining; Datasets; Deep learning; Distant supervision; Enzymes; Humans; Language processing; Life Sciences; Machine learning; Methods; Microarrays; Natural language interfaces; Natural language processing; Noise; Phosphorylation; Post-translation; Post-translational modification; Post-translational modifications; Predictions; Protein interaction; Protein Processing, Post-Translational; Protein-protein interaction; Protein-protein interactions; Proteins; PubMed; Supervision; Test sets; Translation; Uniqueness; Australia; Deep learning; Distant supervision; Natural language processing; Post-translational modifications; Protein-protein interaction; BioBERT
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-021-04504-x

Motivation Protein-protein interactions (PPIs) are critical to normal cellular function and are related to many disease pathways. A range of protein functions are mediated and regulated by protein interactions through post-translational modifications (PTM). However, only 4% of PPIs are annotated with PTMs in biological knowledge databases such as IntAct, mainly performed through manual curation, which is neither time- nor cost-effective. Here we aim to facilitate annotation by extracting PPIs along with their pairwise PTM from the literature by using distantly supervised training data using deep learning to aid human curation. Method We use the IntAct PPI database to create a distant supervised dataset annotated with interacting protein pairs, their corresponding PTM type, and associated abstracts from the PubMed database. We train an ensemble of BioBERT models—dubbed PPI-BioBERT-x10—to improve confidence calibration. We extend the use of ensemble average confidence approach with confidence variation to counteract the effects of class imbalance to extract high confidence predictions. Results and conclusion The PPI-BioBERT-x10 model evaluated on the test set resulted in a modest F1-micro 41.3 (P =5 8.1, R = 32.1). However, by combining high confidence and low variation to identify high quality predictions, tuning the predictions for precision, we retained 19% of the test predictions with 100% precision. We evaluated PPI-BioBERT-x10 on 18 million PubMed abstracts and extracted 1.6 million (546507 unique PTM-PPI triplets) PTM-PPI predictions, and filter ≈ 5700 (4584 unique) high confidence predictions. Of the 5700, human evaluation on a small randomly sampled subset shows that the precision drops to 33.7% despite confidence calibration and highlights the challenges of generalisability beyond the test set even with confidence calibration. We circumvent the problem by only including predictions associated with multiple papers, improving the precision to 58.8%. In this work, we highlight the benefits and challenges of deep learning-based text mining in practice, and the need for increased emphasis on confidence calibration to facilitate human curation efforts.