More Like this

1. A Gated Recurrent Unit based architecture for recognizing ontology concepts from biological literature

   https://doi.org/10.1186/s13040-022-00310-0  

   Devkota, Pratik; Mohanty, Somya D.; Manda, Prashanti (September 2022, BioData Mining)

   Abstract BackgroundAnnotating scientific literature with ontology concepts is a critical task in biology and several other domains for knowledge discovery. Ontology based annotations can power large-scale comparative analyses in a wide range of applications ranging from evolutionary phenotypes to rare human diseases to the study of protein functions. Computational methods that can tag scientific text with ontology terms have included lexical/syntactic methods, traditional machine learning, and most recently, deep learning. ResultsHere, we present state of the art deep learning architectures based on Gated Recurrent Units for annotating text with ontology concepts. We use the Colorado Richly Annotated Full Text Corpus (CRAFT) as a gold standard for training and testing. We explore a number of additional information sources including NCBI’s BioThesauraus and Unified Medical Language System (UMLS) to augment information from CRAFT for increasing prediction accuracy. Our best model results in a 0.84 F1 and semantic similarity. ConclusionThe results shown here underscore the impact for using deep learning architectures for automatically recognizing ontology concepts from literature. The augmentation of the models with biological information beyond that present in the gold standard corpus shows a distinct improvement in prediction accuracy. 

   more » « less
2. Using ontology embeddings with deep learning architectures to improve prediction of ontology concepts from literature

   Devkota, Pratik; Mohanty, Somya; Manda, Prashanti (September 2023, CEUR workshop proceedings)
3. Knowledge of the Ancestors: Intelligent Ontology-aware Annotation of Biological Literature using Semantic Similarity

   Devkota; Pratik; Mohanty, Somya; Manda, Prashanti (January 2022, International Conference on Biomedical Ontology)
4. Knowledge of the Ancestors: Intelligent Ontology-aware Annotation of Biological Literature using Semantic Similarity

   Devkota, Pratik; Mohanty, Somya; Manda, Prashanti (September 2022, International COnference on Biomedical Ontology)
5. Auditing subtype inconsistencies among gene ontology concepts

   https://doi.org/10.1109/BIBM.2017.8217835  

   Abeysinghe, Rashmie; Hinderer, Eugene W.; Moseley, Hunter N.; Cui, Licong (November 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM))