Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics

The identification of chemicals in articles has attracted a large interest in the biomedical scientific community, given its importance in drug development research. Most of previous research have focused on PubMed abstracts, and further investigation using full-text documents is required because these contain additional valuable information that must be explored. The manual expert task of indexing Medical Subject Headings (MeSH) terms to these articles later helps researchers find the most relevant publications for their ongoing work. The BioCreative VII NLM-Chem track fostered the development of systems for chemical identification and indexing in PubMed full-text articles. Chemical identification consisted in identifying the chemical mentions and linking these to unique MeSH identifiers. This manuscript describes our participation system and the post-challenge improvements we made. We propose a three-stage pipeline that individually performs chemical mention detection, entity normalization and indexing. Regarding chemical identification, we adopted a deep-learning solution that utilizes the PubMedBERT contextualized embeddings followed by a multilayer perceptron and a conditional random field tagging layer. For the normalization approach, we use a sieve-based dictionary filtering followed by a deep-learning similarity search strategy. Finally, for the indexing we developed rules for identifying the more relevant MeSH codes for each article. During the challenge, our system obtained the best official results in the normalization and indexing tasks despite the lower performance in the chemical mention recognition task. In a post-contest phase we boosted our results by improving our named entity recognition model with additional techniques. The final system achieved 0.8731, 0.8275 and 0.4849 in the chemical identification, normalization and indexing tasks, respectively. The code to reproduce our experiments and run the pipeline is publicly available. Database URL:



Results from the Paper

Task Dataset Model Metric Name Metric Value Global Rank Uses Extra
Training Data
Chemical Indexing BC7 NLM-Chem Rule-based F1-score (strict) 0.4849 # 1
Entity Linking BC7 NLM-Chem Sieve-based+SapBERT F1-score (strict) 0.8275 # 1
Named Entity Recognition (NER) BC7 NLM-Chem PubMedBERT+MLP+CRF F1-score (strict) 0.8731 # 1


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