Chemical entity extraction using CRF and an ensemble of extractors

Madian Khabsa, C. Lee Giles

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


Background: As we are witnessing a great interest in identifying and extracting chemical entities in academic articles, many approaches have been proposed to solve this problem. In this work we describe a probabilistic framework that allows for the output of multiple information extraction systems to be combined in a systematic way. The identified entities are assigned a probability score that reflects the extractors' confidence, without the need for each individual extractor to generate a probability score. We quantitively compared the performance of multiple chemical tokenizers to measure the effect of tokenization on extraction accuracy. Later, a single Conditional Random Fields (CRF) extractor that utilizes the best performing tokenizer is built using a unique collection of features such as word embeddings and Soundex codes, which, to the best of our knowledge, has not been explored in this context before, Results: The ensemble of multiple extractors outperforms each extractor's individual performance during the CHEMDNER challenge. When the runs were optimized to favor recall, the ensemble approach achieved the second highest recall on unseen entities. As for the single CRF model with novel features, the extractor achieves an F1 score of 83.3% on the test set, without any post processing or abbreviation matching. Conclusions: Ensemble information extraction is effective when multiple stand alone extractors are to be used, and produces higher performance than individual off the shelf extractors. The novel features introduced in the single CRF model are sufficient to achieve very competitive F1 score using a simple standalone extractor.

Original languageEnglish (US)
Article numberS12
JournalJournal of Cheminformatics
StatePublished - 2015

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Library and Information Sciences


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