The Fudan-UIUC participation in the BioASQ Challenge Task 2a: The antinomyra system

Abstract

This paper describes the Antinomyra System that participated in the BioASQ Task 2a Challenge for the large-scale biomedical semantic indexing. The system can automatically annotate MeSH terms for MEDLINE citations using only title and abstract information. With respect to the official test set (batch 3, week 5), based on 1867 annotated citations out of all 4533 citations (June 6, 2014), our best submission achieved 0.6199 in flat Micro F-measure. This is 9.8% higher than the performance of official NLM solution Medical Text Indexer (MTI), which achieved 0.5647 in flat F-measure.