MeSHLabeler and DeepMeSH: Recent Progress in Large-Scale MeSH Indexing

  • Shengwen Peng
  • Hiroshi Mamitsuka
  • Shanfeng ZhuEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1807)


The US National Library of Medicine (NLM) uses the Medical Subject Headings (MeSH) (seeNote 1 ) to index almost all 24 million citations in MEDLINE, which greatly facilitates the application of biomedical information retrieval and text mining. Large-scale automatic MeSH indexing has two challenging aspects: the MeSH side and citation side. For the MeSH side, each citation is annotated by only 12 (on average) out of all 28,000 MeSH terms. For the citation side, all existing methods, including Medical Text Indexer (MTI) by NLM, deal with text by bag-of-words, which cannot capture semantic and context-dependent information well. To solve these two challenges, we developed the MeSHLabeler and DeepMeSH. By utilizing “learning to rank” (LTR) framework, MeSHLabeler integrates multiple types of information to solve the challenge in the MeSH side, while DeepMeSH integrates deep semantic representation to solve the challenge in the citation side. MeSHLabeler achieved the first place in both BioASQ2 and BioASQ3, and DeepMeSH achieved the first place in both BioASQ4 and BioASQ5 challenges. DeepMeSH is available at

Key words

MeSH indexing Text categorization Multi-label classification Medical subject headings MEDLINE Machine learning 



This work has been partially supported by National Natural Science Foundation of China (Grant Nos: 61572139), MEXT KAKENHI #16H02868 and FiDiPro by Tekes.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Shengwen Peng
    • 1
    • 2
  • Hiroshi Mamitsuka
    • 3
    • 4
  • Shanfeng Zhu
    • 1
    • 2
    • 5
    Email author
  1. 1.School of Computer ScienceFudan UniversityShanghaiChina
  2. 2.Shanghai Key Lab of Intelligent Information ProcessingFudan UniversityShanghaiChina
  3. 3.Bioinformatics Center, Institute for Chemical ResearchKyoto UniversityKyotoJapan
  4. 4.Department of Computer ScienceAalto UniversityEspooFinland
  5. 5.Center for Computational System BiologyFudan UniversityShanghaiChina

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