New publication: Journal of Cheminformatics

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The following new publication have been accepted in the Journal of Cheminformatics:

  • [1] CRFVoter: gene and protein related object recognition using a conglomerate of CRF-based tools

[1] [doi] W. Hemati and A. Mehler, “CRFVoter: gene and protein related object recognition using a conglomerate of CRF-based tools,” Journal of Cheminformatics, vol. 11, iss. 1, p. 11, 2019.
[BibTeX]
@article{Hemati:Mehler:2019b,
  author="Hemati, Wahed and Mehler, Alexander",
  title="{{CRFVoter}: gene and protein related object recognition using a conglomerate of CRF-based tools}",
  journal={Journal of Cheminformatics},
  year="2019",
  month="Mar",
  day="14",
  volume="11",
  number="1",
  pages="11",
  abstract="Gene and protein related objects are an important class of entities in biomedical research, whose identification and extraction from scientific articles is attracting increasing interest. In this work, we describe an approach to the BioCreative V.5 challenge regarding the recognition and classification of gene and protein related objects. For this purpose, we transform the task as posed by BioCreative V.5 into a sequence labeling problem. We present a series of sequence labeling systems that we used and adapted in our experiments for solving this task. Our experiments show how to optimize the hyperparameters of the classifiers involved. To this end, we utilize various algorithms for hyperparameter optimization. Finally, we present CRFVoter, a two-stage application of Conditional Random Field (CRF) that integrates the optimized sequence labelers from our study into one ensemble classifier.",
  issn="1758-2946",
  doi="10.1186/s13321-019-0343-x",
  url="https://doi.org/10.1186/s13321-019-0343-x"
}