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arXiv 2003.07424cs.CLcs.IRcs.LG

Parallel sequence tagging for concept recognition

University of Zurich(苏黎世大学);Dalle Molle Institute for Artificial Intelligence Research (IDSIA)(达勒·莫勒人工智能研究所);Swiss Institute of Bioinformatics(瑞士生物信息学研究所)

Lenz Furrer, Joseph Cornelius, Fabio Rinaldi

英文摘要:

Background: Named Entity Recognition (NER) and Normalisation (NEN) are core components of any text-mining system for biomedical texts. In a traditional concept-recognition pipeline, these tasks are combined in a serial way, which is inherently prone to error propagation from NER to NEN. We propose a parallel architecture, where both NER and NEN are modeled as a sequence-labeling task, operating directly on the source text. We examine different harmonisation strategies for merging the predictions of the two classifiers into a single output sequence. Results: We test our approach on the recent Version 4 of the CRAFT corpus. In all 20 annotation sets of the concept-annotation task, our system outperforms the pipeline system reported as a baseline in the CRAFT shared task 2019. Conclusions: Our analysis shows that the strengths of the two classifiers can be combined in a fruitful way. However, prediction harmonisation requires individual calibration on a development set for each annotation set. This allows achieving a good trade-off between established knowledge (training set) and novel information (unseen concepts). Availability and Implementation: Source code freely available for download at https://github.com/OntoGene/craft-st. Supplementary data are available at arXiv online.

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