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Register a new userParallel sequence tagging for concept recognition
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Added by
Lenz Furrer
Publication date
2020
fields
Informatics Engineering
and research's language is
English
Authors
Lenz Furrer
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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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Many domain adaptation approaches rely on learning cross domain shared representations to transfer the knowledge learned in one domain to other domains. Traditional domain adaptation only considers adapting for one task. In this paper, we explore multi-task representation learning under the domain adaptation scenario. We propose a neural network framework that supports domain adaptation for multiple tasks simultaneously, and learns shared representations that better generalize for domain adaptation. We apply the proposed framework to domain adaptation for sequence tagging problems considering two tasks: Chinese word segmentation and named entity recognition. Experiments show that multi-task domain adaptation works better than disjoint domain adaptation for each task, and achieves the state-of-the-art results for both tasks in the social media domain.
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