NLNDE: Enhancing Neural Sequence Taggers with Attention and Noisy Channel for Robust Pharmacological Entity Detection (D19-57)
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| Challenge: | Named entity recognition has been extensively studied on English news texts, but transfer to other domains and languages is still a challenging problem. |
| Approach: | They propose a system that provides a non-standard domain and language setting for pharmacological entity detection in Spanish texts and a sequencelabeling task that requires neither language nor domain expertise. |
| Outcome: | The proposed system achieves up to 88.6% F1 in the PharmaCoNER competition and is based on a sequence labeling task and training on annotated data. |
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| Challenge: | The Named Entity Recognition of drugs, medications and chemical entities in Spanish is a new task in the field of NLP . |
| Approach: | They propose to use SNOMED CT term search engine to classify the entities in Spanish and a neural model for the Named Entity Recognition. |
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When Specialization Helps: Using Pooled Contextualized Embeddings to Detect Chemical and Biomedical Entities in Spanish (D19-57)
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| Challenge: | Existing work on pharmacological entities requires manual annotation of these units. |
| Approach: | They propose an approach to task 1 of the PharmaCoNER Challenge to recognize pharmacological entities on a spanish corpus. |
| Outcome: | The proposed approach achieves 89.76% score on a spanish corpus based on pre-trained embeddings and 90.52% score on domain-specific embeddables. |
Transfer Learning in Biomedical Named Entity Recognition: An Evaluation of BERT in the PharmaCoNER task (D19-57)
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| Challenge: | Existing methods for natural language processing are labor-intensive and skill-dependent . Currently, most biomedical natural language tasks focus on English documents . |
| Approach: | They introduce a BERT benchmark to facilitate the research of PharmaCoNER task . they evaluate two baselines based on Multilingual BERT and BioBERT on the corpus . |
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Linguistically Informed Relation Extraction and Neural Architectures for Nested Named Entity Recognition in BioNLP-OST 2019 (D19-57)
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| Challenge: | Named Entity Recognition (NER) and Relation Extraction (RE) are essential tools in distilling knowledge from biomedical literature. |
| Approach: | They propose to use Named Entities to perform nested entities extraction, Entity Normalization and Relation Extraction to generalize the approach to different languages. |
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PharmaCoNER: Pharmacological Substances, Compounds and proteins Named Entity Recognition track (D19-57)
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Aitor Gonzalez-Agirre, Montserrat Marimon, Ander Intxaurrondo, Obdulia Rabal, Marta Villegas, Martin Krallinger
| Challenge: | Biomedical text mining is one of the most prolific application domains of natural language processing technologies. |
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IxaMed at PharmacoNER Challenge 2019 (D19-57)
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| Challenge: | The aim of this paper is to present our approach in the PharmacoNER 2019 task. |
| Approach: | They propose to use a Bi-LSTM with a CRF to identify named entities from clinical case studies written in Spanish. |
| Outcome: | The proposed approach achieves the best score (86.81 F-Score) combining pretrained word embeddings of Wikipedia and Electronic Health Records with contextual string embedds. |
Deep neural model with enhanced embeddings for pharmaceutical and chemical entities recognition in Spanish clinical text (D19-57)
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| Challenge: | Currently, the number of biomedical literature is growing at an exponential rate. |
| Approach: | They propose a Deep Learning architecture for pharmaceutical and chemical Named Entity Recognition in Spanish clinical cases texts. |
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A Deep Learning-Based System for PharmaCoNER (D19-57)
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Ying Xiong, Yedan Shen, Yuanhang Huang, Shuai Chen, Buzhou Tang, Xiaolong Wang, Qingcai Chen, Jun Yan, Yi Zhou
| Challenge: | Efficient access to mentions of clinical entities is very important for using clinical text. |
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Biomedical Named Entity Recognition with Multilingual BERT (D19-57)
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| Challenge: | a multilingual model is not specifically tailored to either the language nor the application domain. |
| Approach: | They propose a CRF-based baseline approach and multilingual BERT to the task . they achieve an F-score of 88% on the development data and 87% on the test set with BERT . |
| Outcome: | The proposed model achieves an F score of 88% on the development data and 87% on the test set with BERT. |
What Matters for Neural Cross-Lingual Named Entity Recognition: An Empirical Analysis (D19-1)
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| Challenge: | Named entity recognition models are challenging for languages with little training data. |
| Approach: | They propose a simple and efficient neural architecture for cross-lingual named entity recognition models. |
| Outcome: | The proposed model achieves competitive performance with the state-of-the-art on two transferable factors: sequential order and multilingual embedding. |