ArticleDatabase : the journal of biological databases and curation2024
An analysis of FRE @ BC8 SympTEMIST track: named entity recognition.
Article in Database : the journal of biological databases and curation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Advancing Evidence-Based Medicine for Population, Intervention, Comparison, and Outcome Element Recognition and Extraction in Medical Literature: Large Language Model Approach.Journal of medical Internet research · 2026Article
- Updates to the Minimum Information Required for A Glycomics Experiment (MIRAGE) guidelines.Analytical and bioanalytical chemistry · 2026Article
- An analysis of FRE @ BC8 SympTEMIST track: named entity recognition.Database : the journal of biological databases and curation · 2024Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This paper is a more in-depth analysis of the approaches used in our submission (Martínez A, García-Santa N. (2023) FRE @ BC8 SympTEMIST track: Named Entity Recognition Zenodo.) to the 'SympTEMIST' Named Entity Recognition (NER) shared subtask at 'BioCreative 2023'. We participated on the challenge submitting two systems based on a RoBERTa architecture LLM trained on Spanish-language clinical data available at 'HuggingFace' model repository. Before choosing the systems that would be submitted, we tried different combinations of the techniques described here: Conditional Random Fields and Byte-Pair Encoding dropout. In the second system we also included Sub-Subword feature based embeddings (SSW). The test set used in the challenge has now been released (López SL, Sánchez LG, Farré E et al. (2024) SympTEMIST Corpus: Gold Standard annotations for clinical symptoms, signs and findings information extraction. Zenodo), allowing us to analyze more in depth our methods, as well as measuring the impact of introducing data from CARMEN-I (Lima-López S, Farré-Maduell E, Krallinger M. (2023) CARMEN-I: Clinical Entities Annotation Guidelines in Spanish. Zenodo) corpus. Our experiments show the moderate effect of using the Sub-Subword feature based embeddings and the impact of including the symptom NER data from the CARMEN-I dataset. Database URL: https://physionet.org/content/carmen-i/1.0/.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.