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--- |
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language: |
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- en |
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pipeline_tag: token-classification |
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license: apache-2.0 |
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--- |
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Named Entity Recognition (NER) model to recognize disease entities. |
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Please cite our work: |
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``` |
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@article{NILNKER2022, |
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title = {NILINKER: Attention-based approach to NIL Entity Linking}, |
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journal = {Journal of Biomedical Informatics}, |
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volume = {132}, |
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pages = {104137}, |
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year = {2022}, |
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issn = {1532-0464}, |
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doi = {https://doi.org/10.1016/j.jbi.2022.104137}, |
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url = {https://www.sciencedirect.com/science/article/pii/S1532046422001526}, |
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author = {Pedro Ruas and Francisco M. Couto}, |
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} |
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``` |
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[PubMedBERT](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) fine-tuned on the following datasets: |
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- [NCBI Disease Corpus](https://www.ncbi.nlm.nih.gov/research/bionlp/Data/disease/) (train and dev sets) |
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- [PHAEDRA](http://www.nactem.ac.uk/PHAEDRA/) (train, dev, test sets): entity type "Disorder" |
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- [Corpus for Disease Names and Adverse Effects](https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/corpus-for-disease-names-and-adverse-effects.html) (train, dev, test sets): entity types "DISEASE", "ADVERSE" |
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- [RareDis corpus](https://github.com/isegura/NLP4RARE-CM-UC3M/tree/main/corpus) (train, dev, test sets): entity types "DISEASE", "RAREDISEASE", "SYMPTOM" |
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- [CoMAGC](https://github.com/isegura/NLP4RARE-CM-UC3M/tree/main/corpus) (train, dev, test sets): entity type "cancer_term" |
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- [PGxCorpus](https://www.nature.com/articles/s41597-019-0342-9) (train, dev, test sets): |
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- [miRNA-Test-Corpus](https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/download-mirna-test-corpus.html) (train, dev, test sets): entity type "Diseases" |
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- [BC5CDR]() (train and dev sets): entity type "Disease" |
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- [Mantra](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4986661/pdf/ocv037.pdf) (train, dev, test sets): entity type "DISO" |
