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--- |
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language: en |
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license: mit |
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task_categories: |
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- token-classification |
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task_ids: |
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- named-entity-recognition |
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pretty_name: PHEE validation data |
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tags: |
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- pharmacovigilance |
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- adverse-event |
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- medical |
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- ner |
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--- |
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# PHEE validation data |
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## Dataset Description |
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This dataset contains sentences derived from medical case report abstracts |
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curated for adverse events. Split data and CoNLL formatting allows for the |
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**training of language models**, for **named entity recognition.** The dataset |
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includes entity annotations or labels. This subsect is the validation split. |
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The creation of the original PHEE dataset is detailed at: |
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> Sun, Z., Li, J., Pergola, G., Wallace, B. C., John, B., Greene, N., Kim, J., |
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> & He, Y. (2022). PHEE: A dataset for pharmacovigilance event extraction from |
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> text. arXiv preprint arXiv:2210.12560. |
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> https://arxiv.org/pdf/2210.12560. |
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--- |
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## Source Data |
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The port of the original PHEE dataset used for our purposes is detailed here: |
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Original source repository: |
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https://huggingface.co/datasets/sarus-tech/phee |
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--- |
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## Intended Use |
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### Primary Use |
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- Supervised NER training for biomedical NLP tasks |
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### Not Intended For |
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- Clinical or patient-level decision making |
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--- |
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## Dataset Structure |
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- **Language:** English |
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- **Splits:** Train / Test / Validation |
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- **Features:** Text field, BIO label |
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- **Labels:** Adev ~ 'Adverse Event' |
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--- |
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## Preprocessing |
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- Sentence-level segmentation is enforced |
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- Annotations carried out by 15 annotators in data's original creation |
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- Present dataset split into train / test / val |
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- Present dataset labeled in the IOB CoNLL format |
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--- |
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## Limitations |
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- Relatively small corpus size compared to large-scale pretraining datasets |
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- Specific to medical case report abstracts only |
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--- |
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## Ethical Considerations |
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- All content originates from publicly available, open-access scientific datasets |
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- No personal, clinical, or identifiable patient information is included |
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--- |
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## Citation |
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If you use this dataset, please cite the original publication: |
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```bibtex |
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@article{sun2022phee, |
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title = {PHEE: A dataset for pharmacovigilance event extraction from text}, |
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author = {Sun, Z., Li, J., Pergola, G., Wallace, B. C., John, B., Greene, N., Kim, J., & He, Y.}, |
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journal = {arXiv}, |
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year = {2022}, |
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doi = {preprint arXiv:2210.12560} |
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} |
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``` |
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