--- dataset_info: features: - name: text_id dtype: string - name: text dtype: string - name: sentences dtype: string - name: error_flag dtype: bool - name: error_type dtype: string - name: error_sentence_id dtype: int8 - name: error_sentence dtype: string - name: corrected_sentence dtype: string - name: corrected_text dtype: string splits: - name: train num_bytes: 4733960 num_examples: 2189 - name: test num_bytes: 1300714 num_examples: 597 - name: validation num_bytes: 1234271 num_examples: 574 download_size: 2940360 dataset_size: 7268945 configs: - config_name: default data_files: - split: train path: data/train-* - split: test path: data/test-* - split: validation path: data/validation-* license: cc-by-4.0 task_categories: - text-generation - question-answering - text-classification tags: - medical - clinical --- # MEDEC-MS HuggingFace upload of the MEDEC-MS dataset with fixes. If used, please cite the original authors using the citation below. ## Dataset Details ### Dataset Description The dataset contains three splits: **train**, **validation**, **test**. ### Dataset Sources - **Repository:** https://github.com/abachaa/MEDEC - **Paper:** https://arxiv.org/pdf/2412.19260 ### Corrections to the original dataset: - **Added pipes to delimit sentence IDs and sentences in the `sentences` column, as specified in [Prompt #1](https://arxiv.org/pdf/2412.19260#page=5).** - **Removed non-standard characters.** For example, the original `ms-train-19` `text` column had ```txt ...“something crawling on my hand.” The... ``` which is corrected in this dataset to be ``` ..."something crawling on my hand." The... ``` - **Fixed many broken sentences in the original dataset.** For example, the original `ms-test-15` row had a malformed `sentences` column: ```txt 5 Her temperature is 37.5 C 6 (99.5 F ); pulse is 75/min; respiratory rate is 13/min, and blood pressure is 7 115/70 mm 8 Hg. 9 A maculopapular rash is observed over the trunk and limbs. ``` which is corrected in this dataset to be ```txt 5 | Her temperature is 37.5C (99.5 F); pulse is 75/min; respiratory rate is 13/min, and blood pressure is 115/70 mm Hg. 6 | A maculopapular rash is observed over the trunk and limbs. ``` - **Ensured that the `error_sentence` and `corrected_sentence` column contain the full sentences.** For example, `ms-test-551` originally had ```txt error_sentence: "Prazosin is prescribed as his temperature is 99.3 F (37.4 C), blood pressure is 165/118" corrected_sentence: "Phenoxybenzamine is prescribed as his temperature is 99.3 F (37.4 C), blood pressure is 165/118" ``` with `sentences` ```txt 0 A 45-year-old-man presents to the physician with complaints of intermittent episodes of severe headaches and palpitations. 1 During these episodes, he notices that he sweats profusely and becomes pale in complexion. 2 He describes the episodes as coming and going within the past 2 months. 3 Prazosin is prescribed as his temperature is 99.3 F (37.4 C), blood pressure is 165/118 4 mmHg, pulse is 5 126/min, respirations are 18/min, and oxygen saturation is 90% on room air. ``` which is corrected in this dataset to include the full sentences ```txt error_sentence: "Prazosin is prescribed as his temperature is 99.3 F (37.4 C), blood pressure is 165/118 mmHg, pulse is 126/min, respirations are 18/min, and oxygen saturation is 90% on room air." corrected_sentence: "Phenoxybenzamine is prescribed as his temperature is 99.3 F (37.4 C), blood pressure is 165/118 mmHg, pulse is 126/min, respirations are 18/min, and oxygen saturation is 90% on room air." ``` and ```txt 0 | A 45-year-old-man presents to the physician with complaints of intermittent episodes of severe headaches and palpitations. 1 | During these episodes, he notices that he sweats profusely and becomes pale in complexion. 2 | He describes the episodes as coming and going within the past 2 months. 3 | Prazosin is prescribed as his temperature is 99.3 F (37.4 C), blood pressure is 165/118 mmHg, pulse is 126/min, respirations are 18/min, and oxygen saturation is 90% on room air. ``` As you can see, the original `sentences` column had incorrect sentence splits, which the `error_sentence` and `corrected_sentence` at least conformed to. But if you want to specifically test for sentence extraction, especially in the case of raw, unmarked text, we feel it's important to respect sentence boundaries. ### Direct Use ```python import json from datasets import load_dataset if __name__ == "__main__": # load all data dataset = load_dataset("mkieffer/MEDEC") # load only train split dataset_train = load_dataset("mkieffer/MEDEC", split="train") # load only test split dataset_test = load_dataset("mkieffer/MEDEC", split="test") # load only validation split dataset_val = load_dataset("mkieffer/MEDEC", split="validation") print("\nfull dataset:\n", dataset) print("\ntrain split:\n", dataset_train) print("\test split:\n", dataset_test) print("\validation split:\n", dataset_val) print("\ntrain sample:\n", json.dumps(dataset_train[0], indent=2)) print("\test sample:\n", json.dumps(dataset_test[0], indent=2)) print("\validation sample:\n", json.dumps(dataset_val[0], indent=2)) ``` ## Citation ```bibtex @inproceedings{medec, author = {Asma {Ben Abacha} and Wen{-}wai Yim and Yujuan Fu and Zhaoyi Sun and Meliha Yetisgen and Fei Xia and Thomas Lin}, title = {MEDEC: A Benchmark for Medical Error Detection and Correction in Clinical Notes}, booktitle = {Findings of the Association for Computational Linguistics, ACL 2025, Vienna, Austria, July 27 - August 1, 2025}, pages = {22539--22550}, publisher = {Association for Computational Linguistics}, year = {2025}, url = {https://aclanthology.org/2025.findings-acl.1159/} } ```