Datasets:

mkieffer
/

MEDEC-MS

	---
	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
	...â€œsomething crawling on my hand.â€ 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/}
	}
	```