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import datasets |
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import os |
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import json |
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_CITATION = """ |
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@article{chen2020meddiag, |
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title={MedDialog: a large-scale medical dialogue dataset}, |
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author={Chen, Shu and Ju, Zeqian and Dong, Xiangyu and Fang, Hongchao and Wang, Sicheng and Yang, Yue and Zeng, |
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Jiaqi and Zhang, Ruisi and Zhang, Ruoyu and Zhou, Meng and Zhu, Penghui and Xie, Pengtao}, |
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journal={arXiv preprint arXiv:2004.03329}, |
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year={2020} |
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} |
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""" |
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_DESCRIPTION = """ |
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"The MedDialog dataset (English) contains conversations between doctors and patients. |
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It has 0.26 million dialogues. The data is continuously growing and more dialogues will be added. |
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The raw dialogues are from healthcaremagic.com and icliniq.com. All copyrights of the data belong |
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to healthcaremagic.com and icliniq.com." |
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The following is an example from the healthcaremagic.com subset: |
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Patient: I get cramps on top of my left forearm and hand and it causes my hand and fingers to draw up and it |
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hurts. It mainly does this when I bend my arm. I ve been told that I have a slight pinch in a nerve in my neck. |
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Could this be a cause? I don t think so. Doctor: Hi there. It may sound difficult to believe it ,but the nerves |
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which supply your forearms and hand, start at the level of spinal cord and on their way towards the forearm and |
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hand regions which they supply, the course of these nerves pass through difference fascial and muscular planes |
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that can make them susceptible to entrapment neuropathies. Its a group of conditions where a nerve gets |
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compressed between a muscle and a bone, or between the fibers of a muscle that it pierces or passes through. |
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Also, the compression can happen when the nerves are travelling around a blood vessel which can mechanically put |
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pressure on them. Usually patients who would be having such a problem present with a dull aching pain over the |
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arm and forearm. If it is not too severe and does not cause any neurological deficits then conservative management |
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with Pregabalin and Vitamin B complex tablets, activity modifications and physiotherapy can be started which |
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will provide relief. Avoid the activities which exaggerate your problem. |
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Could painful forearms be related to pinched nerve in neck? |
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The following is an example from the icliniq.com subset: |
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Patient: Hello doctor, We are looking for a second opinion on my friend's MRI scan of both the knee joints as he |
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is experiencing excruciating pain just above the patella. He has a sudden onset of severe pain on both the knee |
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joints about two weeks ago. Previously he had a similar episode about two to three months ago and it subsided |
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after resting and painkillers. Doctor: Hi. I viewed the right and left knee MRI images. (attachment removed to |
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protect patient identity). Left knee: The MRI, left knee joint shows a complex tear in the posterior horn of the |
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medial meniscus area and mild left knee joint effusion. There is some fluid between the semimembranous and medial |
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head of gastrocnemius muscles. There is a small area of focal cartilage defect in the upper pole of the patella |
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with mild edematous fat. The anterior and posterior cruciate ligaments are normal. The medial and lateral |
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collateral ligaments are normal. Right knee: The right knee joint shows mild increased signal intensity in the |
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posterior horn of the medial meniscus area and minimal knee joint effusion. There is minimal fluid in the back |
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of the lower thigh and not significant. There is a suspicious strain in the left anterior cruciate ligament |
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interiorly but largely the attachments are normal. The posterior cruciate ligament is normal. There are subtle |
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changes in the upper pole area of the right patella and mild edema. There is mild edema around the bilateral |
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distal quadriceps tendons, but there is no obvious tear of the tendons. |
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My friend has excruciating knee pain. Please interpret his MRI report |
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Paper: https://arxiv.org/abs/2004.03329 |
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Code: https://github.com/UCSD-AI4H/Medical-Dialogue-System |
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@article{chen2020meddiag, |
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title={MedDialog: a large-scale medical dialogue dataset}, |
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author={Chen, Shu and Ju, Zeqian and Dong, Xiangyu and Fang, Hongchao and Wang, Sicheng and Yang, Yue and Zeng, |
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Jiaqi and Zhang, Ruisi and Zhang, Ruoyu and Zhou, Meng and Zhu, Penghui and Xie, Pengtao}, |
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journal={arXiv preprint arXiv:2004.03329}, |
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year={2020} |
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} |
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We used the data preprocessing from "BioBART: Pretraining and Evaluation o A Biomedical Generative Language Model" |
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(Yuan et al.) and generated the following splits: |
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|Dataset | Train | Valid | Test | |
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|--------------- |------------|---------|--------| |
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|HealthCareMagic | 181,122 | 22,641 | 22,642 | |
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|iCliniq | 24,851 | 3,105 | 3,108 | |
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Yuan et al. described, "HealthCareMagic's summaries are more abstractive and are written in a formal style, |
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unlike iCliniq's patient-written summaries." |
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Paper: https://arxiv.org/abs/2204.03905 |
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Code: https://github.com/GanjinZero/BioBART |
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@misc{https://doi.org/10.48550/arxiv.2204.03905, |
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doi = {10.48550/ARXIV.2204.03905}, |
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url = {https://arxiv.org/abs/2204.03905}, |
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author = {Yuan, Hongyi and Yuan, Zheng and Gan, Ruyi and Zhang, Jiaxing and Xie, Yutao and Yu, Sheng}, |
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keywords = {Computation and Language (cs.CL), FOS: Computer and information sciences, |
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FOS: Computer and information sciences}, |
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title = {BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model}, |
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publisher = {arXiv}, |
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year = {2022}, |
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copyright = {arXiv.org perpetual, non-exclusive license} |
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} |
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""" |
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class MedDialog(datasets.GeneratorBasedBuilder): |
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VERSION = datasets.Version("1.0.0") |
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BUILDER_CONFIGS = [ |
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datasets.BuilderConfig(name=name, version=datasets.Version("1.0.0"), description=_DESCRIPTION) |
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for name in ["healthcaremagic", "icliniq"] |
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] |
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def _info(self): |
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features = datasets.Features( |
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{ |
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"tgt": datasets.Value("string"), |
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"src": datasets.Value("string"), |
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"id": datasets.Value("int64"), |
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} |
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) |
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return datasets.DatasetInfo( |
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description=_DESCRIPTION, |
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features=features, |
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homepage="", |
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license="", |
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citation=_CITATION, |
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) |
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def _split_generators(self, dl_manager): |
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train_json = dl_manager.download(os.path.join(self.config.name, "train.json")) |
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valid_json = dl_manager.download(os.path.join(self.config.name, "valid.json")) |
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test_json = dl_manager.download(os.path.join(self.config.name, "test.json")) |
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return [ |
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datasets.SplitGenerator( |
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name=datasets.Split.TRAIN, |
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gen_kwargs={"path": train_json}, |
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), |
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datasets.SplitGenerator( |
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name=datasets.Split.VALIDATION, |
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gen_kwargs={"path": valid_json}, |
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), |
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datasets.SplitGenerator( |
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name=datasets.Split.TEST, |
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gen_kwargs={"path": test_json}, |
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) |
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] |
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def _generate_examples(self, path): |
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with open(path, encoding="utf-8") as f: |
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file = json.load(f) |
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for key, row in enumerate(file["data"]): |
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yield key, row |
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