Med Dialog

med_dialog.py

@@ -0,0 +1,148 @@
+import datasets
+import os
+import json
+
+
+_CITATION = """
+    @article{chen2020meddiag,
+      title={MedDialog: a large-scale medical dialogue dataset},
+      author={Chen, Shu and Ju, Zeqian and Dong, Xiangyu and Fang, Hongchao and Wang, Sicheng and Yang, Yue and Zeng,
+              Jiaqi and Zhang, Ruisi and Zhang, Ruoyu and Zhou, Meng and Zhu, Penghui and Xie, Pengtao},
+      journal={arXiv preprint arXiv:2004.03329},
+      year={2020}
+    }
+"""
+
+_DESCRIPTION = """
+    "The MedDialog dataset (English) contains conversations between doctors and patients.
+    It has 0.26 million dialogues. The data is continuously growing and more dialogues will be added.
+    The raw dialogues are from healthcaremagic.com and icliniq.com. All copyrights of the data belong
+    to healthcaremagic.com and icliniq.com."
+
+    The following is an example from the healthcaremagic.com subset:
+
+    Patient: I get cramps on top of my left forearm and hand and it causes my hand and fingers to draw up and it
+    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.
+    Could this be a cause? I don t think so. Doctor: Hi there. It may sound difficult to believe it ,but the nerves
+    which supply your forearms and hand, start at the level of spinal cord and on their way towards the forearm and
+    hand regions which they supply, the course of these nerves pass through difference fascial and muscular planes
+    that can make them susceptible to entrapment neuropathies. Its a group of conditions where a nerve gets
+    compressed between a muscle and a bone, or between the fibers of a muscle that it pierces or passes through.
+    Also, the compression can happen when the nerves are travelling around a blood vessel which can mechanically put
+    pressure on them. Usually patients who would be having such a problem present with a dull aching pain over the
+    arm and forearm. If it is not too severe and does not cause any neurological deficits then conservative management
+    with Pregabalin and Vitamin B complex tablets, activity modifications and physiotherapy can be started which
+    will provide relief. Avoid the activities which exaggerate your problem.
+
+    Could painful forearms be related to pinched nerve in neck?
+
+
+    The following is an example from the icliniq.com subset:
+
+    Patient: Hello doctor,  We are looking for a second opinion on my friend's MRI scan of both the knee joints as he
+    is experiencing excruciating pain just above the patella. He has a sudden onset of severe pain on both the knee
+    joints about two weeks ago. Previously he had a similar episode about two to three months ago and it subsided
+    after resting and painkillers. Doctor: Hi. I viewed the right and left knee MRI images. (attachment removed to
+    protect patient identity).  Left knee: The MRI, left knee joint shows a complex tear in the posterior horn of the
+    medial meniscus area and mild left knee joint effusion. There is some fluid between the semimembranous and medial
+    head of gastrocnemius muscles. There is a small area of focal cartilage defect in the upper pole of the patella
+    with mild edematous fat. The anterior and posterior cruciate ligaments are normal. The medial and lateral
+    collateral ligaments are normal. Right knee: The right knee joint shows mild increased signal intensity in the
+    posterior horn of the medial meniscus area and minimal knee joint effusion. There is minimal fluid in the back
+    of the lower thigh and not significant. There is a suspicious strain in the left anterior cruciate ligament
+    interiorly but largely the attachments are normal. The posterior cruciate ligament is normal. There are subtle
+    changes in the upper pole area of the right patella and mild edema. There is mild edema around the bilateral
+    distal quadriceps tendons, but there is no obvious tear of the tendons.
+
+    My friend has excruciating knee pain. Please interpret his MRI report
+
+
+    Paper: https://arxiv.org/abs/2004.03329
+    Code: https://github.com/UCSD-AI4H/Medical-Dialogue-System
+
+    @article{chen2020meddiag,
+      title={MedDialog: a large-scale medical dialogue dataset},
+      author={Chen, Shu and Ju, Zeqian and Dong, Xiangyu and Fang, Hongchao and Wang, Sicheng and Yang, Yue and Zeng,
+              Jiaqi and Zhang, Ruisi and Zhang, Ruoyu and Zhou, Meng and Zhu, Penghui and Xie, Pengtao},
+      journal={arXiv preprint arXiv:2004.03329},
+      year={2020}
+    }
+
+    We used the data preprocessing from "BioBART: Pretraining and Evaluation o A Biomedical Generative Language Model"
+    (Yuan et al.) and generated the following splits:
+
+    |Dataset         | Train      | Valid   | Test   |
+    |--------------- |------------|---------|--------|
+    |HealthCareMagic | 181,122    | 22,641  | 22,642 |
+    |iCliniq         | 24,851     | 3,105   | 3,108  |
+
+    Yuan et al. described, "HealthCareMagic's summaries are more abstractive and are written in a formal style,
+    unlike iCliniq's patient-written summaries."
+
+    Paper: https://arxiv.org/abs/2204.03905
+    Code: https://github.com/GanjinZero/BioBART
+
+    @misc{https://doi.org/10.48550/arxiv.2204.03905,
+      doi = {10.48550/ARXIV.2204.03905},
+      url = {https://arxiv.org/abs/2204.03905},
+      author = {Yuan, Hongyi and Yuan, Zheng and Gan, Ruyi and Zhang, Jiaxing and Xie, Yutao and Yu, Sheng},
+      keywords = {Computation and Language (cs.CL), FOS: Computer and information sciences,
+                  FOS: Computer and information sciences},
+      title = {BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model},
+      publisher = {arXiv},
+      year = {2022},
+      copyright = {arXiv.org perpetual, non-exclusive license}
+    }
+"""
+
+class MedDialog(datasets.GeneratorBasedBuilder):
+    VERSION = datasets.Version("1.0.0")
+
+    BUILDER_CONFIGS = [
+        datasets.BuilderConfig(name=name, version=datasets.Version("1.0.0"), description=_DESCRIPTION)
+            for name in ["healthcaremagic", "icliniq"]
+        ]
+
+    def _info(self):
+        features = datasets.Features(
+            {
+                "tgt": datasets.Value("string"),
+                "src": datasets.Value("string"),
+                "id": datasets.Value("int64"),
+
+            }
+        )
+        return datasets.DatasetInfo(
+            description=_DESCRIPTION,
+            features=features,
+            homepage="",
+            license="",
+            citation=_CITATION,
+        )
+
+    def _split_generators(self, dl_manager):
+        train_json = dl_manager.download(os.path.join(self.config.name, "train.json"))
+        valid_json = dl_manager.download(os.path.join(self.config.name, "valid.json"))
+        test_json = dl_manager.download(os.path.join(self.config.name, "test.json"))
+
+        return [
+            datasets.SplitGenerator(
+                name=datasets.Split.TRAIN,
+                gen_kwargs={"path": train_json},
+            ),
+            datasets.SplitGenerator(
+                name=datasets.Split.VALIDATION,
+                gen_kwargs={"path": valid_json},
+            ),
+            datasets.SplitGenerator(
+                name=datasets.Split.TEST,
+                gen_kwargs={"path": test_json},
+            )
+        ]
+
+    # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
+    def _generate_examples(self, path):
+        with open(path, encoding="utf-8") as f:
+            file = json.load(f)
+            for key, row in enumerate(file["data"]):
+                yield key, row