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"""PMC-OA Dataset""" |
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import os |
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import jsonlines |
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import datasets |
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logger = datasets.logging.get_logger(__name__) |
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_CITATION = """\ |
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@article{lin2023pmc, |
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title={PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents}, |
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author={Lin, Weixiong and Zhao, Ziheng and Zhang, Xiaoman and Wu, Chaoyi and Zhang, Ya and Wang, Yanfeng and Xie, Weidi}, |
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journal={arXiv preprint arXiv:2303.07240}, |
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year={2023} |
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} |
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""" |
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_DESCRIPTION = """\ |
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Foundation models trained on large-scale dataset gain a recent surge in CV and NLP. In contrast, development in biomedical domain lags far behind due to data scarcity. |
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To address this issue, we build and release PMC-OA, a biomedical dataset with 1.6M image-caption pairs collected from PubMedCentral's OpenAccess subset, which is 8 times larger than before. |
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PMC-OA covers diverse modalities or diseases, with majority of the image-caption samples aligned at finer-grained level, i.e., subfigure and subcaption. |
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While pretraining a CLIP-style model on PMC-OA, our model named PMC-CLIP achieves state-of-the-art results on various downstream tasks, |
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including image-text retrieval on ROCO, MedMNIST image classification, Medical VQA, i.e. +8.1% R@10 on image-text retrieval, +3.9% accuracy on image classification. |
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""" |
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_HOMEPAGE = "https://weixionglin.github.io/PMC-CLIP/" |
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_URLs = { |
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"images": "https://huggingface.co/datasets/axiong/pmc_oa/resolve/main/images.zip", |
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"demo_images": "https://huggingface.co/datasets/axiong/test/resolve/main/images.zip", |
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"demo_captions": "https://huggingface.co/datasets/axiong/test/resolve/main/mini_dataset.jsonl", |
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"pmc_oa_beta": "https://huggingface.co/datasets/axiong/pmc_oa/resolve/main/pmc_oa_beta.jsonl", |
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"pmc_oa": "https://huggingface.co/datasets/axiong/pmc_oa/resolve/main/pmc_oa.jsonl", |
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} |
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class PMC_OA_Config(datasets.BuilderConfig): |
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"""BuilderConfig for PMC_OA""" |
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def __init__(self, **kwargs): |
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""" |
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Args: |
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**kwargs: keyword arguments forwarded to super. |
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""" |
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super(PMC_OA_Config, self).__init__(version=datasets.Version("1.0.0", ""), **kwargs) |
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class PMC_OA(datasets.GeneratorBasedBuilder): |
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"""PMC_OA Dataset""" |
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VERSION = datasets.Version("1.0.0") |
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BUILDER_CONFIGS = [ |
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PMC_OA_Config( |
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name="demo", |
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description="Demo subset to show dataset samples.", |
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), |
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PMC_OA_Config( |
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name="pmc_oa_beta", |
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description="<subfigure, caption> pairs. Subfigures detected by a DETR model.", |
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), |
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PMC_OA_Config( |
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name="pmc_oa", |
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description="<subfigure, subcaption> pairs. Subfigures detected by a DETR model. Subcaptions detected by ChatGPT and aligned with subfigures.", |
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), |
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] |
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def _info(self): |
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if self.config.name == "demo": |
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return datasets.DatasetInfo( |
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description=_DESCRIPTION, |
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features=datasets.Features( |
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{ |
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"image": datasets.Value("string"), |
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"caption": datasets.Value("string"), |
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} |
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), |
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supervised_keys=None, |
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citation=_CITATION, |
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homepage=_HOMEPAGE, |
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) |
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elif self.config.name == "pmc_oa_beta": |
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return datasets.DatasetInfo( |
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description=_DESCRIPTION, |
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features=datasets.Features( |
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{ |
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"image": datasets.Value("string"), |
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"caption": datasets.Value("string"), |
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} |
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), |
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supervised_keys=None, |
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citation=_CITATION, |
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homepage=_HOMEPAGE, |
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) |
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elif self.config.name == "pmc_oa": |
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return datasets.DatasetInfo( |
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description=_DESCRIPTION, |
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features=datasets.Features( |
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{ |
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"image": datasets.Value("string"), |
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"caption": datasets.Value("string"), |
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} |
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), |
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supervised_keys=None, |
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citation=_CITATION, |
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homepage=_HOMEPAGE, |
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) |
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def _split_generators(self, dl_manager): |
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"""Returns SplitGenerators.""" |
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downloaded_files = dl_manager.download_and_extract(_URLs) |
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if self.config.name == "demo": |
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return [ |
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datasets.SplitGenerator( |
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name=datasets.Split.TRAIN, gen_kwargs={"filepath": downloaded_files["demo_captions"], "image_dir": downloaded_files['demo_images']} |
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) |
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] |
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elif self.config.name == "pmc_oa_beta": |
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return [ |
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datasets.SplitGenerator( |
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name=datasets.Split.TRAIN, gen_kwargs={"filepath": downloaded_files["pmc_oa_beta"], "image_dir": downloaded_files['images']} |
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) |
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] |
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elif self.config.name == "pmc_oa": |
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return [ |
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datasets.SplitGenerator( |
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name=datasets.Split.TRAIN, gen_kwargs={"filepath": downloaded_files["pmc_oa"], "image_dir": downloaded_files['images']} |
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) |
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] |
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def _generate_examples(self, filepath, image_dir): |
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"""Yields examples.""" |
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logger.info("generating examples from = %s", filepath) |
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with jsonlines.open(filepath) as reader: |
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for _id, obj in enumerate(reader): |
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if self.config.name == "demo": |
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relative_image_path = obj['image'] |
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image_path = os.path.join(image_dir, "images", relative_image_path) |
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caption = obj['caption'] |
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yield _id, { |
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"image": { |
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"path": image_path, |
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"bytes": open(image_path, "rb").read(), |
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}, |
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"caption": caption, |
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} |
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elif self.config.name == "pmc_oa_beta": |
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relative_image_path = obj['image'] |
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image_path = os.path.join(image_dir, "caption_T060_filtered_top4_sep_v0_subfigures", relative_image_path) |
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caption = obj['caption'] |
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yield _id, { |
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"image": { |
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"path": image_path, |
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"bytes": open(image_path, "rb").read(), |
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}, |
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"caption": caption, |
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} |
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elif self.config.name == "pmc_oa": |
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relative_image_path = obj['image'] |
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image_path = os.path.join(image_dir, "caption_T060_filtered_top4_sep_v0_subfigures", relative_image_path) |
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caption = obj['caption'] |
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yield _id, { |
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"image": { |
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"path": image_path, |
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"bytes": open(image_path, "rb").read(), |
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}, |
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"caption": caption, |
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} |
