Learning Generalized Medical Image Representations through Image-Graph Contrastive Pretraining (2405.09594v1)
Abstract: Medical image interpretation using deep learning has shown promise but often requires extensive expert-annotated datasets. To reduce this annotation burden, we develop an Image-Graph Contrastive Learning framework that pairs chest X-rays with structured report knowledge graphs automatically extracted from radiology notes. Our approach uniquely encodes the disconnected graph components via a relational graph convolution network and transformer attention. In experiments on the CheXpert dataset, this novel graph encoding strategy enabled the framework to outperform existing methods that use image-text contrastive learning in 1% linear evaluation and few-shot settings, while achieving comparable performance to radiologists. By exploiting unlabeled paired images and text, our framework demonstrates the potential of structured clinical insights to enhance contrastive learning for medical images. This work points toward reducing demands on medical experts for annotations, improving diagnostic precision, and advancing patient care through robust medical image understanding.
- Improved Automated Detection of Diabetic Retinopathy on a Publicly Available Dataset Through Integration of Deep Learning. Investigative Ophthalmology & Visual Science, 57(13):5200–5206, 10 2016. ISSN 1552-5783. 10.1167/iovs.16-19964. URL https://doi.org/10.1167/iovs.16-19964.
- Kernel methods for mining instance data in ontologies. In The Semantic Web: 6th International Semantic Web Conference, 2nd Asian Semantic Web Conference, ISWC 2007+ ASWC 2007, Busan, Korea, November 11-15, 2007. Proceedings, pages 58–71. Springer, 2007.
- Alchemy: A quantum chemistry dataset for benchmarking ai models. arXiv preprint arXiv:1906.09427, 2019a.
- Self-supervised learning for medical image analysis using image context restoration. Medical image analysis, 58:101539, 2019b.
- A simple framework for contrastive learning of visual representations. In International conference on machine learning, pages 1597–1607. PMLR, 2020.
- Machine learning of accurate energy-conserving molecular force fields. Science advances, 3(5):e1603015, 2017.
- Supporting linked data production for cultural heritage institutes: the amsterdam museum case study. In The Semantic Web: Research and Applications: 9th Extended Semantic Web Conference, ESWC 2012, Heraklion, Crete, Greece, May 27-31, 2012. Proceedings 9, pages 733–747. Springer, 2012.
- Clinically applicable deep learning for diagnosis and referral in retinal disease. Nature medicine, 24(9):1342–1350, 2018.
- Structure-activity relationship of mutagenic aromatic and heteroaromatic nitro compounds. correlation with molecular orbital energies and hydrophobicity. Journal of medicinal chemistry, 34(2):786–797, 1991.
- Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805, 2018.
- Retrieval-based chest x-ray report generation using a pre-trained contrastive language-image model. In Machine Learning for Health, pages 209–219. PMLR, 2021.
- Deep residual learning for image recognition. In Proceedings of the IEEE conference on computer vision and pattern recognition, pages 770–778, 2016.
- Densely connected convolutional networks. In Proceedings of the IEEE conference on computer vision and pattern recognition, pages 4700–4708, 2017.
- Gloria: A multimodal global-local representation learning framework for label-efficient medical image recognition. In Proceedings of the IEEE/CVF International Conference on Computer Vision, pages 3942–3951, 2021.
- Chexpert: A large chest radiograph dataset with uncertainty labels and expert comparison. In Proceedings of the AAAI conference on artificial intelligence, volume 33, pages 590–597, 2019.
- Radgraph: Extracting clinical entities and relations from radiology reports. In J. Vanschoren and S. Yeung, editors, Proceedings of the Neural Information Processing Systems Track on Datasets and Benchmarks, volume 1, 2021.
- Chextransfer: performance and parameter efficiency of imagenet models for chest x-ray interpretation. In Proceedings of the conference on health, inference, and learning, pages 116–124, 2021.
- Ishan Misra and Laurens van der Maaten. Self-supervised learning of pretext-invariant representations. In Proceedings of the IEEE/CVF conference on computer vision and pattern recognition, pages 6707–6717, 2020.
- Contrastive language-image pre-training with knowledge graphs. arXiv preprint arXiv:2210.08901, 2022.
- Learning transferable visual models from natural language supervision. In International conference on machine learning, pages 8748–8763. PMLR, 2021.
- Deep learning for chest radiograph diagnosis: A retrospective comparison of the chexnext algorithm to practicing radiologists. PLoS medicine, 15(11):e1002686, 2018.
- Chexpedition: investigating generalization challenges for translation of chest x-ray algorithms to the clinical setting. arXiv preprint arXiv:2002.11379, 2020a.
- Chexaid: deep learning assistance for physician diagnosis of tuberculosis using chest x-rays in patients with hiv. NPJ digital medicine, 3(1):115, 2020b.
- Quantum chemistry structures and properties of 134 kilo molecules. Scientific data, 1(1):1–7, 2014.
- A collection of benchmark datasets for systematic evaluations of machine learning on the semantic web. In The Semantic Web–ISWC 2016: 15th International Semantic Web Conference, Kobe, Japan, October 17–21, 2016, Proceedings, Part II 15, pages 186–194. Springer, 2016.
- Enumeration of 166 billion organic small molecules in the chemical universe database gdb-17. Journal of chemical information and modeling, 52(11):2864–2875, 2012.
- Modeling relational data with graph convolutional networks. In The Semantic Web: 15th International Conference, ESWC 2018, Heraklion, Crete, Greece, June 3–7, 2018, Proceedings 15, pages 593–607. Springer, 2018.
- Simplified transfer learning for chest radiography models using less data. Radiology, 305(2):454–465, 2022.
- Augmenting the national institutes of health chest radiograph dataset with expert annotations of possible pneumonia. Radiology: Artificial Intelligence, 1(1):e180041, 2019.
- Moco pretraining improves representation and transferability of chest x-ray models. In Medical Imaging with Deep Learning, pages 728–744. PMLR, 2021.
- Covid-19 prognosis via self-supervised representation learning and multi-image prediction. arXiv preprint arXiv:2101.04909, 2021.
- Rotate: Knowledge graph embedding by relational rotation in complex space. arXiv preprint arXiv:1902.10197, 2019.
- A survey on deep transfer learning. In Artificial Neural Networks and Machine Learning–ICANN 2018: 27th International Conference on Artificial Neural Networks, Rhodes, Greece, October 4-7, 2018, Proceedings, Part III 27, pages 270–279. Springer, 2018.
- Attention is all you need. Advances in neural information processing systems, 30, 2017.
- Graph attention networks. arXiv preprint arXiv:1710.10903, 2017.
- Medaug: Contrastive learning leveraging patient metadata improves representations for chest x-ray interpretation. In Machine Learning for Healthcare Conference, pages 755–769. PMLR, 2021.
- Covid-net: A tailored deep convolutional neural network design for detection of covid-19 cases from chest x-ray images. Scientific reports, 10(1):1–12, 2020.
- Graph convolutional networks: a comprehensive review. Computational Social Networks, 6(1):1–23, 2019.
- Generalized radiograph representation learning via cross-supervision between images and free-text radiology reports. Nature Machine Intelligence, 4(1):32–40, 2022.
- Sameer Khanna (4 papers)
- Daniel Michael (1 paper)
- Pranav Rajpurkar (69 papers)
- Marinka Zitnik (79 papers)