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Register a new userCats, not CAT scans: a study of dataset similarity in transfer learning for 2D medical image classification
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Added by
Veronika Cheplygina
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Transfer learning is a commonly used strategy for medical image classification, especially via pretraining on source data and fine-tuning on target data. There is currently no consensus on how to choose appropriate source data, and in the literature we can find both evidence of favoring large natural image datasets such as ImageNet, and evidence of favoring more specialized medical datasets. In this paper we perform a systematic study with nine source datasets with natural or medical images, and three target medical datasets, all with 2D images. We find that ImageNet is the source leading to the highest performances, but also that larger datasets are not necessarily better. We also study different definitions of data similarity. We show that common intuitions about similarity may be inaccurate, and therefore not sufficient to predict an appropriate source a priori. Finally, we discuss several steps needed for further research in this field, especially with regard to other types (for example 3D) medical images. Our experiments and pretrained models are available via url{https://www.github.com/vcheplygina/cats-scans}
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Transfer learning is a widely used strategy in medical image analysis. Instead of only training a network with a limited amount of data from the target task of interest, we can first train the network with other, potentially larger source datasets, creating a more robust model. The source datasets do not have to be related to the target task. For a classification task in lung CT images, we could use both head CT images, or images of cats, as the source. While head CT images appear more similar to lung CT images, the number and diversity of cat images might lead to a better model overall. In this survey we review a number of papers that have performed similar comparisons. Although the answer to which strategy is best seems to be it depends, we discuss a number of research directions we need to take as a community, to gain more understanding of this topic.
The accuracy and robustness of image classification with supervised deep learning are dependent on the availability of large-scale, annotated training data. However, there is a paucity of annotated data available due to the complexity of manual annotation. To overcome this problem, a popular approach is to use transferable knowledge across different domains by: 1) using a generic feature extractor that has been pre-trained on large-scale general images (i.e., transfer-learned) but which not suited to capture characteristics from medical images; or 2) fine-tuning generic knowledge with a relatively smaller number of annotated images. Our aim is to reduce the reliance on annotated training data by using a new hierarchical unsupervised feature extractor with a convolutional auto-encoder placed atop of a pre-trained convolutional neural network. Our approach constrains the rich and generic image features from the pre-trained domain to a sophisticated representation of the local image characteristics from the unannotated medical image domain. Our approach has a higher classification accuracy than transfer-learned approaches and is competitive with state-of-the-art supervised fine-tuned methods.
Machine learning (ML) algorithms have made a tremendous impact in the field of medical imaging. While medical imaging datasets have been growing in size, a challenge for supervised ML algorithms that is frequently mentioned is the lack of annotated data. As a result, various methods which can learn with less/other types of supervision, have been proposed. We review semi-supervised, multiple instance, and transfer learning in medical imaging, both in diagnosis/detection or segmentation tasks. We also discuss connections between these learning scenarios, and opportunities for future research.
Transfer learning from supervised ImageNet models has been frequently used in medical image analysis. Yet, no large-scale evaluation has been conducted to benchmark the efficacy of newly-developed pre-training techniques for medical image analysis, leaving several important questions unanswered. As the first step in this direction, we conduct a systematic study on the transferability of models pre-trained on iNat2021, the most recent large-scale fine-grained dataset, and 14 top self-supervised ImageNet models on 7 diverse medical tasks in comparison with the supervised ImageNet model. Furthermore, we present a practical approach to bridge the domain gap between natural and medical images by continually (pre-)training supervised ImageNet models on medical images. Our comprehensive evaluation yields new insights: (1) pre-trained models on fine-grained data yield distinctive local representations that are more suitable for medical segmentation tasks, (2) self-supervised ImageNet models learn holistic features more effectively than supervised ImageNet models, and (3) continual pre-training can bridge the domain gap between natural and medical images. We hope that this large-scale open evaluation of transfer learning can direct the future research of deep learning for medical imaging. As open science, all codes and pre-trained models are available on our GitHub page https://github.com/JLiangLab/BenchmarkTransferLearning.
Recent research in disaster informatics demonstrates a practical and important use case of artificial intelligence to save human lives and sufferings during post-natural disasters based on social media contents (text and images). While notable progress has been made using texts, research on exploiting the images remains relatively under-explored. To advance the image-based approach, we propose MEDIC (available at: https://crisisnlp.qcri.org/medic/index.html), which is the largest social media image classification dataset for humanitarian response consisting of 71,198 images to address four different tasks in a multi-task learning setup. This is the first dataset of its kind: social media image, disaster response, and multi-task learning research. An important property of this dataset is its high potential to contribute research on multi-task learning, which recently receives much interest from the machine learning community and has shown remarkable results in terms of memory, inference speed, performance, and generalization capability. Therefore, the proposed dataset is an important resource for advancing image-based disaster management and multi-task machine learning research.
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