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Register a new userTransfusion: Understanding Transfer Learning for Medical Imaging
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Chiyuan Zhang
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Transfer learning from natural image datasets, particularly ImageNet, using standard large models and corresponding pretrained weights has become a de-facto method for deep learning applications to medical imaging. However, there are fundamental differences in data sizes, features and task specifications between natural image classification and the target medical tasks, and there is little understanding of the effects of transfer. In this paper, we explore properties of transfer learning for medical imaging. A performance evaluation on two large scale medical imaging tasks shows that surprisingly, transfer offers little benefit to performance, and simple, lightweight models can perform comparably to ImageNet architectures. Investigating the learned representations and features, we find that some of the differences from transfer learning are due to the over-parametrization of standard models rather than sophisticated feature reuse. We isolate where useful feature reuse occurs, and outline the implications for more efficient model exploration. We also explore feature independent benefits of transfer arising from weight scalings.
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Medical image processing is one of the most important topics in the field of the Internet of Medical Things (IoMT). Recently, deep learning methods have carried out state-of-the-art performances on medical image tasks. However, conventional deep learning have two main drawbacks: 1) insufficient training data and 2) the domain mismatch between the training data and the testing data. In this paper, we propose a distant domain transfer learning (DDTL) method for medical image classification. Moreover, we apply our methods to a recent issue (Coronavirus diagnose). Several current studies indicate that lung Computed Tomography (CT) images can be used for a fast and accurate COVID-19 diagnosis. However, the well-labeled training data cannot be easily accessed due to the novelty of the disease and a number of privacy policies. Moreover, the proposed method has two components: Reduced-size Unet Segmentation model and Distant Feature Fusion (DFF) classification model. It is related to a not well-investigated but important transfer learning problem, termed Distant Domain Transfer Learning (DDTL). DDTL aims to make efficient transfers even when the domains or the tasks are entirely different. In this study, we develop a DDTL model for COVID-19 diagnose using unlabeled Office-31, Catech-256, and chest X-ray image data sets as the source data, and a small set of COVID-19 lung CT as the target data. The main contributions of this study: 1) the proposed method benefits from unlabeled data collected from distant domains which can be easily accessed, 2) it can effectively handle the distribution shift between the training data and the testing data, 3) it has achieved 96% classification accuracy, which is 13% higher classification accuracy than non-transfer algorithms, and 8% higher than existing transfer and distant transfer algorithms.
Transfer learning is a standard technique to improve performance on tasks with limited data. However, for medical imaging, the value of transfer learning is less clear. This is likely due to the large domain mismatch between the usual natural-image pre-training (e.g. ImageNet) and medical images. However, recent advances in transfer learning have shown substantial improvements from scale. We investigate whether modern methods can change the fortune of transfer learning for medical imaging. For this, we study the class of large-scale pre-trained networks presented by Kolesnikov et al. on three diverse imaging tasks: chest radiography, mammography, and dermatology. We study both transfer performance and critical properties for the deployment in the medical domain, including: out-of-distribution generalization, data-efficiency, sub-group fairness, and uncertainty estimation. Interestingly, we find that for some of these properties transfer from natural to medical images is indeed extremely effective, but only when performed at sufficient scale.
Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this application requires substantial implementation effort. Thus, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups. This work presents the open-source NiftyNet platform for deep learning in medical imaging. The ambition of NiftyNet is to accelerate and simplify the development of these solutions, and to provide a common mechanism for disseminating research outputs for the community to use, adapt and build upon. NiftyNet provides a modular deep-learning pipeline for a range of medical imaging applications including segmentation, regression, image generation and representation learning applications. Components of the NiftyNet pipeline including data loading, data augmentation, network architectures, loss functions and evaluation metrics are tailored to, and take advantage of, the idiosyncracies of medical image analysis and computer-assisted intervention. NiftyNet is built on TensorFlow and supports TensorBoard visualization of 2D and 3D images and computational graphs by default. We present 3 illustrative medical image analysis applications built using NiftyNet: (1) segmentation of multiple abdominal organs from computed tomography; (2) image regression to predict computed tomography attenuation maps from brain magnetic resonance images; and (3) generation of simulated ultrasound images for specified anatomical poses. NiftyNet enables researchers to rapidly develop and distribute deep learning solutions for segmentation, regression, image generation and representation learning applications, or extend the platform to new applications.
Deep neural networks (DNNs) have become popular for medical image analysis tasks like cancer diagnosis and lesion detection. However, a recent study demonstrates that medical deep learning systems can be compromised by carefully-engineered adversarial examples/attacks with small imperceptible perturbations. This raises safety concerns about the deployment of these systems in clinical settings. In this paper, we provide a deeper understanding of adversarial examples in the context of medical images. We find that medical DNN models can be more vulnerable to adversarial attacks compared to models for natural images, according to two different viewpoints. Surprisingly, we also find that medical adversarial attacks can be easily detected, i.e., simple detectors can achieve over 98% detection AUC against state-of-the-art attacks, due to fundamental feature differences compared to normal examples. We believe these findings may be a useful basis to approach the design of more explainable and secure medical deep learning systems.
Advancement in digital pathology and artificial intelligence has enabled deep learning-based computer vision techniques for automated disease diagnosis and prognosis. However, WSIs present unique computational and algorithmic challenges. WSIs are gigapixel-sized, making them infeasible to be used directly for training deep neural networks. Hence, for modeling, a two-stage approach is adopted: Patch representations are extracted first, followed by the aggregation for WSI prediction. These approaches require detailed pixel-level annotations for training the patch encoder. However, obtaining these annotations is time-consuming and tedious for medical experts. Transfer learning is used to address this gap and deep learning architectures pre-trained on ImageNet are used for generating patch-level representation. Even though ImageNet differs significantly from histopathology data, pre-trained networks have been shown to perform impressively on histopathology data. Also, progress in self-supervised and multi-task learning coupled with the release of multiple histopathology data has led to the release of histopathology-specific networks. In this work, we compare the performance of features extracted from networks trained on ImageNet and histopathology data. We use an attention pooling network over these extracted features for slide-level aggregation. We investigate if features learned using more complex networks lead to gain in performance. We use a simple top-k sampling approach for fine-tuning framework and study the representation similarity between frozen and fine-tuned networks using Centered Kernel Alignment. Further, to examine if intermediate block representation is better suited for feature extraction and ImageNet architectures are unnecessarily large for histopathology, we truncate the blocks of ResNet18 and DenseNet121 and examine the performance.
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