Differentiable programming is able to combine different functions or programs in a processing pipeline with the goal of applying end-to-end learning or optimization. A significant impediment is the non-differentiable nature of some algorithms. We propose to use synthetic gradients (SG) to overcome this difficulty. SG uses the universal function approximation property of neural networks. We apply SG to combine convolutional neural network (CNN) with dynamic programming (DP) in end-to-end learning for segmenting left ventricle from short axis view of heart MRI. Our experiments show that end-to-end combination of CNN and DP requires fewer labeled images to achieve a significantly better segmentation accuracy than using only CNN.
Hu @cite_10 proposed to use CNN to learn a level set function (signed distance transform) for salient object detection. Tang @cite_5 used level set in conjunction with deep learning to segment liver CT data and left ventricle from MRI. However, their method does not use end-to-end training for this combination. Deep active contours @cite_28 combined CNN and active contours; the work, however, fell short of an end-to-end training process.
@cite_28 @cite_5 @cite_10
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While deep convolutional neural networks (CNN) have been successfully applied for 2D image analysis, it is still challenging to apply them to 3D anisotropic volumes, especially when the within-slice resolution is much higher than the between-slice resolution and when the amount of 3D volumes is relatively small. On one hand, direct learning of CNN with 3D convolution kernels suffers from the lack of data and likely ends up with poor generalization; insufficient GPU memory limits the model size or representational power. On the other hand, applying 2D CNN with generalizable features to 2D slices ignores between-slice information. Coupling 2D network with LSTM to further handle the between-slice information is not optimal due to the difficulty in LSTM learning. To overcome the above challenges, we propose a 3D Anisotropic Hybrid Network (AH-Net) that transfers convolutional features learned from 2D images to 3D anisotropic volumes. Such a transfer inherits the desired strong generalization capability for within-slice information while naturally exploiting between-slice information for more effective modelling. The focal loss is further utilized for more effective end-to-end learning. We experiment with the proposed 3D AH-Net on two different medical image analysis tasks, namely lesion detection from a Digital Breast Tomosynthesis volume, and liver and liver tumor segmentation from a Computed Tomography volume and obtain the state-of-the-art results. Training a deep convolutional neural network (CNN) from scratch is difficult because it requires a large amount of labeled training data and a great deal of expertise to ensure proper convergence. A promising alternative is to fine-tune a CNN that has been pre-trained using, for instance, a large set of labeled natural images. However, the substantial differences between natural and medical images may advise against such knowledge transfer. In this paper, we seek to answer the following central question in the context of medical image analysis: Can the use of pre-trained deep CNNs with sufficient fine-tuning eliminate the need for training a deep CNN from scratch? To address this question, we considered four distinct medical imaging applications in three specialties (radiology, cardiology, and gastroenterology) involving classification, detection, and segmentation from three different imaging modalities, and investigated how the performance of deep CNNs trained from scratch compared with the pre-trained CNNs fine-tuned in a layer-wise manner. Our experiments consistently demonstrated that 1) the use of a pre-trained CNN with adequate fine-tuning outperformed or, in the worst case, performed as well as a CNN trained from scratch; 2) fine-tuned CNNs were more robust to the size of training sets than CNNs trained from scratch; 3) neither shallow tuning nor deep tuning was the optimal choice for a particular application; and 4) our layer-wise fine-tuning scheme could offer a practical way to reach the best performance for the application at hand based on the amount of available data. Convolutional neural network (CNN) has achieved the state-of-the-art performance in many different visual tasks. Learned from a large-scale training data set, CNN features are much more discriminative and accurate than the handcrafted features. Moreover, CNN features are also transferable among different domains. On the other hand, traditional dictionary-based features (such as BoW and spatial pyramid matching) contain much more local discriminative and structural information, which is implicitly embedded in the images. To further improve the performance, in this paper, we propose to combine CNN with dictionary-based models for scene recognition and visual domain adaptation (DA). Specifically, based on the well-tuned CNN models (e.g., AlexNet and VGG Net), two dictionary-based representations are further constructed, namely, mid-level local representation (MLR) and convolutional Fisher vector (CFV) representation. In MLR, an efficient two-stage clustering method, i.e., weighted spatial and feature space spectral clustering on the parts of a single image followed by clustering all representative parts of all images, is used to generate a class-mixture or a class-specific part dictionary. After that, the part dictionary is used to operate with the multiscale image inputs for generating mid-level representation. In CFV, a multiscale and scale-proportional Gaussian mixture model training strategy is utilized to generate Fisher vectors based on the last convolutional layer of CNN. By integrating the complementary information of MLR, CFV, and the CNN features of the fully connected layer, the state-of-the-art performance can be achieved on scene recognition and DA problems. An interested finding is that our proposed hybrid representation (from VGG net trained on ImageNet) is also complementary to GoogLeNet and or VGG-11 (trained on Place205) greatly. Training deep fully convolutional neural networks (F-CNNs) for semantic image segmentation requires access to abundant labeled data. While large datasets of unlabeled image data are available in medical applications, access to manually labeled data is very limited. We propose to automatically create auxiliary labels on initially unlabeled data with existing tools and to use them for pre-training. For the subsequent fine-tuning of the network with manually labeled data, we introduce error corrective boosting (ECB), which emphasizes parameter updates on classes with lower accuracy. Furthermore, we introduce SkipDeconv-Net (SD-Net), a new F-CNN architecture for brain segmentation that combines skip connections with the unpooling strategy for upsampling. The SD-Net addresses challenges of severe class imbalance and errors along boundaries. With application to whole-brain MRI T1 scan segmentation, we generate auxiliary labels on a large dataset with FreeSurfer and fine-tune on two datasets with manual annotations. Our results show that the inclusion of auxiliary labels and ECB yields significant improvements. SD-Net segments a 3D scan in 7 secs in comparison to 30 hours for the closest multi-atlas segmentation method, while reaching similar performance. It also outperforms the latest state-of-the-art F-CNN models.