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Register a new userColorectal Cancer Segmentation using Atrous Convolution and Residual Enhanced UNet
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Colorectal cancer is a leading cause of death worldwide. However, early diagnosis dramatically increases the chances of survival, for which it is crucial to identify the tumor in the body. Since its imaging uses high-resolution techniques, annotating the tumor is time-consuming and requires particular expertise. Lately, methods built upon Convolutional Neural Networks(CNNs) have proven to be at par, if not better in many biomedical segmentation tasks. For the task at hand, we propose another CNN-based approach, which uses atrous convolutions and residual connections besides the conventional filters. The training and inference were made using an efficient patch-based approach, which significantly reduced unnecessary computations. The proposed AtResUNet was trained on the DigestPath 2019 Challenge dataset for colorectal cancer segmentation with results having a Dice Coefficient of 0.748.
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Deriving interpretable prognostic features from deep-learning-based prognostic histopathology models remains a challenge. In this study, we developed a deep learning system (DLS) for predicting disease specific survival for stage II and III colorectal cancer using 3,652 cases (27,300 slides). When evaluated on two validation datasets containing 1,239 cases (9,340 slides) and 738 cases (7,140 slides) respectively, the DLS achieved a 5-year disease-specific survival AUC of 0.70 (95%CI 0.66-0.73) and 0.69 (95%CI 0.64-0.72), and added significant predictive value to a set of 9 clinicopathologic features. To interpret the DLS, we explored the ability of different human-interpretable features to explain the variance in DLS scores. We observed that clinicopathologic features such as T-category, N-category, and grade explained a small fraction of the variance in DLS scores (R2=18% in both validation sets). Next, we generated human-interpretable histologic features by clustering embeddings from a deep-learning based image-similarity model and showed that they explain the majority of the variance (R2 of 73% to 80%). Furthermore, the clustering-derived feature most strongly associated with high DLS scores was also highly prognostic in isolation. With a distinct visual appearance (poorly differentiated tumor cell clusters adjacent to adipose tissue), this feature was identified by annotators with 87.0-95.5% accuracy. Our approach can be used to explain predictions from a prognostic deep learning model and uncover potentially-novel prognostic features that can be reliably identified by people for future validation studies.
In this work, we propose a new segmentation network by integrating DenseUNet and bidirectional LSTM together with attention mechanism, termed as DA-BDense-UNet. DenseUNet allows learning enough diverse features and enhancing the representative power of networks by regulating the information flow. Bidirectional LSTM is responsible to explore the relationships between the encoded features and the up-sampled features in the encoding and decoding paths. Meanwhile, we introduce attention gates (AG) into DenseUNet to diminish responses of unrelated background regions and magnify responses of salient regions progressively. Besides, the attention in bidirectional LSTM takes into account the contribution differences of the encoded features and the up-sampled features in segmentation improvement, which can in turn adjust proper weights for these two kinds of features. We conduct experiments on liver CT image data sets collected from multiple hospitals by comparing them with state-of-the-art segmentation models. Experimental results indicate that our proposed method DA-BDense-UNet has achieved comparative performance in terms of dice coefficient, which demonstrates its effectiveness.
Recently, a growing interest has been seen in deep learning-based semantic segmentation. UNet, which is one of deep learning networks with an encoder-decoder architecture, is widely used in medical image segmentation. Combining multi-scale features is one of important factors for accurate segmentation. UNet++ was developed as a modified Unet by designing an architecture with nested and dense skip connections. However, it does not explore sufficient information from full scales and there is still a large room for improvement. In this paper, we propose a novel UNet 3+, which takes advantage of full-scale skip connections and deep supervisions. The full-scale skip connections incorporate low-level details with high-level semantics from feature maps in different scales; while the deep supervision learns hierarchical representations from the full-scale aggregated feature maps. The proposed method is especially benefiting for organs that appear at varying scales. In addition to accuracy improvements, the proposed UNet 3+ can reduce the network parameters to improve the computation efficiency. We further propose a hybrid loss function and devise a classification-guided module to enhance the organ boundary and reduce the over-segmentation in a non-organ image, yielding more accurate segmentation results. The effectiveness of the proposed method is demonstrated on two datasets. The code is available at: github.com/ZJUGiveLab/UNet-Version
Microscopic examination of tissues or histopathology is one of the diagnostic procedures for detecting colorectal cancer. The pathologist involved in such an examination usually identifies tissue type based on texture analysis, especially focusing on tumour-stroma ratio. In this work, we automate the task of tissue classification within colorectal cancer histology samples using deep transfer learning. We use discriminative fine-tuning with one-cycle-policy and apply structure-preserving colour normalization to boost our results. We also provide visual explanations of the deep neural networks decision on texture classification. With achieving state-of-the-art test accuracy of 96.2% we also embark on using deployment friendly architecture called SqueezeNet for memory-limited hardware.
Knowledge graph embedding is an important task and it will benefit lots of downstream applications. Currently, deep neural networks based methods achieve state-of-the-art performance. However, most of these existing methods are very complex and need much time for training and inference. To address this issue, we propose a simple but effective atrous convolution based knowledge graph embedding method. Compared with existing state-of-the-art methods, our method has following main characteristics. First, it effectively increases feature interactions by using atrous convolutions. Second, to address the original information forgotten issue and vanishing/exploding gradient issue, it uses the residual learning method. Third, it has simpler structure but much higher parameter efficiency. We evaluate our method on six benchmark datasets with different evaluation metrics. Extensive experiments show that our model is very effective. On these diverse datasets, it achieves better results than the compared state-of-the-art methods on most of evaluation metrics. The source codes of our model could be found at https://github.com/neukg/AcrE.
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