No Arabic abstract
Recent neural-network-based architectures for image segmentation make extensive usage of feature forwarding mechanisms to integrate information from multiple scales. Although yielding good results, even deeper architectures and alternative methods for feature fusion at different resolutions have been scarcely investigated for medical applications. In this work we propose to implement segmentation via an encoder-decoder architecture which differs from any other previously published method since (i) it employs a very deep architecture based on residual learning and (ii) combines features via a convolutional Long Short Term Memory (LSTM), instead of concatenation or summation. The intuition is that the memory mechanism implemented by LSTMs can better integrate features from different scales through a coarse-to-fine strategy; hence the name Coarse-to-Fine Context Memory (CFCM). We demonstrate the remarkable advantages of this approach on two datasets: the Montgomery county lung segmentation dataset, and the EndoVis 2015 challenge dataset for surgical instrument segmentation.
In this paper, we adopt 3D Convolutional Neural Networks to segment volumetric medical images. Although deep neural networks have been proven to be very effective on many 2D vision tasks, it is still challenging to apply them to 3D tasks due to the limited amount of annotated 3D data and limited computational resources. We propose a novel 3D-based coarse-to-fine framework to effectively and efficiently tackle these challenges. The proposed 3D-based framework outperforms the 2D counterpart to a large margin since it can leverage the rich spatial infor- mation along all three axes. We conduct experiments on two datasets which include healthy and pathological pancreases respectively, and achieve the current state-of-the-art in terms of Dice-S{o}rensen Coefficient (DSC). On the NIH pancreas segmentation dataset, we outperform the previous best by an average of over 2%, and the worst case is improved by 7% to reach almost 70%, which indicates the reliability of our framework in clinical applications.
Boundary-based instance segmentation has drawn much attention since of its attractive efficiency. However, existing methods suffer from the difficulty in long-distance regression. In this paper, we propose a coarse-to-fine module to address the problem. Approximate boundary points are generated at the coarse stage and then features of these points are sampled and fed to a refined regressor for fine prediction. It is end-to-end trainable since differential sampling operation is well supported in the module. Furthermore, we design a holistic boundary-aware branch and introduce instance-agnostic supervision to assist regression. Equipped with ResNet-101, our approach achieves 31.7% mask AP on COCO dataset with single-scale training and testing, outperforming the baseline 1.3% mask AP with less than 1% additional parameters and GFLOPs. Experiments also show that our proposed method achieves competitive performance compared to existing boundary-based methods with a lightweight design and a simple pipeline.
3D convolution neural networks (CNN) have been proved very successful in parsing organs or tumours in 3D medical images, but it remains sophisticated and time-consuming to choose or design proper 3D networks given different task contexts. Recently, Neural Architecture Search (NAS) is proposed to solve this problem by searching for the best network architecture automatically. However, the inconsistency between search stage and deployment stage often exists in NAS algorithms due to memory constraints and large search space, which could become more serious when applying NAS to some memory and time consuming tasks, such as 3D medical image segmentation. In this paper, we propose coarse-to-fine neural architecture search (C2FNAS) to automatically search a 3D segmentation network from scratch without inconsistency on network size or input size. Specifically, we divide the search procedure into two stages: 1) the coarse stage, where we search the macro-level topology of the network, i.e. how each convolution module is connected to other modules; 2) the fine stage, where we search at micro-level for operations in each cell based on previous searched macro-level topology. The coarse-to-fine manner divides the search procedure into two consecutive stages and meanwhile resolves the inconsistency. We evaluate our method on 10 public datasets from Medical Segmentation Decalthon (MSD) challenge, and achieve state-of-the-art performance with the network searched using one dataset, which demonstrates the effectiveness and generalization of our searched models.
Previous feature alignment methods in Unsupervised domain adaptation(UDA) mostly only align global features without considering the mismatch between class-wise features. In this work, we propose a new coarse-to-fine feature alignment method using contrastive learning called CFContra. It draws class-wise features closer than coarse feature alignment or class-wise feature alignment only, therefore improves the models performance to a great extent. We build it upon one of the most effective methods of UDA called entropy minimization to further improve performance. In particular, to prevent excessive memory occupation when applying contrastive loss in semantic segmentation, we devise a new way to build and update the memory bank. In this way, we make the algorithm more efficient and viable with limited memory. Extensive experiments show the effectiveness of our method and model trained on the GTA5 to Cityscapes dataset has boost mIOU by 3.5 compared to the MinEnt algorithm. Our code will be publicly available.
Although deep neural networks have been a dominant method for many 2D vision tasks, it is still challenging to apply them to 3D tasks, such as medical image segmentation, due to the limited amount of annotated 3D data and limited computational resources. In this chapter, by rethinking the strategy to apply 3D Convolutional Neural Networks to segment medical images, we propose a novel 3D-based coarse-to-fine framework to efficiently tackle these challenges. The proposed 3D-based framework outperforms their 2D counterparts by a large margin since it can leverage the rich spatial information along all three axes. We further analyze the threat of adversarial attacks on the proposed framework and show how to defense against the attack. We conduct experiments on three datasets, the NIH pancreas dataset, the JHMI pancreas dataset and the JHMI pathological cyst dataset, where the first two and the last one contain healthy and pathological pancreases respectively, and achieve the current state-of-the-art in terms of Dice-Sorensen Coefficient (DSC) on all of them. Especially, on the NIH pancreas segmentation dataset, we outperform the previous best by an average of over $2%$, and the worst case is improved by $7%$ to reach almost $70%$, which indicates the reliability of our framework in clinical applications.