TAN: Temporal Affine Network for Real-Time Left Ventricle Anatomical Structure Analysis Based on 2D Ultrasound Videos

With superiorities on low cost, portability, and free of radiation, echocardiogram is a widely used imaging modality for left ventricle (LV) function quantification. However, automatic LV segmentation and motion tracking is still a challenging task. In addition to fuzzy border definition, low contrast, and abounding artifacts on typical ultrasound images, the shape and size of the LV change significantly in a cardiac cycle. In this work, we propose a temporal affine network (TAN) to perform image analysis in a warped image space, where the shape and size variations due to the cardiac motion as well as other artifacts are largely compensated. Furthermore, we perform three frequent echocardiogram interpretation tasks simultaneously: standard cardiac plane recognition, LV landmark detection, and LV segmentation. Instead of using three networks with one dedicating to each task, we use a multi-task network to perform three tasks simultaneously. Since three tasks share the same encoder, the compact network improves the segmentation accuracy with more supervision. The network is further finetuned with optical flow adjusted annotations to enhance motion coherence in the segmentation result. Experiments on 1,714 2D echocardiographic sequences demonstrate that the proposed method achieves state-of-the-art segmentation accuracy with real-time efficiency

Med3D: Transfer Learning for 3D Medical Image Analysis

The performance on deep learning is significantly affected by volume of training data. Models pre-trained from massive dataset such as ImageNet become a powerful weapon for speeding up training convergence and improving accuracy. Similarly, models based on large dataset are important for the development of deep learning in 3D medical images. However, it is extremely challenging to build a sufficiently large dataset due to difficulty of data acquisition and annotation in 3D medical imaging. We aggregate the dataset from several medical challenges to build 3DSeg-8 dataset with diverse modalities, target organs, and pathologies. To extract general medical three-dimension (3D) features, we design a heterogeneous 3D network called Med3D to co-train multi-domain 3DSeg-8 so as to make a series of pre-trained models. We transfer Med3D pre-trained models to lung segmentation in LIDC dataset, pulmonary nodule classification in LIDC dataset and liver segmentation on LiTS challenge. Experiments show that the Med3D can accelerate the training convergence speed of target 3D medical tasks 2 times compared with model pre-trained on Kinetics dataset, and 10 times compared with training from scratch as well as improve accuracy ranging from 3% to 20%. Transferring our Med3D model on state-the-of-art DenseASPP segmentation network, in case of single model, we achieve 94.6\% Dice coefficient which approaches the result of top-ranged algorithms on the LiTS challenge

A GLCM Embedded CNN Strategy for Computer-aided Diagnosis in Intracerebral Hemorrhage

Computer-aided diagnosis (CADx) systems have been shown to assist radiologists by providing classifications of all kinds of medical images like Computed tomography (CT) and Magnetic resonance (MR). Currently, convolutional neural networks play an important role in CADx. However, since CNN model should have a square-like input, it is usually difficult to directly apply the CNN algorithms on the irregular segmentation region of interests (ROIs) where the radiologists are interested in. In this paper, we propose a new approach to construct the model by extracting and converting the information of the irregular region into a fixed-size Gray-Level Co-Occurrence Matrix (GLCM) and then utilize the GLCM as one input of our CNN model. In this way, as an useful implementary to the original CNN, a couple of GLCM-based features are also extracted by CNN. Meanwhile, the network will pay more attention to the important lesion area and achieve a higher accuracy in classification. Experiments are performed on three classification databases: Hemorrhage, BraTS18 and Cervix to validate the universality of our innovative model. In conclusion, the proposed framework outperforms the corresponding state-of-art algorithms on each database with both test losses and classification accuracy as the evaluation criteria

When Semi-Supervised Learning Meets Transfer Learning: Training Strategies, Models and Datasets

Semi-Supervised Learning (SSL) has been proved to be an effective way to leverage both labeled and unlabeled data at the same time. Recent semi-supervised approaches focus on deep neural networks and have achieved promising results on several benchmarks: CIFAR10, CIFAR100 and SVHN. However, most of their experiments are based on models trained from scratch instead of pre-trained models. On the other hand, transfer learning has demonstrated its value when the target domain has limited labeled data. Here comes the intuitive question: is it possible to incorporate SSL when fine-tuning a pre-trained model? We comprehensively study how SSL methods starting from pretrained models perform under varying conditions, including training strategies, architecture choice and datasets. From this study, we obtain several interesting and useful observations. While practitioners have had an intuitive understanding of these observations, we do a comprehensive emperical analysis and demonstrate that: (1) the gains from SSL techniques over a fully-supervised baseline are smaller when trained from a pre-trained model than when trained from random initialization, (2) when the domain of the source data used to train the pre-trained model differs significantly from the domain of the target task, the gains from SSL are significantly higher and (3) some SSL methods are able to advance fully-supervised baselines (like Pseudo-Label). We hope our studies can deepen the understanding of SSL research and facilitate the process of developing more effective SSL methods to utilize pre-trained models. Code is now available at github.Comment: Technical repor

Learning Crisp Edge Detector Using Logical Refinement Network

Edge detection is a fundamental problem in different computer vision tasks. Recently, edge detection algorithms achieve satisfying improvement built upon deep learning. Although most of them report favorable evaluation scores, they often fail to accurately localize edges and give thick and blurry boundaries. In addition, most of them focus on 2D images and the challenging 3D edge detection is still under-explored. In this work, we propose a novel logical refinement network for crisp edge detection, which is motivated by the logical relationship between segmentation and edge maps and can be applied to both 2D and 3D images. The network consists of a joint object and edge detection network and a crisp edge refinement network, which predicts more accurate, clearer and thinner high quality binary edge maps without any post-processing. Extensive experiments are conducted on the 2D nuclei images from Kaggle 2018 Data Science Bowl and a private 3D microscopy images of a monkey brain, which show outstanding performance compared with state-of-the-art methods.Comment: Accepted by MICCAI202

X2CT-GAN: Reconstructing CT from Biplanar X-Rays with Generative Adversarial Networks

Computed tomography (CT) can provide a 3D view of the patient's internal organs, facilitating disease diagnosis, but it incurs more radiation dose to a patient and a CT scanner is much more cost prohibitive than an X-ray machine too. Traditional CT reconstruction methods require hundreds of X-ray projections through a full rotational scan of the body, which cannot be performed on a typical X-ray machine. In this work, we propose to reconstruct CT from two orthogonal X-rays using the generative adversarial network (GAN) framework. A specially designed generator network is exploited to increase data dimension from 2D (X-rays) to 3D (CT), which is not addressed in previous research of GAN. A novel feature fusion method is proposed to combine information from two X-rays.The mean squared error (MSE) loss and adversarial loss are combined to train the generator, resulting in a high-quality CT volume both visually and quantitatively. Extensive experiments on a publicly available chest CT dataset demonstrate the effectiveness of the proposed method. It could be a nice enhancement of a low-cost X-ray machine to provide physicians a CT-like 3D volume in several niche applications

Distractor-Aware Neuron Intrinsic Learning for Generic 2D Medical Image Classifications

Medical image analysis benefits Computer Aided Diagnosis (CADx). A fundamental analyzing approach is the classification of medical images, which serves for skin lesion diagnosis, diabetic retinopathy grading, and cancer classification on histological images. When learning these discriminative classifiers, we observe that the convolutional neural networks (CNNs) are vulnerable to distractor interference. This is due to the similar sample appearances from different categories (i.e., small inter-class distance). Existing attempts select distractors from input images by empirically estimating their potential effects to the classifier. The essences of how these distractors affect CNN classification are not known. In this paper, we explore distractors from the CNN feature space via proposing a neuron intrinsic learning method. We formulate a novel distractor-aware loss that encourages large distance between the original image and its distractor in the feature space. The novel loss is combined with the original classification loss to update network parameters by back-propagation. Neuron intrinsic learning first explores distractors crucial to the deep classifier and then uses them to robustify CNN inherently. Extensive experiments on medical image benchmark datasets indicate that the proposed method performs favorably against the state-of-the-art approaches.Comment: MICCAI202

A Fully-Automated Pipeline for Detection and Segmentation of Liver Lesions and Pathological Lymph Nodes

We propose a fully-automated method for accurate and robust detection and segmentation of potentially cancerous lesions found in the liver and in lymph nodes. The process is performed in three steps, including organ detection, lesion detection and lesion segmentation. Our method applies machine learning techniques such as marginal space learning and convolutional neural networks, as well as active contour models. The method proves to be robust in its handling of extremely high lesion diversity. We tested our method on volumetric computed tomography (CT) images, including 42 volumes containing liver lesions and 86 volumes containing 595 pathological lymph nodes. Preliminary results under 10-fold cross validation show that for both the liver lesions and the lymph nodes, a total detection sensitivity of 0.53 and average Dice score of $0.71 \pm 0.15$ for segmentation were obtained.Comment: Workshop on Machine Learning in Healthcare, Neural Information Processing Systems (NIPS). Barcelona, Spain, 201

Iterative Multi-domain Regularized Deep Learning for Anatomical Structure Detection and Segmentation from Ultrasound Images

Accurate detection and segmentation of anatomical structures from ultrasound images are crucial for clinical diagnosis and biometric measurements. Although ultrasound imaging has been widely used with superiorities such as low cost and portability, the fuzzy border definition and existence of abounding artifacts pose great challenges for automatically detecting and segmenting the complex anatomical structures. In this paper, we propose a multi-domain regularized deep learning method to address this challenging problem. By leveraging the transfer learning from cross domains, the feature representations are effectively enhanced. The results are further improved by the iterative refinement. Moreover, our method is quite efficient by taking advantage of a fully convolutional network, which is formulated as an end-to-end learning framework of detection and segmentation. Extensive experimental results on a large-scale database corroborated that our method achieved a superior detection and segmentation accuracy, outperforming other methods by a significant margin and demonstrating competitive capability even compared to human performance.Comment: MICCAI 201

Pyramid Network with Online Hard Example Mining for Accurate Left Atrium Segmentation

Accurately segmenting left atrium in MR volume can benefit the ablation procedure of atrial fibrillation. Traditional automated solutions often fail in relieving experts from the labor-intensive manual labeling. In this paper, we propose a deep neural network based solution for automated left atrium segmentation in gadolinium-enhanced MR volumes with promising performance. We firstly argue that, for this volumetric segmentation task, networks in 2D fashion can present great superiorities in time efficiency and segmentation accuracy than networks with 3D fashion. Considering the highly varying shape of atrium and the branchy structure of associated pulmonary veins, we propose to adopt a pyramid module to collect semantic cues in feature maps from multiple scales for fine-grained segmentation. Also, to promote our network in classifying the hard examples, we propose an Online Hard Negative Example Mining strategy to identify voxels in slices with low classification certainties and penalize the wrong predictions on them. Finally, we devise a competitive training scheme to further boost the generalization ability of networks. Extensively verified on 20 testing volumes, our proposed framework achieves an average Dice of 92.83% in segmenting the left atria and pulmonary veins.Comment: 9 pages, 4 figures. MICCAI Workshop on STACOM 201