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Pictures of everyday life are inherently multi-label in nature. Hence, multi-label classification is commonly used to analyze their content. In typical multi-label datasets, each picture contains only a few positive labels, and many negative ones. This positive-negative imbalance can result in under-emphasizing gradients from positive labels during training, leading to poor accuracy. In this paper, we introduce a novel asymmetric loss ("ASL"), that operates differently on positive and negative samples. The loss dynamically down-weights the importance of easy negative samples, causing the optimization process to focus more on the positive samples, and also enables to discard mislabeled negative samples. We demonstrate how ASL leads to a more "balanced" network, with increased average probabilities for positive samples, and show how this balanced network is translated to better mAP scores, compared to commonly used losses. Furthermore, we offer a method that can dynamically adjust the level of asymmetry throughout the training. With ASL, we reach new state-of-the-art results on three common multi-label datasets, including achieving 86.6% on MS-COCO. We also demonstrate ASL applicability for other tasks such as fine-grain single-label classification and object detection. ASL is effective, easy to implement, and does not increase the training time or complexity. Implementation is available at: //github.com/Alibaba-MIIL/ASL.

In this paper, we aim to improve the performance of semantic image segmentation in a semi-supervised setting in which training is effectuated with a reduced set of annotated images and additional non-annotated images. We present a method based on an ensemble of deep segmentation models. Each model is trained on a subset of the annotated data, and uses the non-annotated images to exchange information with the other models, similar to co-training. Even if each model learns on the same non-annotated images, diversity is preserved with the use of adversarial samples. Our results show that this ability to simultaneously train models, which exchange knowledge while preserving diversity, leads to state-of-the-art results on two challenging medical image datasets.

Accurate segmentation of the prostate from magnetic resonance (MR) images provides useful information for prostate cancer diagnosis and treatment. However, automated prostate segmentation from 3D MR images still faces several challenges. For instance, a lack of clear edge between the prostate and other anatomical structures makes it challenging to accurately extract the boundaries. The complex background texture and large variation in size, shape and intensity distribution of the prostate itself make segmentation even further complicated. With deep learning, especially convolutional neural networks (CNNs), emerging as commonly used methods for medical image segmentation, the difficulty in obtaining large number of annotated medical images for training CNNs has become much more pronounced that ever before. Since large-scale dataset is one of the critical components for the success of deep learning, lack of sufficient training data makes it difficult to fully train complex CNNs. To tackle the above challenges, in this paper, we propose a boundary-weighted domain adaptive neural network (BOWDA-Net). To make the network more sensitive to the boundaries during segmentation, a boundary-weighted segmentation loss (BWL) is proposed. Furthermore, an advanced boundary-weighted transfer leaning approach is introduced to address the problem of small medical imaging datasets. We evaluate our proposed model on the publicly available MICCAI 2012 Prostate MR Image Segmentation (PROMISE12) challenge dataset. Our experimental results demonstrate that the proposed model is more sensitive to boundary information and outperformed other state-of-the-art methods.

Medical image segmentation is a primary task in many applications, and the accuracy of the segmentation is a necessity. Recently, many deep learning networks derived from U-Net have been extensively used and have achieved notable results. To further improve and refine the performance of U-Net, parallel decoders along with mask prediction decoder have been carried out and have shown significant improvement with additional advantages. In our work, we utilize the advantages of using a combination of contour and distance map as regularizers. In turn, we propose a novel architecture Psi-Net with a single encoder and three parallel decoders, one decoder to learn the mask and other two to learn the auxiliary tasks of contour detection and distance map estimation. The learning of these auxiliary tasks helps in capturing the shape and boundary. We also propose a new joint loss function for the proposed architecture. The loss function consists of a weighted combination of Negative likelihood and Mean Square Error loss. We have used two publicly available datasets: 1) Origa dataset for the task of optic cup and disc segmentation and 2) Endovis segment dataset for the task of polyp segmentation to evaluate our model. We have conducted extensive experiments using our network to show our model gives better results in terms of segmentation, boundary and shape metrics.

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.

Despite the state-of-the-art performance for medical image segmentation, deep convolutional neural networks (CNNs) have rarely provided uncertainty estimations regarding their segmentation outputs, e.g., model (epistemic) and image-based (aleatoric) uncertainties. In this work, we analyze these different types of uncertainties for CNN-based 2D and 3D medical image segmentation tasks. We additionally propose a test-time augmentation-based aleatoric uncertainty to analyze the effect of different transformations of the input image on the segmentation output. Test-time augmentation has been previously used to improve segmentation accuracy, yet not been formulated in a consistent mathematical framework. Hence, we also propose a theoretical formulation of test-time augmentation, where a distribution of the prediction is estimated by Monte Carlo simulation with prior distributions of parameters in an image acquisition model that involves image transformations and noise. We compare and combine our proposed aleatoric uncertainty with model uncertainty. Experiments with segmentation of fetal brains and brain tumors from 2D and 3D Magnetic Resonance Images (MRI) showed that 1) the test-time augmentation-based aleatoric uncertainty provides a better uncertainty estimation than calculating the test-time dropout-based model uncertainty alone and helps to reduce overconfident incorrect predictions, and 2) our test-time augmentation outperforms a single-prediction baseline and dropout-based multiple predictions.

Data augmentation has been widely used for training deep learning systems for medical image segmentation and plays an important role in obtaining robust and transformation-invariant predictions. However, it has seldom been used at test time for segmentation and not been formulated in a consistent mathematical framework. In this paper, we first propose a theoretical formulation of test-time augmentation for deep learning in image recognition, where the prediction is obtained through estimating its expectation by Monte Carlo simulation with prior distributions of parameters in an image acquisition model that involves image transformations and noise. We then propose a novel uncertainty estimation method based on the formulated test-time augmentation. Experiments with segmentation of fetal brains and brain tumors from 2D and 3D Magnetic Resonance Images (MRI) showed that 1) our test-time augmentation outperforms a single-prediction baseline and dropout-based multiple predictions, and 2) it provides a better uncertainty estimation than calculating the model-based uncertainty alone and helps to reduce overconfident incorrect predictions.

Fully convolutional deep neural networks have been asserted to be fast and precise frameworks with great potential in image segmentation. One of the major challenges in utilizing such networks raises when data is unbalanced, which is common in many medical imaging applications such as lesion segmentation where lesion class voxels are often much lower in numbers than non-lesion voxels. A trained network with unbalanced data may make predictions with high precision and low recall, being severely biased towards the non-lesion class which is particularly undesired in medical applications where false negatives are actually more important than false positives. Various methods have been proposed to address this problem including two step training, sample re-weighting, balanced sampling, and similarity loss functions. In this paper we developed a patch-wise 3D densely connected network with an asymmetric loss function, where we used large overlapping image patches for intrinsic and extrinsic data augmentation, a patch selection algorithm, and a patch prediction fusion strategy based on B-spline weighted soft voting to take into account the uncertainty of prediction in patch borders. We applied this method to lesion segmentation based on the MSSEG 2016 and ISBI 2015 challenges, where we achieved average Dice similarity coefficient of 69.9% and 65.74%, respectively. In addition to the proposed loss, we trained our network with focal and generalized Dice loss functions. Significant improvement in $F_1$ and $F_2$ scores and the APR curve was achieved in test using the asymmetric similarity loss layer and our 3D patch prediction fusion. The asymmetric similarity loss based on $F_\beta$ scores generalizes the Dice similarity coefficient and can be effectively used with the patch-wise strategy developed here to train fully convolutional deep neural networks for highly unbalanced image segmentation.

Convolutional networks (ConvNets) have achieved great successes in various challenging vision tasks. However, the performance of ConvNets would degrade when encountering the domain shift. The domain adaptation is more significant while challenging in the field of biomedical image analysis, where cross-modality data have largely different distributions. Given that annotating the medical data is especially expensive, the supervised transfer learning approaches are not quite optimal. In this paper, we propose an unsupervised domain adaptation framework with adversarial learning for cross-modality biomedical image segmentations. Specifically, our model is based on a dilated fully convolutional network for pixel-wise prediction. Moreover, we build a plug-and-play domain adaptation module (DAM) to map the target input to features which are aligned with source domain feature space. A domain critic module (DCM) is set up for discriminating the feature space of both domains. We optimize the DAM and DCM via an adversarial loss without using any target domain label. Our proposed method is validated by adapting a ConvNet trained with MRI images to unpaired CT data for cardiac structures segmentations, and achieved very promising results.

Image segmentation is the process of partitioning the image into significant regions easier to analyze. Nowadays, segmentation has become a necessity in many practical medical imaging methods as locating tumors and diseases. Hidden Markov Random Field model is one of several techniques used in image segmentation. It provides an elegant way to model the segmentation process. This modeling leads to the minimization of an objective function. Conjugate Gradient algorithm (CG) is one of the best known optimization techniques. This paper proposes the use of the Conjugate Gradient algorithm (CG) for image segmentation, based on the Hidden Markov Random Field. Since derivatives are not available for this expression, finite differences are used in the CG algorithm to approximate the first derivative. The approach is evaluated using a number of publicly available images, where ground truth is known. The Dice Coefficient is used as an objective criterion to measure the quality of segmentation. The results show that the proposed CG approach compares favorably with other variants of Hidden Markov Random Field segmentation algorithms.