Image segmentation is a fundamental problem in medical image analysis. In recent years, deep neural networks achieve impressive performances on many medical image segmentation tasks by supervised learning on large manually annotated data. However, expert annotations on big medical datasets are tedious, expensive or sometimes unavailable. Weakly supervised learning could reduce the effort for annotation but still required certain amounts of expertise. Recently, deep learning shows a potential to produce more accurate predictions than the original erroneous labels. Inspired by this, we introduce a very weakly supervised learning method, for cystic lesion detection and segmentation in lung CT images, without any manual annotation. Our method works in a self-learning manner, where segmentation generated in previous steps (first by unsupervised segmentation then by neural networks) is used as ground truth for the next level of network learning. Experiments on a cystic lung lesion dataset show that the deep learning could perform better than the initial unsupervised annotation, and progressively improve itself after self-learning.
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Applying artificial intelligence techniques in medical imaging is one of the most promising areas in medicine. However, most of the recent success in this area highly relies on large amounts of carefully annotated data, whereas annotating medical images is a costly process. In this paper, we propose a novel method, called FocalMix, which, to the best of our knowledge, is the first to leverage recent advances in semi-supervised learning (SSL) for 3D medical image detection. We conducted extensive experiments on two widely used datasets for lung nodule detection, LUNA16 and NLST. Results show that our proposed SSL methods can achieve a substantial improvement of up to 17.3% over state-of-the-art supervised learning approaches with 400 unlabeled CT scans.
In this work, we study the problem of training deep networks for semantic image segmentation using only a fraction of annotated images, which may significantly reduce human annotation efforts. Particularly, we propose a strategy that exploits the unpaired image style transfer capabilities of CycleGAN in semi-supervised segmentation. Unlike recent works using adversarial learning for semi-supervised segmentation, we enforce cycle consistency to learn a bidirectional mapping between unpaired images and segmentation masks. This adds an unsupervised regularization effect that boosts the segmentation performance when annotated data is limited. Experiments on three different public segmentation benchmarks (PASCAL VOC 2012, Cityscapes and ACDC) demonstrate the effectiveness of the proposed method. The proposed model achieves 2-4% of improvement with respect to the baseline and outperforms recent approaches for this task, particularly in low labeled data regime.
Biomedical image segmentation is an important task in many medical applications. Segmentation methods based on convolutional neural networks attain state-of-the-art accuracy; however, they typically rely on supervised training with large labeled datasets. Labeling datasets of medical images requires significant expertise and time, and is infeasible at large scales. To tackle the lack of labeled data, researchers use techniques such as hand-engineered preprocessing steps, hand-tuned architectures, and data augmentation. However, these techniques involve costly engineering efforts, and are typically dataset-specific. We present an automated data augmentation method for medical images. We demonstrate our method on the task of segmenting magnetic resonance imaging (MRI) brain scans, focusing on the one-shot segmentation scenario -- a practical challenge in many medical applications. Our method requires only a single segmented scan, and leverages other unlabeled scans in a semi-supervised approach. We learn a model of transforms from the images, and use the model along with the labeled example to synthesize additional labeled training examples for supervised segmentation. Each transform is comprised of a spatial deformation field and an intensity change, enabling the synthesis of complex effects such as variations in anatomy and image acquisition procedures. Augmenting the training of a supervised segmenter with these new examples provides significant improvements over state-of-the-art methods for one-shot biomedical image segmentation. Our code is available at //github.com/xamyzhao/brainstorm.
In recent years, object detection has experienced impressive progress. Despite these improvements, there is still a significant gap in the performance between the detection of small and large objects. We analyze the current state-of-the-art model, Mask-RCNN, on a challenging dataset, MS COCO. We show that the overlap between small ground-truth objects and the predicted anchors is much lower than the expected IoU threshold. We conjecture this is due to two factors; (1) only a few images are containing small objects, and (2) small objects do not appear enough even within each image containing them. We thus propose to oversample those images with small objects and augment each of those images by copy-pasting small objects many times. It allows us to trade off the quality of the detector on large objects with that on small objects. We evaluate different pasting augmentation strategies, and ultimately, we achieve 9.7\% relative improvement on the instance segmentation and 7.1\% on the object detection of small objects, compared to the current state of the art method on MS COCO.
3D image segmentation plays an important role in biomedical image analysis. Many 2D and 3D deep learning models have achieved state-of-the-art segmentation performance on 3D biomedical image datasets. Yet, 2D and 3D models have their own strengths and weaknesses, and by unifying them together, one may be able to achieve more accurate results. In this paper, we propose a new ensemble learning framework for 3D biomedical image segmentation that combines the merits of 2D and 3D models. First, we develop a fully convolutional network based meta-learner to learn how to improve the results from 2D and 3D models (base-learners). Then, to minimize over-fitting for our sophisticated meta-learner, we devise a new training method that uses the results of the base-learners as multiple versions of "ground truths". Furthermore, since our new meta-learner training scheme does not depend on manual annotation, it can utilize abundant unlabeled 3D image data to further improve the model. Extensive experiments on two public datasets (the HVSMR 2016 Challenge dataset and the mouse piriform cortex dataset) show that our approach is effective under fully-supervised, semi-supervised, and transductive settings, and attains superior performance over state-of-the-art image segmentation methods.
We propose a method for the weakly supervised detection of objects in paintings. At training time, only image-level annotations are needed. This, combined with the efficiency of our multiple-instance learning method, enables one to learn new classes on-the-fly from globally annotated databases, avoiding the tedious task of manually marking objects. We show on several databases that dropping the instance-level annotations only yields mild performance losses. We also introduce a new database, IconArt, on which we perform detection experiments on classes that could not be learned on photographs, such as Jesus Child or Saint Sebastian. To the best of our knowledge, these are the first experiments dealing with the automatic (and in our case weakly supervised) detection of iconographic elements in paintings. We believe that such a method is of great benefit for helping art historians to explore large digital databases.
Deep learning based object detectors require thousands of diversified bounding box and class annotated examples. Though image object detectors have shown rapid progress in recent years with the release of multiple large-scale static image datasets, object detection on videos still remains an open problem due to scarcity of annotated video frames. Having a robust video object detector is an essential component for video understanding and curating large-scale automated annotations in videos. Domain difference between images and videos makes the transferability of image object detectors to videos sub-optimal. The most common solution is to use weakly supervised annotations where a video frame has to be tagged for presence/absence of object categories. This still takes up manual effort. In this paper we take a step forward by adapting the concept of unsupervised adversarial image-to-image translation to perturb static high quality images to be visually indistinguishable from a set of video frames. We assume the presence of a fully annotated static image dataset and an unannotated video dataset. Object detector is trained on adversarially transformed image dataset using the annotations of the original dataset. Experiments on Youtube-Objects and Youtube-Objects-Subset datasets with two contemporary baseline object detectors reveal that such unsupervised pixel level domain adaptation boosts the generalization performance on video frames compared to direct application of original image object detector. Also, we achieve competitive performance compared to recent baselines of weakly supervised methods. This paper can be seen as an application of image translation for cross domain object detection.
Weakly-supervised semantic segmentation under image tags supervision is a challenging task as it directly associates high-level semantic to low-level appearance. To bridge this gap, in this paper, we propose an iterative bottom-up and top-down framework which alternatively expands object regions and optimizes segmentation network. We start from initial localization produced by classification networks. While classification networks are only responsive to small and coarse discriminative object regions, we argue that, these regions contain significant common features about objects. So in the bottom-up step, we mine common object features from the initial localization and expand object regions with the mined features. To supplement non-discriminative regions, saliency maps are then considered under Bayesian framework to refine the object regions. Then in the top-down step, the refined object regions are used as supervision to train the segmentation network and to predict object masks. These object masks provide more accurate localization and contain more regions of object. Further, we take these object masks as initial localization and mine common object features from them. These processes are conducted iteratively to progressively produce fine object masks and optimize segmentation networks. Experimental results on Pascal VOC 2012 dataset demonstrate that the proposed method outperforms previous state-of-the-art methods by a large margin.
In recent years, deep learning (DL) methods have become powerful tools for biomedical image segmentation. However, high annotation efforts and costs are commonly needed to acquire sufficient biomedical training data for DL models. To alleviate the burden of manual annotation, in this paper, we propose a new weakly supervised DL approach for biomedical image segmentation using boxes only annotation. First, we develop a method to combine graph search (GS) and DL to generate fine object masks from box annotation, in which DL uses box annotation to compute a rough segmentation for GS and then GS is applied to locate the optimal object boundaries. During the mask generation process, we carefully utilize information from box annotation to filter out potential errors, and then use the generated masks to train an accurate DL segmentation network. Extensive experiments on gland segmentation in histology images, lymph node segmentation in ultrasound images, and fungus segmentation in electron microscopy images show that our approach attains superior performance over the best known state-of-the-art weakly supervised DL method and is able to achieve (1) nearly the same accuracy compared to fully supervised DL methods with far less annotation effort, (2) significantly better results with similar annotation time, and (3) robust performance in various applications.
In a weakly-supervised scenario object detectors need to be trained using image-level annotation alone. Since bounding-box-level ground truth is not available, most of the solutions proposed so far are based on an iterative, Multiple Instance Learning framework in which the current classifier is used to select the highest-confidence boxes in each image, which are treated as pseudo-ground truth in the next training iteration. However, the errors of an immature classifier can make the process drift, usually introducing many of false positives in the training dataset. To alleviate this problem, we propose in this paper a training protocol based on the self-paced learning paradigm. The main idea is to iteratively select a subset of images and boxes that are the most reliable, and use them for training. While in the past few years similar strategies have been adopted for SVMs and other classifiers, we are the first showing that a self-paced approach can be used with deep-network-based classifiers in an end-to-end training pipeline. The method we propose is built on the fully-supervised Fast-RCNN architecture and can be applied to similar architectures which represent the input image as a bag of boxes. We show state-of-the-art results on Pascal VOC 2007, Pascal VOC 2010 and ILSVRC 2013. On ILSVRC 2013 our results based on a low-capacity AlexNet network outperform even those weakly-supervised approaches which are based on much higher-capacity networks.
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