Despite its broad availability, volumetric information acquisition from Bright-Field Microscopy (BFM) is inherently difficult due to the projective nature of the acquisition process. We investigate the prediction of 3D cell instances from a set of BFM Z-Stack images. We propose a novel two-stage weakly supervised method for volumetric instance segmentation of cells which only requires approximate cell centroids annotation. Created pseudo-labels are thereby refined with a novel refinement loss with Z-stack guidance. The evaluations show that our approach can generalize not only to BFM Z-Stack data, but to other 3D cell imaging modalities. A comparison of our pipeline against fully supervised methods indicates that the significant gain in reduced data collection and labelling results in minor performance difference.
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Self-supervised, category-agnostic segmentation of real-world images is a challenging open problem in computer vision. Here, we show how to learn static grouping priors from motion self-supervision by building on the cognitive science concept of a Spelke Object: a set of physical stuff that moves together. We introduce the Excitatory-Inhibitory Segment Extraction Network (EISEN), which learns to extract pairwise affinity graphs for static scenes from motion-based training signals. EISEN then produces segments from affinities using a novel graph propagation and competition network. During training, objects that undergo correlated motion (such as robot arms and the objects they move) are decoupled by a bootstrapping process: EISEN explains away the motion of objects it has already learned to segment. We show that EISEN achieves a substantial improvement in the state of the art for self-supervised image segmentation on challenging synthetic and real-world robotics datasets.
Feature-based self-explanatory methods explain their classification in terms of human-understandable features. In the medical imaging community, this semantic matching of clinical knowledge adds significantly to the trustworthiness of the AI. However, the cost of additional annotation of features remains a pressing issue. We address this problem by proposing cRedAnno, a data-/annotation-efficient self-explanatory approach for lung nodule diagnosis. cRedAnno considerably reduces the annotation need by introducing self-supervised contrastive learning to alleviate the burden of learning most parameters from annotation, replacing end-to-end training with two-stage training. When training with hundreds of nodule samples and only 1% of their annotations, cRedAnno achieves competitive accuracy in predicting malignancy, meanwhile significantly surpassing most previous works in predicting nodule attributes. Visualisation of the learned space further indicates that the correlation between the clustering of malignancy and nodule attributes coincides with clinical knowledge. Our complete code is open-source available: //github.com/diku-dk/credanno.
While there have been increased researches using deep learning techniques for the extraction of vascular structure from the 2D en face OCTA, for such approach, it is known that the data annotation process on the curvilinear structure like the retinal vasculature is very costly and time consuming, albeit few tried to address the annotation problem. In this work, we propose the application of the scribble-base weakly-supervised learning method to automate the pixel-level annotation. The proposed method, called OCTAve, combines the weakly-supervised learning using scribble-annotated ground truth augmented with an adversarial and a novel self-supervised deep supervision. Our novel mechanism is designed to utilize the discriminative outputs from the discrimination layer of a UNet-like architecture where the Kullback-Liebler Divergence between the aggregate discriminative outputs and the segmentation map predicate is minimized during the training. This combined method leads to the better localization of the vascular structure as shown in our experiments. We validate our proposed method on the large public datasets i.e., ROSE, OCTA-500. The segmentation performance is compared against both state-of-the-art fully-supervised and scribble-based weakly-supervised approaches. The implementation of our work used in the experiments is located at [LINK].
Object detectors trained with weak annotations are affordable alternatives to fully-supervised counterparts. However, there is still a significant performance gap between them. We propose to narrow this gap by fine-tuning a base pre-trained weakly-supervised detector with a few fully-annotated samples automatically selected from the training set using ``box-in-box'' (BiB), a novel active learning strategy designed specifically to address the well-documented failure modes of weakly-supervised detectors. Experiments on the VOC07 and COCO benchmarks show that BiB outperforms other active learning techniques and significantly improves the base weakly-supervised detector's performance with only a few fully-annotated images per class. BiB reaches 97% of the performance of fully-supervised Fast RCNN with only 10% of fully-annotated images on VOC07. On COCO, using on average 10 fully-annotated images per class, or equivalently 1% of the training set, BiB also reduces the performance gap (in AP) between the weakly-supervised detector and the fully-supervised Fast RCNN by over 70%, showing a good trade-off between performance and data efficiency. Our code is publicly available at //github.com/huyvvo/BiB.
In recent years, video instance segmentation (VIS) has been largely advanced by offline models, while online models gradually attracted less attention possibly due to their inferior performance. However, online methods have their inherent advantage in handling long video sequences and ongoing videos while offline models fail due to the limit of computational resources. Therefore, it would be highly desirable if online models can achieve comparable or even better performance than offline models. By dissecting current online models and offline models, we demonstrate that the main cause of the performance gap is the error-prone association between frames caused by the similar appearance among different instances in the feature space. Observing this, we propose an online framework based on contrastive learning that is able to learn more discriminative instance embeddings for association and fully exploit history information for stability. Despite its simplicity, our method outperforms all online and offline methods on three benchmarks. Specifically, we achieve 49.5 AP on YouTube-VIS 2019, a significant improvement of 13.2 AP and 2.1 AP over the prior online and offline art, respectively. Moreover, we achieve 30.2 AP on OVIS, a more challenging dataset with significant crowding and occlusions, surpassing the prior art by 14.8 AP. The proposed method won first place in the video instance segmentation track of the 4th Large-scale Video Object Segmentation Challenge (CVPR2022). We hope the simplicity and effectiveness of our method, as well as our insight into current methods, could shed light on the exploration of VIS models.
A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.
Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.
Medical image segmentation requires consensus ground truth segmentations to be derived from multiple expert annotations. A novel approach is proposed that obtains consensus segmentations from experts using graph cuts (GC) and semi supervised learning (SSL). Popular approaches use iterative Expectation Maximization (EM) to estimate the final annotation and quantify annotator's performance. Such techniques pose the risk of getting trapped in local minima. We propose a self consistency (SC) score to quantify annotator consistency using low level image features. SSL is used to predict missing annotations by considering global features and local image consistency. The SC score also serves as the penalty cost in a second order Markov random field (MRF) cost function optimized using graph cuts to derive the final consensus label. Graph cut obtains a global maximum without an iterative procedure. Experimental results on synthetic images, real data of Crohn's disease patients and retinal images show our final segmentation to be accurate and more consistent than competing methods.
We introduce a generic framework that reduces the computational cost of object detection while retaining accuracy for scenarios where objects with varied sizes appear in high resolution images. Detection progresses in a coarse-to-fine manner, first on a down-sampled version of the image and then on a sequence of higher resolution regions identified as likely to improve the detection accuracy. Built upon reinforcement learning, our approach consists of a model (R-net) that uses coarse detection results to predict the potential accuracy gain for analyzing a region at a higher resolution and another model (Q-net) that sequentially selects regions to zoom in. Experiments on the Caltech Pedestrians dataset show that our approach reduces the number of processed pixels by over 50% without a drop in detection accuracy. The merits of our approach become more significant on a high resolution test set collected from YFCC100M dataset, where our approach maintains high detection performance while reducing the number of processed pixels by about 70% and the detection time by over 50%.
We consider the task of weakly supervised one-shot detection. In this task, we attempt to perform a detection task over a set of unseen classes, when training only using weak binary labels that indicate the existence of a class instance in a given example. The model is conditioned on a single exemplar of an unseen class and a target example that may or may not contain an instance of the same class as the exemplar. A similarity map is computed by using a Siamese neural network to map the exemplar and regions of the target example to a latent representation space and then computing cosine similarity scores between representations. An attention mechanism weights different regions in the target example, and enables learning of the one-shot detection task using the weaker labels alone. The model can be applied to detection tasks from different domains, including computer vision object detection. We evaluate our attention Siamese networks on a one-shot detection task from the audio domain, where it detects audio keywords in spoken utterances. Our model considerably outperforms a baseline approach and yields a 42.6% average precision for detection across 10 unseen classes. Moreover, architectural developments from computer vision object detection models such as a region proposal network can be incorporated into the model architecture, and results show that performance is expected to improve by doing so.
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