We present a novel method to explicitly incorporate topological prior knowledge into deep learning based segmentation, which is, to our knowledge, the first work to do so. Our method uses the concept of persistent homology, a tool from topological data analysis, to capture high-level topological characteristics of segmentation results in a way which is differentiable with respect to the pixelwise probability of being assigned to a given class. The topological prior knowledge consists of the sequence of desired Betti numbers of the segmentation. As a proof-of-concept we demonstrate our approach by applying it to the problem of left-ventricle segmentation of cardiac MR images of 500 subjects from the UK Biobank dataset, where we show that it improves segmentation performance in terms of topological correctness without sacrificing pixelwise accuracy.
Other approaches have involved encouraging the correct adjacencies of various object classes, whether they were learned from the data as in @cite_15 or provided as a prior as in @cite_0 . Such methods allow the introduction of this simple topological feature into a loss function when performing image segmentation but cannot be easily generalised to any other kinds of higher-order feature such as the presence of holes, handles or voids.
@cite_0 @cite_15
2889890911 2296226447
Semantic instance segmentation remains a challenging task. In this work we propose to tackle the problem with a discriminative loss function, operating at the pixel level, that encourages a convolutional network to produce a representation of the image that can easily be clustered into instances with a simple post-processing step. The loss function encourages the network to map each pixel to a point in feature space so that pixels belonging to the same instance lie close together while different instances are separated by a wide margin. Our approach of combining an off-the-shelf network with a principled loss function inspired by a metric learning objective is conceptually simple and distinct from recent efforts in instance segmentation. In contrast to previous works, our method does not rely on object proposals or recurrent mechanisms. A key contribution of our work is to demonstrate that such a simple setup without bells and whistles is effective and can perform on par with more complex methods. Moreover, we show that it does not suffer from some of the limitations of the popular detect-and-segment approaches. We achieve competitive performance on the Cityscapes and CVPPP leaf segmentation benchmarks. We provide a short introduction to the field of topological data analysis and discuss its possible relevance for the study of complex systems. Topological data analysis provides a set of tools to characterise the shape of data, in terms of the presence of holes or cavities between the points. The methods, based on notion of simplicial complexes, generalise standard network tools by naturally allowing for many-body interactions and providing results robust under continuous deformations of the data. We present strengths and weaknesses of current methods, as well as a range of empirical studies relevant to the field of complex systems, before identifying future methodological challenges to help understand the emergence of collective phenomena. A citing sentence is one that appears in a scientific article and cites previous work. Citing sentences have been studied and used in many applications. For example, they have been used in scientific paper summarization, automatic survey generation, paraphrase identification, and citation function classification. Citing sentences that cite multiple papers are common in scientific writing. This observation should be taken into consideration when using citing sentences in applications. For instance, when a citing sentence is used in a summary of a scientific paper, only the fragments of the sentence that are relevant to the summarized paper should be included in the summary. In this paper, we present and compare three different approaches for identifying the fragments of a citing sentence that are related to a given target reference. Our methods are: word classification, sequence labeling, and segment classification. Our experiments show that segment classification achieves the best results. In this paper, we propose a novel Weakly-Supervised Dual Clustering (WSDC) approach for image semantic segmentation with image-level labels, i.e., collaboratively performing image segmentation and tag alignment with those regions. The proposed approach is motivated from the observation that super pixels belonging to an object class usually exist across multiple images and hence can be gathered via the idea of clustering. In WSDC, spectral clustering is adopted to cluster the super pixels obtained from a set of over-segmented images. At the same time, a linear transformation between features and labels as a kind of discriminative clustering is learned to select the discriminative features among different classes. The both clustering outputs should be consistent as much as possible. Besides, weakly-supervised constraints from image-level labels are imposed to restrict the labeling of super pixels. Finally, the non-convex and non-smooth objective function are efficiently optimized using an iterative CCCP procedure. Extensive experiments conducted on MSRC and Label Me datasets demonstrate the encouraging performance of our method in comparison with some state-of-the-arts. Video sequences contain many cues that may be used to segment objects in them, such as color, gradient, color adjacency, shape, temporal coherence, camera and object motion, and easily-trackable points. This paper introduces LIVEcut, a novel method for interactively selecting objects in video sequences by extracting and leveraging as much of this information as possible. Using a graph-cut optimization framework, LIVEcut propagates the selection forward frame by frame, allowing the user to correct any mistakes along the way if needed. Enhanced methods of extracting many of the features are provided. In order to use the most accurate information from the various potentially-conflicting features, each feature is automatically weighted locally based on its estimated accuracy using the previous implicitly-validated frame. Feature weights are further updated by learning from the user corrections required in the previous frame. The effectiveness of LIVEcut is shown through timing comparisons to other interactive methods, accuracy comparisons to unsupervised methods, and qualitatively through selections on various video sequences. Segmentation involves separating an object from the background in a given image. The use of image information alone often leads to poor segmentation results due to the presence of noise, clutter or occlusion. The introduction of shape priors in the geometric active contour (GAC) framework has proved to be an effective way to ameliorate some of these problems. In this work, we propose a novel segmentation method combining image information with prior shape knowledge, using level-sets. Following the work of , we propose to revisit the use of PCA to introduce prior knowledge about shapes in a more robust manner. We utilize kernel PCA (KPCA) and show that this method outperforms linear PCA by allowing only those shapes that are close enough to the training data. In our segmentation framework, shape knowledge and image information are encoded into two energy functionals entirely described in terms of shapes. This consistent description permits to fully take advantage of the Kernel PCA methodology and leads to promising segmentation results. In particular, our shape-driven segmentation technique allows for the simultaneous encoding of multiple types of shapes, and offers a convincing level of robustness with respect to noise, occlusions, or smearing. We propose a generic and efficient learning framework that is applicable to segment images in which individual objects are mainly discernible by boundary cues. Our approach starts by first hierarchically clustering the image and then explaining the image in terms of a cost-minimal subset of non-overlapping segments. The cost of a segmentation is defined as a weighted sum of features of the selected candidates. This formulation allows us to take into account an extensible set of arbitrary features. The maximally discriminative linear combination of features is learned from training data using a margin-rescaled structured SVM. At the core of our formulation is a novel and simple topology-based structured loss which is a combination of counts and geodesic distance of topological errors (splits, merges, false positives and false negatives) relative to the training set. We demonstrate the generality and accuracy of our approach on three challenging 2D cell segmentation problems, where we improve accuracy compared to the current state of the art. Persistent homology is a mathematical tool from topological data analysis. It performs multi-scale analysis on a set of points and identifies clusters, holes, and voids therein. These latter topological structures complement standard feature representations, making persistent homology an attractive feature extractor for artificial intelligence. Research on persistent homology for AI is in its infancy, and is currently hindered by two issues: the lack of an accessible introduction to AI researchers, and the paucity of applications. In response, the first part of this paper presents a tutorial on persistent homology specifically aimed at a broader audience without sacrificing mathematical rigor. The second part contains one of the first applications of persistent homology to natural language processing. Specifically, our Similarity Filtration with Time Skeleton (SIFTS) algorithm identifies holes that can be interpreted as semantic "tie-backs" in a text document, providing a new document structure representation. We illustrate our algorithm on documents ranging from nursery rhymes to novels, and on a corpus with child and adolescent writings. In this paper we are interested in how semantic segmentation can help object detection. Towards this goal, we propose a novel deformable part-based model which exploits region-based segmentation algorithms that compute candidate object regions by bottom-up clustering followed by ranking of those regions. Our approach allows every detection hypothesis to select a segment (including void), and scores each box in the image using both the traditional HOG filters as well as a set of novel segmentation features. Thus our model blends'' between the detector and segmentation models. Since our features can be computed very efficiently given the segments, we maintain the same complexity as the original DPM. We demonstrate the effectiveness of our approach in PASCAL VOC 2010, and show that when employing only a root filter our approach outperforms Dalal & Triggs detector on all classes, achieving 13 higher average AP. When employing the parts, we outperform the original DPM in @math out of @math classes, achieving an improvement of 8 AP. Furthermore, we outperform the previous state-of-the-art on VOC 2010 test by 4 . We present a method combining affinity prediction with region agglomeration, which improves significantly upon the state of the art of neuron segmentation from electron microscopy (EM) in accuracy and scalability. Our method consists of a 3D U-Net, trained to predict affinities between voxels, followed by iterative region agglomeration. We train using a structured loss based on Malis, encouraging topologically correct segmentations obtained from affinity thresholding. Our extension consists of two parts: First, we present a quasi-linear method to compute the loss gradient, improving over the original quadratic algorithm. Second, we compute the gradient in two separate passes to avoid spurious gradient contributions in early training stages. Our predictions are accurate enough that simple learning-free percentile-based agglomeration outperforms more involved methods used earlier on inferior predictions. We present results on three diverse EM datasets, achieving relative improvements over previous results of 27, 15, and 250 percent. Our findings suggest that a single method can be applied to both nearly isotropic block-face EM data and anisotropic serial sectioned EM data. The runtime of our method scales linearly with the size of the volume and achieves a throughput of @math ∼ 2.6 seconds per megavoxel, qualifying our method for the processing of very large datasets. A key ingredient in the design of visual object classification systems is the identification of relevant class specific aspects while being robust to intra-class variations. While this is a necessity in order to generalize beyond a given set of training images, it is also a very difficult problem due to the high variability of visual appearance within each class. In the last years substantial performance gains on challenging benchmark datasets have been reported in the literature. This progress can be attributed to two developments: the design of highly discriminative and robust image features and the combination of multiple complementary features based on different aspects such as shape, color or texture. In this paper we study several models that aim at learning the correct weighting of different features from training data. These include multiple kernel learning as well as simple baseline methods. Furthermore we derive ensemble methods inspired by Boosting which are easily extendable to several multiclass setting. All methods are thoroughly evaluated on object classification datasets using a multitude of feature descriptors. The key results are that even very simple baseline methods, that are orders of magnitude faster than learning techniques are highly competitive with multiple kernel learning. Furthermore the Boosting type methods are found to produce consistently better results in all experiments. We provide insight of when combination methods can be expected to work and how the benefit of complementary features can be exploited most efficiently. In contrast to the widely studied problem of recognizing an action given a complete sequence, action anticipation aims to identify the action from only partially available videos. As such, it is therefore key to the success of computer vision applications requiring to react as early as possible, such as autonomous navigation. In this paper, we propose a new action anticipation method that achieves high prediction accuracy even in the presence of a very small percentage of a video sequence. To this end, we develop a multi-stage LSTM architecture that leverages context-aware and action-aware features, and introduce a novel loss function that encourages the model to predict the correct class as early as possible. Our experiments on standard benchmark datasets evidence the benefits of our approach; We outperform the state-of-the-art action anticipation methods for early prediction by a relative increase in accuracy of 22.0 on JHMDB-21, 14.0 on UT-Interaction and 49.9 on UCF-101. The Dice score is widely used for binary segmentation due to its robustness to class imbalance. Soft generalisations of the Dice score allow it to be used as a loss function for training convolutional neural networks (CNN). Although CNNs trained using mean-class Dice score achieve state-of-the-art results on multi-class segmentation, this loss function does neither take advantage of inter-class relationships nor multi-scale information. We argue that an improved loss function should balance misclassifications to favour predictions that are semantically meaningful. This paper investigates these issues in the context of multi-class brain tumour segmentation. Our contribution is threefold. (1) We propose a semantically-informed generalisation of the Dice score for multi-class segmentation based on the Wasserstein distance on the probabilistic label space. (2) We propose a holistic CNN that embeds spatial information at multiple scales with deep supervision. (3) We show that the joint use of holistic CNNs and generalised Wasserstein Dice score achieves segmentations that are more semantically meaningful for brain tumour segmentation. We present DeepVesselNet, an architecture tailored to the challenges faced when extracting vessel networks or trees and corresponding features in 3-D angiographic volumes using deep learning. We discuss the problems of low execution speed and high memory requirements associated with full 3-D convolutional networks, high-class imbalance arising from the low percentage of vessel voxels, and unavailability of accurately annotated training data - and offer solutions as the building blocks of DeepVesselNet. First, we formulate 2-D orthogonal cross-hair filters which make use of 3-D context information at a reduced computational burden. Second, we introduce a class balancing cross-entropy loss function with false positive rate correction to handle the high-class imbalance and high false positive rate problems associated with existing loss functions. Finally, we generate synthetic dataset using a computational angiogenesis model capable of generating vascular trees under physiological constraints on local network structure and topology and use these data for transfer learning. DeepVesselNet is optimized for segmenting and analyzing vessels, and we test the performance on a range of angiographic volumes including clinical MRA data of the human brain, as well as X-ray tomographic microscopy scans of the rat brain. Our experiments show that, by replacing 3-D filters with cross-hair filters in our network, we achieve over 23 improvement in speed, lower memory footprint, lower network complexity which prevents overfitting and comparable accuracy (with a Cox-Wilcoxon paired sample significance test p-value of 0.07 when compared to full 3-D filters). Our class balancing metric is crucial for training the network and transfer learning with synthetic data is an efficient, robust, and very generalizable approach leading to a network that excels in a variety of angiography segmentation tasks. We introduce a novel loss max-pooling concept for handling imbalanced training data distributions, applicable as alternative loss layer in the context of deep neural networks for semantic image segmentation. Most real-world semantic segmentation datasets exhibit long tail distributions with few object categories comprising the majority of data and consequently biasing the classifiers towards them. Our method adaptively re-weights the contributions of each pixel based on their observed losses, targeting under-performing classification results as often encountered for under-represented object classes. Our approach goes beyond conventional cost-sensitive learning attempts through adaptive considerations that allow us to indirectly address both, inter- and intra-class imbalances. We provide a theoretical justification of our approach, complementary to experimental analyses on benchmark datasets. In our experiments on the Cityscapes and Pascal VOC 2012 segmentation datasets we find consistently improved results, demonstrating the efficacy of our approach. Models defined using higher-order potentials are becoming increasingly popular in computer vision. However, the exact representation of a general higher-order potential defined over many variables is computationally unfeasible. This has led prior works to adopt parametric potentials that can be compactly represented. This paper proposes a non-parametric higher-order model for image labeling problems that uses a patch-based representation of its potentials. We use the transformation scheme of [11, 25] to convert the higher-order potentials to a pair-wise form that can be handled using traditional inference algorithms. This representation is able to capture structure, geometrical and topological information of labels from training data and to provide more precise segmentations. Other tasks such as image denoising and reconstruction are also possible. We evaluate our method on denoising and segmentation problems with synthetic and real images. Purpose – The purpose of this paper is to suggest an alternative to the widely used Times Cited criterion for analysing citation networks. The approach involves taking account of the natures of the papers that cite a given paper, so as to differentiate between papers that attract the same number of citations.Design methodology approach – ArticleRank is an algorithm that has been derived from Google's PageRank algorithm to measure the influence of journal articles. ArticleRank is applied to two datasets – a citation network based on an early paper on webometrics, and a self‐citation network based on the 19 most cited papers in the Journal of Documentation – using citation data taken from the Web of Knowledge database.Findings – ArticleRank values provide a different ranking of a set of papers from that provided by the corresponding Times Cited values, and overcomes the inability of the latter to differentiate between papers with the same numbers of citations. The difference in rankings between Times Cited ... Split-and-merge algorithms define a class of image segmentation methods. Topological maps are a mathematical model that represents image subdivisions in 2D and 3D. This paper discusses a split-and-merge method for 3D image data based on the topological map model This model allows representations of states of segmentations and of merge and split operations. Indeed, it can be used as data structure for dynamic changes of segmentation. The paper details such an algorithmic approach and analyzes its time complexity. A general introduction into combinatorial and topological maps is given to support the understanding of the proposed algorithms. This paper introduces a probabilistic framework for k-shot image classification. The goal is to generalise from an initial large-scale classification task to a separate task comprising new classes and small numbers of examples. The new approach not only leverages the feature-based representation learned by a neural network from the initial task (representational transfer), but also information about the classes (concept transfer). The concept information is encapsulated in a probabilistic model for the final layer weights of the neural network which acts as a prior for probabilistic k-shot learning. We show that even a simple probabilistic model achieves state-of-the-art on a standard k-shot learning dataset by a large margin. Moreover, it is able to accurately model uncertainty, leading to well calibrated classifiers, and is easily extensible and flexible, unlike many recent approaches to k-shot learning. A major limitation of existing models for semantic segmentation is the inability to identify individual instances of the same class: when labeling pixels with only semantic classes, a set of pixels with the same label could represent a single object or ten. In this work, we introduce a model to perform both semantic and instance segmentation simultaneously. We introduce a new higher-order loss function that directly minimizes the coverage metric and evaluate a variety of region features, including those from a convolutional network. We apply our model to the NYU Depth V2 dataset, obtaining state of the art results.