In medical image analysis, automated segmentation of multi-component anatomical structures, which often have a spectrum of potential anomalies and pathologies, is a challenging task. In this work, we develop a multi-step approach using U-Net-based neural networks to initially detect anomalies (bone marrow lesions, bone cysts) in the distal femur, proximal tibia and patella from 3D magnetic resonance (MR) images of the knee in individuals with varying grades of osteoarthritis. Subsequently, the extracted data are used for downstream tasks involving semantic segmentation of individual bone and cartilage volumes as well as bone anomalies. For anomaly detection, the U-Net-based models were developed to reconstruct the bone profiles of the femur and tibia in images via inpainting so anomalous bone regions could be replaced with close to normal appearances. The reconstruction error was used to detect bone anomalies. A second anomaly-aware network, which was compared to anomaly-na\"ive segmentation networks, was used to provide a final automated segmentation of the femoral, tibial and patellar bones and cartilages from the knee MR images containing a spectrum of bone anomalies. The anomaly-aware segmentation approach provided up to 58% reduction in Hausdorff distances for bone segmentations compared to the results from the anomaly-na\"ive segmentation networks. In addition, the anomaly-aware networks were able to detect bone lesions in the MR images with greater sensitivity and specificity (area under the receiver operating characteristic curve [AUC] up to 0.896) compared to the anomaly-na\"ive segmentation networks (AUC up to 0.874).
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Producing thousands of simulations of the dark matter distribution in the Universe with increasing precision is a challenging but critical task to facilitate the exploitation of current and forthcoming cosmological surveys. Many inexpensive substitutes to full $N$-body simulations have been proposed, even though they often fail to reproduce the statistics of the smaller, non-linear scales. Among these alternatives, a common approximation is represented by the lognormal distribution, which comes with its own limitations as well, while being extremely fast to compute even for high-resolution density fields. In this work, we train a generative deep learning model, mainly made of convolutional layers, to transform projected lognormal dark matter density fields to more realistic dark matter maps, as obtained from full $N$-body simulations. We detail the procedure that we follow to generate highly correlated pairs of lognormal and simulated maps, which we use as our training data, exploiting the information of the Fourier phases. We demonstrate the performance of our model comparing various statistical tests with different field resolutions, redshifts and cosmological parameters, proving its robustness and explaining its current limitations. When evaluated on 100 test maps, the augmented lognormal random fields reproduce the power spectrum up to wavenumbers of $1 \ h \ \rm{Mpc}^{-1}$, and the bispectrum within 10%, and always within the error bars, of the fiducial target simulations. Finally, we describe how we plan to integrate our proposed model with existing tools to yield more accurate spherical random fields for weak lensing analysis.
Purpose: Automated distinct bone segmentation from CT scans is widely used in planning and navigation workflows. U-Net variants are known to provide excellent results in supervised semantic segmentation. However, in distinct bone segmentation from upper body CTs a large field of view and a computationally taxing 3D architecture are required. This leads to low-resolution results lacking detail or localisation errors due to missing spatial context when using high-resolution inputs. Methods: We propose to solve this problem by using end-to-end trainable segmentation networks that combine several 3D U-Nets working at different resolutions. Our approach, which extends and generalizes HookNet and MRN, captures spatial information at a lower resolution and skips the encoded information to the target network, which operates on smaller high-resolution inputs. We evaluated our proposed architecture against single resolution networks and performed an ablation study on information concatenation and the number of context networks. Results: Our proposed best network achieves a median DSC of 0.86 taken over all 125 segmented bone classes and reduces the confusion among similar-looking bones in different locations. These results outperform our previously published 3D U-Net baseline results on the task and distinct-bone segmentation results reported by other groups. Conclusion: The presented multi-resolution 3D U-Nets address current shortcomings in bone segmentation from upper-body CT scans by allowing for capturing a larger field of view while avoiding the cubic growth of the input pixels and intermediate computations that quickly outgrow the computational capacities in 3D. The approach thus improves the accuracy and efficiency of distinct bone segmentation from upper-body CT.
Psychoacoustic experiments have shown that directional properties of the direct sound, salient reflections, and the late reverberation of an acoustic room response can have a distinct influence on the auditory perception of a given room. Spatial room impulse responses (SRIRs) capture those properties and thus are used for direction-dependent room acoustic analysis and virtual acoustic rendering. This work proposes a subspace method that decomposes SRIRs into a direct part, which comprises the direct sound and the salient reflections, and a residual, to facilitate enhanced analysis and rendering methods by providing individual access to these components. The proposed method is based on the generalized singular value decomposition and interprets the residual as noise that is to be separated from the other components of the reverberation. Large generalized singular values are attributed to the direct part, which is then obtained as a low-rank approximation of the SRIR. By advancing from the end of the SRIR toward the beginning while iteratively updating the residual estimate, the method adapts to spatio-temporal variations of the residual. The method is evaluated using a spatio-spectral error measure and simulated SRIRs of different rooms, microphone arrays, and ratios of direct sound to residual energy. The proposed method creates lower errors than existing approaches in all tested scenarios, including a scenario with two simultaneous reflections. A case study with measured SRIRs shows the applicability of the method under real-world acoustic conditions. A reference implementation is provided.
This paper deals with the estimation of population sizes for respondent-driven sampling (RDS), a variant of link-tracing sampling that leverages social networks over a number of waves to recruit individuals from hidden populations. The RDS process is mostly controlled by individual participants who might report on recruitment proposals, or nominations, that they have received or given. By considering all nominations given or received over a time period, one can create a capture-recapture dataset in which units are individuals who have received at least one nomination and capture occasions are either time intervals or recruitment waves, with the goal of estimating the size $N$ of the hidden population. In this paper, we argue that the underlying process that generated the RDS nomination data is that of a capture-recapture experiment. We then proposed a methodology for the estimation of the population size and investigated its performance against departures from classical capture-recapture assumptions.
Graphs are used widely to model complex systems, and detecting anomalies in a graph is an important task in the analysis of complex systems. Graph anomalies are patterns in a graph that do not conform to normal patterns expected of the attributes and/or structures of the graph. In recent years, graph neural networks (GNNs) have been studied extensively and have successfully performed difficult machine learning tasks in node classification, link prediction, and graph classification thanks to the highly expressive capability via message passing in effectively learning graph representations. To solve the graph anomaly detection problem, GNN-based methods leverage information about the graph attributes (or features) and/or structures to learn to score anomalies appropriately. In this survey, we review the recent advances made in detecting graph anomalies using GNN models. Specifically, we summarize GNN-based methods according to the graph type (i.e., static and dynamic), the anomaly type (i.e., node, edge, subgraph, and whole graph), and the network architecture (e.g., graph autoencoder, graph convolutional network). To the best of our knowledge, this survey is the first comprehensive review of graph anomaly detection methods based on GNNs.
Over the past few years, the rapid development of deep learning technologies for computer vision has greatly promoted the performance of medical image segmentation (MedISeg). However, the recent MedISeg publications usually focus on presentations of the major contributions (e.g., network architectures, training strategies, and loss functions) while unwittingly ignoring some marginal implementation details (also known as "tricks"), leading to a potential problem of the unfair experimental result comparisons. In this paper, we collect a series of MedISeg tricks for different model implementation phases (i.e., pre-training model, data pre-processing, data augmentation, model implementation, model inference, and result post-processing), and experimentally explore the effectiveness of these tricks on the consistent baseline models. Compared to paper-driven surveys that only blandly focus on the advantages and limitation analyses of segmentation models, our work provides a large number of solid experiments and is more technically operable. With the extensive experimental results on both the representative 2D and 3D medical image datasets, we explicitly clarify the effect of these tricks. Moreover, based on the surveyed tricks, we also open-sourced a strong MedISeg repository, where each of its components has the advantage of plug-and-play. We believe that this milestone work not only completes a comprehensive and complementary survey of the state-of-the-art MedISeg approaches, but also offers a practical guide for addressing the future medical image processing challenges including but not limited to small dataset learning, class imbalance learning, multi-modality learning, and domain adaptation. The code has been released at: //github.com/hust-linyi/MedISeg
Video anomaly detection under weak labels is formulated as a typical multiple-instance learning problem in previous works. In this paper, we provide a new perspective, i.e., a supervised learning task under noisy labels. In such a viewpoint, as long as cleaning away label noise, we can directly apply fully supervised action classifiers to weakly supervised anomaly detection, and take maximum advantage of these well-developed classifiers. For this purpose, we devise a graph convolutional network to correct noisy labels. Based upon feature similarity and temporal consistency, our network propagates supervisory signals from high-confidence snippets to low-confidence ones. In this manner, the network is capable of providing cleaned supervision for action classifiers. During the test phase, we only need to obtain snippet-wise predictions from the action classifier without any extra post-processing. Extensive experiments on 3 datasets at different scales with 2 types of action classifiers demonstrate the efficacy of our method. Remarkably, we obtain the frame-level AUC score of 82.12% on UCF-Crime.
It is important to detect anomalous inputs when deploying machine learning systems. The use of larger and more complex inputs in deep learning magnifies the difficulty of distinguishing between anomalous and in-distribution examples. At the same time, diverse image and text data are available in enormous quantities. We propose leveraging these data to improve deep anomaly detection by training anomaly detectors against an auxiliary dataset of outliers, an approach we call Outlier Exposure (OE). This enables anomaly detectors to generalize and detect unseen anomalies. In extensive experiments on natural language processing and small- and large-scale vision tasks, we find that Outlier Exposure significantly improves detection performance. We also observe that cutting-edge generative models trained on CIFAR-10 may assign higher likelihoods to SVHN images than to CIFAR-10 images; we use OE to mitigate this issue. We also analyze the flexibility and robustness of Outlier Exposure, and identify characteristics of the auxiliary dataset that improve performance.
Object detection is an important and challenging problem in computer vision. Although the past decade has witnessed major advances in object detection in natural scenes, such successes have been slow to aerial imagery, not only because of the huge variation in the scale, orientation and shape of the object instances on the earth's surface, but also due to the scarcity of well-annotated datasets of objects in aerial scenes. To advance object detection research in Earth Vision, also known as Earth Observation and Remote Sensing, we introduce a large-scale Dataset for Object deTection in Aerial images (DOTA). To this end, we collect $2806$ aerial images from different sensors and platforms. Each image is of the size about 4000-by-4000 pixels and contains objects exhibiting a wide variety of scales, orientations, and shapes. These DOTA images are then annotated by experts in aerial image interpretation using $15$ common object categories. The fully annotated DOTA images contains $188,282$ instances, each of which is labeled by an arbitrary (8 d.o.f.) quadrilateral To build a baseline for object detection in Earth Vision, we evaluate state-of-the-art object detection algorithms on DOTA. Experiments demonstrate that DOTA well represents real Earth Vision applications and are quite challenging.
Image segmentation is still an open problem especially when intensities of the interested objects are overlapped due to the presence of intensity inhomogeneity (also known as bias field). To segment images with intensity inhomogeneities, a bias correction embedded level set model is proposed where Inhomogeneities are Estimated by Orthogonal Primary Functions (IEOPF). In the proposed model, the smoothly varying bias is estimated by a linear combination of a given set of orthogonal primary functions. An inhomogeneous intensity clustering energy is then defined and membership functions of the clusters described by the level set function are introduced to rewrite the energy as a data term of the proposed model. Similar to popular level set methods, a regularization term and an arc length term are also included to regularize and smooth the level set function, respectively. The proposed model is then extended to multichannel and multiphase patterns to segment colourful images and images with multiple objects, respectively. It has been extensively tested on both synthetic and real images that are widely used in the literature and public BrainWeb and IBSR datasets. Experimental results and comparison with state-of-the-art methods demonstrate that advantages of the proposed model in terms of bias correction and segmentation accuracy.
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