Advances in graph machine learning (ML) have been driven by applications in chemistry as graphs have remained the most expressive representations of molecules. While early graph ML methods focused primarily on small organic molecules, recently, the scope of graph ML has expanded to include inorganic materials. Modelling the periodicity and symmetry of inorganic crystalline materials poses unique challenges, which existing graph ML methods are unable to address. Moving to inorganic nanomaterials increases complexity as the scale of number of nodes within each graph can be broad ($10$ to $10^5$). The bulk of existing graph ML focuses on characterising molecules and materials by predicting target properties with graphs as input. However, the most exciting applications of graph ML will be in their generative capabilities, which is currently not at par with other domains such as images or text. We invite the graph ML community to address these open challenges by presenting two new chemically-informed large-scale inorganic (CHILI) nanomaterials datasets: A medium-scale dataset (with overall >6M nodes, >49M edges) of mono-metallic oxide nanomaterials generated from 12 selected crystal types (CHILI-3K) and a large-scale dataset (with overall >183M nodes, >1.2B edges) of nanomaterials generated from experimentally determined crystal structures (CHILI-100K). We define 11 property prediction tasks and 6 structure prediction tasks, which are of special interest for nanomaterial research. We benchmark the performance of a wide array of baseline methods and use these benchmarking results to highlight areas which need future work. To the best of our knowledge, CHILI-3K and CHILI-100K are the first open-source nanomaterial datasets of this scale -- both on the individual graph level and of the dataset as a whole -- and the only nanomaterials datasets with high structural and elemental diversity.
The delimitation of biological species, i.e., deciding which individuals belong to the same species and whether and how many different species are represented in a data set, is key to the conservation of biodiversity. Much existing work uses only genetic data for species delimitation, often employing some kind of cluster analysis. This can be misleading, because geographically distant groups of individuals can be genetically quite different even if they belong to the same species. We investigate the problem of testing whether two potentially separated groups of individuals can belong to a single species or not based on genetic and spatial data. Existing methods such as the partial Mantel test and jackknife-based distance-distance regression are considered. New approaches, i.e., an adaptation of a mixed effects model, a bootstrap approach, and a jackknife version of partial Mantel, are proposed. All these methods address the issue that distance data violate the independence assumption for standard inference regarding correlation and regression; a standard linear regression is also considered. The approaches are compared on simulated meta-populations generated with SLiM and GSpace - two software packages that can simulate spatially-explicit genetic data at an individual level. Simulations show that the new jackknife version of the partial Mantel test provides a good compromise between power and respecting the nominal type I error rate. Mixed-effects models have larger power than jackknife-based methods, but tend to display type I error rates slightly above the significance level. An application on brassy ringlets concludes the paper.
Accurate per-object distance estimation is crucial in safety-critical applications such as autonomous driving, surveillance, and robotics. Existing approaches rely on two scales: local information (i.e., the bounding box proportions) or global information, which encodes the semantics of the scene as well as the spatial relations with neighboring objects. However, these approaches may struggle with long-range objects and in the presence of strong occlusions or unusual visual patterns. In this respect, our work aims to strengthen both local and global cues. Our architecture -- named DistFormer -- builds upon three major components acting jointly: i) a robust context encoder extracting fine-grained per-object representations; ii) a masked encoder-decoder module exploiting self-supervision to promote the learning of useful per-object features; iii) a global refinement module that aggregates object representations and computes a joint, spatially-consistent estimation. To evaluate the effectiveness of DistFormer, we conduct experiments on the standard KITTI dataset and the large-scale NuScenes and MOTSynth datasets. Such datasets cover various indoor/outdoor environments, changing weather conditions, appearances, and camera viewpoints. Our comprehensive analysis shows that DistFormer outperforms existing methods. Moreover, we further delve into its generalization capabilities, showing its regularization benefits in zero-shot synth-to-real transfer.
The current best practice for computing optimal transport (OT) is via entropy regularization and Sinkhorn iterations. This algorithm runs in quadratic time as it requires the full pairwise cost matrix, which is prohibitively expensive for large sets of objects. In this work we propose two effective log-linear time approximations of the cost matrix: First, a sparse approximation based on locality-sensitive hashing (LSH) and, second, a Nystr\"om approximation with LSH-based sparse corrections, which we call locally corrected Nystr\"om (LCN). These approximations enable general log-linear time algorithms for entropy-regularized OT that perform well even for the complex, high-dimensional spaces common in deep learning. We analyse these approximations theoretically and evaluate them experimentally both directly and end-to-end as a component for real-world applications. Using our approximations for unsupervised word embedding alignment enables us to speed up a state-of-the-art method by a factor of 3 while also improving the accuracy by 3.1 percentage points without any additional model changes. For graph distance regression we propose the graph transport network (GTN), which combines graph neural networks (GNNs) with enhanced Sinkhorn. GTN outcompetes previous models by 48% and still scales log-linearly in the number of nodes.
Boundary-based instance segmentation has drawn much attention since of its attractive efficiency. However, existing methods suffer from the difficulty in long-distance regression. In this paper, we propose a coarse-to-fine module to address the problem. Approximate boundary points are generated at the coarse stage and then features of these points are sampled and fed to a refined regressor for fine prediction. It is end-to-end trainable since differential sampling operation is well supported in the module. Furthermore, we design a holistic boundary-aware branch and introduce instance-agnostic supervision to assist regression. Equipped with ResNet-101, our approach achieves 31.7\% mask AP on COCO dataset with single-scale training and testing, outperforming the baseline 1.3\% mask AP with less than 1\% additional parameters and GFLOPs. Experiments also show that our proposed method achieves competitive performance compared to existing boundary-based methods with a lightweight design and a simple pipeline.
This work proposes a multi-task fully convolutional architecture for tree species mapping in dense forests from sparse and scarce polygon-level annotations using hyperspectral UAV-borne data. Our model implements a partial loss function that enables dense tree semantic labeling outcomes from non-dense training samples, and a distance regression complementary task that enforces tree crown boundary constraints and substantially improves the model performance. Our multi-task architecture uses a shared backbone network that learns common representations for both tasks and two task-specific decoders, one for the semantic segmentation output and one for the distance map regression. We report that introducing the complementary task boosts the semantic segmentation performance compared to the single-task counterpart in up to 11% reaching an average user's accuracy of 88.63% and an average producer's accuracy of 88.59%, achieving state-of-art performance for tree species classification in tropical forests.
Cardiac segmentation of atriums, ventricles, and myocardium in computed tomography (CT) images is an important first-line task for presymptomatic cardiovascular disease diagnosis. In several recent studies, deep learning models have shown significant breakthroughs in medical image segmentation tasks. Unlike other organs such as the lungs and liver, the cardiac organ consists of multiple substructures, i.e., ventricles, atriums, aortas, arteries, veins, and myocardium. These cardiac substructures are proximate to each other and have indiscernible boundaries (i.e., homogeneous intensity values), making it difficult for the segmentation network focus on the boundaries between the substructures. In this paper, to improve the segmentation accuracy between proximate organs, we introduce a novel model to exploit shape and boundary-aware features. We primarily propose a shape-aware attention module, that exploits distance regression, which can guide the model to focus on the edges between substructures so that it can outperform the conventional contour-based attention method. In the experiments, we used the Multi-Modality Whole Heart Segmentation dataset that has 20 CT cardiac images for training and validation, and 40 CT cardiac images for testing. The experimental results show that the proposed network produces more accurate results than state-of-the-art networks by improving the Dice similarity coefficient score by 4.97%. Our proposed shape-aware contour attention mechanism demonstrates that distance transformation and boundary features improve the actual attention map to strengthen the responses in the boundary area. Moreover, our proposed method significantly reduces the false-positive responses of the final output, resulting in accurate segmentation.
The existing human pose estimation methods are confronted with inaccurate long-distance regression or high computational cost due to the complex learning objectives. This work proposes a novel deep learning framework for human pose estimation called composite localization to divide the complex learning objective into two simpler ones: a sparse heatmap to find the keypoint's approximate location and two short-distance offsetmaps to obtain its final precise coordinates. To realize the framework, we construct two types of composite localization networks: CLNet-ResNet and CLNet-Hourglass. We evaluate the networks on three benchmark datasets, including the Leeds Sports Pose dataset, the MPII Human Pose dataset, and the COCO keypoints detection dataset. The experimental results show that our CLNet-ResNet50 outperforms SimpleBaseline by 1.14% with about 1/2 GFLOPs. Our CLNet-Hourglass outperforms the original stacked-hourglass by 4.45% on COCO.
Glacier calving front position (CFP) is an important glaciological variable. Traditionally, delineating the CFPs has been carried out manually, which was subjective, tedious and expensive. Automating this process is crucial for continuously monitoring the evolution and status of glaciers. Recently, deep learning approaches have been investigated for this application. However, the current methods get challenged by a severe class-imbalance problem. In this work, we propose to mitigate the class-imbalance between the calving front class and the non-calving front class by reformulating the segmentation problem into a pixel-wise regression task. A Convolutional Neural Network gets optimized to predict the distance values to the glacier front for each pixel in the image. The resulting distance map localizes the CFP and is further post-processed to extract the calving front line. We propose three post-processing methods, one method based on statistical thresholding, a second method based on conditional random fields (CRF), and finally the use of a second U-Net. The experimental results confirm that our approach significantly outperforms the state-of-the-art methods and produces accurate delineation. The Second U-Net obtains the best performance results, resulting in an average improvement of about 21% dice coefficient enhancement.
This paper addresses acoustic vehicle counting using one-channel audio. We predict the pass-by instants of vehicles from local minima of clipped vehicle-to-microphone distance. This distance is predicted from audio using a two-stage (coarse-fine) regression, with both stages realised via neural networks (NNs). Experiments show that the NN-based distance regression outperforms by far the previously proposed support vector regression. The $ 95\% $ confidence interval for the mean of vehicle counting error is within $[0.28\%, -0.55\%]$. Besides the minima-based counting, we propose a deep learning counting that operates on the predicted distance without detecting local minima. Although outperformed in accuracy by the former approach, deep counting has a significant advantage in that it does not depend on minima detection parameters. Results also show that removing low frequencies in features improves the counting performance.
In this paper we present a novel radar-camera sensor fusion framework for accurate object detection and distance estimation in autonomous driving scenarios. The proposed architecture uses a middle-fusion approach to fuse the radar point clouds and RGB images. Our radar object proposal network uses radar point clouds to generate 3D proposals from a set of 3D prior boxes. These proposals are mapped to the image and fed into a Radar Proposal Refinement (RPR) network for objectness score prediction and box refinement. The RPR network utilizes both radar information and image feature maps to generate accurate object proposals and distance estimations. The radar-based proposals are combined with image-based proposals generated by a modified Region Proposal Network (RPN). The RPN has a distance regression layer for estimating distance for every generated proposal. The radar-based and image-based proposals are merged and used in the next stage for object classification. Experiments on the challenging nuScenes dataset show our method outperforms other existing radar-camera fusion methods in the 2D object detection task while at the same time accurately estimates objects' distances.
As a proposal-free approach, instance segmentation through pixel embedding learning and clustering is gaining more emphasis. Compared with bounding box refinement approaches, such as Mask R-CNN, it has potential advantages in handling complex shapes and dense objects. In this work, we propose a simple, yet highly effective, architecture for object-aware embedding learning. A distance regression module is incorporated into our architecture to generate seeds for fast clustering. At the same time, we show that the features learned by the distance regression module are able to promote the accuracy of learned object-aware embeddings significantly. By simply concatenating features of the distance regression module to the images as inputs of the embedding module, the mSBD scores on the CVPPP Leaf Segmentation Challenge can be further improved by more than 8% compared to the identical set-up without concatenation, yielding the best overall result amongst the leaderboard at CodaLab.
In this paper, we introduce an anchor-free and single-shot instance segmentation method, which is conceptually simple with 3 independent branches, fully convolutional and can be used by easily embedding it into mobile and embedded devices. Our method, refer as EOLO, reformulates the instance segmentation problem as predicting semantic segmentation and distinguishing overlapping objects problem, through instance center classification and 4D distance regression on each pixel. Moreover, we propose one effective loss function to deal with sampling a high-quality center of gravity examples and optimization for 4D distance regression, which can significantly improve the mAP performance. Without any bells and whistles, EOLO achieves 27.7$\%$ in mask mAP under IoU50 and reaches 30 FPS on 1080Ti GPU, with a single-model and single-scale training/testing on the challenging COCO2017 dataset. For the first time, we show the different comprehension of instance segmentation in recent methods, in terms of both up-bottom, down-up, and direct-predict paradigms. Then we illustrate our model and present related experiments and results. We hope that the proposed EOLO framework can serve as a fundamental baseline for a single-shot instance segmentation task in Real-time Industrial Scenarios.
Individual tooth segmentation from cone beam computed tomography (CBCT) images is an essential prerequisite for an anatomical understanding of orthodontic structures in several applications, such as tooth reformation planning and implant guide simulations. However, the presence of severe metal artifacts in CBCT images hinders the accurate segmentation of each individual tooth. In this study, we propose a neural network for pixel-wise labeling to exploit an instance segmentation framework that is robust to metal artifacts. Our method comprises of three steps: 1) image cropping and realignment by pose regressions, 2) metal-robust individual tooth detection, and 3) segmentation. We first extract the alignment information of the patient by pose regression neural networks to attain a volume-of-interest (VOI) region and realign the input image, which reduces the inter-overlapping area between tooth bounding boxes. Then, individual tooth regions are localized within a VOI realigned image using a convolutional detector. We improved the accuracy of the detector by employing non-maximum suppression and multiclass classification metrics in the region proposal network. Finally, we apply a convolutional neural network (CNN) to perform individual tooth segmentation by converting the pixel-wise labeling task to a distance regression task. Metal-intensive image augmentation is also employed for a robust segmentation of metal artifacts. The result shows that our proposed method outperforms other state-of-the-art methods, especially for teeth with metal artifacts. The primary significance of the proposed method is two-fold: 1) an introduction of pose-aware VOI realignment followed by a robust tooth detection and 2) a metal-robust CNN framework for accurate tooth segmentation.
In this paper, we introduce an anchor-box free and single shot instance segmentation method, which is conceptually simple, fully convolutional and can be used as a mask prediction module for instance segmentation, by easily embedding it into most off-the-shelf detection methods. Our method, termed PolarMask, formulates the instance segmentation problem as instance center classification and dense distance regression in a polar coordinate. Moreover, we propose two effective approaches to deal with sampling high-quality center examples and optimization for dense distance regression, respectively, which can significantly improve the performance and simplify the training process. Without any bells and whistles, PolarMask achieves 32.9% in mask mAP with single-model and single-scale training/testing on challenging COCO dataset. For the first time, we demonstrate a much simpler and flexible instance segmentation framework achieving competitive accuracy. We hope that the proposed PolarMask framework can serve as a fundamental and strong baseline for single shot instance segmentation tasks. Code is available at: github.com/xieenze/PolarMask.
Understanding visual scenes relies more and more on dense pixel-wise classification obtained via deep fully convolutional neural networks. However, due to the nature of the networks, predictions often suffer from blurry boundaries and ill-segmented shapes, fueling the need for post-processing. This work introduces a new semantic segmentation regularization based on the regression of a distance transform. After computing the distance transform on the label masks, we train a FCN in a multi-task setting in both discrete and continuous spaces by learning jointly classification and distance regression. This requires almost no modification of the network structure and adds a very low overhead to the training process. Learning to approximate the distance transform back-propagates spatial cues that implicitly regularizes the segmentation. We validate this technique with several architectures on various datasets, and we show significant improvements compared to competitive baselines.
It remains challenging to automatically segment kidneys in clinical ultrasound images due to the kidneys' varied shapes and image intensity distributions, although semi-automatic methods have achieved promising performance. In this study, we developed a novel boundary distance regression deep neural network to segment the kidneys, informed by the fact that the kidney boundaries are relatively consistent across images in terms of their appearance. Particularly, we first use deep neural networks pre-trained for classification of natural images to extract high-level image features from ultrasound images, then these feature maps are used as input to learn kidney boundary distance maps using a boundary distance regression network, and finally the predicted boundary distance maps are classified as kidney pixels or non-kidney pixels using a pixel classification network in an end-to-end learning fashion. Experimental results have demonstrated that our method could effectively improve the performance of automatic kidney segmentation, significantly better than deep learning based pixel classification networks.
It remains challenging to automatically segment kidneys in clinical ultrasound (US) images due to the kidneys' varied shapes and image intensity distributions, although semi-automatic methods have achieved promising performance. In this study, we propose subsequent boundary distance regression and pixel classification networks to segment the kidneys, informed by the fact that the kidney boundaries have relatively homogenous texture patterns across images. Particularly, we first use deep neural networks pre-trained for classification of natural images to extract high-level image features from US images, then these features are used as input to learn kidney boundary distance maps using a boundary distance regression network, and finally the predicted boundary distance maps are classified as kidney pixels or non-kidney pixels using a pixel classification network in an end-to-end learning fashion. We also adopted a data-augmentation method based on kidney shape registration to generate enriched training data from a small number of US images with manually segmented kidney labels. Experimental results have demonstrated that our method could effectively improve the performance of automatic kidney segmentation, significantly better than deep learning-based pixel classification networks.