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Multiple sclerosis (MS) is a chronic inflammatory and degenerative disease of the central nervous system, characterized by the appearance of focal lesions in the white and gray matter that topographically correlate with an individual patient's neurological symptoms and signs. Magnetic resonance imaging (MRI) provides detailed in-vivo structural information, permitting the quantification and categorization of MS lesions that critically inform disease management. Traditionally, MS lesions have been manually annotated on 2D MRI slices, a process that is inefficient and prone to inter-/intra-observer errors. Recently, automated statistical imaging analysis techniques have been proposed to detect and segment MS lesions based on MRI voxel intensity. However, their effectiveness is limited by the heterogeneity of both MRI data acquisition techniques and the appearance of MS lesions. By learning complex lesion representations directly from images, deep learning techniques have achieved remarkable breakthroughs in the MS lesion segmentation task. Here, we provide a comprehensive review of state-of-the-art automatic statistical and deep-learning MS segmentation methods and discuss current and future clinical applications. Further, we review technical strategies, such as domain adaptation, to enhance MS lesion segmentation in real-world clinical settings.

In this paper, we propose to employ a Gaussian map representation to estimate precise location and count of 3D surface features, addressing the limitations of state-of-the-art methods based on density estimation which struggle in presence of local disturbances. Gaussian maps indicate probable object location and can be generated directly from keypoint annotations avoiding laborious and costly per-pixel annotations. We apply this method to the 3D spheroidal class of objects which can be projected into 2D shape representation enabling efficient processing by a neural network GNet, an improved UNet architecture, which generates the likely locations of surface features and their precise count. We demonstrate a practical use of this technique for counting strawberry achenes which is used as a fruit quality measure in phenotyping applications. The results of training the proposed system on several hundreds of 3D scans of strawberries from a publicly available dataset demonstrate the accuracy and precision of the system which outperforms the state-of-the-art density-based methods for this application.

Sepsis is an important cause of mortality, especially in intensive care unit (ICU) patients. Developing novel methods to identify early mortality is critical for improving survival outcomes in sepsis patients. Using the MIMIC-III database, we integrated demographic data, physiological measurements and clinical notes. We built and applied several machine learning models to predict the risk of hospital mortality and 30-day mortality in sepsis patients. From the clinical notes, we generated clinically meaningful word representations and embeddings. Supervised learning classifiers and a deep learning architecture were used to construct prediction models. The configurations that utilized both structured and unstructured clinical features yielded competitive F-measure of 0.512. Our results showed that the approaches integrating both structured and unstructured clinical features can be effectively applied to assist clinicians in identifying the risk of mortality in sepsis patients upon admission to the ICU.

Mainstream object detectors based on the fully convolutional network has achieved impressive performance. While most of them still need a hand-designed non-maximum suppression (NMS) post-processing, which impedes fully end-to-end training. In this paper, we give the analysis of discarding NMS, where the results reveal that a proper label assignment plays a crucial role. To this end, for fully convolutional detectors, we introduce a Prediction-aware One-To-One (POTO) label assignment for classification to enable end-to-end detection, which obtains comparable performance with NMS. Besides, a simple 3D Max Filtering (3DMF) is proposed to utilize the multi-scale features and improve the discriminability of convolutions in the local region. With these techniques, our end-to-end framework achieves competitive performance against many state-of-the-art detectors with NMS on COCO and CrowdHuman datasets. The code is available at //github.com/Megvii-BaseDetection/DeFCN .

We present Neural A*, a novel data-driven search method for path planning problems. Despite the recent increasing attention to data-driven path planning, a machine learning approach to search-based planning is still challenging due to the discrete nature of search algorithms. In this work, we reformulate a canonical A* search algorithm to be differentiable and couple it with a convolutional encoder to form an end-to-end trainable neural network planner. Neural A* solves a path planning problem by encoding a problem instance to a guidance map and then performing the differentiable A* search with the guidance map. By learning to match the search results with ground-truth paths provided by experts, Neural A* can produce a path consistent with the ground truth accurately and efficiently. Our extensive experiments confirmed that Neural A* outperformed state-of-the-art data-driven planners in terms of the search optimality and efficiency trade-off, and furthermore, successfully predicted realistic human trajectories by directly performing search-based planning on natural image inputs.

Generating character-level features is an important step for achieving good results in various natural language processing tasks. To alleviate the need for human labor in generating hand-crafted features, methods that utilize neural architectures such as Convolutional Neural Network (CNN) or Recurrent Neural Network (RNN) to automatically extract such features have been proposed and have shown great results. However, CNN generates position-independent features, and RNN is slow since it needs to process the characters sequentially. In this paper, we propose a novel method of using a densely connected network to automatically extract character-level features. The proposed method does not require any language or task specific assumptions, and shows robustness and effectiveness while being faster than CNN- or RNN-based methods. Evaluating this method on three sequence labeling tasks - slot tagging, Part-of-Speech (POS) tagging, and Named-Entity Recognition (NER) - we obtain state-of-the-art performance with a 96.62 F1-score and 97.73% accuracy on slot tagging and POS tagging, respectively, and comparable performance to the state-of-the-art 91.13 F1-score on NER.

Classifying large scale networks into several categories and distinguishing them according to their fine structures is of great importance with several applications in real life. However, most studies of complex networks focus on properties of a single network but seldom on classification, clustering, and comparison between different networks, in which the network is treated as a whole. Due to the non-Euclidean properties of the data, conventional methods can hardly be applied on networks directly. In this paper, we propose a novel framework of complex network classifier (CNC) by integrating network embedding and convolutional neural network to tackle the problem of network classification. By training the classifiers on synthetic complex network data and real international trade network data, we show CNC can not only classify networks in a high accuracy and robustness, it can also extract the features of the networks automatically.

Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.

In this work, we establish dense correspondences between RGB image and a surface-based representation of the human body, a task we refer to as dense human pose estimation. We first gather dense correspondences for 50K persons appearing in the COCO dataset by introducing an efficient annotation pipeline. We then use our dataset to train CNN-based systems that deliver dense correspondence 'in the wild', namely in the presence of background, occlusions and scale variations. We improve our training set's effectiveness by training an 'inpainting' network that can fill in missing groundtruth values and report clear improvements with respect to the best results that would be achievable in the past. We experiment with fully-convolutional networks and region-based models and observe a superiority of the latter; we further improve accuracy through cascading, obtaining a system that delivers highly0accurate results in real time. Supplementary materials and videos are provided on the project page //densepose.org

Superpixel segmentation has become an important research problem in image processing. In this paper, we propose an Iterative Spanning Forest (ISF) framework, based on sequences of Image Foresting Transforms, where one can choose i) a seed sampling strategy, ii) a connectivity function, iii) an adjacency relation, and iv) a seed pixel recomputation procedure to generate improved sets of connected superpixels (supervoxels in 3D) per iteration. The superpixels in ISF structurally correspond to spanning trees rooted at those seeds. We present five ISF methods to illustrate different choices of its components. These methods are compared with approaches from the state-of-the-art in effectiveness and efficiency. The experiments involve 2D and 3D datasets with distinct characteristics, and a high level application, named sky image segmentation. The theoretical properties of ISF are demonstrated in the supplementary material and the results show that some of its methods are competitive with or superior to the best baselines in effectiveness and efficiency.