3D Convolutional Neural Networks for Tumor Segmentation using Long-range 2D Context

We present an efficient deep learning approach for the challenging task of tumor segmentation in multisequence MR images. In recent years, Convolutional Neural Networks (CNN) have achieved state-of-the-art performances in a large variety of recognition tasks in medical imaging. Because of the considerable computational cost of CNNs, large volumes such as MRI are typically processed by subvolumes, for instance slices (axial, coronal, sagittal) or small 3D patches. In this paper we introduce a CNN-based model which efficiently combines the advantages of the short-range 3D context and the long-range 2D context. To overcome the limitations of specific choices of neural network architectures, we also propose to merge outputs of several cascaded 2D-3D models by a voxelwise voting strategy. Furthermore, we propose a network architecture in which the different MR sequences are processed by separate subnetworks in order to be more robust to the problem of missing MR sequences. Finally, a simple and efficient algorithm for training large CNN models is introduced. We evaluate our method on the public benchmark of the BRATS 2017 challenge on the task of multiclass segmentation of malignant brain tumors. Our method achieves good performances and produces accurate segmentations with median Dice scores of 0.918 (whole tumor), 0.883 (tumor core) and 0.854 (enhancing core). Our approach can be naturally applied to various tasks involving segmentation of lesions or organs.Comment: Submitted to the journal Computerized Medical Imaging and Graphic

An Automated Social Graph De-anonymization Technique

We present a generic and automated approach to re-identifying nodes in anonymized social networks which enables novel anonymization techniques to be quickly evaluated. It uses machine learning (decision forests) to matching pairs of nodes in disparate anonymized sub-graphs. The technique uncovers artefacts and invariants of any black-box anonymization scheme from a small set of examples. Despite a high degree of automation, classification succeeds with significant true positive rates even when small false positive rates are sought. Our evaluation uses publicly available real world datasets to study the performance of our approach against real-world anonymization strategies, namely the schemes used to protect datasets of The Data for Development (D4D) Challenge. We show that the technique is effective even when only small numbers of samples are used for training. Further, since it detects weaknesses in the black-box anonymization scheme it can re-identify nodes in one social network when trained on another.Comment: 12 page

Deep roots: Improving CNN efficiency with hierarchical filter groups

We propose a new method for creating computationally efficient and compact convolutional neural networks (CNNs) using a novel sparse connection structure that resembles a tree root. This allows a significant reduction in computational cost and number of parameters compared to state-of-the-art deep CNNs, without compromising accuracy, by exploiting the sparsity of inter-layer filter dependencies. We validate our approach by using it to train more efficient variants of state-of-the-art CNN architectures, evaluated on the CIFAR10 and ILSVRC datasets. Our results show similar or higher accuracy than the baseline architectures with much less computation, as measured by CPU and GPU timings. For example, for ResNet 50, our model has 40% fewer parameters, 45% fewer floating point operations, and is 31% (12%) faster on a CPU (GPU). For the deeper ResNet 200 our model has 25% fewer floating point operations and 44% fewer parameters, while maintaining state-of-the-art accuracy. For GoogLeNet, our model has 7% fewer parameters and is 21% (16%) faster on a CPU (GPU).Microsoft Research PhD Scholarshi

Scene Coordinate Regression with Angle-Based Reprojection Loss for Camera Relocalization

Image-based camera relocalization is an important problem in computer vision and robotics. Recent works utilize convolutional neural networks (CNNs) to regress for pixels in a query image their corresponding 3D world coordinates in the scene. The final pose is then solved via a RANSAC-based optimization scheme using the predicted coordinates. Usually, the CNN is trained with ground truth scene coordinates, but it has also been shown that the network can discover 3D scene geometry automatically by minimizing single-view reprojection loss. However, due to the deficiencies of the reprojection loss, the network needs to be carefully initialized. In this paper, we present a new angle-based reprojection loss, which resolves the issues of the original reprojection loss. With this new loss function, the network can be trained without careful initialization, and the system achieves more accurate results. The new loss also enables us to utilize available multi-view constraints, which further improve performance.Comment: ECCV 2018 Workshop (Geometry Meets Deep Learning

Refining Architectures of Deep Convolutional Neural Networks

© 2016 IEEE. Deep Convolutional Neural Networks (CNNs) have recently evinced immense success for various image recognition tasks [11, 27]. However, a question of paramount importance is somewhat unanswered in deep learning research - is the selected CNN optimal for the dataset in terms of accuracy and model size? In this paper, we intend to answer this question and introduce a novel strategy that alters the architecture of a given CNN for a specified dataset, to potentially enhance the original accuracy while possibly reducing the model size. We use two operations for architecture refinement, viz. stretching and symmetrical splitting. Stretching increases the number of hidden units (nodes) in a given CNN layer, while a symmetrical split of say K between two layers separates the input and output channels into K equal groups, and connects only the corresponding input-output channel groups. Our procedure starts with a pre-trained CNN for a given dataset, and optimally decides the stretch and split factors across the network to refine the architecture. We empirically demonstrate the necessity of the two operations. We evaluate our approach on two natural scenes attributes datasets, SUN Attributes [16] and CAMIT-NSAD [20], with architectures of GoogleNet and VGG-11, that are quite contrasting in their construction. We justify our choice of datasets, and show that they are interestingly distinct from each other, and together pose a challenge to our architectural refinement algorithm. Our results substantiate the usefulness of the proposed method

Bayesian image quality transfer

Image quality transfer (IQT) aims to enhance clinical images of relatively low quality by learning and propagating high-quality structural information from expensive or rare data sets. However,the original framework gives no indication of confidence in its output,which is a significant barrier to adoption in clinical practice and downstream processing. In this article,we present a general Bayesian extension of IQT which enables efficient and accurate quantification of uncertainty,providing users with an essential prediction of the accuracy of enhanced images. We demonstrate the efficacy of the uncertainty quantification through super-resolution of diffusion tensor images of healthy and pathological brains. In addition,the new method displays improved performance over the original IQT and standard interpolation techniques in both reconstruction accuracy and robustness to anomalies in input images

Discriminative segmentation-based evaluation through shape dissimilarity.

Segmentation-based scores play an important role in the evaluation of computational tools in medical image analysis. These scores evaluate the quality of various tasks, such as image registration and segmentation, by measuring the similarity between two binary label maps. Commonly these measurements blend two aspects of the similarity: pose misalignments and shape discrepancies. Not being able to distinguish between these two aspects, these scores often yield similar results to a widely varying range of different segmentation pairs. Consequently, the comparisons and analysis achieved by interpreting these scores become questionable. In this paper, we address this problem by exploring a new segmentation-based score, called normalized Weighted Spectral Distance (nWSD), that measures only shape discrepancies using the spectrum of the Laplace operator. Through experiments on synthetic and real data we demonstrate that nWSD provides additional information for evaluating differences between segmentations, which is not captured by other commonly used scores. Our results demonstrate that when jointly used with other scores, such as Dices similarity coefficient, the additional information provided by nWSD allows richer, more discriminative evaluations. We show for the task of registration that through this addition we can distinguish different types of registration errors. This allows us to identify the source of errors and discriminate registration results which so far had to be treated as being of similar quality in previous evaluation studies. © 2012 IEEE

Homography-based ground plane detection using a single on-board camera

This study presents a robust method for ground plane detection in vision-based systems with a non-stationary camera. The proposed method is based on the reliable estimation of the homography between ground planes in successive images. This homography is computed using a feature matching approach, which in contrast to classical approaches to on-board motion estimation does not require explicit ego-motion calculation. As opposed to it, a novel homography calculation method based on a linear estimation framework is presented. This framework provides predictions of the ground plane transformation matrix that are dynamically updated with new measurements. The method is specially suited for challenging environments, in particular traffic scenarios, in which the information is scarce and the homography computed from the images is usually inaccurate or erroneous. The proposed estimation framework is able to remove erroneous measurements and to correct those that are inaccurate, hence producing a reliable homography estimate at each instant. It is based on the evaluation of the difference between the predicted and the observed transformations, measured according to the spectral norm of the associated matrix of differences. Moreover, an example is provided on how to use the information extracted from ground plane estimation to achieve object detection and tracking. The method has been successfully demonstrated for the detection of moving vehicles in traffic environments