Abstract: Quantification of tumor heterogeneity is essential to better understand cancer progression and to adapt therapeutic treatments to patient specificities. Bioinformatic tools to assess the different cell populations from single-omic datasets as bulk transcriptome or methylome samples have been recently developed, including reference-based and reference-free methods. Improved methods using multi-omic datasets are yet to be developed in the future and the community would need systematic tools to perform a comparative evaluation of these algorithms on controlled data.

Abstract: Background: Eating disorders are psychological conditions characterized by unhealthy eating habits. Anorexia nervosa (AN) is defined as the belief of being overweight despite being dangerously underweight. The psychological signs involve emotional and behavioral issues. There is evidence that signs and symptoms can manifest on social media, wherein both harmful and beneficial content is shared daily.

Abstract: This work addresses the problem of Question Answering (QA) on handwritten document collections. Unlike typical QA and Visual Question Answering (VQA) formulations where the answer is a short text, we aim to locate a document snippet where the answer lies. The proposed approach works without recognizing the text in the documents. We argue that the recognition-free approach is suitable for handwritten documents and historical collections where robust text recognition is often difficult. At the same time, for human users, document image snippets containing answers act as a valid alternative to textual answers. The proposed approach uses an off-the-shelf deep embedding network which can project both textual words and word images into a common sub-space. This embedding bridges the textual and visual domains and helps us retrieve document snippets that potentially answer a question. We evaluate results of the proposed approach on two new datasets: (i) HW-SQuAD: a synthetic, handwritten document image counterpart of SQuAD1.0 dataset and (ii) BenthamQA: a smaller set of QA pairs defined on documents from the popular Bentham manuscripts collection. We also present a thorough analysis of the proposed recognition-free approach compared to a recognition-based approach which uses text recognized from the images using an OCR. Datasets presented in this work are available to download at docvqa.org.

Abstract: Modern computer vision requires processing large amounts of data, both while training the model and/or during inference, once the model is deployed. Scenarios where images are captured and processed in physically separated locations are increasingly common (e.g. autonomous vehicles, cloud computing). In addition, many devices suffer from limited resources to store or transmit data (e.g. storage space, channel capacity). In these scenarios, lossy image compression plays a crucial role to effectively increase the number of images collected under such constraints. However, lossy compression entails some undesired degradation of the data that may harm the performance of the downstream analysis task at hand, since important semantic information may be lost in the process. Moreover, we may only have compressed images at training time but are able to use original images at inference time, or vice versa, and in such a case, the downstream model suffers from covariate shift. In this paper, we analyze this phenomenon, with a special focus on vision-based perception for autonomous driving as a paradigmatic scenario. We see that loss of semantic information and covariate shift do indeed exist, resulting in a drop in performance that depends on the compression rate. In order to address the problem, we propose dataset restoration, based on image restoration with generative adversarial networks (GANs). Our method is agnostic to both the particular image compression method and the downstream task; and has the advantage of not adding additional cost to the deployed models, which is particularly important in resource-limited devices. The presented experiments focus on semantic segmentation as a challenging use case, cover a broad range of compression rates and diverse datasets, and show how our method is able to significantly alleviate the negative effects of compression on the downstream visual task.

Abstract: This article presents a GPU-accelerated software design of the recently proposed model of Slanted Stixels, which represents the geometric and semantic information of a scene in a compact and accurate way. We reformulate the measurement depth model to reduce the computational complexity of the algorithm, relying on the confidence of the depth estimation and the identification of invalid values to handle outliers. The proposed massively parallel scheme and data layout for the irregular computation pattern that corresponds to a Dynamic Programming paradigm is described and carefully analyzed in performance terms. Performance is shown to scale gracefully on current generation embedded GPUs. We assess the proposed methods in terms of semantic and geometric accuracy as well as run-time performance on three publicly available benchmark datasets. Our approach achieves real-time performance with high accuracy for 2048 × 1024 image sizes and 4 × 4 Stixel resolution on the low-power embedded GPU of an NVIDIA Tegra Xavier.

Abstract: The emergence of deep learning has considerably advanced the state-of-the-art in cardiac magnetic resonance (CMR) segmentation. Many techniques have been proposed over the last few years, bringing the accuracy of automated segmentation close to human performance. However, these models have been all too often trained and validated using cardiac imaging samples from single clinical centres or homogeneous imaging protocols. This has prevented the development and validation of models that are generalizable across different clinical centres, imaging conditions or scanner vendors. To promote further research and scientific benchmarking in the field of generalizable deep learning for cardiac segmentation, this paper presents the results of the Multi-Centre, Multi-Vendor and Multi-Disease Cardiac Segmentation (M&Ms) Challenge, which was recently organized as part of the MICCAI 2020 Conference. A total of 14 teams submitted different solutions to the problem, combining various baseline models, data augmentation strategies, and domain adaptation techniques. The obtained results indicate the importance of intensity-driven data augmentation, as well as the need for further research to improve generalizability towards unseen scanner vendors or new imaging protocols. Furthermore, we present a new resource of 375 heterogeneous CMR datasets acquired by using four different scanner vendors in six hospitals and three different countries (Spain, Canada and Germany), which we provide as open-access for the community to enable future research in the field.

Abstract: BACKGROUND : Artificial intelligence (AI) research in colonoscopy is progressing rapidly but widespread clinical implementation is not yet a reality. We aimed to identify the top implementation research priorities. METHODS : An established modified Delphi approach for research priority setting was used. Fifteen international experts, including endoscopists and translational computer scientists/engineers, from nine countries participated in an online survey over 9 months. Questions related to AI implementation in colonoscopy were generated as a long-list in the first round, and then scored in two subsequent rounds to identify the top 10 research questions. RESULTS : The top 10 ranked questions were categorized into five themes. Theme 1: clinical trial design/end points (4 questions), related to optimum trial designs for polyp detection and characterization, determining the optimal end points for evaluation of AI, and demonstrating impact on interval cancer rates. Theme 2: technological developments (3 questions), including improving detection of more challenging and advanced lesions, reduction of false-positive rates, and minimizing latency. Theme 3: clinical adoption/integration (1 question), concerning the effective combination of detection and characterization into one workflow. Theme 4: data access/annotation (1 question), concerning more efficient or automated data annotation methods to reduce the burden on human experts. Theme 5: regulatory approval (1 question), related to making regulatory approval processes more efficient. CONCLUSIONS : This is the first reported international research priority setting exercise for AI in colonoscopy. The study findings should be used as a framework to guide future research with key stakeholders to accelerate the clinical implementation of AI in endoscopy.

Abstract: Medical image fusion plays an important role in the clinical diagnosis of several critical neurological diseases by merging complementary information available in multimodal images. In this paper, a novel CT-MR neurological image fusion framework is proposed using an optimized biologically inspired feedforward neural model in two-scale hybrid ℓ1 − ℓ0 decomposition domain using gray wolf optimization to preserve the structural as well as texture information present in source CT and MR images. Initially, the source images are subjected to two-scale ℓ1 − ℓ0 decomposition with optimized parameters, giving a scale-1 detail layer, a scale-2 detail layer and a scale-2 base layer. Two detail layers at scale-1 and 2 are fused using an optimized biologically inspired neural model and weighted average scheme based on local energy and modified spatial frequency to maximize the preservation of edges and local textures, respectively, while the scale-2 base layer gets fused using choose max rule to preserve the background information. To optimize the hyper-parameters of hybrid ℓ1 − ℓ0 decomposition and biologically inspired neural model, a fitness function is evaluated based on spatial frequency and edge index of the resultant fused image obtained by adding all the fused components. The fusion performance is analyzed by conducting extensive experiments on different CT-MR neurological images. Experimental results indicate that the proposed method provides better-fused images and outperforms the other state-of-the-art fusion methods in both visual and quantitative assessments.