Motivation: During the last decade, improvements in high-throughput sequencing have generated a wealth of genomic data. Functionally interpreting these sequences and finding the biological signals that are hallmarks of gene function and regulation is currently mostly done using automated genome annotation platforms, which mainly rely on integrated machine learning frameworks to identify different functional sites of interest, including splice sites. Splicing is an essential step in the gene regulation process, and the correct identification of splice sites is a major cornerstone in a genome annotation system. Results: In this paper, we present SpliceRover, a predictive deep learning approach that outperforms the state-of-the-art in splice site prediction. SpliceRover uses convolutional neural networks (CNNs), which have been shown to obtain cutting edge performance on a wide variety of prediction tasks. We adapted this approach to deal with genomic sequence inputs, and show it consistently outperforms already existing approaches, with relative improvements in prediction effectiveness of up to 80.9% when measured in terms of false discovery rate. However, a major criticism of CNNs concerns their ‘black box’ nature, as mechanisms to obtain insight into their reasoning processes are limited. To facilitate interpretability of the SpliceRover models, we introduce an approach to visualize the biologically relevant information learnt. We show that our visualization approach is able to recover features known to be important for splice site prediction (binding motifs around the splice site, presence of polypyrimidine tracts and branch points), as well as reveal new features (e.g. several types of exclusion patterns near splice sites). Availability and implementation: SpliceRover is available as a web service. The prediction tool and instructions can be found at http://bioit2.irc.ugent.be/splicerover/. Supplementary information: Supplementary data are available at Bioinformatics online.

This paper discusses a privacy-protected video surveillance system that makes use of JPEG extended range (JPEG XR). JPEG XR offers a low-complexity solution for the scalable coding of high-resolution images. To address privacy concerns, face regions are detected and scrambled in the transform domain, taking into account the quality and spatial scalability features of JPEG XR. Experiments were conducted to investigate the performance of our surveillance system, considering visual distortion, bit stream overhead, and security aspects. Our results demonstrate that subband-adaptive scrambling is able to conceal privacy-sensitive face regions with a feasible level of protection. In addition, our results show that subband-adaptive scrambling of face regions outperforms subband-adaptive scrambling of frames in terms of coding efficiency, except when low video bit rates are in use.

Using face annotation for effective management of personal photos in online social networks (OSNs) is currently of considerable practical interest. In this paper, we propose a novel collaborative face recognition (FR) framework, improving the accuracy of face annotation by effectively making use of multiple FR engines available in an OSN. Our collaborative FR framework consists of two major parts: selection of FR engines and merging (or fusion) of multiple FR results. The selection of FR engines aims at determining a set of personalized FR engines that are suitable for recognizing query face images belonging to a particular member of the OSN. For this purpose, we exploit both social network context in an OSN and social context in personal photo collections. In addition, to take advantage of the availability of multiple FR results retrieved from the selected FR engines, we devise two effective solutions for merging FR results, adopting traditional techniques for combining multiple classifier results. Experiments were conducted using 547 991 personal photos collected from an existing OSN. Our results demonstrate that the proposed collaborative FR method is able to significantly improve the accuracy of face annotation, compared to conventional FR approaches that only make use of a single FR engine. Further, we demonstrate that our collaborative FR framework has a low computational cost and comes with a design that is suited for deployment in a decentralized OSN.

Glaucoma is a leading eye disease, causing vision loss by gradually affecting peripheral vision if left untreated. Current diagnosis of glaucoma is performed by ophthalmologists, human experts who typically need to analyze different types of medical images generated by different types of medical equipment: fundus, Retinal Nerve Fiber Layer (RNFL), Optical Coherence Tomography (OCT) disc, OCT macula, perimetry, and/or perimetry deviation. Capturing and analyzing these medical images is labor intensive and time consuming. In this paper, we present a novel approach for glaucoma diagnosis and localization, only relying on fundus images that are analyzed by making use of state-of-the-art deep learning techniques. Specifically, our approach towards glaucoma diagnosis and localization leverages Convolutional Neural Networks (CNNs) and Gradient-weighted Class Activation Mapping (Grad-CAM), respectively. We built and evaluated different predictive models using a large set of fundus images, collected and labeled by ophthalmologists at Samsung Medical Center (SMC). Our experimental results demonstrate that our most effective predictive model is able to achieve a high diagnosis accuracy of 96%, as well as a high sensitivity of 96% and a high specificity of 100% for Dataset-Optic Disc (OD), a set of center-cropped fundus images highlighting the optic disc. Furthermore, we present Medinoid, a publicly-available prototype web application for computer-aided diagnosis and localization of glaucoma, integrating our most effective predictive model in its back-end.