Evangelia I. Zacharaki

Ilja Gubins, Marten L. Chaillet, Gijs van der Schot et al.

Cryo-electron tomography (cryo-ET) is an imaging technique that allows three-dimensional visualization of macro-molecular assemblies under near-native conditions. Cryo-ET comes with a number of challenges, mainly low signal-to-noise and inability to obtain images from all angles. Computational methods are key to analyze cryo-electron tomograms. To promote innovation in computational methods, we generate a novel simulated dataset to benchmark different methods of localization and classification of biological macromolecules in tomograms. Our publicly available dataset contains ten tomographic reconstructions of simulated cell-like volumes. Each volume contains twelve different types of complexes, varying in size, function and structure. In this paper, we have evaluated seven different methods of finding and classifying proteins. Seven research groups present results obtained with learning-based methods and trained on the simulated dataset, as well as a baseline template matching (TM), a traditional method widely used in cryo-ET research. We show that learning-based approaches can achieve notably better localization and classification performance than TM. We also experimentally confirm that there is a negative relationship between particle size and performance for all methods.

Nikos D. Fakotakis, Stavros Nousias, Gerasimos Arvanitis et al.

Asthma is a common, usually long-term respiratory disease with negative impact on global society and economy. Treatment involves using medical devices (inhalers) that distribute medication to the airways and its efficiency depends on the precision of the inhalation technique. There is a clinical need for objective methods to assess the inhalation technique, during clinical consultation. Integrated health monitoring systems, equipped with sensors, enable the recognition of drug actuation, embedded with sound signal detection, analysis and identification, from intelligent structures, that could provide powerful tools for reliable content management. Health monitoring systems equipped with sensors, embedded with sound signal detection, enable the recognition of drug actuation and could be used for effective audio content analysis. This paper revisits sound pattern recognition with machine learning techniques for asthma medication adherence assessment and presents the Respiratory and Drug Actuation (RDA) Suite (https://gitlab.com/vvr/monitoring-medication-adherence/rda-benchmark) for benchmarking and further research. The RDA Suite includes a set of tools for audio processing, feature extraction and classification procedures and is provided along with a dataset, consisting of respiratory and drug actuation sounds. The classification models in RDA are implemented based on conventional and advanced machine learning and deep networks' architectures. This study provides a comparative evaluation of the implemented approaches, examines potential improvements and discusses on challenges and future tendencies.

Gerasimos Arvanitis, Nikolaos Stagakis, Evangelia I. Zacharaki et al.

Autonomous vehicles are expected to operate safely in real-life road conditions in the next years. Nevertheless, unanticipated events such as the existence of unexpected objects in the range of the road, can put safety at risk. The advancement of sensing and communication technologies and Internet of Things may facilitate the recognition of hazardous situations and information exchange in a cooperative driving scheme, providing new opportunities for the increase of collaborative situational awareness. Safe and unobtrusive visualization of the obtained information may nowadays be enabled through the adoption of novel Augmented Reality (AR) interfaces in the form of windshields. Motivated by these technological opportunities, we propose in this work a saliency-based distributed, cooperative obstacle detection and rendering scheme for increasing the driver's situational awareness through (i) automated obstacle detection, (ii) AR visualization and (iii) information sharing (upcoming potential dangers) with other connected vehicles or road infrastructure. An extensive evaluation study using a variety of real datasets for pothole detection showed that the proposed method provides favorable results and features compared to other recent and relevant approaches.

Afshine Amidi, Shervine Amidi, Dimitrios Vlachakis et al.

During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data Bank has increased more than 15 fold since 1999, which enabled the expansion of models that aim at predicting enzymatic function via their amino acid composition. Amino acid sequence however is less conserved in nature than protein structure and therefore considered a less reliable predictor of protein function. This paper presents EnzyNet, a novel 3D-convolutional neural networks classifier that predicts the Enzyme Commission number of enzymes based only on their voxel-based spatial structure. The spatial distribution of biochemical properties was also examined as complementary information. The 2-layer architecture was investigated on a large dataset of 63,558 enzymes from the Protein Data Bank and achieved an accuracy of 78.4% by exploiting only the binary representation of the protein shape. Code and datasets are available at https://github.com/shervinea/enzynet.