Design and evaluation of a person-centric heart monitoring system over fog computing infrastructure

Heart disease and stroke are becoming the leading cause of death worldwide. Electrocardiography monitoring devices (ECG) are the only tool that helps physicians diagnose cardiac abnormalities. Although the design of ECGs has followed closely the electronics miniaturization evolution over the years, existing wearable ECG have limited accuracy and rely on external resources to analyze the signal and evaluate heart activity. In this paper, we work towards empowering the wearable device with processing capabilities to locally analyze the signal and identify abnormal behavior. The ability to differentiate between normal and abnormal heart activity significantly reduces (a) the need to store the signals, (b) the data transmitted to the cloud and (c) the overall power consumption. Based on this concept, the HEART platform is presented that combines wearable embedded devices, mobile edge devices, and cloud services to provide on-the-spot, reliable, accurate and instant monitoring of the heart. The performance of the system is evaluated concerning the accuracy of detecting abnormal events and the power consumption of the wearable device. Results indicate that a very high percentage of success can be achieved in terms of event detection ratio and the device being operative up to a several days without the need for a recharge

Deploying AI Frameworks on Secure HPC Systems with Containers

The increasing interest in the usage of Artificial Intelligence techniques (AI) from the research community and industry to tackle "real world" problems, requires High Performance Computing (HPC) resources to efficiently compute and scale complex algorithms across thousands of nodes. Unfortunately, typical data scientists are not familiar with the unique requirements and characteristics of HPC environments. They usually develop their applications with high-level scripting languages or frameworks such as TensorFlow and the installation process often requires connection to external systems to download open source software during the build. HPC environments, on the other hand, are often based on closed source applications that incorporate parallel and distributed computing API's such as MPI and OpenMP, while users have restricted administrator privileges, and face security restrictions such as not allowing access to external systems. In this paper we discuss the issues associated with the deployment of AI frameworks in a secure HPC environment and how we successfully deploy AI frameworks on SuperMUC-NG with Charliecloud.Comment: 6 pages, 2 figures, 2019 IEEE High Performance Extreme Computing Conferenc

Video-based assistance system for training in minimally invasive surgery

In this paper, the development of an assisting system for laparoscopic surgical training is presented. With this system, we expect to facilitate the training process at the first stages of training in laparoscopic surgery and to contribute to an objective evaluation of surgical skills. To achieve this, we propose the insertion of multimedia contents and outlines of work adapted to the level of experience of trainees and the detection of the movements of the laparoscopic instrument into the monitored image. A module to track the instrument is implemented focusing on the tip of the laparoscopic tool. This tracking method does not need the presence of artificial marks or special colours to distinguish the instruments. Similarly, the system has another method based on visual tracking to localize support multimedia content in a stable position of the field of vision. Therefore, this position of the support content is adapted to the movements of the camera or the working area. Experimental results are presented to show the feasibility of the proposed system for assisting in laparoscopic surgical training

Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions

Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages, and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we 1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and 2) provide guidelines for determining the appropriate tools for each step. We analyze various combinations of different tools and expose the tradeoffs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious and effective choices for each step of the genome assembly pipeline using nanopore sequence data. Also, with the help of bottlenecks we have found, developers can improve the current tools or build new ones that are both accurate and fast, in order to overcome the high error rates of the nanopore sequencing technology.Comment: To appear in Briefings in Bioinformatics (BIB), 201

An LLVM Instrumentation Plug-in for Score-P

Reducing application runtime, scaling parallel applications to higher numbers of processes/threads, and porting applications to new hardware architectures are tasks necessary in the software development process. Therefore, developers have to investigate and understand application runtime behavior. Tools such as monitoring infrastructures that capture performance relevant data during application execution assist in this task. The measured data forms the basis for identifying bottlenecks and optimizing the code. Monitoring infrastructures need mechanisms to record application activities in order to conduct measurements. Automatic instrumentation of the source code is the preferred method in most application scenarios. We introduce a plug-in for the LLVM infrastructure that enables automatic source code instrumentation at compile-time. In contrast to available instrumentation mechanisms in LLVM/Clang, our plug-in can selectively include/exclude individual application functions. This enables developers to fine-tune the measurement to the required level of detail while avoiding large runtime overheads due to excessive instrumentation.Comment: 8 page