Bayesian Optimization with Dimension Scheduling: Application to Biological Systems

Bayesian Optimization (BO) is a data-efficient method for global black-box optimization of an expensive-to-evaluate fitness function. BO typically assumes that computation cost of BO is cheap, but experiments are time consuming or costly. In practice, this allows us to optimize ten or fewer critical parameters in up to 1,000 experiments. But experiments may be less expensive than BO methods assume: In some simulation models, we may be able to conduct multiple thousands of experiments in a few hours, and the computational burden of BO is no longer negligible compared to experimentation time. To address this challenge we introduce a new Dimension Scheduling Algorithm (DSA), which reduces the computational burden of BO for many experiments. The key idea is that DSA optimizes the fitness function only along a small set of dimensions at each iteration. This DSA strategy (1) reduces the necessary computation time, (2) finds good solutions faster than the traditional BO method, and (3) can be parallelized straightforwardly. We evaluate the DSA in the context of optimizing parameters of dynamic models of microalgae metabolism and show faster convergence than traditional BO

Bayesian Optimization with Dimension Scheduling: Application to Biological Systems

Bayesian Optimization (BO) is a data-efficient method for global black-box optimization of an expensive-to-evaluate fitness function. BO typically assumes that computation cost of BO is cheap, but experiments are time consuming or costly. In practice, this allows us to optimize ten or fewer critical parameters in up to 1,000 experiments. But experiments may be less expensive than BO methods assume: In some simulation models, we may be able to conduct multiple thousands of experiments in a few hours, and the computational burden of BO is no longer negligible compared to experimentation time. To address this challenge we introduce a new Dimension Scheduling Algorithm (DSA), which reduces the computational burden of BO for many experiments. The key idea is that DSA optimizes the fitness function only along a small set of dimensions at each iteration. This DSA strategy (1) reduces the necessary computation time, (2) finds good solutions faster than the traditional BO method, and (3) can be parallelized straightforwardly. We evaluate the DSA in the context of optimizing parameters of dynamic models of microalgae metabolism and show faster convergence than traditional BO

Traffic Management Algorithms in Differentiated Services Networks

The Differentiated Services (DiffServ) Architecture, a Quality of Service (QoS) solution being worked on by an IETF work group, is aimed to solve the increasing problems with no service guarantees in the current Internet. New services such as video-on-demand and IP-telephony will be unusable without some sort of service guarantees on which to build applications on. A replacement architecture for the Integrated Services (IntServ) Architecture is needed because of its problems with overhead and scalability. This master thesis studies and evaluates traffic algorithms, specifically scheduling and active queue management algorithms, within the Differentiated Services area using the Network Simulator. The studies investigate Differentiated Services network stability and performance through noise influenced simulations. Results show that against unresponsive users network stability and performance mainly depends on the used scheduling algorithm

Scheduling of Two Real-Time Tasks with Non-Fixed Sampling Rates Modelled on an Unmanned Air Vehicle with Autonomous Navigation and Image Processing Capabilities

Control tasks and scheduling problems are usually treated in separate contexts, but when they are implemented in a real-time system their co-design becomes essential, as it will allow a better use of the limited computational resources. This project regards the creation of a scheduling algorithm for two real-time tasks sharing the same Processing Unit. Once a theoretical solution has been developed, it will be applied to a realistic scenario: UAV control with image processing abilities.ope

Guidance and control of sounding rockets

Includes abstract.Includes bibliographical references.This dissertation presents the design, fabrication and testing of a sounding rocket flight computer for the South African Astronomical Observatory (SAAO). Sounding rockets carry instruments with which to take measurements in the Earth’s atmosphere in sub-orbital flight. The South African Astronomical Observatory (SAAO) requires a flight computer for their sounding rockets. This flight computer is to replace the current commercial flight computer currently in use improving on its functionality and expandability

A Unified And Green Platform For Smartphone Sensing

Smartphones have become key communication and entertainment devices in people\u27s daily life. Sensors on (or attached to) smartphones can enable attractive sensing applications in different domains, including environmental monitoring, social networking, healthcare, transportation, etc. Most existing smartphone sensing systems are application-specific. How to leverage smartphones\u27 sensing capability to make them become unified information providers for various applications has not yet been fully explored. This dissertation presents a unified and green platform for smartphone sensing, which has the following desirable features: 1) It can support various smartphone sensing applications; 2) It is personalizable; 2) It is energy-efficient; and 3) It can be easily extended to support new sensors. Two novel sensing applications are built and integrated into this unified platform: SOR and LIPS. SOR is a smartphone Sensing based Objective Ranking (SOR) system. Different from a few subjective online review and recommendation systems (such as Yelp and TripAdvisor), SOR ranks a target place based on data collected via smartphone sensing. LIPS is a system that learns the LIfestyles of mobile users via smartPhone Sensing (LIPS). Combining both unsupervised and supervised learning, a hybrid scheme is proposed to characterize lifestyle and predict future activities of mobile users. This dissertation also studies how to use the cloud as a coordinator to assist smartphones for sensing collaboratively with the objective of reducing sensing energy consumption. A novel probabilistic model is built to address the GPS-less energy-efficient crowd sensing problem. Provably-good approximation algorithms are presented to enable smartphones to sense collaboratively without accurate locations such that sensing coverage requirements can be met with limited energy consumption

Navigation Recommender:Real-Time iGNSS QoS Prediction for Navigation Services

Global Navigation Satellite Systems (GNSSs), especially Global Positioning System (GPS), have become commonplace in mobile devices and are the most preferred geo-positioning sensors for many location-based applications. Besides GPS, other GNSSs under development or deployment are GLONASS, Galileo, and Compass. These four GNSSs are planned to be integrated in the near future. It is anticipated that integrated GNSSs (iGNSSs) will improve the overall satellite-based geo-positioning performance. However, one major shortcoming of any GNSS and iGNSSs is Quality of Service (QoS) degradation due to signal blockage and attenuation by the surrounding environments, particularly in obstructed areas. GNSS QoS uncertainty is the root cause of positioning ambiguity, poor localization performance, application freeze, and incorrect guidance in navigation applications. In this research, a methodology, called iGNSS QoS prediction, that can provide GNSS QoS on desired and prospective routes is developed. Six iGNSS QoS parameters suitable for navigation are defined: visibility, availability, accuracy, continuity, reliability, and flexibility. The iGNSS QoS prediction methodology, which includes a set of algorithms, encompasses four modules: segment sampling, point-based iGNSS QoS prediction, tracking-based iGNSS QoS prediction, and iGNSS QoS segmentation. Given that iGNSS QoS prediction is data- and compute-intensive and navigation applications require real-time solutions, an efficient satellite selection algorithm is developed and distributed computing platforms, mainly grids and clouds, for achieving real-time performance are explored. The proposed methodology is unique in several respects: it specifically addresses the iGNSS positioning requirements of navigation systems/services; it provides a new means for route choices and routing in navigation systems/services; it is suitable for different modes of travel such as driving and walking; it takes high-resolution 3D data into account for GNSS positioning; and it is based on efficient algorithms and can utilize high-performance and scalable computing platforms such as grids and clouds to provide real-time solutions. A number of experiments were conducted to evaluate the developed methodology and the algorithms using real field test data (GPS coordinates). The experimental results show that the methodology can predict iGNSS QoS in various areas, especially in problematic areas

Machine Learning in Wireless Sensor Networks: Algorithms, Strategies, and Applications

Wireless sensor networks monitor dynamic environments that change rapidly over time. This dynamic behavior is either caused by external factors or initiated by the system designers themselves. To adapt to such conditions, sensor networks often adopt machine learning techniques to eliminate the need for unnecessary redesign. Machine learning also inspires many practical solutions that maximize resource utilization and prolong the lifespan of the network. In this paper, we present an extensive literature review over the period 2002-2013 of machine learning methods that were used to address common issues in wireless sensor networks (WSNs). The advantages and disadvantages of each proposed algorithm are evaluated against the corresponding problem. We also provide a comparative guide to aid WSN designers in developing suitable machine learning solutions for their specific application challenges.Comment: Accepted for publication in IEEE Communications Surveys and Tutorial

A Novel Side-Channel in Real-Time Schedulers

We demonstrate the presence of a novel scheduler side-channel in preemptive, fixed-priority real-time systems (RTS); examples of such systems can be found in automotive systems, avionic systems, power plants and industrial control systems among others. This side-channel can leak important timing information such as the future arrival times of real-time tasks.This information can then be used to launch devastating attacks, two of which are demonstrated here (on real hardware platforms). Note that it is not easy to capture this timing information due to runtime variations in the schedules, the presence of multiple other tasks in the system and the typical constraints (e.g., deadlines) in the design of RTS. Our ScheduLeak algorithms demonstrate how to effectively exploit this side-channel. A complete implementation is presented on real operating systems (in Real-time Linux and FreeRTOS). Timing information leaked by ScheduLeak can significantly aid other, more advanced, attacks in better accomplishing their goals