Nonlinear system identification provides insight into protein folding

Much like the shape of a tool suggests its intended purpose, knowledge of a protein's structure can provide substantial insight into its function. Therefore, computational prediction of protein structure based solely on protein sequence data is a challenge of fundamental importance to biomedical research. An effective solution promises significant advances in computational drug discovery and an increased understanding of complex disease processes such as cancer. We have recently developed a novel approach to determining the secondary structure of proteins from protein sequence data which makes use of Parallel Cascade Identification (PCI), a powerful method of nonlinear system identification. PCI is used to create two layers of dynamic nonlinear systems that map divergent evolutionary profile input data into secondary structure assignment output data. PCI prediction accuracy compares well with eleven top contemporary methods over a dataset of new protein structures. Furthermore, PCI is a highly effective means to combine multiple experts achieving the highest observed accuracy over two test datasets and also the lowest rate of occurrence of a particularly detrimental class of errors. One limitation of the PCI classifiers is that approximately 13% of all amino acids cannot readily be assigned predictions due to settling times introduced by the dynamic linear component in each cascade model. In this paper we describe a number of methods designed to overcome this limitation. While zero-padding of the input sequence data proved to be the most effective solution in terms of prediction accuracy, an analysis of causal, anti-causal, and mixed cascades provides interesting insights into the biological mechanism of protein folding

Dynamic online-calibrated radio maps for indoor positioning in wireless local area networks

Context-awareness and Location-Based-Services are of great importance in mobile computing environments. Although fingerprinting provides accurate indoor positioning in Wireless Local Area Networks (WLAN), difficulty of offline site surveys and the dynamic environment changes prevent it from being practically implemented and commercially adopted. This paper introduces a novel client/server-based system that dynamically estimates and continuously calibrates a fine radio map for indoor positioning without extra network hardware or prior knowledge about the area and without time-consuming offline surveys. A modified Bayesian regression algorithm is introduced to estimate a posterior signal strength probability distribution over all locations based on online observations from WLAN access points (AP) assuming Gaussian prior centered over a logarithmic pass loss mean. To continuously adapt to dynamic changes, Bayesian kernels parameters are continuously updated and optimized genetically based on recent APs observations. The radio map is further optimized by a fast features reduction algorithm to select the most informative APs. Additionally, the system provides reliable integrity monitor (accuracy measure). Two different experiments on IEEE 802.11 networks show that the dynamic radio map provides 2-3m accuracy, which is comparable to results of an up-to-date offline radio map. Also results show the consistency of estimated accuracy measure with actual positioning accuracy

Dynamic propagation modeling for mobile users' position and heading estimation in wireless local area networks

A system for mobile users' position and heading estimation in IEEE 802.11 WLAN (WiFi) using received signal strength (RSS) approach is introduced. The basic contribution the system introduces is that it doesn't need offline training or extra special hardware. It makes use of the fact that only few online RSS measurements from visible access points (AP) around the user is needed to build local propagation model at run-time. Gaussian Process Regression (GPR) is used as a non-parametric modeling that handles non-equally spaced sparse data. Due to the few learning data points, Gaussian kernels calibration and prediction happen in a single step. This enables the system to autonomously adapt to environment changes. The estimated ranges from multiple access points (AP) are used to determine position using weighted least squares. Then, the rate of change of signal strength from multiple APs is used by a novel algorithm to estimate heading. Experiments show reliable meter-level positioning accuracy and heading estimation accuracy of 16.5 degrees

Model-based design: a report from the trenches of the DARPA Urban Challenge

The impact of model-based design on the software engineering community is impressive, and recent research in model transformations, and elegant behavioral specifications of systems has the potential to revolutionize the way in which systems are designed. Such techniques aim to raise the level of abstraction at which systems are specified, to remove the burden of producing application-specific programs with general-purpose programming. For complex real-time systems, however, the impact of model-driven approaches is not nearly so widespread. In this paper, we present a perspective of model-based design researchers who joined with software experts in robotics to enter the DARPA Urban Challenge, and to what extent model-based design techniques were used. Further, we speculate on why, according to our experience and the testimonies of many teams, the full promises of model-based design were not widely realized for the competition. Finally, we present some thoughts for the future of model-based design in complex systems such as these, and what advancements in modeling are needed to motivate small-scale projects to use model-based design in these domains