Matching Items (28)
Description
Signal processing techniques have been used extensively in many engineering problems and in recent years its application has extended to non-traditional research fields such as biological systems. Many of these applications require extraction of a signal or parameter of interest from degraded measurements. One such application is mass spectrometry immunoassay (MSIA) which has been one of the primary methods of biomarker discovery techniques. MSIA analyzes protein molecules as potential biomarkers using time of flight mass spectrometry (TOF-MS). Peak detection in TOF-MS is important for biomarker analysis and many other MS related application. Though many peak detection algorithms exist, most of them are based on heuristics models. One of the ways of detecting signal peaks is by deploying stochastic models of the signal and noise observations. Likelihood ratio test (LRT) detector, based on the Neyman-Pearson (NP) lemma, is an uniformly most powerful test to decision making in the form of a hypothesis test. The primary goal of this dissertation is to develop signal and noise models for the electrospray ionization (ESI) TOF-MS data. A new method is proposed for developing the signal model by employing first principles calculations based on device physics and molecular properties. The noise model is developed by analyzing MS data from careful experiments in the ESI mass spectrometer. A non-flat baseline in MS data is common. The reasons behind the formation of this baseline has not been fully comprehended. A new signal model explaining the presence of baseline is proposed, though detailed experiments are needed to further substantiate the model assumptions. Signal detection schemes based on these signal and noise models are proposed. A maximum likelihood (ML) method is introduced for estimating the signal peak amplitudes. The performance of the detection methods and ML estimation are evaluated with Monte Carlo simulation which shows promising results. An application of these methods is proposed for fractional abundance calculation for biomarker analysis, which is mathematically robust and fundamentally different than the current algorithms. Biomarker panels for type 2 diabetes and cardiovascular disease are analyzed using existing MS analysis algorithms. Finally, a support vector machine based multi-classification algorithm is developed for evaluating the biomarkers' effectiveness in discriminating type 2 diabetes and cardiovascular diseases and is shown to perform better than a linear discriminant analysis based classifier.
ContributorsBuddi, Sai (Author) / Taylor, Thomas (Thesis advisor) / Cochran, Douglas (Thesis advisor) / Nelson, Randall (Committee member) / Duman, Tolga (Committee member) / Arizona State University (Publisher)
Created2012
Description
This project is to develop a new method to generate GPS waypoints for better terrain mapping efficiency using an UAV. To create a map of a desired terrain, an UAV is used to capture images at particular GPS locations. These images are then stitched together to form a complete map of the terrain. To generate a good map using image stitching, the images are desired to have a certain percentage of overlap between them. In high windy condition, an UAV may not capture image at desired GPS location, which in turn interferes with the desired percentage of overlap between images; both frontal and sideways; thus causing discrepancies while stitching the images together. The information about the exact GPS locations at which the images are captured can be found on the flight logs that are stored in the Ground Control Station and the Auto pilot board. The objective is to look at the flight logs, predict the waypoints at which the UAV might have swayed from the desired flight path. If there are locations where flight swayed from intended path, the code should generate a new set of waypoints for a correction flight. This will save the time required for stitching the images together, thus making the whole process faster and more efficient.
ContributorsGhadage, Prasannakumar Prakashrao (Author) / Saripalli, Srikanth (Thesis advisor) / Berman, Spring M (Thesis advisor) / Thangavelautham, Jekanthan (Committee member) / Arizona State University (Publisher)
Created2014
Description
Immunosignaturing is a new immunodiagnostic technology that uses random-sequence peptide microarrays to profile the humoral immune response. Though the peptides have little sequence homology to any known protein, binding of serum antibodies may be detected, and the pattern correlated to disease states. The aim of my dissertation is to analyze the factors affecting the binding patterns using monoclonal antibodies and determine how much information may be extracted from the sequences. Specifically, I examined the effects of antibody concentration, competition, peptide density, and antibody valence. Peptide binding could be detected at the low concentrations relevant to immunosignaturing, and a monoclonal's signature could even be detected in the presences of 100 fold excess naive IgG. I also found that peptide density was important, but this effect was not due to bivalent binding. Next, I examined in more detail how a polyreactive antibody binds to the random sequence peptides compared to protein sequence derived peptides, and found that it bound to many peptides from both sets, but with low apparent affinity. An in depth look at how the peptide physicochemical properties and sequence complexity revealed that there were some correlations with properties, but they were generally small and varied greatly between antibodies. However, on a limited diversity but larger peptide library, I found that sequence complexity was important for antibody binding. The redundancy on that library did enable the identification of specific sub-sequences recognized by an antibody. The current immunosignaturing platform has little repetition of sub-sequences, so I evaluated several methods to infer antibody epitopes. I found two methods that had modest prediction accuracy, and I developed a software application called GuiTope to facilitate the epitope prediction analysis. None of the methods had sufficient accuracy to identify an unknown antigen from a database. In conclusion, the characteristics of the immunosignaturing platform observed through monoclonal antibody experiments demonstrate its promise as a new diagnostic technology. However, a major limitation is the difficulty in connecting the signature back to the original antigen, though larger peptide libraries could facilitate these predictions.
ContributorsHalperin, Rebecca (Author) / Johnston, Stephen A. (Thesis advisor) / Bordner, Andrew (Committee member) / Taylor, Thomas (Committee member) / Stafford, Phillip (Committee member) / Arizona State University (Publisher)
Created2011
Description
This dissertation describes a novel, low cost strategy of using particle streak (track) images for accurate micro-channel velocity field mapping. It is shown that 2-dimensional, 2-component fields can be efficiently obtained using the spatial variation of particle track lengths in micro-channels. The velocity field is a critical performance feature of many microfluidic devices. Since it is often the case that un-modeled micro-scale physics frustrates principled design methodologies, particle based velocity field estimation is an essential design and validation tool. Current technologies that achieve this goal use particle constellation correlation strategies and rely heavily on costly, high-speed imaging hardware. The proposed image/ video processing based method achieves comparable accuracy for fraction of the cost. In the context of micro-channel velocimetry, the usability of particle streaks has been poorly studied so far. Their use has remained restricted mostly to bulk flow measurements and occasional ad-hoc uses in microfluidics. A second look at the usability of particle streak lengths in this work reveals that they can be efficiently used, after approximately 15 years from their first use for micro-channel velocimetry. Particle tracks in steady, smooth microfluidic flows is mathematically modeled and a framework for using experimentally observed particle track lengths for local velocity field estimation is introduced here, followed by algorithm implementation and quantitative verification. Further, experimental considerations and image processing techniques that can facilitate the proposed methods are also discussed in this dissertation. Unavailability of benchmarked particle track image data motivated the implementation of a simulation framework with the capability to generate exposure time controlled particle track image sequence for velocity vector fields. This dissertation also describes this work and shows that arbitrary velocity fields designed in computational fluid dynamics software tools can be used to obtain such images. Apart from aiding gold-standard data generation, such images would find use for quick microfluidic flow field visualization and help improve device designs.
ContributorsMahanti, Prasun (Author) / Cochran, Douglas (Thesis advisor) / Taylor, Thomas (Thesis advisor) / Hayes, Mark (Committee member) / Zhang, Junshan (Committee member) / Arizona State University (Publisher)
Created2011
Description
This thesis examines the application of statistical signal processing approaches to data arising from surveys intended to measure psychological and sociological phenomena underpinning human social dynamics. The use of signal processing methods for analysis of signals arising from measurement of social, biological, and other non-traditional phenomena has been an important and growing area of signal processing research over the past decade. Here, we explore the application of statistical modeling and signal processing concepts to data obtained from the Global Group Relations Project, specifically to understand and quantify the effects and interactions of social psychological factors related to intergroup conflicts. We use Bayesian networks to specify prospective models of conditional dependence. Bayesian networks are determined between social psychological factors and conflict variables, and modeled by directed acyclic graphs, while the significant interactions are modeled as conditional probabilities. Since the data are sparse and multi-dimensional, we regress Gaussian mixture models (GMMs) against the data to estimate the conditional probabilities of interest. The parameters of GMMs are estimated using the expectation-maximization (EM) algorithm. However, the EM algorithm may suffer from over-fitting problem due to the high dimensionality and limited observations entailed in this data set. Therefore, the Akaike information criterion (AIC) and the Bayesian information criterion (BIC) are used for GMM order estimation. To assist intuitive understanding of the interactions of social variables and the intergroup conflicts, we introduce a color-based visualization scheme. In this scheme, the intensities of colors are proportional to the conditional probabilities observed.
ContributorsLiu, Hui (Author) / Taylor, Thomas (Thesis advisor) / Cochran, Douglas (Thesis advisor) / Zhang, Junshan (Committee member) / Arizona State University (Publisher)
Created2012
Description
Toward the ambitious long-term goal of a fleet of cooperating Flexible Autonomous Machines operating in an uncertain Environment (FAME), this thesis addresses various perception and control problems in autonomous aerial robotics. The objective of this thesis is to motivate the use of perspective cues in single images for the planning and control of quadrotors in indoor environments. In addition to providing empirical evidence for the abundance of such cues in indoor environments, the usefulness of these perspective cues is demonstrated by designing a control algorithm for navigating a quadrotor in indoor corridors. An Extended Kalman Filter (EKF), implemented on top of the vision algorithm, serves to improve the robustness of the algorithm to changing illumination.
In this thesis, vanishing points are the perspective cues used to control and navigate a quadrotor in an indoor corridor. Indoor corridors are an abundant source of parallel lines. As a consequence of perspective projection, parallel lines in the real world, that are not parallel to the plane of the camera, intersect at a point in the image. This point is called the vanishing point of the image. The vanishing point is sensitive to the lateral motion of the camera and hence the quadrotor. By tracking the position of the vanishing point in every image frame, the quadrotor can navigate along the center of the corridor.
Experiments are conducted using the Augmented Reality (AR) Drone 2.0. The drone is equipped with the following componenets: (1) 720p forward facing camera for vanishing point detection, (2) 240p downward facing camera, (3) Inertial Measurement Unit (IMU) for attitude control , (4) Ultrasonic sensor for estimating altitude, (5) On-board 1 GHz Processor for processing low level commands. The reliability of the vision algorithm is presented by flying the drone in indoor corridors.
In this thesis, vanishing points are the perspective cues used to control and navigate a quadrotor in an indoor corridor. Indoor corridors are an abundant source of parallel lines. As a consequence of perspective projection, parallel lines in the real world, that are not parallel to the plane of the camera, intersect at a point in the image. This point is called the vanishing point of the image. The vanishing point is sensitive to the lateral motion of the camera and hence the quadrotor. By tracking the position of the vanishing point in every image frame, the quadrotor can navigate along the center of the corridor.
Experiments are conducted using the Augmented Reality (AR) Drone 2.0. The drone is equipped with the following componenets: (1) 720p forward facing camera for vanishing point detection, (2) 240p downward facing camera, (3) Inertial Measurement Unit (IMU) for attitude control , (4) Ultrasonic sensor for estimating altitude, (5) On-board 1 GHz Processor for processing low level commands. The reliability of the vision algorithm is presented by flying the drone in indoor corridors.
ContributorsRavishankar, Nikhilesh (Author) / Rodriguez, Armando A (Thesis advisor) / Tsakalis, Konstantinos (Committee member) / Berman, Spring M (Committee member) / Arizona State University (Publisher)
Created2018
Description
In the past decade, real-world applications of Vertical Take-Off and Landing (VTOL) Unmanned Aerial Vehicles (UAV) have increased significantly. There has been growing interest in one of these types of UAVs, called a tail-sitter UAV, due to its VTOL and cruise capabilities. This thesis presents the fabrication of a spherical tail-sitter UAV and derives a nonlinear mathematical model of its dynamics. The singularity in the attitude kinematics of the vehicle is avoided using Modified Rodrigues Parameters (MRP). The model parameters of the fabricated vehicle are calculated using the bifilar pendulum method, a motor stand, and ANSYS simulation software. Then the trim conditions at hover are calculated for the nonlinear model, and the rotational dynamics of the model are linearized around the equilibrium state with the calculated trim conditions. Robust controllers are designed to stabilize the UAV in hover using the H2 control and H-infinity control methodologies. For H2 control design, Linear Quadratic Gaussian (LQG) control is used. For the H infinity control design, Linear Matrix Inequalities (LMI) with frequency-dependent weights are derived and solved using the MATLAB toolbox YALMIP. In addition, a nonlinear controller is designed using the Sum-of-Squares (SOS) method to implement large-angle maneuvers for transitions between horizontal flight and vertical flight. Finally, the linear controllers are implemented in the fabricated spherical tail-sitter UAV for experimental validation. The performance trade-offs and the response of the UAV with the linear and nonlinear controllers are discussed in detail.
ContributorsRamasubramaniyan, Sri Ram Prasath (Author) / Berman, Spring M (Thesis advisor) / Mignolet, Marc P (Committee member) / Tsakalis, Konstantinos S (Committee member) / Arizona State University (Publisher)
Created2018
Description
Robotic swarms can potentially perform complicated tasks such as exploration and mapping at large space and time scales in a parallel and robust fashion. This thesis presents strategies for mapping environmental features of interest – specifically obstacles, collision-free paths, generating a metric map and estimating scalar density fields– in an unknown domain using data obtained by a swarm of resource-constrained robots. First, an approach was developed for mapping a single obstacle using a swarm of point-mass robots with both directed and random motion. The swarm population dynamics are modeled by a set of advection-diffusion-reaction partial differential equations (PDEs) in which a spatially-dependent indicator function marks the presence or absence of the obstacle in the domain. The indicator function is estimated by solving an optimization problem with PDEs as constraints. Second, a methodology for constructing a topological map of an unknown environment was proposed, which indicates collision-free paths for navigation, from data collected by a swarm of finite-sized robots. As an initial step, the number of topological features in the domain was quantified by applying tools from algebraic topology, to a probability function over the explored region that indicates the presence of obstacles. A topological map of the domain is then generated using a graph-based wave propagation algorithm. This approach is further extended, enabling the technique to construct a metric map of an unknown domain with obstacles using uncertain position data collected by a swarm of resource-constrained robots, filtered using intensity measurements of an external signal. Next, a distributed method was developed to construct the occupancy grid map of an unknown environment using a swarm of inexpensive robots or mobile sensors with limited communication. In addition to this, an exploration strategy which combines information theoretic ideas with Levy walks was also proposed. Finally, the problem of reconstructing a two-dimensional scalar field using observations from a subset of a sensor network in which each node communicates its local measurements to its neighboring nodes was addressed. This problem reduces to estimating the initial condition of a large interconnected system with first-order linear dynamics, which can be solved as an optimization problem.
ContributorsRamachandran, Ragesh Kumar (Author) / Berman, Spring M (Thesis advisor) / Mignolet, Marc (Committee member) / Artemiadis, Panagiotis (Committee member) / Marvi, Hamid (Committee member) / Robinson, Michael (Committee member) / Arizona State University (Publisher)
Created2018
Description
Toward the ambitious long-term goal of developing a robotic circus, this thesis addresses key steps toward the development of a ground robot that can catch a ball. Toward this end, we examine nonlinear quadratic drag trajectories for a tossed ball. Relevant least square error fits are provided. It is also shown how a Kalman filter and Extended Kalman filter can be used to generate estimates for the ball trajectory.
Several simple ball intercept policies are examined. This includes open loop and closed loop policies. It is also shown how a low-cost differential-drive research grade robot can be built, modeled and controlled. Directions for developing more complex xy planar intercept policies are also briefly discussed. In short, the thesis establishes a foundation for future work on developing a practical ball catching robot.
Several simple ball intercept policies are examined. This includes open loop and closed loop policies. It is also shown how a low-cost differential-drive research grade robot can be built, modeled and controlled. Directions for developing more complex xy planar intercept policies are also briefly discussed. In short, the thesis establishes a foundation for future work on developing a practical ball catching robot.
ContributorsDAS, NIRANGKUSH (Author) / Rodriguez, Armando A (Thesis advisor) / Berman, Spring M (Thesis advisor) / Artemiadis, Panagiotis (Committee member) / Arizona State University (Publisher)
Created2018
Description
Aberrant glycosylation has been shown to be linked to specific cancers, and using this idea, it was proposed that the levels of glycans in the blood could predict stage I adenocarcinoma. To track this glycosylation, glycan were broken down into glycan nodes via methylation analysis. This analysis utilized information from N-, O-, and lipid linked glycans detected from gas chromatography-mass spectrometry. The resulting glycan node-ratios represent the initial quantitative data that were used in this experiment.
For this experiment, two Sets of 50 µl blood plasma samples were provided by NYU Medical School. These samples were then analyzed by Dr. Borges’s lab so that they contained normalized biomarker levels from patients with stage 1 adenocarcinoma and control patients with matched age, smoking status, and gender were examined. An ROC curve was constructed under individual and paired conditions and AUC calculated in Wolfram Mathematica 10.2. Methods such as increasing size of training set, using hard vs. soft margins, and processing biomarkers together and individually were used in order to increase the AUC. Using a soft margin for this particular data set was proved to be most useful compared to the initial set hard margin, raising the AUC from 0.6013 to 0.6585. In regards to which biomarkers yielded the better value, 6-Glc/6-Man and 3,6-Gal glycan node ratios had the best with 0.7687 AUC and a sensitivity of .7684 and specificity of .6051. While this is not enough accuracy to become a primary diagnostic tool for diagnosing stage I adenocarcinoma, the methods examined in the paper should be evaluated further. . By comparison, the current clinical standard blood test for prostate cancer that has an AUC of only 0.67.
For this experiment, two Sets of 50 µl blood plasma samples were provided by NYU Medical School. These samples were then analyzed by Dr. Borges’s lab so that they contained normalized biomarker levels from patients with stage 1 adenocarcinoma and control patients with matched age, smoking status, and gender were examined. An ROC curve was constructed under individual and paired conditions and AUC calculated in Wolfram Mathematica 10.2. Methods such as increasing size of training set, using hard vs. soft margins, and processing biomarkers together and individually were used in order to increase the AUC. Using a soft margin for this particular data set was proved to be most useful compared to the initial set hard margin, raising the AUC from 0.6013 to 0.6585. In regards to which biomarkers yielded the better value, 6-Glc/6-Man and 3,6-Gal glycan node ratios had the best with 0.7687 AUC and a sensitivity of .7684 and specificity of .6051. While this is not enough accuracy to become a primary diagnostic tool for diagnosing stage I adenocarcinoma, the methods examined in the paper should be evaluated further. . By comparison, the current clinical standard blood test for prostate cancer that has an AUC of only 0.67.
ContributorsDe Jesus, Celine Spicer (Author) / Taylor, Thomas (Thesis director) / Borges, Chad (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05