Enhancing Estimates of Breakpoints in Genome Copy Number Alteration using Confidence Masks

Chromosomal structural changes in human body known as copy number alteration (CNA) are often associated with diseases, such as various forms of cancer. Therefore, accurate estimation of breakpoints of the CNAs is important to understand the genetic basis of many diseases. The high‐resolution comparative genomic hybridization (HR‐CGH) and single‐nucleotide polymorphism (SNP) technologies enable cost‐efficient and high‐throughput CNA detection. However, probing provided using these profiles gives data highly contaminated by intensive Gaussian noise having white properties. We observe the probabilistic properties of CNA in HR‐CGH and SNP measurements and show that jitter in the breakpoints can statistically be described with either the discrete skew Laplace distribution when the segmental signal‐to‐noise ratio (SNR) exceeds unity or modified Bessel function‐based approximation when SNR is <1. Based upon these approaches, the confidence masks can be developed and used to enhance the estimates of the CNAs for the given confidence probability by removing some unlikely existing breakpoints

A Parametric Sound Object Model for Sound Texture Synthesis

This thesis deals with the analysis and synthesis of sound textures based on parametric sound objects. An overview is provided about the acoustic and perceptual principles of textural acoustic scenes, and technical challenges for analysis and synthesis are considered. Four essential processing steps for sound texture analysis are identifi ed, and existing sound texture systems are reviewed, using the four-step model as a guideline. A theoretical framework for analysis and synthesis is proposed. A parametric sound object synthesis (PSOS) model is introduced, which is able to describe individual recorded sounds through a fi xed set of parameters. The model, which applies to harmonic and noisy sounds, is an extension of spectral modeling and uses spline curves to approximate spectral envelopes, as well as the evolution of parameters over time. In contrast to standard spectral modeling techniques, this representation uses the concept of objects instead of concatenated frames, and it provides a direct mapping between sounds of diff erent length. Methods for automatic and manual conversion are shown. An evaluation is presented in which the ability of the model to encode a wide range of di fferent sounds has been examined. Although there are aspects of sounds that the model cannot accurately capture, such as polyphony and certain types of fast modulation, the results indicate that high quality synthesis can be achieved for many different acoustic phenomena, including instruments and animal vocalizations. In contrast to many other forms of sound encoding, the parametric model facilitates various techniques of machine learning and intelligent processing, including sound clustering and principal component analysis. Strengths and weaknesses of the proposed method are reviewed, and possibilities for future development are discussed

Analysis of Embedded Controllers Subject to Computational Overruns

Microcontrollers have become an integral part of modern everyday embedded systems, such as smart bikes, cars, and drones. Typically, microcontrollers operate under real-time constraints, which require the timely execution of programs on the resource-constrained hardware. As embedded systems are becoming increasingly more complex, microcontrollers run the risk of violating their timing constraints, i.e., overrunning the program deadlines. Breaking these constraints can cause severe damage to both the embedded system and the humans interacting with the device. Therefore, it is crucial to analyse embedded systems properly to ensure that they do not pose any significant danger if the microcontroller overruns a few deadlines.However, there are very few tools available for assessing the safety and performance of embedded control systems when considering the implementation of the microcontroller. This thesis aims to fill this gap in the literature by presenting five papers on the analysis of embedded controllers subject to computational overruns. Details about the real-time operating system's implementation are included into the analysis, such as what happens to the controller's internal state representation when the timing constraints are violated. The contribution includes theoretical and computational tools for analysing the embedded system's stability, performance, and real-time properties.The embedded controller is analysed under three different types of timing violations: blackout events (when no control computation is completed during long periods), weakly-hard constraints (when the number of deadline overruns is constrained over a window), and stochastic overruns (when violations of timing constraints are governed by a probabilistic process). These scenarios are combined with different implementation policies to reduce the gap between the analysis and its practical applicability. The analyses are further validated with a comprehensive experimental campaign performed on both a set of physical processes and multiple simulations.In conclusion, the findings of this thesis reveal that the effect deadline overruns have on the embedded system heavily depends the implementation details and the system's dynamics. Additionally, the stability analysis of embedded controllers subject to deadline overruns is typically conservative, implying that additional insights can be gained by also analysing the system's performance

Machine Learning

Machine Learning can be defined in various ways related to a scientific domain concerned with the design and development of theoretical and implementation tools that allow building systems with some Human Like intelligent behavior. Machine learning addresses more specifically the ability to improve automatically through experience

The Telecommunications and Data Acquisition Report

This quarterly publication (July-Sept. 1986) provides archival reports on developments in programs managed by JPL's Office of Telecommunications and Data Acquisition (TDA). In space communications, radio navigation, radio science, and ground-based radio astronomy, it reports on activities of the Deep Space Network (DSN) and its associated Ground Communications Facility (GCF) in planning, in supporting research and technology, in implementation, and in operations. This work is performed for NASA's Office of Space Tracking and Data Systems (OSTDS). In geodynamics, the publication reports on the application of radio interferometry at microwave frequencies for geodynamic measurements. In the search for extraterrestrial intelligence (SETI), it reports on implementation and operations for searching the microwave spectrum. The latter two programs are performed for NASA's Office of Space Science and Applications (OSSA)

Simulation Studies of Digital Filters for the Phase-II Upgrade of the Liquid-Argon Calorimeters of the ATLAS Detector at the High-Luminosity LHC

Am Large Hadron Collider und am ATLAS-Detektor werden umfangreiche Aufrüstungsarbeiten vorgenommen. Diese Arbeiten sind in mehrere Phasen gegliedert und umfassen unter Anderem Änderungen an der Ausleseelektronik der Flüssigargonkalorimeter; insbesondere ist es geplant, während der letzten Phase ihren Primärpfad vollständig auszutauschen. Die Elektronik besteht aus einem analogen und einem digitalen Teil: während ersterer die Signalpulse verstärkt und sie zur leichteren Abtastung verformt, führt letzterer einen Algorithmus zur Energierekonstruktion aus. Beide Teile müssen während der Aufrüstung verbessert werden, damit der Detektor interessante Kollisionsereignisse präzise rekonstruieren und uninteressante effizient verwerfen kann. In dieser Dissertation werden Simulationsstudien präsentiert, die sowohl die analoge als auch die digitale Auslese der Flüssigargonkalorimeter optimieren. Die Korrektheit der Simulation wird mithilfe von Kalibrationsdaten geprüft, die im sog. Run 2 des ATLAS-Detektors aufgenommen worden sind. Der Einfluss verschiedener Parameter der Signalverformung auf die Energieauflösung wird analysiert und die Nützlichkeit einer erhöhten Abtastrate von 80 MHz untersucht. Des Weiteren gibt diese Arbeit eine Übersicht über lineare und nichtlineare Energierekonstruktionsalgorithmen. Schließlich wird eine Auswahl von ihnen hinsichtlich ihrer Leistungsfähigkeit miteinander verglichen. Es wird gezeigt, dass ein Erhöhen der Ordnung des Optimalfilters, der gegenwärtig verwendete Algorithmus, die Energieauflösung um 2 bis 3 % verbessern kann, und zwar in allen Regionen des Detektors. Der Wiener Filter mit Vorwärtskorrektur, ein nichtlinearer Algorithmus, verbessert sie um bis zu 10 % in einigen Regionen, verschlechtert sie aber in anderen. Ein Zusammenhang dieses Verhaltens mit der Wahrscheinlichkeit fälschlich detektierter Kalorimetertreffer wird aufgezeigt und mögliche Lösungen werden diskutiert.:1 Introduction 2 An Overview of High-Energy Particle Physics 2.1 The Standard Model of Particle Physics 2.2 Verification of the Standard Model 2.3 Beyond the Standard Model 3 LHC, ATLAS, and the Liquid-Argon Calorimeters 3.1 The Large Hadron Collider 3.2 The ATLAS Detector 3.3 The ATLAS Liquid-Argon Calorimeters 4 Upgrades to the ATLAS Liquid-Argon Calorimeters 4.1 Physics Goals 4.2 Phase-I Upgrade 4.3 Phase-II Upgrade 5 Noise Suppression With Digital Filters 5.1 Terminology 5.2 Digital Filters 5.3 Wiener Filter 5.4 Matched Wiener Filter 5.5 Matched Wiener Filter Without Bias 5.6 Timing Reconstruction, Optimal Filtering, and Selection Criteria 5.7 Forward Correction 5.8 Sparse Signal Restoration 5.9 Artificial Neural Networks 6 Simulation of the ATLAS Liquid-Argon Calorimeter Readout Electronics 6.1 AREUS 6.2 Hit Generation and Sampling 6.3 Pulse Shapes 6.4 Thermal Noise 6.5 Quantization 6.6 Digital Filters 6.7 Statistical Analysis 7 Results of the Readout Electronics Simulation Studies 7.1 Statistical Treatment 7.2 Simulation Verification Using Run-2 Data 7.3 Dependence of the Noise on the Shaping Time 7.4 The Analog Readout Electronics and the ADC 7.5 The Optimal Filter (OF) 7.6 The Wiener Filter 7.7 The Wiener Filter with Forward Correction (WFFC) 7.8 Final Comparison and Conclusions 8 Conclusions and Outlook AppendicesThe Large Hadron Collider and the ATLAS detector are undergoing a comprehensive upgrade split into multiple phases. This effort also affects the liquid-argon calorimeters, whose main readout electronics will be replaced completely during the final phase. The electronics consist of an analog and a digital portion: the former amplifies the signal and shapes it to facilitate sampling, the latter executes an energy reconstruction algorithm. Both must be improved during the upgrade so that the detector may accurately reconstruct interesting collision events and efficiently suppress uninteresting ones. In this thesis, simulation studies are presented that optimize both the analog and the digital readout of the liquid-argon calorimeters. The simulation is verified using calibration data that has been measured during Run 2 of the ATLAS detector. The influence of several parameters of the analog shaping stage on the energy resolution is analyzed and the utility of an increased signal sampling rate of 80 MHz is investigated. Furthermore, a number of linear and non-linear energy reconstruction algorithms is reviewed and the performance of a selection of them is compared. It is demonstrated that increasing the order of the Optimal Filter, the algorithm currently in use, improves energy resolution by 2 to 3 % in all detector regions. The Wiener filter with forward correction, a non-linear algorithm, gives an improvement of up to 10 % in some regions, but degrades the resolution in others. A link between this behavior and the probability of falsely detected calorimeter hits is shown and possible solutions are discussed.:1 Introduction 2 An Overview of High-Energy Particle Physics 2.1 The Standard Model of Particle Physics 2.2 Verification of the Standard Model 2.3 Beyond the Standard Model 3 LHC, ATLAS, and the Liquid-Argon Calorimeters 3.1 The Large Hadron Collider 3.2 The ATLAS Detector 3.3 The ATLAS Liquid-Argon Calorimeters 4 Upgrades to the ATLAS Liquid-Argon Calorimeters 4.1 Physics Goals 4.2 Phase-I Upgrade 4.3 Phase-II Upgrade 5 Noise Suppression With Digital Filters 5.1 Terminology 5.2 Digital Filters 5.3 Wiener Filter 5.4 Matched Wiener Filter 5.5 Matched Wiener Filter Without Bias 5.6 Timing Reconstruction, Optimal Filtering, and Selection Criteria 5.7 Forward Correction 5.8 Sparse Signal Restoration 5.9 Artificial Neural Networks 6 Simulation of the ATLAS Liquid-Argon Calorimeter Readout Electronics 6.1 AREUS 6.2 Hit Generation and Sampling 6.3 Pulse Shapes 6.4 Thermal Noise 6.5 Quantization 6.6 Digital Filters 6.7 Statistical Analysis 7 Results of the Readout Electronics Simulation Studies 7.1 Statistical Treatment 7.2 Simulation Verification Using Run-2 Data 7.3 Dependence of the Noise on the Shaping Time 7.4 The Analog Readout Electronics and the ADC 7.5 The Optimal Filter (OF) 7.6 The Wiener Filter 7.7 The Wiener Filter with Forward Correction (WFFC) 7.8 Final Comparison and Conclusions 8 Conclusions and Outlook Appendice

Hidden Markov Models

Hidden Markov Models (HMMs), although known for decades, have made a big career nowadays and are still in state of development. This book presents theoretical issues and a variety of HMMs applications in speech recognition and synthesis, medicine, neurosciences, computational biology, bioinformatics, seismology, environment protection and engineering. I hope that the reader will find this book useful and helpful for their own research

Advances in Image Processing, Analysis and Recognition Technology

For many decades, researchers have been trying to make computers’ analysis of images as effective as the system of human vision is. For this purpose, many algorithms and systems have previously been created. The whole process covers various stages, including image processing, representation and recognition. The results of this work can be applied to many computer-assisted areas of everyday life. They improve particular activities and provide handy tools, which are sometimes only for entertainment, but quite often, they significantly increase our safety. In fact, the practical implementation of image processing algorithms is particularly wide. Moreover, the rapid growth of computational complexity and computer efficiency has allowed for the development of more sophisticated and effective algorithms and tools. Although significant progress has been made so far, many issues still remain, resulting in the need for the development of novel approaches