Automated extraction of chemical structure information from digital raster images

Background: To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results: This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader -- a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion: The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links to scientific research articles.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90875/1/Saitou8.pd

A Self-timed Ring Based True Random Number Generator

International audienceSelf-timed rings are oscillators in which several events can evolve evenly-spaced in time thanks to analog effects inherent to the ring stage structure. One of their interesting features is that they provide precise high-speed multiphase signals. This paper presents a true random number generator that exploits the jitter of events propagating in a self-timed ring with a high entropy. Designs implemented in Altera Cyclone III and Xilinx Virtex 5 devices provide high quality random bit sequences passing FIPS 140-1 and NIST SP 800-22 statistical tests at a high bit rate

Time-domain optimization of amplifiers based on distributed genetic algorithms

Thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Electrical and Computer EngineeringThe work presented in this thesis addresses the task of circuit optimization, helping the designer facing the high performance and high efficiency circuits demands of the market and technology evolution. A novel framework is introduced, based on time-domain analysis, genetic algorithm optimization, and distributed processing. The time-domain optimization methodology is based on the step response of the amplifier. The main advantage of this new time-domain methodology is that, when a given settling-error is reached within the desired settling-time, it is automatically guaranteed that the amplifier has enough open-loop gain, AOL, output-swing (OS), slew-rate (SR), closed loop bandwidth and closed loop stability. Thus, this simplification of the circuit‟s evaluation helps the optimization process to converge faster. The method used to calculate the step response expression of the circuit is based on the inverse Laplace transform applied to the transfer function, symbolically, multiplied by 1/s (which represents the unity input step). Furthermore, may be applied to transfer functions of circuits with unlimited number of zeros/poles, without approximation in order to keep accuracy. Thus, complex circuit, with several design/optimization degrees of freedom can also be considered. The expression of the step response, from the proposed methodology, is based on the DC bias operating point of the devices of the circuit. For this, complex and accurate device models (e.g. BSIM3v3) are integrated. During the optimization process, the time-domain evaluation of the amplifier is used by the genetic algorithm, in the classification of the genetic individuals. The time-domain evaluator is integrated into the developed optimization platform, as independent library, coded using C programming language. The genetic algorithms have demonstrated to be a good approach for optimization since they are flexible and independent from the optimization-objective. Different levels of abstraction can be optimized either system level or circuit level. Optimization of any new block is basically carried-out by simply providing additional configuration files, e.g. chromosome format, in text format; and the circuit library where the fitness value of each individual of the genetic algorithm is computed. Distributed processing is also employed to address the increasing processing time demanded by the complex circuit analysis, and the accurate models of the circuit devices. The communication by remote processing nodes is based on Message Passing interface (MPI). It is demonstrated that the distributed processing reduced the optimization run-time by more than one order of magnitude. Platform assessment is carried by several examples of two-stage amplifiers, which have been optimized and successfully used, embedded, in larger systems, such as data converters. A dedicated example of an inverter-based self-biased two-stage amplifier has been designed, laid-out and fabricated as a stand-alone circuit and experimentally evaluated. The measured results are a direct demonstration of the effectiveness of the proposed time-domain optimization methodology.Portuguese Foundation for the Science and Technology (FCT

D2.1 - Report on Selected TRNG and PUF Principles

This report represents the final version of Deliverable 2.1 of the HECTOR work package WP2. It is a result of discussions and work on Task 2.1 of all HECTOR partners involved in WP2. The aim of the Deliverable 2.1 is to select principles of random number generators (RNGs) and physical unclonable functions (PUFs) that fulfill strict technology, design and security criteria. For example, the selected RNGs must be suitable for implementation in logic devices according to the German AIS20/31 standard. Correspondingly, the selected PUFs must be suitable for applying similar security approach. A standard PUF evaluation approach does not exist, yet, but it should be proposed in the framework of the project. Selected RNGs and PUFs should be then thoroughly evaluated from the point of view of security and the most suitable principles should be implemented in logic devices, such as Field Programmable Logic Arrays (FPGAs) and Application Specific Integrated Circuits (ASICs) during the next phases of the project

Linearization of Time-encoded ADCs Architectures for Smart MEMS Sensors in Low Power CMOS Technology

Mención Internacional en el título de doctorIn the last few years, the development of mobile technologies and machine learning applications has increased the demand of MEMS-based digital microphones. Mobile devices have several microphones enabling noise canceling, acoustic beamforming and speech recognition. With the development of machine learning applications the interest to integrate sensors with neural networks has increased. This has driven the interest to develop digital microphones in nanometer CMOS nodes where the microphone analog-front end and digital processing, potentially including neural networks, is integrated on the same chip. Traditionally, analog-to-digital converters (ADCs) in digital microphones have been implemented using high order Sigma-Delta modulators. The most common technique to implement these high order Sigma-Selta modulators is switchedcapacitor CMOS circuits. Recently, to reduce power consumption and make them more suitable for tasks that require always-on operation, such as keyword recognition, switched-capacitor circuits have been improved using inverter-based operational amplifier integrators. Alternatively, switched-capacitor based Sigma- Delta modulators have been replaced by continuous time Sigma-Delta converters. Nevertheless, in both implementations the input signal is voltage encoded across the modulator, making the integration in smaller CMOS nodes more challenging due to the reduced voltage supply. An alternative technique consists on encoding the input signal on time (or frequency) instead of voltage. This is what time-encoded converters do. Lately, time-encoding converters have gained popularity as they are more suitable to nanometer CMOS nodes than Sigma-Delta converters. Among the ones that have drawn more interest we find voltage-controlled oscillator based ADCs (VCOADCs). VCO-ADCs can be implemented using CMOS inverter based ring oscillators (RO) and digital circuitry. They also show noise-shaping properties. This makes them a very interesting alternative for implementation of ADCs in nanometer CMOS nodes. Nevertheless, two main circuit impairments are present in VCO-ADCs, and both come from the oscillator non-idealities. The first of them is the oscillator phase noise, that reduces the resolution of the ADC. The second is the non-linear tuning curve of the oscillator, that results in harmonic distortion at medium to high input amplitudes. In this thesis we analyze the use of time encoding ADCs for MEMS microphones with special focus on ring oscillator based ADCs (RO-ADCs). Firstly, we study the use of a dual-slope based SAR noise shaped quantizer (SAR-NSQ) in sigma-delta loops. This quantizer adds and extra level of noise-shaping to the modulator, improving the resolution. The quantizer is explained, and equations for the noise transfer function (NTF) of a third order sigma-delta using a second order filter and the NSQ are presented. Secondly, we move our attention to the topic of RO-ADCs. We present a high dynamic range MEMS microphone 130nm CMOS chip based on an open-loop VCO-ADC. This dissertation shows the implementation of the analog front-end that includes the oscillator and the MEMS interface, with a focus on achieving low power consumption with low noise and a high dynamic range. The digital circuitry is left to be explained by the coauthor of the chip in his dissertation. The chip achieves a 80dBA peak SNDR and 108dB dynamic range with a THD of 1.5% at 128 dBSPL with a power consumption of 438μW. After that, we analyze the use of a frequency-dependent-resistor (FDR) to implement an unsampled feedback loop around the oscillator. The objective is to reduce distortion. Additionally phase noise mitigation is achieved. A first topology including an operational amplifier to increase the loop gain is analyzed. The design is silicon proven in a 130 nm CMOS chip that achieves a 84 dBA peak SNDR with an analog power consumption of 600μW. A second topology without the operational amplifier is also analyzed. Two chips are designed with this topology. The first chip in 130 nm CMOS is a full VCO-ADC including the frequencyto- digital converter (F2D). This chip achieves a peak SNDR of 76.6 dBA with a power consumption of 482μW. The second chip includes only the oscillator and is implemented in 55nm CMOS. The peak SNDR is 78.15 dBA and the analog power consumption is 153μW. To finish this thesis, two circuits that use an FDR with a ring oscillator are presented. The first is a capacity-to-digital converter (CDC). The second is a filter made with an FDR and an oscillator intended for voice activity detection tasks (VAD).En los últimos años, el desarrollo de las tecnologías móviles y las aplicaciones de machine-learning han aumentado la demanda de micrófonos digitales basados en MEMS. Los dipositivos móviles tienen varios micrófonos que permiten la cancelación de ruido, el beamforming o conformación de haces y el reconocimiento de voz. Con el desarrollo de aplicaciones de aprendizaje automático, el interés por integrar sensores con redes neuronales ha aumentado. Esto ha impulsado el interés por desarrollar micrófonos digitales en nodos CMOS nanométricos donde el front-end analógico y el procesamiento digital del micrófono, que puede incluir redes neuronales, está integrado en el mismo chip. Tradicionalmente, los convertidores analógicos-digitales (ADC) en micrófonos digitales han sido implementados utilizando moduladores Sigma-Delta de orden elevado. La técnica más común para implementar estos moduladores Sigma- Delta es el uso de circuitos CMOS de capacidades conmutadas. Recientemente, para reducir el consumo de potencia y hacerlos más adecuados para las tareas que requieren una operación continua, como el reconocimiento de palabras clave, los convertidores Sigma-Delta de capacidades conmutadas has sido mejorados con el uso de integradores implementados con amplificadores operacionales basados en inversores CMOS. Alternativamente, los Sigma-Delta de capacidades conmutadas han sido reemplazados por moduladores en tiempo continuo. No obstante, en ambas implementaciones, la señal de entrada es codificada en voltaje durante el proceso de conversión, lo que hace que la integración en nodos CMOS más pequeños sea complicada debido a la menor tensión de alimentación. Una técnica alternativa consiste en codificar la señal de entrada en tiempo (o frecuencia) en lugar de tensión. Esto es lo que hacen los convertidores de codificación temporal. Recientemente, los convertidores de codificación temporal han ganado popularidad ya que son más adecuados para nodos CMOS nanométricos que los convertidores Sigma-Delta. Entre los que más interés han despertado encontramos los ADCs basados en osciladores controlados por tensión (VCO-ADC). Los VCO-ADC se pueden implementar usando osciladores en anillo (RO) implementados con inversores CMOS y circuitos digitales. Esta familia de convertidores también tiene conformado de ruido. Esto los convierte en una alternativa muy interesante para la implementación de convertidores en nodos CMOS nanométricos. Sin embargo, dos problemas principales están presentes en este tipo de ADCs debidos ambos a las no idealidades del oscilador. El primero de los problemas es la presencia de ruido de fase en el oscilador, lo que reduce la resolución del ADC. El segundo es la curva de conversion voltaje-frecuencia no lineal del oscilador, lo que causa distorsión a amplitudes medias y altas. En esta tesis analizamos el uso de ADCs de codificación temporal para micrófonos MEMS, con especial interés en ADCS basados en osciladores de anillo (RO-ADC). En primer lugar, estudiamos el uso de un cuantificador SAR con conformado de ruido (SAR-NSQ) en moduladores Sigma-Delta. Este cuantificador agrega un orden adicional de conformado de ruido al modulador, mejorando la resolución. En este documento se explica el cuantificador y obtienen las ecuaciones para la función de transferencia de ruido (NTF) de un sigma-delta de tercer orden usando un filtro de segundo orden y el NSQ. En segundo lugar, dirigimos nuestra atención al tema de los RO-ADC. Presentamos el chip de un micrófono MEMS de alto rango dinámico en CMOS de 130 nm basado en un VCO-ADC de bucle abierto. En esta tesis se explica la implementación del front-end analógico que incluye el oscilador y la interfaz con el MEMS. Esta implementación se ha llevado a cabo con el objetivo de lograr un bajo consumo de potencia, un bajo nivel de ruido y un alto rango dinámico. La descripción del back-end digital se deja para la tesis del couator del chip. La SNDR de pico del chip es de 80dBA y el rango dinámico de 108dB con una THD de 1,5% a 128 dBSPL y un consumo de potencia de 438μW. Finalmente, se analiza el uso de una resistencia dependiente de frecuencia (FDR) para implementar un bucle de realimentación no muestreado alrededor del oscilador. El objetivo es reducir la distorsión. Además, también se logra la mitigación del ruido de fase del oscilador. Se analyza una primera topologia de realimentación incluyendo un amplificador operacional para incrementar la ganancia de bucle. Este diseño se prueba en silicio en un chip CMOS de 130nm que logra un pico de SNDR de 84 dBA con un consumo de potencia de 600μW en la parte analógica. Seguidamente, se analiza una segunda topología sin el amplificador operacional. Se fabrican y miden dos chips diseñados con esta topologia. El primero de ellos en CMOS de 130 nm es un VCO-ADC completo que incluye el convertidor de frecuencia a digital (F2D). Este chip alcanza un pico SNDR de 76,6 dBA con un consumo de potencia de 482μW. El segundo incluye solo el oscilador y está implementado en CMOS de 55nm. El pico SNDR es 78.15 dBA y el el consumo de potencia analógica es de 153μW. Para cerrar esta tesis, se presentan dos circuitos que usan la FDR con un oscilador en anillo. El primero es un convertidor de capacidad a digital (CDC). El segundo es un filtro realizado con una FDR y un oscilador, enfocado a tareas de detección de voz (VAD).Programa de Doctorado en Ingeniería Eléctrica, Electrónica y Automática por la Universidad Carlos III de MadridPresidente: Antonio Jesús Torralba Silgado.- Secretaria: María Luisa López Vallejo.- Vocal: Pieter Rombout

Musings on Symbol Recognition

This paper does not pretend to be yet another survey on symbol recognition methods. It will rather try to take a step back, look at the main efforts done in that area throughout the years and propose some interesting directions to investigate

Design and Control of Power Converters 2020

In this book, nine papers focusing on different fields of power electronics are gathered, all of which are in line with the present trends in research and industry. Given the generality of the Special Issue, the covered topics range from electrothermal models and losses models in semiconductors and magnetics to converters used in high-power applications. In this last case, the papers address specific problems such as the distortion due to zero-current detection or fault investigation using the fast Fourier transform, all being focused on analyzing the topologies of high-power high-density applications, such as the dual active bridge or the H-bridge multilevel inverter. All the papers provide enough insight in the analyzed issues to be used as the starting point of any research. Experimental or simulation results are presented to validate and help with the understanding of the proposed ideas. To summarize, this book will help the reader to solve specific problems in industrial equipment or to increase their knowledge in specific fields

Probabilistic Image Models and their Massively Parallel Architectures : A Seamless Simulation- and VLSI Design-Framework Approach

Algorithmic robustness in real-world scenarios and real-time processing capabilities are the two essential and at the same time contradictory requirements modern image-processing systems have to fulfill to go significantly beyond state-of-the-art systems. Without suitable image processing and analysis systems at hand, which comply with the before mentioned contradictory requirements, solutions and devices for the application scenarios of the next generation will not become reality. This issue would eventually lead to a serious restraint of innovation for various branches of industry. This thesis presents a coherent approach to the above mentioned problem. The thesis at first describes a massively parallel architecture template and secondly a seamless simulation- and semiconductor-technology-independent design framework for a class of probabilistic image models, which are formulated on a regular Markovian processing grid. The architecture template is composed of different building blocks, which are rigorously derived from Markov Random Field theory with respect to the constraints of \it massively parallel processing \rm and \it technology independence\rm. This systematic derivation procedure leads to many benefits: it decouples the architecture characteristics from constraints of one specific semiconductor technology; it guarantees that the derived massively parallel architecture is in conformity with theory; and it finally guarantees that the derived architecture will be suitable for VLSI implementations. The simulation-framework addresses the unique hardware-relevant simulation needs of MRF based processing architectures. Furthermore the framework ensures a qualified representation for simulation of the image models and their massively parallel architectures by means of their specific simulation modules. This allows for systematic studies with respect to the combination of numerical, architectural, timing and massively parallel processing constraints to disclose novel insights into MRF models and their hardware architectures. The design-framework rests upon a graph theoretical approach, which offers unique capabilities to fulfill the VLSI demands of massively parallel MRF architectures: the semiconductor technology independence guarantees a technology uncommitted architecture for several design steps without restricting the design space too early; the design entry by means of behavioral descriptions allows for a functional representation without determining the architecture at the outset; and the topology-synthesis simplifies and separates the data- and control-path synthesis. Detailed results discussed in the particular chapters together with several additional results collected in the appendix will further substantiate the claims made in this thesis