Heterogeneous multicore systems for signal processing

This thesis explores the capabilities of heterogeneous multi-core systems, based on multiple Graphics Processing Units (GPUs) in a standard desktop framework. Multi-GPU accelerated desk side computers are an appealing alternative to other high performance computing (HPC) systems: being composed of commodity hardware components fabricated in large quantities, their price-performance ratio is unparalleled in the world of high performance computing. Essentially bringing “supercomputing to the masses”, this opens up new possibilities for application fields where investing in HPC resources had been considered unfeasible before. One of these is the field of bioelectrical imaging, a class of medical imaging technologies that occupy a low-cost niche next to million-dollar systems like functional Magnetic Resonance Imaging (fMRI). In the scope of this work, several computational challenges encountered in bioelectrical imaging are tackled with this new kind of computing resource, striving to help these methods approach their true potential. Specifically, the following main contributions were made: Firstly, a novel dual-GPU implementation of parallel triangular matrix inversion (TMI) is presented, addressing an crucial kernel in computation of multi-mesh head models of encephalographic (EEG) source localization. This includes not only a highly efficient implementation of the routine itself achieving excellent speedups versus an optimized CPU implementation, but also a novel GPU-friendly compressed storage scheme for triangular matrices. Secondly, a scalable multi-GPU solver for non-hermitian linear systems was implemented. It is integrated into a simulation environment for electrical impedance tomography (EIT) that requires frequent solution of complex systems with millions of unknowns, a task that this solution can perform within seconds. In terms of computational throughput, it outperforms not only an highly optimized multi-CPU reference, but related GPU-based work as well. Finally, a GPU-accelerated graphical EEG real-time source localization software was implemented. Thanks to acceleration, it can meet real-time requirements in unpreceeded anatomical detail running more complex localization algorithms. Additionally, a novel implementation to extract anatomical priors from static Magnetic Resonance (MR) scansions has been included

Fast algorithm for real-time rings reconstruction

The GAP project is dedicated to study the application of GPU in several contexts in which real-time response is important to take decisions. The definition of real-time depends on the application under study, ranging from answer time of μs up to several hours in case of very computing intensive task. During this conference we presented our work in low level triggers [1] [2] and high level triggers [3] in high energy physics experiments, and specific application for nuclear magnetic resonance (NMR) [4] [5] and cone-beam CT [6]. Apart from the study of dedicated solution to decrease the latency due to data transport and preparation, the computing algorithms play an essential role in any GPU application. In this contribution, we show an original algorithm developed for triggers application, to accelerate the ring reconstruction in RICH detector when it is not possible to have seeds for reconstruction from external trackers

Accelerating Radiation Dose Calculation with High Performance Computing and Machine Learning for Large-scale Radiotherapy Treatment Planning

Radiation therapy is powered by modern techniques in precise planning and executionof radiation delivery, which are being rapidly improved to maximize its benefit to cancerpatients. In the last decade, radiotherapy experienced the introduction of advanced methodsfor automatic beam orientation optimization, real-time tumor tracking, daily planadaptation, and many others, which improve the radiation delivery precision, planning easeand reproducibility, and treatment efficacy. However, such advanced paradigms necessitatethe calculation of orders of magnitude more causal dose deposition data, increasing the timerequirement of all pre-planning dose calculation. Principles of high-performance computingand machine learning were applied to address the insufficient speeds of widely-used dosecalculation algorithms to facilitate translation of these advanced treatment paradigms intoclinical practice.To accelerate CT-guided X-ray therapies, Collapsed-Cone Convolution-Superposition(CCCS), a state-of-the-art analytical dose calculation algorithm, was accelerated through itsnovel implementation on highly parallelized GPUs. This context-based GPU-CCCS approachtakes advantage of X-ray dose deposition compactness to parallelize calculation acrosshundreds of beamlets, reducing hardware-specific overheads, and enabling acceleration bytwo to three orders of magnitude compared to existing GPU-based beamlet-by-beamletapproaches. Near-linear increases in acceleration are achieved with a distributed, multi-GPUimplementation of context-based GPU-CCCS.Dose calculation for MR-guided treatment is complicated by electron return effects(EREs), exhibited by ionizing electrons in the strong magnetic field of the MRI scanner. EREsnecessitate the use of much slower Monte Carlo (MC) dose calculation, limiting the clinicalapplication of advanced treatment paradigms due to time restrictions. An automaticallydistributed framework for very-large-scale MC dose calculation was developed, grantinglinear scaling of dose calculation speed with the number of utilized computational cores. Itwas then harnessed to efficiently generate a large dataset of paired high- and low-noise MCdoses in a 1.5 tesla magnetic field, which were used to train a novel deep convolutionalneural network (CNN), DeepMC, to predict low-noise dose from faster high-noise MC-simulation. DeepMC enables 38-fold acceleration of MR-guided X-ray beamlet dosecalculation, while remaining synergistic with existing MC acceleration techniques to achievemultiplicative speed improvements.This work redefines the expectation of X-ray dose calculation speed, making it possibleto apply new highly-beneficial treatment paradigms to standard clinical practice for the firsttime

Event-based Vision: A Survey

Event cameras are bio-inspired sensors that differ from conventional frame cameras: Instead of capturing images at a fixed rate, they asynchronously measure per-pixel brightness changes, and output a stream of events that encode the time, location and sign of the brightness changes. Event cameras offer attractive properties compared to traditional cameras: high temporal resolution (in the order of microseconds), very high dynamic range (140 dB vs. 60 dB), low power consumption, and high pixel bandwidth (on the order of kHz) resulting in reduced motion blur. Hence, event cameras have a large potential for robotics and computer vision in challenging scenarios for traditional cameras, such as low-latency, high speed, and high dynamic range. However, novel methods are required to process the unconventional output of these sensors in order to unlock their potential. This paper provides a comprehensive overview of the emerging field of event-based vision, with a focus on the applications and the algorithms developed to unlock the outstanding properties of event cameras. We present event cameras from their working principle, the actual sensors that are available and the tasks that they have been used for, from low-level vision (feature detection and tracking, optic flow, etc.) to high-level vision (reconstruction, segmentation, recognition). We also discuss the techniques developed to process events, including learning-based techniques, as well as specialized processors for these novel sensors, such as spiking neural networks. Additionally, we highlight the challenges that remain to be tackled and the opportunities that lie ahead in the search for a more efficient, bio-inspired way for machines to perceive and interact with the world

Modelling of a System for the Detection of Weak Signals Through Text Mining and NLP. Proposal of Improvement by a Quantum Variational Circuit

Tesis por compendio[ES] En esta tesis doctoral se propone y evalúa un sistema para detectar señales débiles (weak signals) relacionadas con cambios futuros trascendentales. Si bien la mayoría de las soluciones conocidas se basan en el uso de datos estructurados, el sistema propuesto detecta cuantitativamente estas señales utilizando información heterogénea y no estructurada de fuentes científicas, periodísticas y de redes sociales. La predicción de nuevas tendencias en un medio tiene muchas aplicaciones. Por ejemplo, empresas y startups se enfrentan a cambios constantes en sus mercados que son muy difíciles de predecir. Por esta razón, el desarrollo de sistemas para detectar automáticamente cambios futuros significativos en una etapa temprana es relevante para que cualquier organización tome decisiones acertadas a tiempo. Este trabajo ha sido diseñado para obtener señales débiles del futuro en cualquier campo dependiendo únicamente del conjunto de datos de entrada de documentos. Se aplican técnicas de minería de textos y procesamiento del lenguaje natural para procesar todos estos documentos. Como resultado, se obtiene un mapa con un ranking de términos, una lista de palabras clave clasificadas automáticamente y una lista de expresiones formadas por múltiples palabras. El sistema completo se ha probado en cuatro sectores diferentes: paneles solares, inteligencia artificial, sensores remotos e imágenes médicas. Este trabajo ha obtenido resultados prometedores, evaluados con dos metodologías diferentes. Como resultado, el sistema ha sido capaz de detectar de forma satisfactoria nuevas tendencias en etapas muy tempranas que se han vuelto cada vez más importantes en la actualidad. La computación cuántica es un nuevo paradigma para una multitud de aplicaciones informáticas. En esta tesis doctoral también se presenta un estudio de las tecnologías disponibles en la actualidad para la implementación física de qubits y puertas cuánticas, estableciendo sus principales ventajas y desventajas, y los marcos disponibles para la programación e implementación de circuitos cuánticos. Con el fin de mejorar la efectividad del sistema, se describe un diseño de un circuito cuántico basado en máquinas de vectores de soporte (SVM) para la resolución de problemas de clasificación. Este circuito está especialmente diseñado para los ruidosos procesadores cuánticos de escala intermedia (NISQ) que están disponibles actualmente. Como experimento, el circuito ha sido probado en un computador cuántico real basado en qubits superconductores por IBM como una mejora para el subsistema de minería de texto en la detección de señales débiles. Los resultados obtenidos con el experimento cuántico muestran también conclusiones interesantes y una mejora en el rendimiento de cerca del 20% sobre los sistemas convencionales, pero a su vez confirman que aún se requiere un desarrollo tecnológico continuo para aprovechar al máximo la computación cuántica.[CA] En aquesta tesi doctoral es proposa i avalua un sistema per detectar senyals febles (weak signals) relacionats amb canvis futurs transcendentals. Si bé la majoria de solucions conegudes es basen en l'ús de dades estructurades, el sistema proposat detecta quantitativament aquests senyals utilitzant informació heterogènia i no estructurada de fonts científiques, periodístiques i de xarxes socials. La predicció de noves tendències en un medi té moltes aplicacions. Per exemple, empreses i startups s'enfronten a canvis constants als seus mercats que són molt difícils de predir. Per això, el desenvolupament de sistemes per detectar automàticament canvis futurs significatius en una etapa primerenca és rellevant perquè les organitzacions prenguen decisions encertades a temps. Aquest treball ha estat dissenyat per obtenir senyals febles del futur a qualsevol camp depenent únicament del conjunt de dades d'entrada de documents. S'hi apliquen tècniques de mineria de textos i processament del llenguatge natural per processar tots aquests documents. Com a resultat, s'obté un mapa amb un rànquing de termes, un llistat de paraules clau classificades automàticament i un llistat d'expressions formades per múltiples paraules. El sistema complet s'ha provat en quatre sectors diferents: panells solars, intel·ligència artificial, sensors remots i imatges mèdiques. Aquest treball ha obtingut resultats prometedors, avaluats amb dues metodologies diferents. Com a resultat, el sistema ha estat capaç de detectar de manera satisfactòria noves tendències en etapes molt primerenques que s'han tornat cada cop més importants actualment. La computació quàntica és un paradigma nou per a una multitud d'aplicacions informàtiques. En aquesta tesi doctoral també es presenta un estudi de les tecnologies disponibles actualment per a la implementació física de qubits i portes quàntiques, establint-ne els principals avantatges i desavantatges, i els marcs disponibles per a la programació i implementació de circuits quàntics. Per tal de millorar l'efectivitat del sistema, es descriu un disseny d'un circuit quàntic basat en màquines de vectors de suport (SVM) per resoldre problemes de classificació. Aquest circuit està dissenyat especialment per als sorollosos processadors quàntics d'escala intermèdia (NISQ) que estan disponibles actualment. Com a experiment, el circuit ha estat provat en un ordinador quàntic real basat en qubits superconductors per IBM com una millora per al subsistema de mineria de text. Els resultats obtinguts amb l'experiment quàntic també mostren conclusions interessants i una millora en el rendiment de prop del 20% sobre els sistemes convencionals, però a la vegada confirmen que encara es requereix un desenvolupament tecnològic continu per aprofitar al màxim la computació quàntica.[EN] In this doctoral thesis, a system to detect weak signals related to future transcendental changes is proposed and tested. While most known solutions are based on the use of structured data, the proposed system quantitatively detects these signals using heterogeneous and unstructured information from scientific, journalistic, and social sources. Predicting new trends in an environment has many applications. For instance, companies and startups face constant changes in their markets that are very difficult to predict. For this reason, developing systems to automatically detect significant future changes at an early stage is relevant for any organization to make right decisions on time. This work has been designed to obtain weak signals of the future in any field depending only on the input dataset of documents. Text mining and natural language processing techniques are applied to process all these documents. As a result, a map of ranked terms, a list of automatically classified keywords and a list of multi-word expressions are obtained. The overall system has been tested in four different sectors: solar panels, artificial intelligence, remote sensing, and medical imaging. This work has obtained promising results that have been evaluated with two different methodologies. As a result, the system was able to successfully detect new trends at a very early stage that have become more and more important today. Quantum computing is a new paradigm for a multitude of computing applications. This doctoral thesis also presents a study of the technologies that are currently available for the physical implementation of qubits and quantum gates, establishing their main advantages and disadvantages and the available frameworks for programming and implementing quantum circuits. In order to improve the effectiveness of the system, a design of a quantum circuit based on support vector machines (SVMs) is described for the resolution of classification problems. This circuit is specially designed for the noisy intermediate-scale quantum (NISQ) computers that are currently available. As an experiment, the circuit has been tested on a real quantum computer based on superconducting qubits by IBM as an improvement for the text mining subsystem in the detection of weak signals. The results obtained with the quantum experiment show interesting outcomes with an improvement of close to 20% better performance than conventional systems, but also confirm that ongoing technological development is still required to take full advantage of quantum computing.Griol Barres, I. (2022). Modelling of a System for the Detection of Weak Signals Through Text Mining and NLP. Proposal of Improvement by a Quantum Variational Circuit [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/183029TESISCompendi

Developments in PET-MRI for Radiotherapy Planning Applications

The hybridization of magnetic resonance imaging (MRI) and positron emission tomography (PET) provides the benefit of soft-tissue contrast and specific molecular information in a simultaneous acquisition. The applications of PET-MRI in radiotherapy are only starting to be realised. However, quantitative accuracy of PET relies on accurate attenuation correction (AC) of, not only the patient anatomy but also MRI hardware and current methods, which are prone to artefacts caused by dense materials. Quantitative accuracy of PET also relies on full characterization of patient motion during the scan. The simultaneity of PET-MRI makes it especially suited for motion correction. However, quality assurance (QA) procedures for such corrections are lacking. Therefore, a dynamic phantom that is PET and MR compatible is required. Additionally, respiratory motion characterization is needed for conformal radiotherapy of lung. 4D-CT can provide 3D motion characterization but suffers from poor soft-tissue contrast. In this thesis, I examine these problems, and present solutions in the form of improved MR-hardware AC techniques, a PET/MRI/CT-compatible tumour respiratory motion phantom for QA measurements, and a retrospective 4D-PET-MRI technique to characterise respiratory motion. Chapter 2 presents two techniques to improve upon current AC methods that use a standard helical CT scan for MRI hardware in PET-MRI. One technique uses a dual-energy computed tomography (DECT) scan to construct virtual monoenergetic image volumes and the other uses a tomotherapy linear accelerator to create CT images at megavoltage energies (1.0 MV) of the RF coil. The DECT-based technique reduced artefacts in the images translating to improved μ-maps. The MVCT-based technique provided further improvements in artefact reduction, resulting in artefact free μ-maps. This led to more AC of the breast coil. In chapter 3, I present a PET-MR-CT motion phantom for QA of motion-correction protocols. This phantom is used to evaluate a clinically available real-time dynamic MR images and a respiratory-triggered PET-MRI protocol. The results show the protocol to perform well under motion conditions. Additionally, the phantom provided a good model for performing QA of respiratory-triggered PET-MRI. Chapter 4 presents a 4D-PET/MRI technique, using MR sequences and PET acquisition methods currently available on hybrid PET/MRI systems. This technique is validated using the motion phantom presented in chapter 3 with three motion profiles. I conclude that our 4D-PET-MRI technique provides information to characterise tumour respiratory motion while using a clinically available pulse sequence and PET acquisition method

Recent developments in X-ray diffraction/scattering computed tomography for materials science

X-ray diffraction/scattering computed tomography (XDS-CT) methods are a non-destructive class of chemical imaging techniques that have the capacity to provide reconstructions of sample cross-sections with spatially resolved chemical information. While X-ray diffraction CT (XRD-CT) is the most well-established method, recent advances in instrumentation and data reconstruction have seen greater use of related techniques like small angle X-ray scattering CT and pair distribution function CT. Additionally, the adoption of machine learning techniques for tomographic reconstruction and data analysis are fundamentally disrupting how XDS-CT data is processed. The following narrative review highlights recent developments and applications of XDS-CT with a focus on studies in the last five years. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'

Recent developments in X-ray diffraction/scattering computed tomography for materials science

X-ray diffraction/scattering computed tomography (XDS-CT) methods are a non-destructive class of chemical imaging techniques that have the capacity to provide reconstructions of sample cross-sections with spatially resolved chemical information. While X-ray diffraction CT (XRD-CT) is the most well-established method, recent advances in instrumentation and data reconstruction have seen greater use of related techniques like small angle X-ray scattering CT and pair distribution function CT. Additionally, the adoption of machine learning techniques for tomographic reconstruction and data analysis are fundamentally disrupting how XDS-CT data is processed. The following narrative review highlights recent developments and applications of XDS-CT with a focus on studies in the last five years. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'