An investigation of the performance of a new Mechanical thrombectomy device using Bond Graph modelling: application to the extraction of blood clots in the middle cerebral artery

A number of thrombectomy devices using a variety of methods have now been developed to facilitate clot removal. We present research involving one such experimental device recently developed in the UK, called a ‘GP’ Thrombus Aspiration Device (GPTAD). This device has the potential to bring about the extraction of a thrombus. Although the device is at a relatively early stage of development, the results look encouraging. In this work, we present an analysis and modeling of the GPTAD by means of the bond graph technique; it seems to be a highly effective method of simulating the device under a variety of conditions. Such modeling is useful in optimizing the GPTAD and predicting the result of clot extraction. The aim of this simulation model is to obtain the minimum pressure necessary to extract the clot and to verify that both the pressure and the time required to complete the clot extraction are realistic for use in clinical situations, and are consistent with any experimentally obtained data. We therefore consider aspects of rheology and mechanics in our modeling.

Uniformly Reweighted Belief Propagation: A Factor Graph Approach

Tree-reweighted belief propagation is a message passing method that has certain advantages compared to traditional belief propagation (BP). However, it fails to outperform BP in a consistent manner, does not lend itself well to distributed implementation, and has not been applied to distributions with higher-order interactions. We propose a method called uniformly-reweighted belief propagation that mitigates these drawbacks. After having shown in previous works that this method can substantially outperform BP in distributed inference with pairwise interaction models, in this paper we extend it to higher-order interactions and apply it to LDPC decoding, leading performance gains over BP.

A graph-based approach for latency modeling and optimization in multiview video encoding

We present a novel framework for encoding latency analysis of arbitrary multiview video coding prediction structures. This framework avoids the need to consider an specific encoder architecture for encoding latency analysis by assuming an unlimited processing capacity on the multiview encoder. Under this assumption, only the influence of the prediction structure and the processing times have to be considered, and the encoding latency is solved systematically by means of a graph model. The results obtained with this model are valid for a multiview encoder with sufficient processing capacity and serve as a lower bound otherwise. Furthermore, with the objective of low latency encoder design with low penalty on rate-distortion performance, the graph model allows us to identify the prediction relationships that add higher encoding latency to the encoder. Experimental results for JMVM prediction structures illustrate how low latency prediction structures with a low rate-distortion penalty can be derived in a systematic manner using the new model.

Probabilistic Atlas Based Segmentation Using Affine Moment Descriptors and Graph-Cuts

We show a procedure for constructing a probabilistic atlas based on affine moment descriptors. It uses a normalization procedure over the labeled atlas. The proposed linear registration is defined by closed-form expressions involving only geometric moments. This procedure applies both to atlas construction as atlas-based segmentation. We model the likelihood term for each voxel and each label using parametric or nonparametric distributions and the prior term is determined by applying the vote-rule. The probabilistic atlas is built with the variability of our linear registration. We have two segmentation strategy: a) it applies the proposed affine registration to bring the target image into the coordinate frame of the atlas or b) the probabilistic atlas is non-rigidly aligning with the target image, where the probabilistic atlas is previously aligned to the target image with our affine registration. Finally, we adopt a graph cut - Bayesian framework for implementing the atlas-based segmentation.

Graph based study of allergen cross-reactivity of plant lipid transfer proteins (LTPs) using microarray in a multicenter study.

The study of cross-reactivity in allergy is key to both understanding. the allergic response of many patients and providing them with a rational treatment In the present study, protein microarrays and a co-sensitization graph approach were used in conjunction with an allergen microarray immunoassay. This enabled us to include a wide number of proteins and a large number of patients, and to study sensitization profiles among members of the LTP family. Fourteen LTPs from the most frequent plant food-induced allergies in the geographical area studied were printed into a microarray specifically designed for this research. 212 patients with fruit allergy and 117 food-tolerant pollen allergic subjects were recruited from seven regions of Spain with different pollen profiles, and their sera were tested with allergen microarray. This approach has proven itself to be a good tool to study cross-reactivity between members of LTP family, and could become a useful strategy to analyze other families of allergens.

Time series irreversibility: a visibility graph approach

We propose a method to measure real-valued time series irreversibility which combines two different tools: the horizontal visibility algorithm and the Kullback-Leibler divergence. This method maps a time series to a directed network according to a geometric criterion. The degree of irreversibility of the series is then estimated by the Kullback-Leibler divergence (i.e. the distinguishability) between the in and out degree distributions of the associated graph. The method is computationally efficient and does not require any ad hoc symbolization process. We find that the method correctly distinguishes between reversible and irreversible stationary time series, including analytical and numerical studies of its performance for: (i) reversible stochastic processes (uncorrelated and Gaussian linearly correlated), (ii) irreversible stochastic processes (a discrete flashing ratchet in an asymmetric potential), (iii) reversible (conservative) and irreversible (dissipative) chaotic maps, and (iv) dissipative chaotic maps in the presence of noise. Two alternative graph functionals, the degree and the degree-degree distributions, can be used as the Kullback-Leibler divergence argument. The former is simpler and more intuitive and can be used as a benchmark, but in the case of an irreversible process with null net current, the degree-degree distribution has to be considered to identify the irreversible nature of the series

Segmentation of RV in 4D Cardiac MR Volumes using region-merging graph cuts

Non-invasive quantitative assessment of the right ventricular anatomical and functional parameters is a challenging task. We present a semi-automatic approach for right ventricle (RV) segmentation from 4D MR images in two variants, which differ in the amount of user interaction. The method consists of three main phases: First, foreground and background markers are generated from the user input. Next, an over-segmented region image is obtained applying a watershed transform. Finally, these regions are merged using 4D graph-cuts with an intensity based boundary term. For the first variant the user outlines the inside of the RV wall in a few end-diastole slices, for the second two marker pixels serve as starting point for a statistical atlas application. Results were obtained by blind evaluation on 16 testing 4D MR volumes. They prove our method to be robust against markers location and place it favourably in the ranks of existing approaches.

Hierarchical graph maps for visualization of collaborative recommender systems

In this paper we provide a method that allows the visualization of similarity relationships present between items of collaborative filtering recommender systems, as well as the relative importance of each of these. The objective is to offer visual representations of the recommender system?s set of items and of their relationships; these graphs show us where the most representative information can be found and which items are rated in a more similar way by the recommender system?s community of users. The visual representations achieved take the shape of phylogenetic trees, displaying the numerical similarity and the reliability between each pair of items considered to be similar. As a case study we provide the results obtained using the public database Movielens 1M, which contains 3900 movies.

A new label fusion method using graph cuts: application to hippocampus segmentation

The aim of this paper is to develop a probabilistic modeling framework for the segmentation of structures of interest from a collection of atlases. Given a subset of registered atlases into the target image for a particular Region of Interest (ROI), a statistical model of appearance and shape is computed for fusing the labels. Segmentations are obtained by minimizing an energy function associated with the proposed model, using a graph-cut technique. We test different label fusion methods on publicly available MR images of human brains.

Heterogeneous architecture for the optimization of large-scale graph processing data centres

Con el auge del Cloud Computing, las aplicaciones de proceso de datos han sufrido un incremento de demanda, y por ello ha cobrado importancia lograr m�ás eficiencia en los Centros de Proceso de datos. El objetivo de este trabajo es la obtenci�ón de herramientas que permitan analizar la viabilidad y rentabilidad de diseñar Centros de Datos especializados para procesamiento de datos, con una arquitectura, sistemas de refrigeraci�ón, etc. adaptados. Algunas aplicaciones de procesamiento de datos se benefician de las arquitecturas software, mientras que en otras puede ser m�ás eficiente un procesamiento con arquitectura hardware. Debido a que ya hay software con muy buenos resultados en el procesamiento de grafos, como el sistema XPregel, en este proyecto se realizará una arquitectura hardware en VHDL, implementando el algoritmo PageRank de Google de forma escalable. Se ha escogido este algoritmo ya que podr��á ser m�ás eficiente en arquitectura hardware, debido a sus características concretas que se indicaráan m�ás adelante. PageRank sirve para ordenar las p�áginas por su relevancia en la web, utilizando para ello la teorí��a de grafos, siendo cada página web un vértice de un grafo; y los enlaces entre páginas, las aristas del citado grafo. En este proyecto, primero se realizará un an�álisis del estado de la técnica. Se supone que la implementaci�ón en XPregel, un sistema de procesamiento de grafos, es una de las m�ás eficientes. Por ello se estudiará esta �ultima implementaci�ón. Sin embargo, debido a que Xpregel procesa, en general, algoritmos que trabajan con grafos; no tiene en cuenta ciertas caracterí��sticas del algoritmo PageRank, por lo que la implementaci�on no es �optima. Esto es debido a que en PageRank, almacenar todos los datos que manda un mismo v�értice es un gasto innecesario de memoria ya que todos los mensajes que manda un vértice son iguales entre sí e iguales a su PageRank. Se realizará el diseño en VHDL teniendo en cuenta esta caracter��ística del citado algoritmo,evitando almacenar varias veces los mensajes que son iguales. Se ha elegido implementar PageRank en VHDL porque actualmente las arquitecturas de los sistemas operativos no escalan adecuadamente. Se busca evaluar si con otra arquitectura se obtienen mejores resultados. Se realizará un diseño partiendo de cero, utilizando la memoria ROM de IPcore de Xillinx (Software de desarrollo en VHDL), generada autom�áticamente. Se considera hacer cuatro tipos de módulos para que as�� el procesamiento se pueda hacer en paralelo. Se simplificar�á la estructura de XPregel con el fin de intentar aprovechar la particularidad de PageRank mencionada, que hace que XPregel no le saque el m�aximo partido. Despu�és se escribirá el c�ódigo, realizando una estructura escalable, ya que en la computación intervienen millones de páginas web. A continuación, se sintetizar�á y se probará el código en una FPGA. El �ultimo paso será una evaluaci�ón de la implementaci�ón, y de posibles mejoras en cuanto al consumo.

VHDL-based system design of a cognitive sensorimotor loop (CSL) for haptic Human-Machine Interaction (HMI)

This document is a summary of the Bachelor thesis titled “VHDL-Based System Design of a Cognitive Sensorimotor Loop (CSL) for Haptic Human-Machine Interaction (HMI)” written by Pablo de Miguel Morales, Electronics Engineering student at the Universidad Politécnica de Madrid (UPM Madrid, Spain) during an Erasmus+ Exchange Program at the Beuth Hochschule für Technik (BHT Berlin, Germany). The tutor of this project is Dr. Prof. Hild. This project has been developed inside the Neurobotics Research Laboratory (NRL) in close collaboration with Benjamin Panreck, a member of the NRL, and another exchange student from the UPM Pablo Gabriel Lezcano. For a deeper comprehension of the content of the thesis, a deeper look in the document is needed as well as the viewing of the videos and the VHDL design. In the growing field of automation, a large amount of workforce is dedicated to improve, adapt and design motor controllers for a wide variety of applications. In the specific field of robotics or other machinery designed to interact with humans or their environment, new needs and technological solutions are often being discovered due to the existing, relatively unexplored new scenario it is. The project consisted of three main parts: Two VHDL-based systems and one short experiment on the haptic perception. Both VHDL systems are based on a Cognitive Sensorimotor Loop (CSL) which is a control loop designed by the NRL and mainly developed by Dr. Prof. Hild. The CSL is a control loop whose main characteristic is the fact that it does not use any external sensor to measure the speed or position of the motor but the motor itself. The motor always generates a voltage that is proportional to its angular speed so it does not need calibration. This method is energy efficient and simplifies control loops in complex systems. The first system, named CSL Stay In Touch (SIT), consists in a one DC motor system controller by a FPGA Board (Zynq ZYBO 7000) whose aim is to keep contact with any external object that touches its Sensing Platform in both directions. Apart from the main behavior, three features (Search Mode, Inertia Mode and Return Mode) have been designed to enhance the haptic interaction experience. Additionally, a VGA-Screen is also controlled by the FPGA Board for the monitoring of the whole system. This system has been completely developed, tested and improved; analyzing its timing and consumption properties. The second system, named CSL Fingerlike Mechanism (FM), consists in a fingerlike mechanical system controlled by two DC motors (Each controlling one part of the finger). The behavior is similar to the first system but in a more complex structure. This system was optional and not part of the original objectives of the thesis and it could not be properly finished and tested due to the lack of time. The haptic perception experiment was an experiment conducted to have an insight into the complexity of human haptic perception in order to implement this knowledge into technological applications. The experiment consisted in testing the capability of the subjects to recognize different objects and shapes while being blindfolded and with their ears covered. Two groups were done, one had full haptic perception while the other had to explore the environment with a plastic piece attached to their finger to create a haptic handicap. The conclusion of the thesis was that a haptic system based only on a CSL-based system is not enough to retrieve valuable information from the environment and that other sensors are needed (temperature, pressure, etc.) but that a CSL-based system is very useful to control the force applied by the system to interact with haptic sensible surfaces such as skin or tactile screens. RESUMEN. Este documento es un resumen del proyecto fin de grado titulado “VHDL-Based System Design of a Cognitive Sensorimotor Loop (CSL) for Haptic Human-Machine Interaction (HMI)” escrito por Pablo de Miguel, estudiante de Ingeniería Electrónica de Comunicaciones en la Universidad Politécnica de Madrid (UPM Madrid, España) durante un programa de intercambio Erasmus+ en la Beuth Hochschule für Technik (BHT Berlin, Alemania). El tutor de este proyecto ha sido Dr. Prof. Hild. Este proyecto se ha desarrollado dentro del Neurorobotics Research Laboratory (NRL) en estrecha colaboración con Benjamin Panreck (un miembro del NRL) y con Pablo Lezcano (Otro estudiante de intercambio de la UPM). Para una comprensión completa del trabajo es necesaria una lectura detenida de todo el documento y el visionado de los videos y análisis del diseño VHDL incluidos en el CD adjunto. En el creciente sector de la automatización, una gran cantidad de esfuerzo está dedicada a mejorar, adaptar y diseñar controladores de motor para un gran rango de aplicaciones. En el campo específico de la robótica u otra maquinaria diseñada para interactuar con los humanos o con su entorno, nuevas necesidades y soluciones tecnológicas se siguen desarrollado debido al relativamente inexplorado y nuevo escenario que supone. El proyecto consta de tres partes principales: Dos sistemas basados en VHDL y un pequeño experimento sobre la percepción háptica. Ambos sistemas VHDL están basados en el Cognitive Sesnorimotor Loop (CSL) que es un lazo de control creado por el NRL y cuyo desarrollador principal ha sido Dr. Prof. Hild. El CSL es un lazo de control cuya principal característica es la ausencia de sensores externos para medir la velocidad o la posición del motor, usando el propio motor como sensor. El motor siempre genera un voltaje proporcional a su velocidad angular de modo que no es necesaria calibración. Este método es eficiente en términos energéticos y simplifica los lazos de control en sistemas complejos. El primer sistema, llamado CSL Stay In Touch (SIT), consiste en un sistema formado por un motor DC controlado por una FPGA Board (Zynq ZYBO 7000) cuyo objetivo es mantener contacto con cualquier objeto externo que toque su plataforma sensible en ambas direcciones. Aparte del funcionamiento básico, tres modos (Search Mode, Inertia Mode y Return Mode) han sido diseñados para mejorar la interacción. Adicionalmente, se ha diseñado el control a través de la FPGA Board de una pantalla VGA para la monitorización de todo el sistema. El sistema ha sido totalmente desarrollado, testeado y mejorado; analizando su propiedades de timing y consumo energético. El segundo sistema, llamado CSL Fingerlike Mechanism (FM), consiste en un mecanismo similar a un dedo controlado por dos motores DC (Cada uno controlando una falange). Su comportamiento es similar al del primer sistema pero con una estructura más compleja. Este sistema no formaba parte de los objetivos iniciales del proyecto y por lo tanto era opcional. No pudo ser plenamente desarrollado debido a la falta de tiempo. El experimento de percepción háptica fue diseñado para profundizar en la percepción háptica humana con el objetivo de aplicar este conocimiento en aplicaciones tecnológicas. El experimento consistía en testear la capacidad de los sujetos para reconocer diferentes objetos, formas y texturas en condiciones de privación del sentido del oído y la vista. Se crearon dos grupos, en uno los sujetos tenían plena percepción háptica mientras que en el otro debían interactuar con los objetos a través de una pieza de plástico para generar un hándicap háptico. La conclusión del proyecto fue que un sistema háptico basado solo en sistemas CSL no es suficiente para recopilar información valiosa del entorno y que debe hacer uso de otros sensores (temperatura, presión, etc.). En cambio, un sistema basado en CSL es idóneo para el control de la fuerza aplicada por el sistema durante la interacción con superficies hápticas sensibles tales como la piel o pantallas táctiles.

Development of a sensorimotor algorithm able to deal with unforeseen pushes and its implementation based on VHDL

Development of a Sensorimotor Algorithm Able to Deal with Unforeseen Pushes and Its Implementation Based on VHDL is the title of my thesis which concludes my Bachelor Degree in the Escuela Técnica Superior de Ingeniería y Sistemas de Telecomunicación of the Universidad Politécnica de Madrid. It encloses the overall work I did in the Neurorobotics Research Laboratory from the Beuth Hochschule für Technik Berlin during my ERASMUS year in 2015. This thesis is focused on the field of robotics, specifically an electronic circuit called Cognitive Sensorimotor Loop (CSL) and its control algorithm based on VHDL hardware description language. The reason that makes the CSL special resides in its ability to operate a motor both as a sensor and an actuator. This way, it is possible to achieve a balanced position in any of the robot joints (e.g. the robot manages to stand) without needing any conventional sensor. In other words, the back electromotive force (EMF) induced by the motor coils is measured and the control algorithm responds depending on its magnitude. The CSL circuit contains mainly an analog-to-digital converter (ADC) and a driver. The ADC consists on a delta-sigma modulation which generates a series of bits with a certain percentage of 1's and 0's, proportional to the back EMF. The control algorithm, running in a FPGA, processes the bit frame and outputs a signal for the driver. This driver, which has an H bridge topology, gives the motor the ability to rotate in both directions while it's supplied with the power needed. The objective of this thesis is to document the experiments and overall work done on push ignoring contractive sensorimotor algorithms, meaning sensorimotor algorithms that ignore large magnitude forces (compared to gravity) applied in a short time interval on a pendulum system. This main objective is divided in two sub-objectives: (1) developing a system based on parameterized thresholds and (2) developing a system based on a push bypassing filter. System (1) contains a module that outputs a signal which blocks the main Sensorimotor algorithm when a push is detected. This module has several different parameters as inputs e.g. the back EMF increment to consider a force as a push or the time interval between samples. System (2) consists on a low-pass Infinite Impulse Response digital filter. It cuts any frequency considered faster than a certain push oscillation. This filter required an intensive study on how to implement some functions and data types (fixed or floating point data) not supported by standard VHDL packages. Once this was achieved, the next challenge was to simplify the solution as much as possible, without using non-official user made packages. Both systems behaved with a series of interesting advantages and disadvantages for the elaboration of the document. Stability, reaction time, simplicity or computational load are one of the many factors to be studied in the designed systems. RESUMEN. Development of a Sensorimotor Algorithm Able to Deal with Unforeseen Pushes and Its Implementation Based on VHDL es un Proyecto de Fin de Grado (PFG) que concluye mis estudios en la Escuela Técnica Superior de Ingeniería y Sistemas de Telecomunicación de la Universidad Politécnica de Madrid. En él se documenta el trabajo de investigación que realicé en el Neurorobotics Research Laboratory de la Beuth Hochschule für Technik Berlin durante el año 2015 mediante el programa de intercambio ERASMUS. Este PFG se centra en el campo de la robótica y en concreto en un circuito electrónico llamado Cognitive Sensorimotor Loop (CSL) y su algoritmo de control basado en lenguaje de modelado hardware VHDL. La particularidad del CSL reside en que se consigue que un motor haga las veces tanto de sensor como de actuador. De esta manera es posible que las articulaciones de un robot alcancen una posición de equilibrio (p.ej. el robot se coloca erguido) sin la necesidad de sensores en el sentido estricto de la palabra. Es decir, se mide la propia fuerza electromotriz (FEM) inducida sobre el motor y el algoritmo responde de acuerdo a su magnitud. El circuito CSL se compone de un convertidor analógico-digital (ADC) y un driver. El ADC consiste en un modulador sigma-delta, que genera una serie de bits con un porcentaje de 1's y 0's determinado, en proporción a la magnitud de la FEM inducida. El algoritmo de control, que se ejecuta en una FPGA, procesa esta cadena de bits y genera una señal para el driver. El driver, que posee una topología en puente H, provee al motor de la potencia necesaria y le otorga la capacidad de rotar en cualquiera de las dos direcciones. El objetivo de este PFG es documentar los experimentos y en general el trabajo realizado en algoritmos Sensorimotor que puedan ignorar fuerzas de gran magnitud (en comparación con la gravedad) y aplicadas en una corta ventana de tiempo. En otras palabras, ignorar empujones conservando el comportamiento original frente a la gravedad. Para ello se han desarrollado dos sistemas: uno basado en umbrales parametrizados (1) y otro basado en un filtro de corte ajustable (2). El sistema (1) contiene un módulo que, en el caso de detectar un empujón, genera una señal que bloquea el algoritmo Sensorimotor. Este módulo recibe diferentes parámetros como el incremento necesario de la FEM para que se considere un empujón o la ventana de tiempo para que se considere la existencia de un empujón. El sistema (2) consiste en un filtro digital paso-bajo de respuesta infinita que corta cualquier variación que considere un empujón. Para crear este filtro se requirió un estudio sobre como implementar ciertas funciones y tipos de datos (coma fija o flotante) no soportados por las librerías básicas de VHDL. Tras esto, el objetivo fue simplificar al máximo la solución del problema, sin utilizar paquetes de librerías añadidos. En ambos sistemas aparecen una serie de ventajas e inconvenientes de interés para el documento. La estabilidad, el tiempo de reacción, la simplicidad o la carga computacional son algunas de las muchos factores a estudiar en los sistemas diseñados. Para concluir, también han sido documentadas algunas incorporaciones a los sistemas: una interfaz visual en VGA, un módulo que compensa el offset del ADC o la implementación de una batería de faders MIDI entre otras.

Pedestrian Motion Prediction: A Graph Based Approach

A novel pedestrian motion prediction technique is presented in this paper. Its main achievement regards to none previous observation, any knowledge of pedestrian trajectories nor the existence of possible destinations is required; hence making it useful for autonomous surveillance applications. Prediction only requires initial position of the pedestrian and a 2D representation of the scenario as occupancy grid. First, it uses the Fast Marching Method (FMM) to calculate the pedestrian arrival time for each position in the map and then, the likelihood that the pedestrian reaches those positions is estimated. The technique has been tested with synthetic and real scenarios. In all cases, accurate probability maps as well as their representative graphs were obtained with low computational cost.