Comparison of climate field reconstruction techniques: Application to Europe

This paper presents a comparison of principal component (PC) regression and regularized expectation maximization (RegEM) to reconstruct European summer and winter surface air temperature over the past millennium. Reconstruction is performed within a surrogate climate using the National Center for Atmospheric Research (NCAR) Climate System Model (CSM) 1.4 and the climate model ECHO-G 4, assuming different white and red noise scenarios to define the distortion of pseudoproxy series. We show how sensitivity tests lead to valuable “a priori” information that provides a basis for improving real world proxy reconstructions. Our results emphasize the need to carefully test and evaluate reconstruction techniques with respect to the temporal resolution and the spatial scale they are applied to. Furthermore, we demonstrate that uncertainties inherent to the predictand and predictor data have to be more rigorously taken into account. The comparison of the two statistical techniques, in the specific experimental setting presented here, indicates that more skilful results are achieved with RegEM as low frequency variability is better preserved. We further detect seasonal differences in reconstruction skill for the continental scale, as e.g. the target temperature average is more adequately reconstructed for summer than for winter. For the specific predictor network given in this paper, both techniques underestimate the target temperature variations to an increasing extent as more noise is added to the signal, albeit RegEM less than with PC regression. We conclude that climate field reconstruction techniques can be improved and need to be further optimized in future applications.

Differential dynamic properties of scleroderma fibroblasts in response to perturbation of environmental stimuli.

Diseases are believed to arise from dysregulation of biological systems (pathways) perturbed by environmental triggers. Biological systems as a whole are not just the sum of their components, rather ever-changing, complex and dynamic systems over time in response to internal and external perturbation. In the past, biologists have mainly focused on studying either functions of isolated genes or steady-states of small biological pathways. However, it is systems dynamics that play an essential role in giving rise to cellular function/dysfunction which cause diseases, such as growth, differentiation, division and apoptosis. Biological phenomena of the entire organism are not only determined by steady-state characteristics of the biological systems, but also by intrinsic dynamic properties of biological systems, including stability, transient-response, and controllability, which determine how the systems maintain their functions and performance under a broad range of random internal and external perturbations. As a proof of principle, we examine signal transduction pathways and genetic regulatory pathways as biological systems. We employ widely used state-space equations in systems science to model biological systems, and use expectation-maximization (EM) algorithms and Kalman filter to estimate the parameters in the models. We apply the developed state-space models to human fibroblasts obtained from the autoimmune fibrosing disease, scleroderma, and then perform dynamic analysis of partial TGF-beta pathway in both normal and scleroderma fibroblasts stimulated by silica. We find that TGF-beta pathway under perturbation of silica shows significant differences in dynamic properties between normal and scleroderma fibroblasts. Our findings may open a new avenue in exploring the functions of cells and mechanism operative in disease development.

Differential dynamic properties of scleroderma fibroblasts in response to perturbation of environmental stimuli.

Diseases are believed to arise from dysregulation of biological systems (pathways) perturbed by environmental triggers. Biological systems as a whole are not just the sum of their components, rather ever-changing, complex and dynamic systems over time in response to internal and external perturbation. In the past, biologists have mainly focused on studying either functions of isolated genes or steady-states of small biological pathways. However, it is systems dynamics that play an essential role in giving rise to cellular function/dysfunction which cause diseases, such as growth, differentiation, division and apoptosis. Biological phenomena of the entire organism are not only determined by steady-state characteristics of the biological systems, but also by intrinsic dynamic properties of biological systems, including stability, transient-response, and controllability, which determine how the systems maintain their functions and performance under a broad range of random internal and external perturbations. As a proof of principle, we examine signal transduction pathways and genetic regulatory pathways as biological systems. We employ widely used state-space equations in systems science to model biological systems, and use expectation-maximization (EM) algorithms and Kalman filter to estimate the parameters in the models. We apply the developed state-space models to human fibroblasts obtained from the autoimmune fibrosing disease, scleroderma, and then perform dynamic analysis of partial TGF-beta pathway in both normal and scleroderma fibroblasts stimulated by silica. We find that TGF-beta pathway under perturbation of silica shows significant differences in dynamic properties between normal and scleroderma fibroblasts. Our findings may open a new avenue in exploring the functions of cells and mechanism operative in disease development.

Probabilistic mapping with mobile robots in structured environments

La mayor parte de los entornos diseñados por el hombre presentan características geométricas específicas. En ellos es frecuente encontrar formas poligonales, rectangulares, circulares . . . con una serie de relaciones típicas entre distintos elementos del entorno. Introducir este tipo de conocimiento en el proceso de construcción de mapas de un robot móvil puede mejorar notablemente la calidad y la precisión de los mapas resultantes. También puede hacerlos más útiles de cara a un razonamiento de más alto nivel. Cuando la construcción de mapas se formula en un marco probabilístico Bayesiano, una especificación completa del problema requiere considerar cierta información a priori sobre el tipo de entorno. El conocimiento previo puede aplicarse de varias maneras, en esta tesis se presentan dos marcos diferentes: uno basado en el uso de primitivas geométricas y otro que emplea un método de representación cercano al espacio de las medidas brutas. Un enfoque basado en características geométricas supone implícitamente imponer un cierto modelo a priori para el entorno. En este sentido, el desarrollo de una solución al problema SLAM mediante la optimización de un grafo de características geométricas constituye un primer paso hacia nuevos métodos de construcción de mapas en entornos estructurados. En el primero de los dos marcos propuestos, el sistema deduce la información a priori a aplicar en cada caso en base a una extensa colección de posibles modelos geométricos genéricos, siguiendo un método de Maximización de la Esperanza para hallar la estructura y el mapa más probables. La representación de la estructura del entorno se basa en un enfoque jerárquico, con diferentes niveles de abstracción para los distintos elementos geométricos que puedan describirlo. Se llevaron a cabo diversos experimentos para mostrar la versatilidad y el buen funcionamiento del método propuesto. En el segundo marco, el usuario puede definir diferentes modelos de estructura para el entorno mediante grupos de restricciones y energías locales entre puntos vecinos de un conjunto de datos del mismo. El grupo de restricciones que se aplica a cada grupo de puntos depende de la topología, que es inferida por el propio sistema. De este modo, se pueden incorporar nuevos modelos genéricos de estructura para el entorno con gran flexibilidad y facilidad. Se realizaron distintos experimentos para demostrar la flexibilidad y los buenos resultados del enfoque propuesto. Abstract Most human designed environments present specific geometrical characteristics. In them, it is easy to find polygonal, rectangular and circular shapes, with a series of typical relations between different elements of the environment. Introducing this kind of knowledge in the mapping process of mobile robots can notably improve the quality and accuracy of the resulting maps. It can also make them more suitable for higher level reasoning applications. When mapping is formulated in a Bayesian probabilistic framework, a complete specification of the problem requires considering a prior for the environment. The prior over the structure of the environment can be applied in several ways; this dissertation presents two different frameworks, one using a feature based approach and another one employing a dense representation close to the measurements space. A feature based approach implicitly imposes a prior for the environment. In this sense, feature based graph SLAM was a first step towards a new mapping solution for structured scenarios. In the first framework, the prior is inferred by the system from a wide collection of feature based priors, following an Expectation-Maximization approach to obtain the most probable structure and the most probable map. The representation of the structure of the environment is based on a hierarchical model with different levels of abstraction for the geometrical elements describing it. Various experiments were conducted to show the versatility and the good performance of the proposed method. In the second framework, different priors can be defined by the user as sets of local constraints and energies for consecutive points in a range scan from a given environment. The set of constraints applied to each group of points depends on the topology, which is inferred by the system. This way, flexible and generic priors can be incorporated very easily. Several tests were carried out to demonstrate the flexibility and the good results of the proposed approach.

Classical segmentation methods on novel MR imaging: a study of brain tissue segmentation of MP2RAGE vs MPRAGE

MP2RAGE has proven to be a bias-free MR acquisition with excellent contrast between grey and white matter. We investigated the ability of three state-of-the-art algorithms to automatically extract white matter (WM), grey matter (GM) and cerebrospinal fluid (CSF) from MPRAGE and MP2RAGE images: unified Segmentation (S) in SPM82 , its extension New Segment (NS), and an in-house Expectation-Maximization Markov Random Field tissue classification3 (EM-MRF) with Graph Cut (GC) optimization4 . Our goal is to quantify the differences between MPRAGE and MP2RAGE-based brain tissue probability maps.

ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins

The adenylate uridylate-rich elements (AREs) mediate the rapid turnover of mRNAs encoding proteins that regulate cellular growth and body response to exogenous agents such as microbes, inflammatory and environmental stimuli. However, the full repertoire of ARE-containing mRNAs is unknown. Here, we explore the distribution of AREs in human mRNA sequences. Computational derivation of a 13-bp ARE pattern was performed using multiple expectation maximization for motif elicitations (MEME) and consensus analyses. This pattern was statistically validated for the specificity towards the 3′-untranslated region and not coding region. The computationally derived ARE pattern is the basis of a database which contains non-redundant full-length ARE-mRNAs. The ARE-mRNA database (ARED; http://rc.kfshrc.edu.sa/ared) reveals that ARE-mRNAs encode a wide repertoire of functionally diverse proteins that belong to different biological processes and are important in several disease states. Cluster analysis was performed using the ARE sequences to demonstrate potential relationships between the type and number of ARE motifs, and the functional characteristics of the proteins.

Estudio y mejora de métodos de registro 3D: aceleración sobre unidades de procesamiento gráfico y caracterización del espacio de transformaciones iniciales

Durante los últimos años ha sido creciente el uso de las unidades de procesamiento gráfico, más conocidas como GPU (Graphic Processing Unit), en aplicaciones de propósito general, dejando a un lado el objetivo para el que fueron creadas y que no era otro que el renderizado de gráficos por computador. Este crecimiento se debe en parte a la evolución que han experimentado estos dispositivos durante este tiempo y que les ha dotado de gran potencia de cálculo, consiguiendo que su uso se extienda desde ordenadores personales a grandes cluster. Este hecho unido a la proliferación de sensores RGB-D de bajo coste ha hecho que crezca el número de aplicaciones de visión que hacen uso de esta tecnología para la resolución de problemas, así como también para el desarrollo de nuevas aplicaciones. Todas estas mejoras no solamente se han realizado en la parte hardware, es decir en los dispositivos, sino también en la parte software con la aparición de nuevas herramientas de desarrollo que facilitan la programación de estos dispositivos GPU. Este nuevo paradigma se acuñó como Computación de Propósito General sobre Unidades de Proceso Gráfico (General-Purpose computation on Graphics Processing Units, GPGPU). Los dispositivos GPU se clasifican en diferentes familias, en función de las distintas características hardware que poseen. Cada nueva familia que aparece incorpora nuevas mejoras tecnológicas que le permite conseguir mejor rendimiento que las anteriores. No obstante, para sacar un rendimiento óptimo a un dispositivo GPU es necesario configurarlo correctamente antes de usarlo. Esta configuración viene determinada por los valores asignados a una serie de parámetros del dispositivo. Por tanto, muchas de las implementaciones que hoy en día hacen uso de los dispositivos GPU para el registro denso de nubes de puntos 3D, podrían ver mejorado su rendimiento con una configuración óptima de dichos parámetros, en función del dispositivo utilizado. Es por ello que, ante la falta de un estudio detallado del grado de afectación de los parámetros GPU sobre el rendimiento final de una implementación, se consideró muy conveniente la realización de este estudio. Este estudio no sólo se realizó con distintas configuraciones de parámetros GPU, sino también con diferentes arquitecturas de dispositivos GPU. El objetivo de este estudio es proporcionar una herramienta de decisión que ayude a los desarrolladores a la hora implementar aplicaciones para dispositivos GPU. Uno de los campos de investigación en los que más prolifera el uso de estas tecnologías es el campo de la robótica ya que tradicionalmente en robótica, sobre todo en la robótica móvil, se utilizaban combinaciones de sensores de distinta naturaleza con un alto coste económico, como el láser, el sónar o el sensor de contacto, para obtener datos del entorno. Más tarde, estos datos eran utilizados en aplicaciones de visión por computador con un coste computacional muy alto. Todo este coste, tanto el económico de los sensores utilizados como el coste computacional, se ha visto reducido notablemente gracias a estas nuevas tecnologías. Dentro de las aplicaciones de visión por computador más utilizadas está el registro de nubes de puntos. Este proceso es, en general, la transformación de diferentes nubes de puntos a un sistema de coordenadas conocido. Los datos pueden proceder de fotografías, de diferentes sensores, etc. Se utiliza en diferentes campos como son la visión artificial, la imagen médica, el reconocimiento de objetos y el análisis de imágenes y datos de satélites. El registro se utiliza para poder comparar o integrar los datos obtenidos en diferentes mediciones. En este trabajo se realiza un repaso del estado del arte de los métodos de registro 3D. Al mismo tiempo, se presenta un profundo estudio sobre el método de registro 3D más utilizado, Iterative Closest Point (ICP), y una de sus variantes más conocidas, Expectation-Maximization ICP (EMICP). Este estudio contempla tanto su implementación secuencial como su implementación paralela en dispositivos GPU, centrándose en cómo afectan a su rendimiento las distintas configuraciones de parámetros GPU. Como consecuencia de este estudio, también se presenta una propuesta para mejorar el aprovechamiento de la memoria de los dispositivos GPU, permitiendo el trabajo con nubes de puntos más grandes, reduciendo el problema de la limitación de memoria impuesta por el dispositivo. El funcionamiento de los métodos de registro 3D utilizados en este trabajo depende en gran medida de la inicialización del problema. En este caso, esa inicialización del problema consiste en la correcta elección de la matriz de transformación con la que se iniciará el algoritmo. Debido a que este aspecto es muy importante en este tipo de algoritmos, ya que de él depende llegar antes o no a la solución o, incluso, no llegar nunca a la solución, en este trabajo se presenta un estudio sobre el espacio de transformaciones con el objetivo de caracterizarlo y facilitar la elección de la transformación inicial a utilizar en estos algoritmos.

Non-linear hierarchical visualisation

This thesis applies a hierarchical latent trait model system to a large quantity of data. The motivation for it was lack of viable approaches to analyse High Throughput Screening datasets which maybe include thousands of data points with high dimensions. High Throughput Screening (HTS) is an important tool in the pharmaceutical industry for discovering leads which can be optimised and further developed into candidate drugs. Since the development of new robotic technologies, the ability to test the activities of compounds has considerably increased in recent years. Traditional methods, looking at tables and graphical plots for analysing relationships between measured activities and the structure of compounds, have not been feasible when facing a large HTS dataset. Instead, data visualisation provides a method for analysing such large datasets, especially with high dimensions. So far, a few visualisation techniques for drug design have been developed, but most of them just cope with several properties of compounds at one time. We believe that a latent variable model (LTM) with a non-linear mapping from the latent space to the data space is a preferred choice for visualising a complex high-dimensional data set. As a type of latent variable model, the latent trait model can deal with either continuous data or discrete data, which makes it particularly useful in this domain. In addition, with the aid of differential geometry, we can imagine the distribution of data from magnification factor and curvature plots. Rather than obtaining the useful information just from a single plot, a hierarchical LTM arranges a set of LTMs and their corresponding plots in a tree structure. We model the whole data set with a LTM at the top level, which is broken down into clusters at deeper levels of t.he hierarchy. In this manner, the refined visualisation plots can be displayed in deeper levels and sub-clusters may be found. Hierarchy of LTMs is trained using expectation-maximisation (EM) algorithm to maximise its likelihood with respect to the data sample. Training proceeds interactively in a recursive fashion (top-down). The user subjectively identifies interesting regions on the visualisation plot that they would like to model in a greater detail. At each stage of hierarchical LTM construction, the EM algorithm alternates between the E- and M-step. Another problem that can occur when visualising a large data set is that there may be significant overlaps of data clusters. It is very difficult for the user to judge where centres of regions of interest should be put. We address this problem by employing the minimum message length technique, which can help the user to decide the optimal structure of the model. In this thesis we also demonstrate the applicability of the hierarchy of latent trait models in the field of document data mining.

Visualisation of heterogeneous data with simultaneous feature saliency using Generalised Generative Topographic Mapping

Most machine-learning algorithms are designed for datasets with features of a single type whereas very little attention has been given to datasets with mixed-type features. We recently proposed a model to handle mixed types with a probabilistic latent variable formalism. This proposed model describes the data by type-specific distributions that are conditionally independent given the latent space and is called generalised generative topographic mapping (GGTM). It has often been observed that visualisations of high-dimensional datasets can be poor in the presence of noisy features. In this paper we therefore propose to extend the GGTM to estimate feature saliency values (GGTMFS) as an integrated part of the parameter learning process with an expectation-maximisation (EM) algorithm. The efficacy of the proposed GGTMFS model is demonstrated both for synthetic and real datasets.

Expectation Conditional Maximization-Based Deformable Shape Registration

This paper addresses the issue of matching statistical and non-rigid shapes, and introduces an Expectation Conditional Maximization-based deformable shape registration (ECM-DSR) algorithm. Similar to previous works, we cast the statistical and non-rigid shape registration problem into a missing data framework and handle the unknown correspondences with Gaussian Mixture Models (GMM). The registration problem is then solved by fitting the GMM centroids to the data. But unlike previous works where equal isotropic covariances are used, our new algorithm uses heteroscedastic covariances whose values are iteratively estimated from the data. A previously introduced virtual observation concept is adopted here to simplify the estimation of the registration parameters. Based on this concept, we derive closed-form solutions to estimate parameters for statistical or non-rigid shape registrations in each iteration. Our experiments conducted on synthesized and real data demonstrate that the ECM-DSR algorithm has various advantages over existing algorithms.

A Study of Ordered Gene Problems Featuring DNA Error Correction and DNA Fragment Assembly with a Variety of Heuristics, Genetic Algorithm Variations, and Dynamic Representations

Ordered gene problems are a very common classification of optimization problems. Because of their popularity countless algorithms have been developed in an attempt to find high quality solutions to the problems. It is also common to see many different types of problems reduced to ordered gene style problems as there are many popular heuristics and metaheuristics for them due to their popularity. Multiple ordered gene problems are studied, namely, the travelling salesman problem, bin packing problem, and graph colouring problem. In addition, two bioinformatics problems not traditionally seen as ordered gene problems are studied: DNA error correction and DNA fragment assembly. These problems are studied with multiple variations and combinations of heuristics and metaheuristics with two distinct types or representations. The majority of the algorithms are built around the Recentering- Restarting Genetic Algorithm. The algorithm variations were successful on all problems studied, and particularly for the two bioinformatics problems. For DNA Error Correction multiple cases were found with 100% of the codes being corrected. The algorithm variations were also able to beat all other state-of-the-art DNA Fragment Assemblers on 13 out of 16 benchmark problem instances.

Design and analysis of distributed utility maximization algorithm for multihop wireless network with inaccurate feedback

Distributed network utility maximization (NUM) is receiving increasing interests for cross-layer optimization problems in multihop wireless networks. Traditional distributed NUM algorithms rely heavily on feedback information between different network elements, such as traffic sources and routers. Because of the distinct features of multihop wireless networks such as time-varying channels and dynamic network topology, the feedback information is usually inaccurate, which represents as a major obstacle for distributed NUM application to wireless networks. The questions to be answered include if distributed NUM algorithm can converge with inaccurate feedback and how to design effective distributed NUM algorithm for wireless networks. In this paper, we first use the infinitesimal perturbation analysis technique to provide an unbiased gradient estimation on the aggregate rate of traffic sources at the routers based on locally available information. On the basis of that, we propose a stochastic approximation algorithm to solve the distributed NUM problem with inaccurate feedback. We then prove that the proposed algorithm can converge to the optimum solution of distributed NUM with perfect feedback under certain conditions. The proposed algorithm is applied to the joint rate and media access control problem for wireless networks. Numerical results demonstrate the convergence of the proposed algorithm. © 2013 John Wiley & Sons, Ltd.

Design and analysis of distributed utility maximization algorithm for multihop wireless network with inaccurate feedback

Distributed network utility maximization (NUM) is receiving increasing interests for cross-layer optimization problems in multihop wireless networks. Traditional distributed NUM algorithms rely heavily on feedback information between different network elements, such as traffic sources and routers. Because of the distinct features of multihop wireless networks such as time-varying channels and dynamic network topology, the feedback information is usually inaccurate, which represents as a major obstacle for distributed NUM application to wireless networks. The questions to be answered include if distributed NUM algorithm can converge with inaccurate feedback and how to design effective distributed NUM algorithm for wireless networks. In this paper, we first use the infinitesimal perturbation analysis technique to provide an unbiased gradient estimation on the aggregate rate of traffic sources at the routers based on locally available information. On the basis of that, we propose a stochastic approximation algorithm to solve the distributed NUM problem with inaccurate feedback. We then prove that the proposed algorithm can converge to the optimum solution of distributed NUM with perfect feedback under certain conditions. The proposed algorithm is applied to the joint rate and media access control problem for wireless networks. Numerical results demonstrate the convergence of the proposed algorithm. © 2013 John Wiley & Sons, Ltd.

Em Algorithm for MLE of a Probit Model for Multiple Ordinal Outcomes

The correlated probit model is frequently used for multiple ordered data since it allows to incorporate seamlessly different correlation structures. The estimation of the probit model parameters based on direct maximization of the limited information maximum likelihood is a numerically intensive procedure. We propose an extension of the EM algorithm for obtaining maximum likelihood estimates for a correlated probit model for multiple ordinal outcomes. The algorithm is implemented in the free software environment for statistical computing and graphics R. We present two simulation studies to examine the performance of the developed algorithm. We apply the model to data on 121 women with cervical or endometrial cancer. Patients developed normal tissue reactions as a result of post-operative external beam pelvic radiotherapy. In this work we focused on modeling the effects of a genetic factor on early skin and early urogenital tissue reactions and on assessing the strength of association between the two types of reactions. We established that there was an association between skin reactions and polymorphism XRCC3 codon 241 (C>T) (rs861539) and that skin and urogenital reactions were positively correlated. ACM Computing Classification System (1998): G.3.

Implementation of the EM Algorithm for Maximum Likelihood Estimation of a Random Effects Model for One Longitudinal Ordinal Outcome

2010 Mathematics Subject Classification: 62J99.