Brain tissue segmentation on Diffusion Weighted Magnetic Resonance data

Introduction Diffusion weighted Imaging (DWI) techniques are able to measure, in vivo and non-invasively, the diffusivity of water molecules inside the human brain. DWI has been applied on cerebral ischemia, brain maturation, epilepsy, multiple sclerosis, etc. [1]. Nowadays, there is a very high availability of these images. DWI allows the identification of brain tissues, so its accurate segmentation is a common initial step for the referred applications. Materials and Methods We present a validation study on automated segmentation of DWI based on the Gaussian mixture and hidden Markov random field models. This methodology is widely solved with iterative conditional modes algorithm, but some studies suggest [2] that graph-cuts (GC) algorithms improve the results when initialization is not close to the final solution. We implemented a segmentation tool integrating ITK with a GC algorithm [3], and a validation software using fuzzy overlap measures [4]. Results Segmentation accuracy of each tool is tested against a gold-standard segmentation obtained from a T1 MPRAGE magnetic resonance image of the same subject, registered to the DWI space. The proposed software shows meaningful improvements by using the GC energy minimization approach on DTI and DSI (Diffusion Spectrum Imaging) data. Conclusions The brain tissues segmentation on DWI is a fundamental step on many applications. Accuracy and robustness improvements are achieved with the proposed software, with high impact on the application’s final result.

MBIS: Multivariate Bayesian Image Segmentation Tool

We present MBIS (Multivariate Bayesian Image Segmentation tool), a clustering tool based on the mixture of multivariate normal distributions model. MBIS supports multi-channel bias field correction based on a B-spline model. A second methodological novelty is the inclusion of graph-cuts optimization for the stationary anisotropic hidden Markov random field model. Along with MBIS, we release an evaluation framework that contains three different experiments on multi-site data. We first validate the accuracy of segmentation and the estimated bias field for each channel. MBIS outperforms a widely used segmentation tool in a cross-comparison evaluation. The second experiment demonstrates the robustness of results on atlas-free segmentation of two image sets from scan-rescan protocols on 21 healthy subjects. Multivariate segmentation is more replicable than the monospectral counterpart on T1-weighted images. Finally, we provide a third experiment to illustrate how MBIS can be used in a large-scale study of tissue volume change with increasing age in 584 healthy subjects. This last result is meaningful as multivariate segmentation performs robustly without the need for prior knowledge.

Propuesta, implementación y evaluación de la biometría de firma en el aire como sistema de verificación en teléfonos móviles

En esta tesis doctoral se propone una técnica biométrica de verificación en teléfonos móviles consistente en realizar una firma en el aire con la mano que sujeta el teléfono móvil. Los acelerómetros integrados en el dispositivo muestrean las aceleraciones del movimiento de la firma en el aire, generando tres señales temporales que pueden utilizarse para la verificación del usuario. Se proponen varios enfoques para la implementación del sistema de verificación, a partir de los enfoques más utilizados en biometría de firma manuscrita: correspondencia de patrones, con variantes de los algoritmos de Needleman-Wusch (NW) y Dynamic Time Warping (DTW), modelos ocultos de Markov (HMM) y clasificador estadístico basado en Máquinas de Vector Soporte (SVM). Al no existir bases de datos públicas de firmas en el aire y con el fin de evaluar los métodos propuestos en esta tesis doctoral, se han capturado dos con distintas características; una con falsificaciones reales a partir del estudio de las grabaciones de usuarios auténticos y otra con muestras de usuarios obtenidas en diferentes sesiones a lo largo del tiempo. Utilizando estas bases de datos se han evaluado una gran cantidad de algoritmos para implementar un sistema de verificación basado en firma en el aire. Esta evaluación se ha realizado de acuerdo con el estándar ISO/IEC 19795, añadiendo el caso de verificación en mundo abierto no incluido en la norma. Además, se han analizado las características que hacen que una firma sea suficientemente segura. Por otro lado, se ha estudiado la permanencia de las firmas en el aire a lo largo del tiempo, proponiendo distintos métodos de actualización, basados en una adaptación dinámica del patrón, para mejorar su rendimiento. Finalmente, se ha implementado un prototipo de la técnica de firma en el aire para teléfonos Android e iOS. Los resultados de esta tesis doctoral han tenido un gran impacto, generando varias publicaciones en revistas internacionales, congresos y libros. La firma en el aire ha sido nombrada también en varias revistas de divulgación, portales de noticias Web y televisión. Además, se han obtenido varios premios en competiciones de ideas innovadoras y se ha firmado un acuerdo de explotación de la tecnología con una empresa extranjera. ABSTRACT This thesis proposes a biometric verification technique on mobile phones consisting on making a signature in the air with the hand holding a mobile phone. The accelerometers integrated in the device capture the movement accelerations, generating three temporal signals that can be used for verification. This thesis suggests several approaches for implementing the verification system, based on the most widely used approaches in handwritten signature biometrics: template matching, with a lot of variations of the Needleman- Wusch (NW) and Dynamic Time Warping (DTW) algorithms, Hidden Markov Models (HMM) and Supported Vector Machines (SVM). As there are no public databases of in-air signatures and with the aim of assessing the proposed methods, there have been captured two databases; one. with real falsification attempts from the study of recordings captured when genuine users made their signatures in front of a camera, and other, with samples obtained in different sessions over a long period of time. These databases have been used to evaluate a lot of algorithms in order to implement a verification system based on in-air signatures. This evaluation has been conducted according to the standard ISO/IEC 19795, adding the open-set verification scenario not included in the norm. In addition, the characteristics of a secure signature are also investigated, as well as the permanence of in-air signatures over time, proposing several updating strategies to improve its performance. Finally, a prototype of in-air signature has been developed for iOS and Android phones. The results of this thesis have achieved a high impact, publishing several articles in SCI journals, conferences and books. The in-air signature deployed in this thesis has been also referred in numerous media. Additionally, this technique has won several awards in the entrepreneurship field and also an exploitation agreement has been signed with a foreign company.

Generating segmental foreign accent

For most of us, speaking in a non-native language involves deviating to some extent from native pronunciation norms. However, the detailed basis for foreign accent (FA) remains elusive, in part due to methodological challenges in isolating segmental from suprasegmental factors. The current study examines the role of segmental features in conveying FA through the use of a generative approach in which accent is localised to single consonantal segments. Three techniques are evaluated: the first requires a highly-proficiency bilingual to produce words with isolated accented segments; the second uses cross-splicing of context-dependent consonants from the non-native language into native words; the third employs hidden Markov model synthesis to blend voice models for both languages. Using English and Spanish as the native/non-native languages respectively, listener cohorts from both languages identified words and rated their degree of FA. All techniques were capable of generating accented words, but to differing degrees. Naturally-produced speech led to the strongest FA ratings and synthetic speech the weakest, which we interpret as the outcome of over-smoothing. Nevertheless, the flexibility offered by synthesising localised accent encourages further development of the method.

Human activity recognition by inertial signals obtained from a smartphone

Human Activity Recognition (HAR) is an emerging research field with the aim to identify the actions carried out by a person given a set of observations and the surrounding environment. The wide growth in this research field inside the scientific community is mainly explained by the high number of applications that are arising in the last years. A great part of the most promising applications are related to the healthcare field, where it is possible to track the mobility of patients with motor dysfunction as also the physical activity in patients with cardiovascular risk. Until a few years ago, by using distinct kind of sensors, a patient follow-up was possible. However, far from being a long-term solution and with the smartphone irruption, that monitoring can be achieved in a non-invasive way by using the embedded smartphone’s sensors. For these reasons this Final Degree Project arises with the main target to evaluate new feature extraction techniques in order to carry out an activity and user recognition, and also an activity segmentation. The recognition is done thanks to the inertial signals integration obtained by two widespread sensors in the greater part of smartphones: accelerometer and gyroscope. In particular, six different activities are evaluated walking, walking-upstairs, walking-downstairs, sitting, standing and lying. Furthermore, a segmentation task is carried out taking into account the activities performed by thirty users. This can be done by using Hidden Markov Models and also a set of tools tested satisfactory in speech recognition: HTK (Hidden Markov Model Toolkit).

Human activity recognition by inertial signals obtained from a smartphone

El Reconocimiento de Actividades Humanas es un área de investigación emergente, cuyo objetivo principal es identificar las acciones realizadas por un sujeto analizando las señales obtenidas a partir de unos sensores. El rápido crecimiento de este área de investigación dentro de la comunidad científica se explica, en parte, por el elevado número de aplicaciones que están surgiendo en los últimos años. Gran parte de las aplicaciones más prometedoras se encuentran en el campo de la salud, donde se puede hacer un seguimiento del nivel de movilidad de pacientes con trastornos motores, así como monitorizar el nivel de actividad física en pacientes con riesgo cardiovascular. Hasta hace unos años, mediante el uso de distintos tipos de sensores se podía hacer un seguimiento del paciente. Sin embargo, lejos de ser una solución a largo plazo y gracias a la irrupción del teléfono inteligente, este seguimiento se puede hacer de una manera menos invasiva, haciendo uso de la gran variedad de sensores integrados en este tipo de dispositivos. En este contexto nace este Trabajo de Fin de Grado, cuyo principal objetivo es evaluar nuevas técnicas de extracción de características para llevar a cabo un reconocimiento de actividades y usuarios así como una segmentación de aquellas. Este reconocimiento se hace posible mediante la integración de señales inerciales obtenidas por dos sensores presentes en la gran mayoría de teléfonos inteligentes: acelerómetro y giróscopo. Concretamente, se evalúan seis tipos de actividades realizadas por treinta usuarios: andar, subir escaleras, bajar escaleras, estar sentado, estar de pie y estar tumbado. Además y de forma paralela, se realiza una segmentación temporal de los distintos tipos de actividades realizadas por dichos usuarios. Todo ello se llevará a cabo haciendo uso de los Modelos Ocultos de Markov, así como de un conjunto de herramientas probadas satisfactoriamente en reconocimiento del habla: HTK (Hidden Markov Model Toolkit).

Identification of a human nuclear receptor defines a new signaling pathway for CYP3A induction

Nuclear receptors regulate metabolic pathways in response to changes in the environment by appropriate alterations in gene expression of key metabolic enzymes. Here, a computational search approach based on iteratively built hidden Markov models of nuclear receptors was used to identify a human nuclear receptor, termed hPAR, that is expressed in liver and intestines. hPAR was found to be efficiently activated by pregnanes and by clinically used drugs including rifampicin, an antibiotic known to selectively induce human but not murine CYP3A expression. The CYP3A drug-metabolizing enzymes are expressed in gut and liver in response to environmental chemicals and clinically used drugs. Interestingly, hPAR is not activated by pregnenolone 16α-carbonitrile, which is a potent inducer of murine CYP3A genes and an activator of the mouse receptor PXR.1. Furthermore, hPAR was found to bind to and trans-activate through a conserved regulatory sequence present in human but not murine CYP3A genes. These results provide evidence that hPAR and PXR.1 may represent orthologous genes from different species that have evolved to regulate overlapping target genes in response to pharmacologically distinct CYP3A activators, and have potential implications for the in vitro identification of drug interactions important to humans.

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1 000 000 hits from 462 500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk.

TIGRFAMs: a protein family resource for the functional identification of proteins

TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional identification of proteins by sequence homology. We introduce the term ‘equivalog’ to describe members of a set of homologous proteins that are conserved with respect to function since their last common ancestor. Related proteins are grouped into equivalog families where possible, and otherwise into protein families with other hierarchically defined homology types. TIGRFAMs currently contains over 800 protein families, available for searching or downloading at www.tigr.org/TIGRFAMs. Classification by equivalog family, where achievable, complements classification by orthology, superfamily, domain or motif. It provides the information best suited for automatic assignment of specific functions to proteins from large-scale genome sequencing projects.

Identification of the yeast cytidine deaminase CDD1 as an orphan C→U RNA editase

Yeast co-expressing rat APOBEC-1 and a fragment of human apolipoprotein B (apoB) mRNA assembled functional editosomes and deaminated C6666 to U in a mooring sequence-dependent fashion. The occurrence of APOBEC-1-complementing proteins suggested a naturally occurring mRNA editing mechanism in yeast. Previously, a hidden Markov model identified seven yeast genes encoding proteins possessing putative zinc-dependent deaminase motifs. Here, only CDD1, a cytidine deaminase, is shown to have the capacity to carry out C→U editing on a reporter mRNA. This is only the second report of a cytidine deaminase that can use mRNA as a substrate. CDD1-dependent editing was growth phase regulated and demonstrated mooring sequence-dependent editing activity. Candidate yeast mRNA substrates were identified based on their homology with the mooring sequence-containing tripartite motif at the editing site of apoB mRNA and their ability to be edited by ectopically expressed APOBEC-1. Naturally occurring yeast mRNAs edited to a significant extent by CDD1 were, however, not detected. We propose that CDD1 be designated an orphan C→U editase until its native RNA substrate, if any, can be identified and that it be added to the CDAR (cytidine deaminase acting on RNA) family of editing enzymes.

Training and search methods for speech recognition.

Speech recognition involves three processes: extraction of acoustic indices from the speech signal, estimation of the probability that the observed index string was caused by a hypothesized utterance segment, and determination of the recognized utterance via a search among hypothesized alternatives. This paper is not concerned with the first process. Estimation of the probability of an index string involves a model of index production by any given utterance segment (e.g., a word). Hidden Markov models (HMMs) are used for this purpose [Makhoul, J. & Schwartz, R. (1995) Proc. Natl. Acad. Sci. USA 92, 9956-9963]. Their parameters are state transition probabilities and output probability distributions associated with the transitions. The Baum algorithm that obtains the values of these parameters from speech data via their successive reestimation will be described in this paper. The recognizer wishes to find the most probable utterance that could have caused the observed acoustic index string. That probability is the product of two factors: the probability that the utterance will produce the string and the probability that the speaker will wish to produce the utterance (the language model probability). Even if the vocabulary size is moderate, it is impossible to search for the utterance exhaustively. One practical algorithm is described [Viterbi, A. J. (1967) IEEE Trans. Inf. Theory IT-13, 260-267] that, given the index string, has a high likelihood of finding the most probable utterance.

Cortical activity flips among quasi-stationary states.

Parallel recordings of spike trains of several single cortical neurons in behaving monkeys were analyzed as a hidden Markov process. The parallel spike trains were considered as a multivariate Poisson process whose vector firing rates change with time. As a consequence of this approach, the complete recording can be segmented into a sequence of a few statistically discriminated hidden states, whose dynamics are modeled as a first-order Markov chain. The biological validity and benefits of this approach were examined in several independent ways: (i) the statistical consistency of the segmentation and its correspondence to the behavior of the animals; (ii) direct measurement of the collective flips of activity, obtained by the model; and (iii) the relation between the segmentation and the pair-wise short-term cross-correlations between the recorded spike trains. Comparison with surrogate data was also carried out for each of the above examinations to assure their significance. Our results indicated the existence of well-separated states of activity, within which the firing rates were approximately stationary. With our present data we could reliably discriminate six to eight such states. The transitions between states were fast and were associated with concomitant changes of firing rates of several neurons. Different behavioral modes and stimuli were consistently reflected by different states of neural activity. Moreover, the pair-wise correlations between neurons varied considerably between the different states, supporting the hypothesis that these distinct states were brought about by the cooperative action of many neurons.

Contexto e modularização em redes neurais recorrentes para aprendizagem de seqüências temporais

Este trabalho apresenta um sistema neural modular, que processa separadamente informações de contexto espacial e temporal, para a tarefa de reprodução de sequências temporais. Para o desenvolvimento do sistema neural foram considerados redes neurais recorrentes, modelos estocásticos, sistemas neurais modulares e processamento de informações de contexto. Em seguida, foram estudados três modelos com abordagens distintas para aprendizagem de seqüências temporais: uma rede neural parcialmente recorrente, um exemplo de sistema neural modular e um modelo estocástico utilizando a teoria de modelos markovianos escondidos. Com base nos estudos e modelos apresentados, esta pesquisa propõe um sistema formado por dois módulos sucessivos distintos. Uma rede de propagação direta (módulo estimador de contexto espacial) realiza o processamento de contexto espacial identificando a seqüência a ser reproduzida e fornecendo um protótipo do contexto para o segundo módulo. Este é formado por uma rede parcialmente recorrente (módulo de reprodução de sequências temporais) para aprender as informações de contexto temporal e reproduzir em suas saídas a seqüência identificada pelo módulo anterior. Para a finalidade mencionada, este mestrado utiliza a distribuição de Gibbs na saída do módulo para contexto espacial de forma que este forneça probabilidades de contexto espacial, indicando o grau de certeza do módulo e possibilitando a utilização de procedimentos especiais para os casos de dúvida. O sistema neural foi testado em conjuntos contendo trajetórias abertas, fechadas, e com diferentes situações de ambigüidade e complexidade. Duas situações distintas foram avaliadas: (a) capacidade do sistema em reproduzir trajetórias a partir de pontos iniciais treinados; e (b) capacidade de generalização do sistema reproduzindo trajetórias considerando pontos iniciais ou finais em situações não treinadas. A situação (b) é um problema de difícil ) solução em redes neurais devido à falta de contexto temporal, essencial na reprodução de seqüências. Foram realizados experimentos comparando o desempenho do sistema modular proposto com o de uma rede parcialmente recorrente operando sozinha e um sistema modular neural (TOTEM). Os resultados sugerem que o sistema proposto apresentou uma capacidade de generalização significamente melhor, sem que houvesse uma deterioração na capacidade de reproduzir seqüências treinadas. Esses resultados foram obtidos em sistema mais simples que o TOTEM.

Human Motion Analysis Based on Sequential Modeling of Radar Signal and Stereo Image Features

Falls are one of the greatest threats to elderly health in their daily living routines and activities. Therefore, it is very important to detect falls of an elderly in a timely and accurate manner, so that immediate response and proper care can be provided, by sending fall alarms to caregivers. Radar is an effective non-intrusive sensing modality which is well suited for this purpose, which can detect human motions in all types of environments, penetrate walls and fabrics, preserve privacy, and is insensitive to lighting conditions. Micro-Doppler features are utilized in radar signal corresponding to human body motions and gait to detect falls using a narrowband pulse-Doppler radar. Human motions cause time-varying Doppler signatures, which are analyzed using time-frequency representations and matching pursuit decomposition (MPD) for feature extraction and fall detection. The extracted features include MPD features and the principal components of the time-frequency signal representations. To analyze the sequential characteristics of typical falls, the extracted features are used for training and testing hidden Markov models (HMM) in different falling scenarios. Experimental results demonstrate that the proposed algorithm and method achieve fast and accurate fall detections. The risk of falls increases sharply when the elderly or patients try to exit beds. Thus, if a bed exit can be detected at an early stage of this motion, the related injuries can be prevented with a high probability. To detect bed exit for fall prevention, the trajectory of head movements is used for recognize such human motion. A head detector is trained using the histogram of oriented gradient (HOG) features of the head and shoulder areas from recorded bed exit images. A data association algorithm is applied on the head detection results to eliminate head detection false alarms. Then the three dimensional (3D) head trajectories are constructed by matching scale-invariant feature transform (SIFT) keypoints in the detected head areas from both the left and right stereo images. The extracted 3D head trajectories are used for training and testing an HMM based classifier for recognizing bed exit activities. The results of the classifier are presented and discussed in the thesis, which demonstrates the effectiveness of the proposed stereo vision based bed exit detection approach.

La movilidad social de los emigrantes españoles en Europa

La migración española de la segunda mitad del siglo XX se ha caracterizado en un primer momento por su carácter masivo y poco cualificado, seguido por un interregno de procesos de retorno y finalmente por una migración estable, no masiva pero altamente cualificada. La atención prestada a la inmigración masiva que recibe España a finales del siglo XX relegó a un segundo plano esta emigración cualificada de españoles. En este artículo se considera la relación entre movilidad espacial (migración de españoles) y su posible consecuencia sobre la movilidad social ascendente que experimentan. Para ello se utilizan los datos procedentes de la encuesta internacional EIMSS (European Internal Migrations Social Survey) y los procedimientos de escalamiento de clase social basados en la ocupación de Goldthorpe. El análisis se complementa con una simulación sobre la movilidad de clase, con la finalidad de visualizar y comparar los efectos sobre la movilidad social de la emigración de españoles a Francia, Alemania, Italia y Gran Bretaña.