Classifying GABAergic interneurons with semi-supervised projected model-based clustering

Objectives: A recently introduced pragmatic scheme promises to be a useful catalog of interneuron names.We sought to automatically classify digitally reconstructed interneuronal morphologies according tothis scheme. Simultaneously, we sought to discover possible subtypes of these types that might emergeduring automatic classification (clustering). We also investigated which morphometric properties weremost relevant for this classification.Materials and methods: A set of 118 digitally reconstructed interneuronal morphologies classified into thecommon basket (CB), horse-tail (HT), large basket (LB), and Martinotti (MA) interneuron types by 42 of theworld?s leading neuroscientists, quantified by five simple morphometric properties of the axon and fourof the dendrites. We labeled each neuron with the type most commonly assigned to it by the experts. Wethen removed this class information for each type separately, and applied semi-supervised clustering tothose cells (keeping the others? cluster membership fixed), to assess separation from other types and lookfor the formation of new groups (subtypes). We performed this same experiment unlabeling the cells oftwo types at a time, and of half the cells of a single type at a time. The clustering model is a finite mixtureof Gaussians which we adapted for the estimation of local (per-cluster) feature relevance. We performedthe described experiments on three different subsets of the data, formed according to how many expertsagreed on type membership: at least 18 experts (the full data set), at least 21 (73 neurons), and at least26 (47 neurons).Results: Interneurons with more reliable type labels were classified more accurately. We classified HTcells with 100% accuracy, MA cells with 73% accuracy, and CB and LB cells with 56% and 58% accuracy,respectively. We identified three subtypes of the MA type, one subtype of CB and LB types each, andno subtypes of HT (it was a single, homogeneous type). We got maximum (adapted) Silhouette widthand ARI values of 1, 0.83, 0.79, and 0.42, when unlabeling the HT, CB, LB, and MA types, respectively,confirming the quality of the formed cluster solutions. The subtypes identified when unlabeling a singletype also emerged when unlabeling two types at a time, confirming their validity. Axonal morphometricproperties were more relevant that dendritic ones, with the axonal polar histogram length in the [pi, 2pi) angle interval being particularly useful.Conclusions: The applied semi-supervised clustering method can accurately discriminate among CB, HT, LB, and MA interneuron types while discovering potential subtypes, and is therefore useful for neuronal classification. The discovery of potential subtypes suggests that some of these types are more heteroge-neous that previously thought. Finally, axonal variables seem to be more relevant than dendritic ones fordistinguishing among the CB, HT, LB, and MA interneuron types.

Identification of pore spaces in 3D CT soil images using a PFCM partitional clustering

Recent advances in non-destructive imaging techniques, such as X-ray computed tomography (CT), make it possible to analyse pore space features from the direct visualisation from soil structures. A quantitative characterisation of the three-dimensional solid-pore architecture is important to understand soil mechanics, as they relate to the control of biological, chemical, and physical processes across scales. This analysis technique therefore offers an opportunity to better interpret soil strata, as new and relevant information can be obtained. In this work, we propose an approach to automatically identify the pore structure of a set of 200-2D images that represent slices of an original 3D CT image of a soil sample, which can be accomplished through non-linear enhancement of the pixel grey levels and an image segmentation based on a PFCM (Possibilistic Fuzzy C-Means) algorithm. Once the solids and pore spaces have been identified, the set of 200-2D images is then used to reconstruct an approximation of the soil sample by projecting only the pore spaces. This reconstruction shows the structure of the soil and its pores, which become more bounded, less bounded, or unbounded with changes in depth. If the soil sample image quality is sufficiently favourable in terms of contrast, noise and sharpness, the pore identification is less complicated, and the PFCM clustering algorithm can be used without additional processing; otherwise, images require pre-processing before using this algorithm. Promising results were obtained with four soil samples, the first of which was used to show the algorithm validity and the additional three were used to demonstrate the robustness of our proposal. The methodology we present here can better detect the solid soil and pore spaces on CT images, enabling the generation of better 2D?3D representations of pore structures from segmented 2D images.

Fast 2D to 3D conversion using a clustering-based hierarchical search in a machine learning framework

Automatic 2D-to-3D conversion is an important application for filling the gap between the increasing number of 3D displays and the still scant 3D content. However, existing approaches have an excessive computational cost that complicates its practical application. In this paper, a fast automatic 2D-to-3D conversion technique is proposed, which uses a machine learning framework to infer the 3D structure of a query color image from a training database with color and depth images. Assuming that photometrically similar images have analogous 3D structures, a depth map is estimated by searching the most similar color images in the database, and fusing the corresponding depth maps. Large databases are desirable to achieve better results, but the computational cost also increases. A clustering-based hierarchical search using compact SURF descriptors to characterize images is proposed to drastically reduce search times. A significant computational time improvement has been obtained regarding other state-of-the-art approaches, maintaining the quality results.

Insertion of impairments in test video sequences for quality assessment based on psychovisual characteristics

Assessing video quality is a complex task. While most pixel-based metrics do not present enough correlation between objective and subjective results, algorithms need to correspond to human perception when analyzing quality in a video sequence. For analyzing the perceived quality derived from concrete video artifacts in determined region of interest we present a novel methodology for generating test sequences which allow the analysis of impact of each individual distortion. Through results obtained after subjective assessment it is possible to create psychovisual models based on weighting pixels belonging to different regions of interest distributed by color, position, motion or content. Interesting results are obtained in subjective assessment which demonstrates the necessity of new metrics adapted to human visual system.

Quality and productivity analysis in a very small enterprise using TSPi

This article shows the benefits of developing a software project using TSPi in a "Very Small Enterprise" based in quality and productivity measures. An adapted process from the current process based on the TSPi was defined and the team was trained in it. The pilot project had schedule and budget constraints. The workaround began by gathering historical data from previous projects in order to get a measurement repository, and then the project metrics were collected. Finally, the process, product and quality improvements were verified

Analysis of quality of experience in 3D video systems

Esta tesis presenta un estudio exhaustivo sobre la evaluación de la calidad de experiencia (QoE, del inglés Quality of Experience) percibida por los usuarios de sistemas de vídeo 3D, analizando el impacto de los efectos introducidos por todos los elementos de la cadena de procesamiento de vídeo 3D. Por lo tanto, se presentan varias pruebas de evaluación subjetiva específicamente diseñadas para evaluar los sistemas considerados, teniendo en cuenta todos los factores perceptuales relacionados con la experiencia visual tridimensional, tales como la percepción de profundidad y la molestia visual. Concretamente, se describe un test subjetivo basado en la evaluación de degradaciones típicas que pueden aparecer en el proceso de creación de contenidos de vídeo 3D, por ejemplo debidas a calibraciones incorrectas de las cámaras o a algoritmos de procesamiento de la señal de vídeo (p. ej., conversión de 2D a 3D). Además, se presenta el proceso de generación de una base de datos de vídeos estereoscópicos de alta calidad, disponible gratuitamente para la comunidad investigadora y que ha sido utilizada ampliamente en diferentes trabajos relacionados con vídeo 3D. Asimismo, se presenta otro estudio subjetivo, realizado entre varios laboratorios, con el que se analiza el impacto de degradaciones causadas por la codificación de vídeo, así como diversos formatos de representación de vídeo 3D. Igualmente, se describen tres pruebas subjetivas centradas en el estudio de posibles efectos causados por la transmisión de vídeo 3D a través de redes de televisión sobre IP (IPTV, del inglés Internet Protocol Television) y de sistemas de streaming adaptativo de vídeo. Para estos casos, se ha propuesto una innovadora metodología de evaluación subjetiva de calidad vídeo, denominada Content-Immersive Evaluation of Transmission Impairments (CIETI), diseñada específicamente para evaluar eventos de transmisión simulando condiciones realistas de visualización de vídeo en ámbitos domésticos, con el fin de obtener conclusiones más representativas sobre la experiencia visual de los usuarios finales. Finalmente, se exponen dos experimentos subjetivos comparando varias tecnologías actuales de televisores 3D disponibles en el mercado de consumo y evaluando factores perceptuales de sistemas Super Multiview Video (SMV), previstos a ser la tecnología futura de televisores 3D de consumo, gracias a una prometedora visualización de contenido 3D sin necesidad de gafas específicas. El trabajo presentado en esta tesis ha permitido entender los factores perceptuales y técnicos relacionados con el procesamiento y visualización de contenidos de vídeo 3D, que pueden ser de utilidad en el desarrollo de nuevas tecnologías y técnicas de evaluación de la QoE, tanto metodologías subjetivas como métricas objetivas. ABSTRACT This thesis presents a comprehensive study of the evaluation of the Quality of Experience (QoE) perceived by the users of 3D video systems, analyzing the impact of effects introduced by all the elements of the 3D video processing chain. Therefore, various subjective assessment tests are presented, particularly designed to evaluate the systems under consideration, and taking into account all the perceptual factors related to the 3D visual experience, such as depth perception and visual discomfort. In particular, a subjective test is presented, based on evaluating typical degradations that may appear during the content creation, for instance due to incorrect camera calibration or video processing algorithms (e.g., 2D to 3D conversion). Moreover, the process of generation of a high-quality dataset of 3D stereoscopic videos is described, which is freely available for the research community, and has been already widely used in different works related with 3D video. In addition, another inter-laboratory subjective study is presented analyzing the impact of coding impairments and representation formats of stereoscopic video. Also, three subjective tests are presented studying the effects of transmission events that take place in Internet Protocol Television (IPTV) networks and adaptive streaming scenarios for 3D video. For these cases, a novel subjective evaluation methodology, called Content-Immersive Evaluation of Transmission Impairments (CIETI), was proposed, which was especially designed to evaluate transmission events simulating realistic home-viewing conditions, to obtain more representative conclusions about the visual experience of the end users. Finally, two subjective experiments are exposed comparing various current 3D displays available in the consumer market, and evaluating perceptual factors of Super Multiview Video (SMV) systems, expected to be the future technology for consumer 3D displays thanks to a promising visualization of 3D content without specific glasses. The work presented in this thesis has allowed to understand perceptual and technical factors related to the processing and visualization of 3D video content, which may be useful in the development of new technologies and approaches for QoE evaluation, both subjective methodologies and objective metrics.

Visual attention and perception models for assessing quality in 2D and 3D stereoscopic video

La medida de calidad de vídeo sigue siendo necesaria para definir los criterios que caracterizan una señal que cumpla los requisitos de visionado impuestos por el usuario. Las nuevas tecnologías, como el vídeo 3D estereoscópico o formatos más allá de la alta definición, imponen nuevos criterios que deben ser analizadas para obtener la mayor satisfacción posible del usuario. Entre los problemas detectados durante el desarrollo de esta tesis doctoral se han determinado fenómenos que afectan a distintas fases de la cadena de producción audiovisual y tipo de contenido variado. En primer lugar, el proceso de generación de contenidos debe encontrarse controlado mediante parámetros que eviten que se produzca el disconfort visual y, consecuentemente, fatiga visual, especialmente en lo relativo a contenidos de 3D estereoscópico, tanto de animación como de acción real. Por otro lado, la medida de calidad relativa a la fase de compresión de vídeo emplea métricas que en ocasiones no se encuentran adaptadas a la percepción del usuario. El empleo de modelos psicovisuales y diagramas de atención visual permitirían ponderar las áreas de la imagen de manera que se preste mayor importancia a los píxeles que el usuario enfocará con mayor probabilidad. Estos dos bloques se relacionan a través de la definición del término saliencia. Saliencia es la capacidad del sistema visual para caracterizar una imagen visualizada ponderando las áreas que más atractivas resultan al ojo humano. La saliencia en generación de contenidos estereoscópicos se refiere principalmente a la profundidad simulada mediante la ilusión óptica, medida en términos de distancia del objeto virtual al ojo humano. Sin embargo, en vídeo bidimensional, la saliencia no se basa en la profundidad, sino en otros elementos adicionales, como el movimiento, el nivel de detalle, la posición de los píxeles o la aparición de caras, que serán los factores básicos que compondrán el modelo de atención visual desarrollado. Con el objetivo de detectar las características de una secuencia de vídeo estereoscópico que, con mayor probabilidad, pueden generar disconfort visual, se consultó la extensa literatura relativa a este tema y se realizaron unas pruebas subjetivas preliminares con usuarios. De esta forma, se llegó a la conclusión de que se producía disconfort en los casos en que se producía un cambio abrupto en la distribución de profundidades simuladas de la imagen, aparte de otras degradaciones como la denominada “violación de ventana”. A través de nuevas pruebas subjetivas centradas en analizar estos efectos con diferentes distribuciones de profundidades, se trataron de concretar los parámetros que definían esta imagen. Los resultados de las pruebas demuestran que los cambios abruptos en imágenes se producen en entornos con movimientos y disparidades negativas elevadas que producen interferencias en los procesos de acomodación y vergencia del ojo humano, así como una necesidad en el aumento de los tiempos de enfoque del cristalino. En la mejora de las métricas de calidad a través de modelos que se adaptan al sistema visual humano, se realizaron también pruebas subjetivas que ayudaron a determinar la importancia de cada uno de los factores a la hora de enmascarar una determinada degradación. Los resultados demuestran una ligera mejora en los resultados obtenidos al aplicar máscaras de ponderación y atención visual, los cuales aproximan los parámetros de calidad objetiva a la respuesta del ojo humano. ABSTRACT Video quality assessment is still a necessary tool for defining the criteria to characterize a signal with the viewing requirements imposed by the final user. New technologies, such as 3D stereoscopic video and formats of HD and beyond HD oblige to develop new analysis of video features for obtaining the highest user’s satisfaction. Among the problems detected during the process of this doctoral thesis, it has been determined that some phenomena affect to different phases in the audiovisual production chain, apart from the type of content. On first instance, the generation of contents process should be enough controlled through parameters that avoid the occurrence of visual discomfort in observer’s eye, and consequently, visual fatigue. It is especially necessary controlling sequences of stereoscopic 3D, with both animation and live-action contents. On the other hand, video quality assessment, related to compression processes, should be improved because some objective metrics are adapted to user’s perception. The use of psychovisual models and visual attention diagrams allow the weighting of image regions of interest, giving more importance to the areas which the user will focus most probably. These two work fields are related together through the definition of the term saliency. Saliency is the capacity of human visual system for characterizing an image, highlighting the areas which result more attractive to the human eye. Saliency in generation of 3DTV contents refers mainly to the simulated depth of the optic illusion, i.e. the distance from the virtual object to the human eye. On the other hand, saliency is not based on virtual depth, but on other features, such as motion, level of detail, position of pixels in the frame or face detection, which are the basic features that are part of the developed visual attention model, as demonstrated with tests. Extensive literature involving visual comfort assessment was looked up, and the development of new preliminary subjective assessment with users was performed, in order to detect the features that increase the probability of discomfort to occur. With this methodology, the conclusions drawn confirmed that one common source of visual discomfort was when an abrupt change of disparity happened in video transitions, apart from other degradations, such as window violation. New quality assessment was performed to quantify the distribution of disparities over different sequences. The results confirmed that abrupt changes in negative parallax environment produce accommodation-vergence mismatches derived from the increasing time for human crystalline to focus the virtual objects. On the other side, for developing metrics that adapt to human visual system, additional subjective tests were developed to determine the importance of each factor, which masks a concrete distortion. Results demonstrated slight improvement after applying visual attention to objective metrics. This process of weighing pixels approximates the quality results to human eye’s response.

Convergence analysis and validation of low cost distance metrics for computational cost reduction of the Iterative Closest Point algorithm

The Iterative Closest Point algorithm (ICP) is commonly used in engineering applications to solve the rigid registration problem of partially overlapped point sets which are pre-aligned with a coarse estimate of their relative positions. This iterative algorithm is applied in many areas such as the medicine for volumetric reconstruction of tomography data, in robotics to reconstruct surfaces or scenes using range sensor information, in industrial systems for quality control of manufactured objects or even in biology to study the structure and folding of proteins. One of the algorithm’s main problems is its high computational complexity (quadratic in the number of points with the non-optimized original variant) in a context where high density point sets, acquired by high resolution scanners, are processed. Many variants have been proposed in the literature whose goal is the performance improvement either by reducing the number of points or the required iterations or even enhancing the complexity of the most expensive phase: the closest neighbor search. In spite of decreasing its complexity, some of the variants tend to have a negative impact on the final registration precision or the convergence domain thus limiting the possible application scenarios. The goal of this work is the improvement of the algorithm’s computational cost so that a wider range of computationally demanding problems from among the ones described before can be addressed. For that purpose, an experimental and mathematical convergence analysis and validation of point-to-point distance metrics has been performed taking into account those distances with lower computational cost than the Euclidean one, which is used as the de facto standard for the algorithm’s implementations in the literature. In that analysis, the functioning of the algorithm in diverse topological spaces, characterized by different metrics, has been studied to check the convergence, efficacy and cost of the method in order to determine the one which offers the best results. Given that the distance calculation represents a significant part of the whole set of computations performed by the algorithm, it is expected that any reduction of that operation affects significantly and positively the overall performance of the method. As a result, a performance improvement has been achieved by the application of those reduced cost metrics whose quality in terms of convergence and error has been analyzed and validated experimentally as comparable with respect to the Euclidean distance using a heterogeneous set of objects, scenarios and initial situations.

Statistical Hurdle Models for Single Cell Gene Expression: Differential Expression and Graphical Modeling

Thesis (Ph.D.)--University of Washington, 2016-06

Symptom prevalence and clustering of symptoms in people living with chronic hepatitis C infection

Quality of life has been shown to be poor among people living with chronic hepatitis C However, it is not clear how this relates to the presence of symptoms and their severity. The aim of this study was to describe the typology of a broad array of symptoms that were attributed to hepatitis C virus (HCV) infection. Phase I used qualitative methods to identify symptoms. In Phase 2, 188 treatment-naive people living with HCV participated in a quantitative survey. The most prevalent symptom was physical tiredness (86%) followed by irritability (75%), depression (70%), mental tiredness (70%), and abdominal pain (68%). Temporal clustering of symptoms was reported in 62% of participants. Principal components analysis identified four symptom clusters: neuropsychiatric (mental tiredness, poor concentration, forgetfulness, depression, irritability, physical tiredness, and sleep problems); gastrointestinal (day sweats, nausea, food intolerance, night sweats, abdominal pain, poor appetite, and diarrhea); algesic (joint pain, muscle pain, and general body pain); and dysesthetic (noise sensitivity, light sensitivity, skin. problems, and headaches). These data demonstrate that symptoms are prevalent in treatment-naive people with HCV and support the hypothesis that symptom clustering occurs.

Managing the quality, value and impact of academic libraries: the role of external standards

Purpose – The purpose of this paper is to explore the role and relevance of external standards in demonstrating the value and impact of academic library services to their stakeholders. Design/methodology/approach – Two UK standards, Charter Mark and Customer Service Excellence, are evaluated via an exploratory case study, employing multiple data collection techniques. Methods and results of phases 1-2 of a three phase research project are outlined. Findings – Despite some limitations, standards may assist the manager in demonstrating the value, impact and quality of academic libraries in a recessional environment. Active engagement and partnership with customers is imperative if academic libraries are to be viewed as vital to their parent organisations and thus survive. Originality/value – This paper provides a systematic evaluation of the role of external accreditation standards in measuring academic library service value and impact.

Metrics and models to support the development of hybrid information systems

The research described here concerns the development of metrics and models to support the development of hybrid (conventional/knowledge based) integrated systems. The thesis argues from the point that, although it is well known that estimating the cost, duration and quality of information systems is a difficult task, it is far from clear what sorts of tools and techniques would adequately support a project manager in the estimation of these properties. A literature review shows that metrics (measurements) and estimating tools have been developed for conventional systems since the 1960s while there has been very little research on metrics for knowledge based systems (KBSs). Furthermore, although there are a number of theoretical problems with many of the `classic' metrics developed for conventional systems, it also appears that the tools which such metrics can be used to develop are not widely used by project managers. A survey was carried out of large UK companies which confirmed this continuing state of affairs. Before any useful tools could be developed, therefore, it was important to find out why project managers were not using these tools already. By characterising those companies that use software cost estimating (SCE) tools against those which could but do not, it was possible to recognise the involvement of the client/customer in the process of estimation. Pursuing this point, a model of the early estimating and planning stages (the EEPS model) was developed to test exactly where estimating takes place. The EEPS model suggests that estimating could take place either before a fully-developed plan has been produced, or while this plan is being produced. If it were the former, then SCE tools would be particularly useful since there is very little other data available from which to produce an estimate. A second survey, however, indicated that project managers see estimating as being essentially the latter at which point project management tools are available to support the process. It would seem, therefore, that SCE tools are not being used because project management tools are being used instead. The issue here is not with the method of developing an estimating model or tool, but; in the way in which "an estimate" is intimately tied to an understanding of what tasks are being planned. Current SCE tools are perceived by project managers as targetting the wrong point of estimation, A model (called TABATHA) is then presented which describes how an estimating tool based on an analysis of tasks would thus fit into the planning stage. The issue of whether metrics can be usefully developed for hybrid systems (which also contain KBS components) is tested by extending a number of "classic" program size and structure metrics to a KBS language, Prolog. Measurements of lines of code, Halstead's operators/operands, McCabe's cyclomatic complexity, Henry & Kafura's data flow fan-in/out and post-release reported errors were taken for a set of 80 commercially-developed LPA Prolog programs: By re~defining the metric counts for Prolog it was found that estimates of program size and error-proneness comparable to the best conventional studies are possible. This suggests that metrics can be usefully applied to KBS languages, such as Prolog and thus, the development of metncs and models to support the development of hybrid information systems is both feasible and useful.

Clustering web documents using hierarchical representation with multi-granularity

Web document cluster analysis plays an important role in information retrieval by organizing large amounts of documents into a small number of meaningful clusters. Traditional web document clustering is based on the Vector Space Model (VSM), which takes into account only two-level (document and term) knowledge granularity but ignores the bridging paragraph granularity. However, this two-level granularity may lead to unsatisfactory clustering results with “false correlation”. In order to deal with the problem, a Hierarchical Representation Model with Multi-granularity (HRMM), which consists of five-layer representation of data and a twophase clustering process is proposed based on granular computing and article structure theory. To deal with the zero-valued similarity problemresulted from the sparse term-paragraphmatrix, an ontology based strategy and a tolerance-rough-set based strategy are introduced into HRMM. By using granular computing, structural knowledge hidden in documents can be more efficiently and effectively captured in HRMM and thus web document clusters with higher quality can be generated. Extensive experiments show that HRMM, HRMM with tolerancerough-set strategy, and HRMM with ontology all outperform VSM and a representative non VSM-based algorithm, WFP, significantly in terms of the F-Score.

Clustering algorithm based on minimal path loss ratio for vehicular communication

Emerging vehicular comfort applications pose a host of completely new set of requirements such as maintaining end-to-end connectivity, packet routing, and reliable communication for internet access while on the move. One of the biggest challenges is to provide good quality of service (QoS) such as low packet delay while coping with the fast topological changes. In this paper, we propose a clustering algorithm based on minimal path loss ratio (MPLR) which should help in spectrum efficiency and reduce data congestion in the network. The vehicular nodes which experience minimal path loss are selected as the cluster heads. The performance of the MPLR clustering algorithm is calculated by rate of change of cluster heads, average number of clusters and average cluster size. Vehicular traffic models derived from the Traffic Wales data are fed as input to the motorway simulator. A mathematical analysis for the rate of change of cluster head is derived which validates the MPLR algorithm and is compared with the simulated results. The mathematical and simulated results are in good agreement indicating the stability of the algorithm and the accuracy of the simulator. The MPLR system is also compared with V2R system with MPLR system performing better. © 2013 IEEE.

Multi-level visualisation using Gaussian process latent variable models

Projection of a high-dimensional dataset onto a two-dimensional space is a useful tool to visualise structures and relationships in the dataset. However, a single two-dimensional visualisation may not display all the intrinsic structure. Therefore, hierarchical/multi-level visualisation methods have been used to extract more detailed understanding of the data. Here we propose a multi-level Gaussian process latent variable model (MLGPLVM). MLGPLVM works by segmenting data (with e.g. K-means, Gaussian mixture model or interactive clustering) in the visualisation space and then fitting a visualisation model to each subset. To measure the quality of multi-level visualisation (with respect to parent and child models), metrics such as trustworthiness, continuity, mean relative rank errors, visualisation distance distortion and the negative log-likelihood per point are used. We evaluate the MLGPLVM approach on the ‘Oil Flow’ dataset and a dataset of protein electrostatic potentials for the ‘Major Histocompatibility Complex (MHC) class I’ of humans. In both cases, visual observation and the quantitative quality measures have shown better visualisation at lower levels.