BUILDING DSS USING KNOWLEDGE DISCOVERY IN DATABASE APPLIED TO ADMISSION & REGISTRATION FUNCTIONS

This research investigates the practical issues surrounding the development and implementation of Decision Support Systems (DSS). The research describes the traditional development approaches analyzing their drawbacks and introduces a new DSS development methodology. The proposed DSS methodology is based upon four modules; needs' analysis, data warehouse (DW), knowledge discovery in database (KDD), and a DSS module. The proposed DSS methodology is applied to and evaluated using the admission and registration functions in Egyptian Universities. The research investigates the organizational requirements that are required to underpin these functions in Egyptian Universities. These requirements have been identified following an in-depth survey of the recruitment process in the Egyptian Universities. This survey employed a multi-part admission and registration DSS questionnaire (ARDSSQ) to identify the required data sources together with the likely users and their information needs. The questionnaire was sent to senior managers within the Egyptian Universities (both private and government) with responsibility for student recruitment, in particular admission and registration. Further, access to a large database has allowed the evaluation of the practical suitability of using a data warehouse structure and knowledge management tools within the decision making framework. 1600 students' records have been analyzed to explore the KDD process, and another 2000 records have been used to build and test the data mining techniques within the KDD process. Moreover, the research has analyzed the key characteristics of data warehouses and explored the advantages and disadvantages of such data structures. This evaluation has been used to build a data warehouse for the Egyptian Universities that handle their admission and registration related archival data. The decision makers' potential benefits of the data warehouse within the student recruitment process will be explored. The design of the proposed admission and registration DSS (ARDSS) will be developed and tested using Cool: Gen (5.0) CASE tools by Computer Associates (CA), connected to a MSSQL Server (6.5), in a Windows NT (4.0) environment. Crystal Reports (4.6) by Seagate will be used as a report generation tool. CLUST AN Graphics (5.0) by CLUST AN software will also be used as a clustering package. Finally, the contribution of this research is found in the following areas: A new DSS development methodology; The development and validation of a new research questionnaire (i.e. ARDSSQ); The development of the admission and registration data warehouse; The evaluation and use of cluster analysis proximities and techniques in the KDD process to find knowledge in the students' records; And the development of the ARDSS software that encompasses the advantages of the KDD and DW and submitting these advantages to the senior admission and registration managers in the Egyptian Universities. The ARDSS software could be adjusted for usage in different countries for the same purpose, it is also scalable to handle new decision situations and can be integrated with other systems

Analytical fusion of multimodal magnetic resonance imaging to identify pathological states in genetically selected Marchigian Sardinian alcohol-preferring (msP) rats

[EN] Alcohol abuse is one of the most alarming issues for the health authorities. It is estimated that at least 23 million of European citizens are affected by alcoholism causing a cost around 270 million euros. Excessive alcohol consumption is related with physical harm and, although it damages the most of body organs, liver, pancreas, and brain are more severally affected. Not only physical harm is associated to alcohol-related disorders, but also other psychiatric disorders such as depression are often comorbiding. As well, alcohol is present in many of violent behaviors and traffic injures. Altogether reflects the high complexity of alcohol-related disorders suggesting the involvement of multiple brain systems. With the emergence of non-invasive diagnosis techniques such as neuroimaging or EEG, many neurobiological factors have been evidenced to be fundamental in the acquisition and maintenance of addictive behaviors, relapsing risk, and validity of available treatment alternatives. Alterations in brain structure and function reflected in non-invasive imaging studies have been repeatedly investigated. However, the extent to which imaging measures may precisely characterize and differentiate pathological stages of the disease often accompanied by other pathologies is not clear. The use of animal models has elucidated the role of neurobiological mechanisms paralleling alcohol misuses. Thus, combining animal research with non-invasive neuroimaging studies is a key tool in the advance of the disorder understanding. As the volume of data from very diverse nature available in clinical and research settings increases, an integration of data sets and methodologies is required to explore multidimensional aspects of psychiatric disorders. Complementing conventional mass-variate statistics, interests in predictive power of statistical machine learning to neuroimaging data is currently growing among scientific community. This doctoral thesis has covered most of the aspects mentioned above. Starting from a well-established animal model in alcohol research, Marchigian Sardinian rats, we have performed multimodal neuroimaging studies at several stages of alcohol-experimental design including the etiological mechanisms modulating high alcohol consumption (in comparison to Wistar control rats), alcohol consumption, and treatment with the opioid antagonist Naltrexone, a well-established drug in clinics but with heterogeneous response. Multimodal magnetic resonance imaging acquisition included Diffusion Tensor Imaging, structural imaging, and the calculation of magnetic-derived relaxometry maps. We have designed an analytical framework based on widely used algorithms in neuroimaging field, Random Forest and Support Vector Machine, combined in a wrapping fashion. Designed approach was applied on the same dataset with two different aims: exploring the validity of the approach to discriminate experimental stages running at subject-level and establishing predictive models at voxel-level to identify key anatomical regions modified during the experiment course. As expected, combination of multiple magnetic resonance imaging modalities resulted in an enhanced predictive power (between 3 and 16%) with heterogeneous modality contribution. Surprisingly, we have identified some inborn alterations correlating high alcohol preference and thalamic neuroadaptations related to Naltrexone efficacy. As well, reproducible contribution of DTI and relaxometry -related biomarkers has been repeatedly identified guiding further studies in alcohol research. In summary, along this research we demonstrate the feasibility of incorporating multimodal neuroimaging, machine learning algorithms, and animal research in the advance of the understanding alcohol-related disorders.[ES] El abuso de alcohol es una de las mayores preocupaciones de las autoridades sanitarias en la Unión Europea. El consumo de alcohol en exceso afecta en mayor o menor medida la totalidad del organismo siendo el páncreas e hígado los más severamente afectados. Además de estos, el sistema nervioso central sufre deterioros relacionados con el alcohol y con frecuencia se presenta en paralelo con otras patologías psiquiátricas como la depresión u otras adicciones como la ludopatía. La presencia de estas comorbidades demuestra la complejidad de la patología en la que multitud de sistemas neuronales interaccionan entre sí. El uso imágenes de resonancia magnética (RM) han ayudado en el estudio de enfermedades psiquiátricas facilitando el descubrimiento de mecanismos neurológicos fundamentales en el desarrollo y mantenimiento de la adicción al alcohol, recaídas y el efecto de los tratamientos disponibles. A pesar de los avances, todavía se necesita investigar más para identificar las bases biológicas que contribuyen a la enfermedad. En este sentido, los modelos animales sirven, por lo tanto, a discriminar aquellos factores únicamente relacionados con el alcohol controlando otros factores que facilitan el desarrollo del alcoholismo. Estudios de resonancia magnética en animales de laboratorio y su posterior evaluación en humanos juegan un papel fundamental en el entendimiento de las patologías psiquatricas como la addicción al alcohol. La imagen por resonancia magnética se ha integrado en entornos clínicos como prueba diagnósticas no invasivas. A medida que el volumen de datos se va incrementando, se necesitan herramientas y metodologías capaces de fusionar información de muy distinta naturaleza y así establecer criterios diagnósticos cada vez más exactos. El poder predictivo de herramientas derivadas de la inteligencia artificial como el aprendizaje automático sirven de complemento a tradicionales métodos estadísticos. En este trabajo se han abordado la mayoría de estos aspectos. Se han obtenido datos multimodales de resonancia magnética de un modelo validado en la investigación de patologías derivadas del consumo del alcohol, las ratas Marchigian-Sardinian desarrolladas en la Universidad de Camerino (Italia) y con consumos de alcohol comparables a los humanos. Para cada animal se han adquirido datos antes y después del consumo de alcohol y bajo dos condiciones de abstinencia (con y sin tratamiento de Naltrexona, una medicaciones anti-recaídas usada como farmacoterapia en el alcoholismo). Los datos de resonancia magnética multimodal consistentes en imágenes de difusión, de relaxometría y estructurales se han fusionado en un esquema analítico multivariable incorporando dos herramientas generalmente usadas en datos derivados de neuroimagen, Random Forest y Support Vector Machine. Nuestro esquema fue aplicado con dos objetivos diferenciados. Por un lado, determinar en qué fase experimental se encuentra el sujeto a partir de biomarcadores y por el otro, identificar sistemas cerebrales susceptibles de alterarse debido a una importante ingesta de alcohol y su evolución durante la abstinencia. Nuestros resultados demostraron que cuando biomarcadores derivados de múltiples modalidades de neuroimagen se fusionan en un único análisis producen diagnósticos más exactos que los derivados de una única modalidad (hasta un 16% de mejora). Biomarcadores derivados de imágenes de difusión y relaxometría discriminan estados experimentales. También se han identificado algunos aspectos innatos que están relacionados con posteriores comportamientos con el consumo de alcohol o la relación entre la respuesta al tratamiento y los datos de resonancia magnética. Resumiendo, a lo largo de esta tesis, se demuestra que el uso de datos de resonancia magnética multimodales en modelos animales combinados en esquemas analíticos multivariados es una herramienta válida en el entendimiento de patologías[CAT] L'abús de alcohol es una de les majors preocupacions per part de les autoritats sanitàries de la Unió Europea. Malgrat la dificultat de establir xifres exactes, se estima que uns 23 milions de europeus actualment sofreixen de malalties derivades del alcoholisme amb un cost que supera els 150.000 milions de euros per a la societat. Un consum de alcohol en excés afecta en major o menor mesura el cos humà sent el pàncreas i el fetge el més afectats. A més, el cervell sofreix de deterioraments produïts per l'alcohol i amb freqüència coexisteixen amb altres patologies com depressió o altres addiccions com la ludopatia. Tot aquest demostra la complexitat de la malaltia en la que múltiple sistemes neuronals interactuen entre si. Tècniques no invasives com el encefalograma (EEG) o imatges de ressonància magnètica (RM) han ajudat en l'estudi de malalties psiquiàtriques facilitant el descobriment de mecanismes neurològics fonamentals en el desenvolupament i manteniment de la addició, recaiguda i la efectivitat dels tractaments disponibles. Tot i els avanços, encara es necessiten més investigacions per identificar les bases biològiques que contribueixen a la malaltia. En aquesta direcció, el models animals serveixen per a identificar únicament dependents del abús del alcohol. Estudis de ressonància magnètica en animals de laboratori i posterior avaluació en humans jugarien un paper fonamental en l' enteniment de l'ús del alcohol. L'ús de probes diagnostiques no invasives en entorns clínics has sigut integrades. A mesura que el volum de dades es incrementa, eines i metodologies per a la fusió d' informació de molt distinta natura i per tant, establir criteris diagnòstics cada vegada més exactes. La predictibilitat de eines desenvolupades en el camp de la intel·ligència artificial com la aprenentatge automàtic serveixen de complement a mètodes estadístics tradicionals. En aquesta investigació se han abordat tots aquestes aspectes. Dades multimodals de ressonància magnètica se han obtingut de un model animal validat en l'estudi de patologies relacionades amb el consum d'alcohol, les rates Marchigian-Sardinian desenvolupades en la Universitat de Camerino (Italià) i amb consums d'alcohol comparables als humans. Per a cada animal es van adquirir dades previs i després al consum de alcohol i dos condicions diferents de abstinència (amb i sense tractament anti-recaiguda). Dades de ressonància magnètica multimodal constituides per imatges de difusió, de relaxometria magnètica i estructurals van ser fusionades en esquemes analítics multivariats incorporant dues metodologies validades en el camp de neuroimatge, Random Forest i Support Vector Machine. Nostre esquema ha sigut aplicat amb dos objectius diferenciats. El primer objectiu es determinar en quina fase experimental es troba el subjecte a partir de biomarcadors obtinguts per neuroimatge. Per l'altra banda, el segon objectiu es identificar el sistemes cerebrals susceptibles de ser alterats durant una important ingesta de alcohol i la seua evolució durant la fase del tractament. El nostres resultats demostraren que l'ús de biomarcadors derivats de varies modalitats de neuroimatge fusionades en un anàlisis multivariat produeixen diagnòstics més exactes que els derivats de una única modalitat (fins un 16% de millora). Biomarcadors derivats de imatges de difusió i relaxometria van contribuir de distints estats experimentals. També s'han identificat aspectes innats que estan relacionades amb posterior preferències d'alcohol o la relació entre la resposta al tractament anti-recaiguda i les dades de ressonància magnètica. En resum, al llarg de aquest treball, es demostra que l'ús de dades de ressonància magnètica multimodal en models animals combinats en esquemes analítics multivariats són una eina molt valida en l'enteniment i avanç de patologies psiquiàtriques com l'alcoholisme.Cosa Liñán, A. (2017). Analytical fusion of multimodal magnetic resonance imaging to identify pathological states in genetically selected Marchigian Sardinian alcohol-preferring (msP) rats [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/90523TESI

Machine learning for efficient recognition of anatomical structures and abnormalities in biomedical images

Three studies have been carried out to investigate new approaches to efficient image segmentation and anomaly detection. The first study investigates the use of deep learning in patch based segmentation. Current approaches to patch based segmentation use low level features such as the sum of squared differences between patches. We argue that better segmentation can be achieved by harnessing the power of deep neural networks. Currently these networks make extensive use of convolutional layers. However, we argue that in the context of patch based segmentation, convolutional layers have little advantage over the canonical artificial neural network architecture. This is because a patch is small, and does not need decomposition and thus will not benefit from convolution. Instead, we make use of the canonical architecture in which neurons only compute dot products, but also incorporate modern techniques of deep learning. The resulting classifier is much faster and less memory-hungry than convolution based networks. In a test application to the segmentation of hippocampus in human brain MR images, we significantly outperformed prior art with a median Dice score up to 90.98% at a near real-time speed (<1s). The second study is an investigation into mouse phenotyping, and develops a high-throughput framework to detect morphological abnormality in mouse embryo micro-CT images. Existing work in this line is centred on, either the detection of phenotype-specific features or comparative analytics. The former approach lacks generality and the latter can often fail, for example, when the abnormality is not associated with severe volume variation. Both these approaches often require image segmentation as a pre-requisite, which is very challenging when applied to embryo phenotyping. A new approach to this problem in which non-rigid registration is combined with robust principal component analysis (RPCA), is proposed. The new framework is able to efficiently perform abnormality detection in a batch of images. It is sensitive to both volumetric and non-volumetric variations, and does not require image segmentation. In a validation study, it successfully distinguished the abnormal VSD and polydactyly phenotypes from the normal, respectively, at 85.19% and 88.89% specificities, with 100% sensitivity in both cases. The third study investigates the RPCA technique in more depth. RPCA is an extension of PCA that tolerates certain levels of data distortion during feature extraction, and is able to decompose images into regular and singular components. It has previously been applied to many computer vision problems (e.g. video surveillance), attaining excellent performance. However these applications commonly rest on a critical condition: in the majority of images being processed, there is a background with very little variation. By contrast in biomedical imaging there is significant natural variation across different images, resulting from inter-subject variability and physiological movements. Non-rigid registration can go some way towards reducing this variance, but cannot eliminate it entirely. To address this problem we propose a modified framework (RPCA-P) that is able to incorporate natural variation priors and adjust outlier tolerance locally, so that voxels associated with structures of higher variability are compensated with a higher tolerance in regularity estimation. An experimental study was applied to the same mouse embryo micro-CT data, and notably improved the detection specificity to 94.12% for the VSD and 90.97% for the polydactyly, while maintaining the sensitivity at 100%.Open Acces

The Murine Accessory Olfactory Bulb as a Model Chemosensory System: Experimental and Computational Analysis of Chemosensory Representations

A common challenge across sensory processing modalities is forming meaningful associations between the neural responses and the outside world. These neural representations of the world must then be integrated across different sensory systems contributing to each individuals perceptual experience. While there has been considerable study of sensory representations in the visual system of humans and multiple model organisms, other sensory domains, including olfaction, are less well understood. In this thesis, I set out to better understand the sensory representations of the mouse accessory olfactory system (AOS), a part of the olfactory system. The mouse AOS, our model chemosensory system, comprises peripheral vomeronasal sensory neurons (VSNs), the accessory olfactory bulb (AOB), and downstream effectors. Our work describes the neural representations of multiple sensory inputs in the AOS, specifically the representations of odorants in high dimensional chemical sensory space in the AOB, and how these representations are shaped by interactions within the circuit. Given the complex nature of olfactory chemosensory representations, the features of our model system may give new perspectives on the neural representation of the outside world. In a neural representation of olfactory information, both the interactions between each receptor and odor compounds as well as the circuit mediated interactions could potentially affect the neural representations of the outside world. The initial neural response comprises component interactions between each receptor and the odor; chemical signals must interact with physical receptors. However, chemosensory processing, such as olfaction, requires interpreting a large variety of potentially overlapping chemical cues from the environment with only a finite number of receptor types. This means that each chemical cue does not necessarily activate only one receptor type or region of the circuit, but rather the cue is likely to be represented by multiple receptor and odor component interactions. Also, the component parts of odors may be processed differently when presented in isolation versus in a more complex mixture, thus allowing the response to a particular odor to vary with chemical context. Moreover, once these component representations exist, interactions within the neural circuit may further shape these responses. For example, one might expect component parts of a complex odor to specifically inhibit other component parts. In the case of the accessory olfactory system this inhibition could be at the receptor level or at the level of the sensory representation in the accessory olfactory bulb (AOB). In Chapter 3, I describe the overall organization of chemosensory representations in the accessory olfactory bulb (AOB), which is found to be a modular map in which the primary associations of functional sensory responses are spatially organized relative to one another. I find these primary associations are condensations of the first order sensory neuron axon terminals, which form population response pooling structures called glomeruli. In these glomeruli, similar response types from those sensory neurons expressing one of the approximately 300 receptor types in the vomeronasal organ (VNO) co-converge. One purpose of converging inputs of neurons expressing the same receptor is likely to minimize noise, and I demonstrate that pooling of like receptor responses into glomeruli does increase neural signal relative to noise. However, I also observed a modular organization among and between glomeruli in which certain types or patterns of chemosensory responses are always spatially adjacent to one another, while others are much farther apart than would be expected by chance. I found this spatial modularity for both ethological stimuli (urine collected from conspecifics with widely divergent physiological endocrine status) and individual sulfated steroids. In Chapter 4, I explore the consequences of changing sensory context, specifically the presentation of multiple compounds, and the role that inhibition plays in the neural representation of the sensory stimuli. First, I tested whether the circuit responds differently to demands to represent a single odor than to demands to represent multiple odors by using odors that activate glomeruli both inside and outside of modules. I found that responses to mixtures rapidly diverge from the responses of individual component parts. Moreover, there was an effect of inhibition in modulating the response to preferred stimuli in all glomeruli. However, initial analysis of one type of pregnanolone responsive glomeruli demonstrated that the divergent response to mixtures in this type of glomerulus was not mediated by inhibition at the glomerular level, but was rather attributable to bottom-up effects from the interactions of multiple ligands with chemosensory receptors in the VNO. Nonetheless, I also demonstrated that in the AOB, the axon terminals of the same sensory neurons (glomeruli) are organized into modules that allow for feedback inhibition. Significant ionotropic glutamate receptor signal modulation was observed within modules, demonstrating that there are inhibition mediated effects in the representation of complex mixtures when glomeruli are co-locally arranged. Specifically, at both the level of the VSNs and also in AOB glomeruli, the response to allopregnanolone sulfate is inhibited by co-presentation with estradiol sulfate. This both significantly increases the relative representation of estradiol sulfate and shifts representation of allopregnanolone primarily within modules. These types of context dependent interactions depend on the spatial organization described in Chapter 3 as well as mixture context, and have the potential to optimize the representation of some chemical cues in a context specific manner

An investigation of functional MRI activation reproducibility

Imperial Users onl

Proceedings of the Fourth International Workshop on Mathematical Foundations of Computational Anatomy - Geometrical and Statistical Methods for Biological Shape Variability Modeling (MFCA 2013), Nagoya, Japan

International audienceComputational anatomy is an emerging discipline at the interface of geometry, statistics and image analysis which aims at modeling and analyzing the biological shape of tissues and organs. The goal is to estimate representative organ anatomies across diseases, populations, species or ages, to model the organ development across time (growth or aging), to establish their variability, and to correlate this variability information with other functional, genetic or structural information. The Mathematical Foundations of Computational Anatomy (MFCA) workshop aims at fostering the interactions between the mathematical community around shapes and the MICCAI community in view of computational anatomy applications. It targets more particularly researchers investigating the combination of statistical and geometrical aspects in the modeling of the variability of biological shapes. The workshop is a forum for the exchange of the theoretical ideas and aims at being a source of inspiration for new methodological developments in computational anatomy. A special emphasis is put on theoretical developments, applications and results being welcomed as illustrations. Following the first edition of this workshop in 2006, second edition in New-York in 2008, the third edition in Toronto in 2011, the forth edition was held in Nagoya Japan on September 22 2013

Novel Texture-based Probabilistic Object Recognition and Tracking Techniques for Food Intake Analysis and Traffic Monitoring

More complex image understanding algorithms are increasingly practical in a host of emerging applications. Object tracking has value in surveillance and data farming; and object recognition has applications in surveillance, data management, and industrial automation. In this work we introduce an object recognition application in automated nutritional intake analysis and a tracking application intended for surveillance in low quality videos. Automated food recognition is useful for personal health applications as well as nutritional studies used to improve public health or inform lawmakers. We introduce a complete, end-to-end system for automated food intake measurement. Images taken by a digital camera are analyzed, plates and food are located, food type is determined by neural network, distance and angle of food is determined and 3D volume estimated, the results are cross referenced with a nutritional database, and before and after meal photos are compared to determine nutritional intake. We compare against contemporary systems and provide detailed experimental results of our system\u27s performance. Our tracking systems consider the problem of car and human tracking on potentially very low quality surveillance videos, from fixed camera or high flying \acrfull{uav}. Our agile framework switches among different simple trackers to find the most applicable tracker based on the object and video properties. Our MAPTrack is an evolution of the agile tracker that uses soft switching to optimize between multiple pertinent trackers, and tracks objects based on motion, appearance, and positional data. In both cases we provide comparisons against trackers intended for similar applications i.e., trackers that stress robustness in bad conditions, with competitive results

Automatic classification of attention-deficit/hyperactivity disorder using brain activation

Nowadays, there is an active fi eld of research in neuroscience trying to fi nd relations between neurofunctional abnormalities of brain structures and neurological disorders. Previous statistical studies on brain functional Magnetic Resonance Images (fMRI) have found Attention Defi cit Hyperactivity Disorder (ADHD) patients are characterized by reduced activity in the inferior frontal gyrus (IFG) during response inhibition tasks and in the Ventral Striatum (VStr) during reward anticipation tasks. Interpreting brain image experiments using fMRI requires analysis of complex data and diff erent univariate or multivariate approaches can be chosen. Recently, one analysis approach that has grown in popularity is the use of machine learning algorithms to train classifiers to discriminate abnormal behavior or other variables of interest from fMRI data. The purpose of this work is to apply machine learning techniques to perform fMRI group analysis in an adult population. We propose a multivariate classifi er using diff erent discriminative features. Furthermore, we show how temporal information of fMRI data can be taken into account to improve the discrimination. We demonstrate that our new approach is able to diagnose the ADHD characteristics based on the activation in the executive functions. Previous results on the response inhibition task did not find di fferences between activation responses. Opposite to these results, we achieve accurate classifi cation performance for this task. Moreover, in this case, we show that classi fication rates can be signi cantly improved by incorporating temporal information into the classi fier