Contributions to Bayesian network learning with applications to neuroscience

Neuronal morphology is a key feature in the study of brain circuits, as it is highly related to information processing and functional identification. Neuronal morphology affects the process of integration of inputs from other neurons and determines the neurons which receive the output of the neurons. Different parts of the neurons can operate semi-independently according to the spatial location of the synaptic connections. As a result, there is considerable interest in the analysis of the microanatomy of nervous cells since it constitutes an excellent tool for better understanding cortical function. However, the morphologies, molecular features and electrophysiological properties of neuronal cells are extremely variable. Except for some special cases, this variability makes it hard to find a set of features that unambiguously define a neuronal type. In addition, there are distinct types of neurons in particular regions of the brain. This morphological variability makes the analysis and modeling of neuronal morphology a challenge. Uncertainty is a key feature in many complex real-world problems. Probability theory provides a framework for modeling and reasoning with uncertainty. Probabilistic graphical models combine statistical theory and graph theory to provide a tool for managing domains with uncertainty. In particular, we focus on Bayesian networks, the most commonly used probabilistic graphical model. In this dissertation, we design new methods for learning Bayesian networks and apply them to the problem of modeling and analyzing morphological data from neurons. The morphology of a neuron can be quantified using a number of measurements, e.g., the length of the dendrites and the axon, the number of bifurcations, the direction of the dendrites and the axon, etc. These measurements can be modeled as discrete or continuous data. The continuous data can be linear (e.g., the length or the width of a dendrite) or directional (e.g., the direction of the axon). These data may follow complex probability distributions and may not fit any known parametric distribution. Modeling this kind of problems using hybrid Bayesian networks with discrete, linear and directional variables poses a number of challenges regarding learning from data, inference, etc. In this dissertation, we propose a method for modeling and simulating basal dendritic trees from pyramidal neurons using Bayesian networks to capture the interactions between the variables in the problem domain. A complete set of variables is measured from the dendrites, and a learning algorithm is applied to find the structure and estimate the parameters of the probability distributions included in the Bayesian networks. Then, a simulation algorithm is used to build the virtual dendrites by sampling values from the Bayesian networks, and a thorough evaluation is performed to show the model’s ability to generate realistic dendrites. In this first approach, the variables are discretized so that discrete Bayesian networks can be learned and simulated. Then, we address the problem of learning hybrid Bayesian networks with different kinds of variables. Mixtures of polynomials have been proposed as a way of representing probability densities in hybrid Bayesian networks. We present a method for learning mixtures of polynomials approximations of one-dimensional, multidimensional and conditional probability densities from data. The method is based on basis spline interpolation, where a density is approximated as a linear combination of basis splines. The proposed algorithms are evaluated using artificial datasets. We also use the proposed methods as a non-parametric density estimation technique in Bayesian network classifiers. Next, we address the problem of including directional data in Bayesian networks. These data have some special properties that rule out the use of classical statistics. Therefore, different distributions and statistics, such as the univariate von Mises and the multivariate von Mises–Fisher distributions, should be used to deal with this kind of information. In particular, we extend the naive Bayes classifier to the case where the conditional probability distributions of the predictive variables given the class follow either of these distributions. We consider the simple scenario, where only directional predictive variables are used, and the hybrid case, where discrete, Gaussian and directional distributions are mixed. The classifier decision functions and their decision surfaces are studied at length. Artificial examples are used to illustrate the behavior of the classifiers. The proposed classifiers are empirically evaluated over real datasets. We also study the problem of interneuron classification. An extensive group of experts is asked to classify a set of neurons according to their most prominent anatomical features. A web application is developed to retrieve the experts’ classifications. We compute agreement measures to analyze the consensus between the experts when classifying the neurons. Using Bayesian networks and clustering algorithms on the resulting data, we investigate the suitability of the anatomical terms and neuron types commonly used in the literature. Additionally, we apply supervised learning approaches to automatically classify interneurons using the values of their morphological measurements. Then, a methodology for building a model which captures the opinions of all the experts is presented. First, one Bayesian network is learned for each expert, and we propose an algorithm for clustering Bayesian networks corresponding to experts with similar behaviors. Then, a Bayesian network which represents the opinions of each group of experts is induced. Finally, a consensus Bayesian multinet which models the opinions of the whole group of experts is built. A thorough analysis of the consensus model identifies different behaviors between the experts when classifying the interneurons in the experiment. A set of characterizing morphological traits for the neuronal types can be defined by performing inference in the Bayesian multinet. These findings are used to validate the model and to gain some insights into neuron morphology. Finally, we study a classification problem where the true class label of the training instances is not known. Instead, a set of class labels is available for each instance. This is inspired by the neuron classification problem, where a group of experts is asked to individually provide a class label for each instance. We propose a novel approach for learning Bayesian networks using count vectors which represent the number of experts who selected each class label for each instance. These Bayesian networks are evaluated using artificial datasets from supervised learning problems. Resumen La morfología neuronal es una característica clave en el estudio de los circuitos cerebrales, ya que está altamente relacionada con el procesado de información y con los roles funcionales. La morfología neuronal afecta al proceso de integración de las señales de entrada y determina las neuronas que reciben las salidas de otras neuronas. Las diferentes partes de la neurona pueden operar de forma semi-independiente de acuerdo a la localización espacial de las conexiones sinápticas. Por tanto, existe un interés considerable en el análisis de la microanatomía de las células nerviosas, ya que constituye una excelente herramienta para comprender mejor el funcionamiento de la corteza cerebral. Sin embargo, las propiedades morfológicas, moleculares y electrofisiológicas de las células neuronales son extremadamente variables. Excepto en algunos casos especiales, esta variabilidad morfológica dificulta la definición de un conjunto de características que distingan claramente un tipo neuronal. Además, existen diferentes tipos de neuronas en regiones particulares del cerebro. La variabilidad neuronal hace que el análisis y el modelado de la morfología neuronal sean un importante reto científico. La incertidumbre es una propiedad clave en muchos problemas reales. La teoría de la probabilidad proporciona un marco para modelar y razonar bajo incertidumbre. Los modelos gráficos probabilísticos combinan la teoría estadística y la teoría de grafos con el objetivo de proporcionar una herramienta con la que trabajar bajo incertidumbre. En particular, nos centraremos en las redes bayesianas, el modelo más utilizado dentro de los modelos gráficos probabilísticos. En esta tesis hemos diseñado nuevos métodos para aprender redes bayesianas, inspirados por y aplicados al problema del modelado y análisis de datos morfológicos de neuronas. La morfología de una neurona puede ser cuantificada usando una serie de medidas, por ejemplo, la longitud de las dendritas y el axón, el número de bifurcaciones, la dirección de las dendritas y el axón, etc. Estas medidas pueden ser modeladas como datos continuos o discretos. A su vez, los datos continuos pueden ser lineales (por ejemplo, la longitud o la anchura de una dendrita) o direccionales (por ejemplo, la dirección del axón). Estos datos pueden llegar a seguir distribuciones de probabilidad muy complejas y pueden no ajustarse a ninguna distribución paramétrica conocida. El modelado de este tipo de problemas con redes bayesianas híbridas incluyendo variables discretas, lineales y direccionales presenta una serie de retos en relación al aprendizaje a partir de datos, la inferencia, etc. En esta tesis se propone un método para modelar y simular árboles dendríticos basales de neuronas piramidales usando redes bayesianas para capturar las interacciones entre las variables del problema. Para ello, se mide un amplio conjunto de variables de las dendritas y se aplica un algoritmo de aprendizaje con el que se aprende la estructura y se estiman los parámetros de las distribuciones de probabilidad que constituyen las redes bayesianas. Después, se usa un algoritmo de simulación para construir dendritas virtuales mediante el muestreo de valores de las redes bayesianas. Finalmente, se lleva a cabo una profunda evaluaci ón para verificar la capacidad del modelo a la hora de generar dendritas realistas. En esta primera aproximación, las variables fueron discretizadas para poder aprender y muestrear las redes bayesianas. A continuación, se aborda el problema del aprendizaje de redes bayesianas con diferentes tipos de variables. Las mixturas de polinomios constituyen un método para representar densidades de probabilidad en redes bayesianas híbridas. Presentamos un método para aprender aproximaciones de densidades unidimensionales, multidimensionales y condicionales a partir de datos utilizando mixturas de polinomios. El método se basa en interpolación con splines, que aproxima una densidad como una combinación lineal de splines. Los algoritmos propuestos se evalúan utilizando bases de datos artificiales. Además, las mixturas de polinomios son utilizadas como un método no paramétrico de estimación de densidades para clasificadores basados en redes bayesianas. Después, se estudia el problema de incluir información direccional en redes bayesianas. Este tipo de datos presenta una serie de características especiales que impiden el uso de las técnicas estadísticas clásicas. Por ello, para manejar este tipo de información se deben usar estadísticos y distribuciones de probabilidad específicos, como la distribución univariante von Mises y la distribución multivariante von Mises–Fisher. En concreto, en esta tesis extendemos el clasificador naive Bayes al caso en el que las distribuciones de probabilidad condicionada de las variables predictoras dada la clase siguen alguna de estas distribuciones. Se estudia el caso base, en el que sólo se utilizan variables direccionales, y el caso híbrido, en el que variables discretas, lineales y direccionales aparecen mezcladas. También se estudian los clasificadores desde un punto de vista teórico, derivando sus funciones de decisión y las superficies de decisión asociadas. El comportamiento de los clasificadores se ilustra utilizando bases de datos artificiales. Además, los clasificadores son evaluados empíricamente utilizando bases de datos reales. También se estudia el problema de la clasificación de interneuronas. Desarrollamos una aplicación web que permite a un grupo de expertos clasificar un conjunto de neuronas de acuerdo a sus características morfológicas más destacadas. Se utilizan medidas de concordancia para analizar el consenso entre los expertos a la hora de clasificar las neuronas. Se investiga la idoneidad de los términos anatómicos y de los tipos neuronales utilizados frecuentemente en la literatura a través del análisis de redes bayesianas y la aplicación de algoritmos de clustering. Además, se aplican técnicas de aprendizaje supervisado con el objetivo de clasificar de forma automática las interneuronas a partir de sus valores morfológicos. A continuación, se presenta una metodología para construir un modelo que captura las opiniones de todos los expertos. Primero, se genera una red bayesiana para cada experto y se propone un algoritmo para agrupar las redes bayesianas que se corresponden con expertos con comportamientos similares. Después, se induce una red bayesiana que modela la opinión de cada grupo de expertos. Por último, se construye una multired bayesiana que modela las opiniones del conjunto completo de expertos. El análisis del modelo consensuado permite identificar diferentes comportamientos entre los expertos a la hora de clasificar las neuronas. Además, permite extraer un conjunto de características morfológicas relevantes para cada uno de los tipos neuronales mediante inferencia con la multired bayesiana. Estos descubrimientos se utilizan para validar el modelo y constituyen información relevante acerca de la morfología neuronal. Por último, se estudia un problema de clasificación en el que la etiqueta de clase de los datos de entrenamiento es incierta. En cambio, disponemos de un conjunto de etiquetas para cada instancia. Este problema está inspirado en el problema de la clasificación de neuronas, en el que un grupo de expertos proporciona una etiqueta de clase para cada instancia de manera individual. Se propone un método para aprender redes bayesianas utilizando vectores de cuentas, que representan el número de expertos que seleccionan cada etiqueta de clase para cada instancia. Estas redes bayesianas se evalúan utilizando bases de datos artificiales de problemas de aprendizaje supervisado.

PUE attack detection in CWSN using collaboration and learning behavior

Cognitive Wireless Sensor Network (CWSN) is a new paradigm which integrates cognitive features in traditional Wireless Sensor Networks (WSNs) to mitigate important problems such as spectrum occupancy. Security in Cognitive Wireless Sensor Networks is an important problem because these kinds of networks manage critical applications and data. Moreover, the specific constraints of WSN make the problem even more critical. However, effective solutions have not been implemented yet. Among the specific attacks derived from new cognitive features, the one most studied is the Primary User Emulation (PUE) attack. This paper discusses a new approach, based on anomaly behavior detection and collaboration, to detect the PUE attack in CWSN scenarios. A nonparametric CUSUM algorithm, suitable for low resource networks like CWSN, has been used in this work. The algorithm has been tested using a cognitive simulator that brings important results in this area. For example, the result shows that the number of collaborative nodes is the most important parameter in order to improve the PUE attack detection rates. If the 20% of the nodes collaborates, the PUE detection reaches the 98% with less than 1% of false positives.

Integrating science and management through collaborative learning and better information management

Achieving more sustainable land and water use depends on high-quality information and its improved use. In other words, better linkages are needed between science and management. Since many stakeholders with different relationships to the natural resources are inevitably involved, we suggest that collaborative learning environments and improved information management are prerequisites for integrating science and management. Case studies that deal with resource management issues are presented that illustrate the creation of collaborative learning environments through systems analyses with communities, and an integration of scientific and experiential knowledge of components of the system. This new knowledge needs to be captured and made accessible through innovative information management systems designed collaboratively with users, in forms which fit the users' 'mental models' of how their systems work. A model for linking science and resource management more effectively is suggested. This model entails systems thinking in a collaborative learning environment, and processes to help convergence of views and value systems, and make scientists and different kinds of managers aware of their interdependence. Adaptive management provides a mechanism for applying and refining scientists' and managers' knowledge. Copyright (C) 2003 John Wiley Sons, Ltd.

An examination of learning processes during critical incident training: Implications for the development of adaptable trainees

Three experiments are reported that examined the process by which trainees learn decision-making skills during a critical incident training program. Formal theories of category learning were used to identify two processes that may be responsible for the acquisition of decision-making skills: rule learning and exemplar learning. Experiments I and 2 used the process dissociation procedure (L. L. Jacoby, 1998) to evaluate the contribution of these processes to performance. The results suggest that trainees used a mixture of rule and exemplar learning. Furthermore, these learning processes were influenced by different aspects of training structure and design. The goal of Experiment 3 was to develop training techniques that enable trainees to use a rule adaptively. Trainees were tested on cases that represented exceptions to the rule. Unexpectedly, the results suggest that providing general instruction regarding the kinds of conditions in which a decision rule does not apply caused them to fixate on the specific conditions mentioned and impaired their ability to identify other conditions in which the rule might not apply. The theoretical, methodological, and practical implications of the results are discussed.

Building partnerships with families and communities to support children's numeracy learning

The importance of building home, school and community partnerships is increasingly acknowledged since family and community involvement in education is thought to be associated with children’s success at school. This paper reports on aspects of an Australian Government commissioned research project that analysed educational partnerships aiming to enhance children’s numeracy education. Snapshots of two school case studies are presented to highlight features of effective partnerships and the kinds of numeracy learning they supported.

Engaging tutors in using e-repositories for learning and teaching

Universities which set up online repositories for the management of learning and teaching resources commonly find that uptake is poor. Tutors are often reluctant to upload their materials to e-repositories, even though the same tutors are happy to upload resources to the virtual learning environment (e.g. Blackboard, Moodle, Sakai) and happy to upload their research papers to the university’s research publications repository. The paper reviews this phenomenon and suggests constructive ways in which tutors can be encouraged to engage with an e-repository. The authors have recently completed a major project “Developing Repositories at Worcester” which is part of a group of similar projects in the UK. The paper includes the feedback and the lessons learned from these projects, based on the publications and reports they have produced. They cover ways of embedding repository use into institutional working practice, and give examples of different types of repository designed to meet the needs of those using different kinds of learning and teaching resources. As well as this specific experience, the authors summarise some of the main findings from UK publications, in particular the December 2008 report of Joint Information Systems Committee: Good intentions: improving the evidence base in support of sharing learning materials and Online Innovation in Higher Education, Ron Cooke’s report to a UK government initiative on the future of Higher Education. The issues covered include the development of Web 2.0 style repositories rather than conventionally structured ones, the use of tags rather than metadata, the open resources initiative, the best use for conventional repositories, links to virtual learning environments, and the processes for the management and support of repositories within universities. In summary the paper presents an optimistic, constructive view of how to embed the use of e-repositories into the working practices of university tutors. Equally, the authors are aware of the considerable difficulties in making progress and are realistic about what can be achieved. The paper uses evidence and experience drawn from those working in this field to suggest a strategic vision in which the management of e-learning resources is productive, efficient and meets the needs of both tutors and their students.

Lexical learning and dysgraphia in a group of adults with developmental dyslexia

We investigated the ability to learn new words in a group of 22 adults with developmental dyslexia/dysgraphia and the relationship between their learning and spelling problems. We identified a deficit that affected the ability to learn both spoken and written new words (lexical learning deficit). There were no comparable problems in learning other kinds of representations (lexical/semantic and visual) and the deficit could not be explained in terms of more traditional phonological deficits associated with dyslexia (phonological awareness, phonological STM). Written new word learning accounted for further variance in the severity of the dysgraphia after phonological abilities had been partialled out. We suggest that lexical learning may be an independent ability needed to create lexical/formal representations from a series of independent units. Theoretical and clinical implications are discussed. © 2005 Psychology Press Ltd.

Supply chain learning needs:towards a port community perspective

The traditional role of ports in the wider supply chain context is currently being subject to a process of radical review. In broad terms, the traditional model is being replaced by a model which focuses on higher value and more knowledge intensive activities. This trend requires a change in the way in which new knowledge and skills are developed by staff in companies of all kinds within port communities. Traditional models need to be re-evaluated to reflect the increasing importance of knowledge and skills acquisition, particularly in relation to the supply chain management (SCM) concept and the evolving role of information and communications technology (ICT) in improving supply chain capability. This paper describes the case of NITL’s Foundation Certificate Programme (FCP) learning programme with specific reference to its use in addressing some of current shortcomings related to supply chain knowledge and skills in port communities. The FCP rationale is based on the need to move from traditional approaches of supply chain organisation where the various links in the chain were measured and managed in isolation from each other and thus tended to operate at cross purposes, towards more cooperative and integrated approaches.

Understanding Teacher and Student Learning Situated in a School-wide Implementation of Fractions Instruction

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

Music Learning Networks: Supporting the Music Learning of Adolescents

Thesis (Ph.D.)--University of Washington, 2016-08

Conditions for Teaching and Learning in Religious Education (RE) : Perspectives of Teachers and Pupils at the Beginning of the 6th Grade in Sweden

In this article empirical findings from interviews with teachers of three classes of 12-year-old pupils are presented, together with questionnaire-responses from these 54 pupils. The interviews focus on teaching aims for Religious Education (RE), a subject that in Sweden, besides dealing with religion, also explores other kinds of beliefs, ethics and life questions. In the questionnaire the pupils are asked to solve four RE tasks with content that is central from a Swedish curriculum perspective. The research involves pupils at the beginning of the sixth grade and the purpose of this article is to look at the teachers’ aims and the pupils’ responses, and consider what these may indicate about conditions for teaching and learning RE in these classes. The findings show that the perspectives of the pupils at the beginning of the sixth grade seem to be rather far from the expectations of the RE syllabus. The pupils’ statements are rather vague with regard to religion as a phenomenon and there are few examples of pupils interpreting religious symbols in a way that is useful in further analysis. While existential and ethical plots, messages and point of views are comparatively easy to describe, it is harder to express multiple perspectives, reasons, comparisons and questions. A problem for the teachers in developing the perspectives of their pupils is that they find it hard to say what kind of general difficulties pupils have in RE, a fact that makes it hard to direct the teaching. Another challenge is that the teachers’ RE-aims are rather overarching and primarily related to fostering fundamental values. What improves the conditions for teaching and learning is the teachers’ concern for the pupils and their relationships with the teacher and with each other, a factor which is of vital importance for learning and which can also be used as a specific teaching method in subject matter education.

Do children copy an expert or a majority? Examining selective learning in instrumental and normative contexts

This study examined whether instrumental and normative learning contexts differentially influence 4- to 7-year-old children’s social learning strategies; specifically, their dispositions to copy an expert versus a majority consensus. Experiment 1 (N = 44) established that children copied a relatively competent “expert” individual over an incompetent individual in both kinds of learning context. In experiment 2 (N = 80) we then tested whether children would copy a competent individual versus a majority, in each of the two different learning contexts. Results showed that individual children differed in strategy, preferring with significant consistency across two different test trials to copy either the competent individual or the majority. This study is the first to show that children prefer to copy more competent individuals when shown competing methods of achieving an instrumental goal (Experiment 1) and provides new evidence that children, at least in our “individualist” culture, may consistently express either a competency or majority bias in learning both instrumental and normative information (Experiment 2). This effect was similar in the instrumental and normative learning contexts we applied.

Socratic flipped classroom : What types of questions and tasks promote learning?

Socratic questioning stresses the importance of questioning for learning. Flipped Classroom pedagogy generates a need for effective questions and tasks in order to promote active learning. This paper describes a project aimed at finding out how different kinds of questions and tasks support students’ learning in a flipped classroom context. In this study, during the flipped courses, both the questions and tasks were distributed together with video recordings. Answers and solutions were presented and discussed in seminars, with approximately 10 participating students in each seminar. Information Systems students from three flipped classroom courses at three different levels were interviewed in focus groups about their perceptions of how different kinds of questions and tasks supported their learning process. The selected courses were organized differently, with various kinds of questions and tasks. Course one included open questions that were answered and presented at the seminar. Students also solved a task and presented the solution to the group. Course two included open questions and a task. Answers and solutions were discussed at the seminars where students also reviewed each other’s answers and solutions. Course three included online single- and multiple choice questions with real-time feedback. Answers were discussed at the seminar, with the focus on any misconceptions. In this paper we categorized the questions in accordance with Wilson (2016) as factual, convergent, divergent, evaluative, or a combination of these. In all, we found that any comprehensible question that initiates a dialogue, preferably with a set of Socratic questions, is perceived as promoting learning. This is why seminars that allow such questions and discussion are effective. We found no differences between the different kinds of Socratic questions. They were seen to promote learning so long as they made students reflect and problematize the questions. To conclude, we found that questions and tasks promote learning when they are answered and solved in a process that is characterized by comprehensibility, variation, repetition and activity.