Structure learning of graphical models for task-oriented robot grasping

In the collective imaginaries a robot is a human like machine as any androids in science fiction. However the type of robots that you will encounter most frequently are machinery that do work that is too dangerous, boring or onerous. Most of the robots in the world are of this type. They can be found in auto, medical, manufacturing and space industries. Therefore a robot is a system that contains sensors, control systems, manipulators, power supplies and software all working together to perform a task. The development and use of such a system is an active area of research and one of the main problems is the development of interaction skills with the surrounding environment, which include the ability to grasp objects. To perform this task the robot needs to sense the environment and acquire the object informations, physical attributes that may influence a grasp. Humans can solve this grasping problem easily due to their past experiences, that is why many researchers are approaching it from a machine learning perspective finding grasp of an object using information of already known objects. But humans can select the best grasp amongst a vast repertoire not only considering the physical attributes of the object to grasp but even to obtain a certain effect. This is why in our case the study in the area of robot manipulation is focused on grasping and integrating symbolic tasks with data gained through sensors. The learning model is based on Bayesian Network to encode the statistical dependencies between the data collected by the sensors and the symbolic task. This data representation has several advantages. It allows to take into account the uncertainty of the real world, allowing to deal with sensor noise, encodes notion of causality and provides an unified network for learning. Since the network is actually implemented and based on the human expert knowledge, it is very interesting to implement an automated method to learn the structure as in the future more tasks and object features can be introduced and a complex network design based only on human expert knowledge can become unreliable. Since structure learning algorithms presents some weaknesses, the goal of this thesis is to analyze real data used in the network modeled by the human expert, implement a feasible structure learning approach and compare the results with the network designed by the expert in order to possibly enhance it.

A Pseudolikelihood Approach for Simultaneous Analysis of Array Comparative Genomic Hybridizations (aCGH)

DNA sequence copy number has been shown to be associated with cancer development and progression. Array-based Comparative Genomic Hybridization (aCGH) is a recent development that seeks to identify the copy number ratio at large numbers of markers across the genome. Due to experimental and biological variations across chromosomes and across hybridizations, current methods are limited to analyses of single chromosomes. We propose a more powerful approach that borrows strength across chromosomes and across hybridizations. We assume a Gaussian mixture model, with a hidden Markov dependence structure, and with random effects to allow for intertumoral variation, as well as intratumoral clonal variation. For ease of computation, we base estimation on a pseudolikelihood function. The method produces quantitative assessments of the likelihood of genetic alterations at each clone, along with a graphical display for simple visual interpretation. We assess the characteristics of the method through simulation studies and through analysis of a brain tumor aCGH data set. We show that the pseudolikelihood approach is superior to existing methods both in detecting small regions of copy number alteration and in accurately classifying regions of change when intratumoral clonal variation is present.

Checking Assumptions in Latent Class Regression Models via a Markov Chain Monte Carlo Estimation Approach: An Application to Depression and Socio-Economic Status

Latent class regression models are useful tools for assessing associations between covariates and latent variables. However, evaluation of key model assumptions cannot be performed using methods from standard regression models due to the unobserved nature of latent outcome variables. This paper presents graphical diagnostic tools to evaluate whether or not latent class regression models adhere to standard assumptions of the model: conditional independence and non-differential measurement. An integral part of these methods is the use of a Markov Chain Monte Carlo estimation procedure. Unlike standard maximum likelihood implementations for latent class regression model estimation, the MCMC approach allows us to calculate posterior distributions and point estimates of any functions of parameters. It is this convenience that allows us to provide the diagnostic methods that we introduce. As a motivating example we present an analysis focusing on the association between depression and socioeconomic status, using data from the Epidemiologic Catchment Area study. We consider a latent class regression analysis investigating the association between depression and socioeconomic status measures, where the latent variable depression is regressed on education and income indicators, in addition to age, gender, and marital status variables. While the fitted latent class regression model yields interesting results, the model parameters are found to be invalid due to the violation of model assumptions. The violation of these assumptions is clearly identified by the presented diagnostic plots. These methods can be applied to standard latent class and latent class regression models, and the general principle can be extended to evaluate model assumptions in other types of models.

Code and readme of a MATLAB-based graphical user interface program for computing functionals of the geopotential

We present a novel graphical user interface program GrafLab (GRAvity Field LABoratory) for spherical harmonic synthesis (SHS) created in MATLAB®. This program allows to comfortably compute 38 various functionals of the geopotential up to ultra-high degrees and orders of spherical harmonic expansion. For the most difficult part of the SHS, namely the evaluation of the fully normalized associated Legendre functions (fnALFs), we used three different approaches according to required maximum degree: (i) the standard forward column method (up to maximum degree 1800, in some cases up to degree 2190); (ii) the modified forward column method combined with Horner's scheme (up to maximum degree 2700); (iii) the extended-range arithmetic (up to an arbitrary maximum degree). For the maximum degree 2190, the SHS with fnALFs evaluated using the extended-range arithmetic approach takes only approximately 2-3 times longer than its standard arithmetic counterpart, i.e. the standard forward column method. In the GrafLab, the functionals of the geopotential can be evaluated on a regular grid or point-wise, while the input coordinates can either be read from a data file or entered manually. For the computation on a regular grid we decided to apply the lumped coefficients approach due to significant time-efficiency of this method. Furthermore, if a full variance-covariance matrix of spherical harmonic coefficients is available, it is possible to compute the commission errors of the functionals. When computing on a regular grid, the output functionals or their commission errors may be depicted on a map using automatically selected cartographic projection.

Markov blanket-based approach for learning multi-dimensional Bayesian network classifiers: An application to predict the European Quality of Life-5 Dimensions (EQ-5D) from the 39-item Parkinson's Disease Questionnaire (PDQ-39)

Multi-dimensional Bayesian network classifiers (MBCs) are probabilistic graphical models recently proposed to deal with multi-dimensional classification problems, where each instance in the data set has to be assigned to more than one class variable. In this paper, we propose a Markov blanket-based approach for learning MBCs from data. Basically, it consists of determining the Markov blanket around each class variable using the HITON algorithm, then specifying the directionality over the MBC subgraphs. Our approach is applied to the prediction problem of the European Quality of Life-5 Dimensions (EQ-5D) from the 39-item Parkinson’s Disease Questionnaire (PDQ-39) in order to estimate the health-related quality of life of Parkinson’s patients. Fivefold cross-validation experiments were carried out on randomly generated synthetic data sets, Yeast data set, as well as on a real-world Parkinson’s disease data set containing 488 patients. The experimental study, including comparison with additional Bayesian network-based approaches, back propagation for multi-label learning, multi-label k-nearest neighbor, multinomial logistic regression, ordinary least squares, and censored least absolute deviations, shows encouraging results in terms of predictive accuracy as well as the identification of dependence relationships among class and feature variables.

A phylogenomic approach to microbial evolution

To study the origin and evolution of biochemical pathways in microorganisms, we have developed methods and software for automatic, large-scale reconstructions of phylogenetic relationships. We define the complete set of phylogenetic trees derived from the proteome of an organism as the phylome and introduce the term phylogenetic connection as a concept that describes the relative relationships between taxa in a tree. A query system has been incorporated into the system so as to allow searches for defined categories of trees within the phylome. As a complement, we have developed the pyphy system for visualising the results of complex queries on phylogenetic connections, genomic locations and functional assignments in a graphical format. Our phylogenomics approach, which links phylogenetic information to the flow of biochemical pathways within and among microbial species, has been used to examine more than 8000 phylogenetic trees from seven microbial genomes. The results have revealed a rich web of phylogenetic connections. However, the separation of Bacteria and Archaea into two separate domains remains robust.

Drought policy: a graphical analysis

The standard approach to modelling production under uncertainty has relied on the concept of the stochastic production function. In the present paper, it is argued that a state-contingent production model is more flexible and realistic. The model is applied to the problem of drought policy.

A contour plot approach that uses data accumulated during routine monitoring to obtain insights into lagoon behaviour

Regular monitoring of wastewater characteristics is undertaken on most wastewater treatment plants. The data acquired during this process are usually filed and forgotten. However, systematic analysis of these data can provide useful insights into plant behaviour. Conventional graphical techniques are inadequate to give a good overall picture of how wastewater characteristics vary, with time and along the lagoon system. An approach based on the use of contour plots was devised that largely overcomes this problem. Superimposition of contour plots for different parameters can be used to gain a qualitative understanding of the nature and strength of relationships between the parameters. This is illustrated in an analysis of monitoring data for lagoon 115 East at the Western Treatment Plant, near Melbourne, Australia. In this illustrative analysis, relationships between ammonia removal rates and parameters such as chlorophyll a level and temperature are explored using a contour plot superimposition approach. It is concluded that this approach can help improve our understanding, not only of lagoon systems, but of other wastewater treatment systems as well.

A graphical specification of model transformations with triple graph grammars

Models and model transformations are the core concepts of OMG's MDA (TM) approach. Within this approach, most models are derived from the MOF and have a graph-based nature. In contrast, most of the current model transformations are specified textually. To enable a graphical specification of model transformation rules, this paper proposes to use triple graph grammars as declarative specification formalism. These triple graph grammars can be specified within the FUJABA tool and we argue that these rules can be more easily specified and they become more understandable and maintainable. To show the practicability of our approach, we present how to generate Tefkat rules from triple graph grammar rules, which helps to integrate triple graph grammars with a state of a art model transformation tool and shows the expressiveness of the concept.

A co-ordinated business object approach for supporting tactical level management decisions

The proliferation of data throughout the strategic, tactical and operational areas within many organisations, has provided a need for the decision maker to be presented with structured information that is appropriate for achieving allocated tasks. However, despite this abundance of data, managers at all levels in the organisation commonly encounter a condition of ‘information overload’, that results in a paucity of the correct information. Specifically, this thesis will focus upon the tactical domain within the organisation and the information needs of management who reside at this level. In doing so, it will argue that the link between decision making at the tactical level in the organisation, and low-level transaction processing data, should be through a common object model that used a framework based upon knowledge leveraged from co-ordination theory. In order to achieve this, the Co-ordinated Business Object Model (CBOM) was created. Detailing a two-tier framework, the first tier models data based upon four interactive object models, namely, processes, activities, resources and actors. The second tier analyses the data captured by the four object models, and returns information that can be used to support tactical decision making. In addition, the Co-ordinated Business Object Support System (CBOSS), is a prototype tool that has been developed in order to both support the CBOM implementation, and to also demonstrate the functionality of the CBOM as a modelling approach for supporting tactical management decision making. Containing a graphical user interface, the system’s functionality allows the user to create and explore alternative implementations of an identified tactical level process. In order to validate the CBOM, three verification tests have been completed. The results provide evidence that the CBOM framework helps bridge the gap between low level transaction data, and the information that is used to support tactical level decision making.

An operational approach to object-oriented software development

The traditional waterfall software life cycle model has several weaknesses. One problem is that a working version of a system is unavailable until a late stage in the development; any omissions and mistakes in the specification undetected until that stage can be costly to maintain. The operational approach which emphasises the construction of executable specifications can help to remedy this problem. An operational specification may be exercised to generate the behaviours of the specified system, thereby serving as a prototype to facilitate early validation of the system's functional requirements. Recent ideas have centred on using an existing operational method such as JSD in the specification phase of object-oriented development. An explicit transformation phase following specification is necessary in this approach because differences in abstractions between the two domains need to be bridged. This research explores an alternative approach of developing an operational specification method specifically for object-oriented development. By incorporating object-oriented concepts in operational specifications, the specifications have the advantage of directly facilitating implementation in an object-oriented language without requiring further significant transformations. In addition, object-oriented concepts can help the developer manage the complexity of the problem domain specification, whilst providing the user with a specification that closely reflects the real world and so the specification and its execution can be readily understood and validated. A graphical notation has been developed for the specification method which can capture the dynamic properties of an object-oriented system. A tool has also been implemented comprising an editor to facilitate the input of specifications, and an interpreter which can execute the specifications and graphically animate the behaviours of the specified systems.

Development of a probabilistic graphical structure from a model of mental health clinical expertise

This thesis explores the process of developing a principled approach for translating a model of mental-health risk expertise into a probabilistic graphical structure. Probabilistic graphical structures can be a combination of graph and probability theory that provide numerous advantages when it comes to the representation of domains involving uncertainty, domains such as the mental health domain. In this thesis the advantages that probabilistic graphical structures offer in representing such domains is built on. The Galatean Risk Screening Tool (GRiST) is a psychological model for mental health risk assessment based on fuzzy sets. In this thesis the knowledge encapsulated in the psychological model was used to develop the structure of the probability graph by exploiting the semantics of the clinical expertise. This thesis describes how a chain graph can be developed from the psychological model to provide a probabilistic evaluation of risk that complements the one generated by GRiST’s clinical expertise by the decomposing of the GRiST knowledge structure in component parts, which were in turned mapped into equivalent probabilistic graphical structures such as Bayesian Belief Nets and Markov Random Fields to produce a composite chain graph that provides a probabilistic classification of risk expertise to complement the expert clinical judgements

Developing a probabilistic graphical structure from a model of mental-health clinical risk expertise

This paper explores the process of developing a principled approach for translating a model of mental-health risk expertise into a probabilistic graphical structure. The Galatean Risk Screening Tool [1] is a psychological model for mental health risk assessment based on fuzzy sets. This paper details how the knowledge encapsulated in the psychological model was used to develop the structure of the probability graph by exploiting the semantics of the clinical expertise. These semantics are formalised by a detailed specification for an XML structure used to represent the expertise. The component parts were then mapped to equivalent probabilistic graphical structures such as Bayesian Belief Nets and Markov Random Fields to produce a composite chain graph that provides a probabilistic classification of risk expertise to complement the expert clinical judgements. © Springer-Verlag 2010.

Dialog Based on Graphical Static Scenes Managed by an Ontology

A new method to implementation of dialog based on graphical static scenes using an ontology-based approach to user interface development is proposed. The main idea of the approach is to form necessary to the user interface development and implementation information using ontologies and then based on this high-level specification to generate the user interface.

Probabilistic Graphical Modelling for Software Product Lines: A Frameweork for Modeling and Reasoning under Uncertainty

This work provides a holistic investigation into the realm of feature modeling within software product lines. The work presented identifies limitations and challenges within the current feature modeling approaches. Those limitations include, but not limited to, the dearth of satisfactory cognitive presentation, inconveniency in scalable systems, inflexibility in adapting changes, nonexistence of predictability of models behavior, as well as the lack of probabilistic quantification of model’s implications and decision support for reasoning under uncertainty. The work in this thesis addresses these challenges by proposing a series of solutions. The first solution is the construction of a Bayesian Belief Feature Model, which is a novel modeling approach capable of quantifying the uncertainty measures in model parameters by a means of incorporating probabilistic modeling with a conventional modeling approach. The Bayesian Belief feature model presents a new enhanced feature modeling approach in terms of truth quantification and visual expressiveness. The second solution takes into consideration the unclear support for the reasoning under the uncertainty process, and the challenging constraint satisfaction problem in software product lines. This has been done through the development of a mathematical reasoner, which was designed to satisfy the model constraints by considering probability weight for all involved parameters and quantify the actual implications of the problem constraints. The developed Uncertain Constraint Satisfaction Problem approach has been tested and validated through a set of designated experiments. Profoundly stating, the main contributions of this thesis include the following: • Develop a framework for probabilistic graphical modeling to build the purported Bayesian belief feature model. • Extend the model to enhance visual expressiveness throughout the integration of colour degree variation; in which the colour varies with respect to the predefined probabilistic weights. • Enhance the constraints satisfaction problem by the uncertainty measuring of the parameters truth assumption. • Validate the developed approach against different experimental settings to determine its functionality and performance.