Model-Based Multiple 3D Object Recognition in Range Data

Vision guided systems are relevant for many industrial application areas, including manufacturing, medicine, service robots etc. A task common to these applications consists of detecting and localizing known objects in cluttered scenes. This amounts to solve the "chicken and egg" problem consisting of data assignment and parameter estimation, that is to localize an object and to determine its pose. In this work, we consider computer vision techniques for the special scenario of industrial bin-picking applications where the goal is to accurately estimate the positions of multiple instances of arbitrary, known objects that are randomly assembled in a bin. Although a-priori knowledge of the objects simplifies the problem, model symmetries, mutual occlusion as well as noise, unstructured measurements and run-time constraints render the problem far from being trivial. A common strategy to cope with this problem is to apply a two-step approach that consists of rough initialization estimation for each objects' position followed by subsequent refinement steps. Established initialization procedures only take into account single objects, however. Hence, they cannot resolve contextual constraints caused by multiple object instances and thus yield poor estimates of the objects' pose in many settings. Inaccurate initial configurations, on the other hand, cause state-of-the-art refinement algorithms to be unable to identify the objects' pose, such that the entire two-step approach is likely to fail. In this thesis, we propose a novel approach for obtaining initial estimates of all object positions jointly. Additionally, we investigate a new local, individual refinement procedure that copes with the shortcomings of state-of-the-art approaches while yielding fast and accurate registration results as well as a large region of attraction. Both stages are designed using advanced numerical techniques such as large-scale convex programming and geometric optimization on the curved space of Euclidean transformations, respectively. They complement each other in that conflicting interpretations are resolved through non-local convex processing, followed by accurate non-convex local optimization based on sufficiently good initializations. Exhaustive numerical evaluation on artificial and real-world measurements experimentally confirms the proposed two-step approach and demonstrates the robustness to noise, unstructured measurements and occlusions as well as showing the potential to meet run-time constraints of real-world industrial applications

Computational Methods for Segmentation of Multi-Modal Multi-Dimensional Cardiac Images

Segmentation of the heart structures helps compute the cardiac contractile function quantified via the systolic and diastolic volumes, ejection fraction, and myocardial mass, representing a reliable diagnostic value. Similarly, quantification of the myocardial mechanics throughout the cardiac cycle, analysis of the activation patterns in the heart via electrocardiography (ECG) signals, serve as good cardiac diagnosis indicators. Furthermore, high quality anatomical models of the heart can be used in planning and guidance of minimally invasive interventions under the assistance of image guidance. The most crucial step for the above mentioned applications is to segment the ventricles and myocardium from the acquired cardiac image data. Although the manual delineation of the heart structures is deemed as the gold-standard approach, it requires significant time and effort, and is highly susceptible to inter- and intra-observer variability. These limitations suggest a need for fast, robust, and accurate semi- or fully-automatic segmentation algorithms. However, the complex motion and anatomy of the heart, indistinct borders due to blood flow, the presence of trabeculations, intensity inhomogeneity, and various other imaging artifacts, makes the segmentation task challenging. In this work, we present and evaluate segmentation algorithms for multi-modal, multi-dimensional cardiac image datasets. Firstly, we segment the left ventricle (LV) blood-pool from a tri-plane 2D+time trans-esophageal (TEE) ultrasound acquisition using local phase based filtering and graph-cut technique, propagate the segmentation throughout the cardiac cycle using non-rigid registration-based motion extraction, and reconstruct the 3D LV geometry. Secondly, we segment the LV blood-pool and myocardium from an open-source 4D cardiac cine Magnetic Resonance Imaging (MRI) dataset by incorporating average atlas based shape constraint into the graph-cut framework and iterative segmentation refinement. The developed fast and robust framework is further extended to perform right ventricle (RV) blood-pool segmentation from a different open-source 4D cardiac cine MRI dataset. Next, we employ convolutional neural network based multi-task learning framework to segment the myocardium and regress its area, simultaneously, and show that segmentation based computation of the myocardial area is significantly better than that regressed directly from the network, while also being more interpretable. Finally, we impose a weak shape constraint via multi-task learning framework in a fully convolutional network and show improved segmentation performance for LV, RV and myocardium across healthy and pathological cases, as well as, in the challenging apical and basal slices in two open-source 4D cardiac cine MRI datasets. We demonstrate the accuracy and robustness of the proposed segmentation methods by comparing the obtained results against the provided gold-standard manual segmentations, as well as with other competing segmentation methods

Gaussian Process Regression for Materials and Molecules.

We provide an introduction to Gaussian process regression (GPR) machine-learning methods in computational materials science and chemistry. The focus of the present review is on the regression of atomistic properties: in particular, on the construction of interatomic potentials, or force fields, in the Gaussian Approximation Potential (GAP) framework; beyond this, we also discuss the fitting of arbitrary scalar, vectorial, and tensorial quantities. Methodological aspects of reference data generation, representation, and regression, as well as the question of how a data-driven model may be validated, are reviewed and critically discussed. A survey of applications to a variety of research questions in chemistry and materials science illustrates the rapid growth in the field. A vision is outlined for the development of the methodology in the years to come

Toward a scalable Bayesian workflow

A scalable Bayesian workflow needs the combination of fast but reliable computing, efficient but targeted model evaluation, and extensive but directed model building and expansion. In this thesis, I develop a sequence of methods to push the scalability frontier of the workflow. First, I study diagnostics of Bayesian computing. The Pareto smoothed importance sampling stabilizes importance weights using a generalized Pareto distribution fit to the upper tail of the distribution of the simulated importance ratios. The method, which empirically performs better than existing methods for stabilizing importance sampling estimates, includes stabilized effective sample size estimates, Monte Carlo error estimates and convergence diagnostics. For variational inference, I propose two diagnostic algorithms. The Pareto smoothed importance sampling diagnostic gives a goodness of fit measurement for joint distributions, while the variational simulation-based calibration assesses the average performance of point estimates. I further apply this importance sampling strategy to causal inference and develop diagnostics for covariate imbalance in observational studies. Second, I develop a solution to continuous model expansion using adaptive path sampling and tempering. This development is relevant to both model-building and computing in the workflow. For the former, I provide an automated way to connect models via a geometric bridge such that a supermodel encompasses individual models as a special case. For the latter, I use adaptive path sampling as a preferred strategy to estimating the normalizing constant and marginal density, based on which I propose two metastable sampling schemes. The continuous simulated tempering aims at multimodal posterior sampling, and the implicit divide-and-conquer sampler aims for a funnel-shaped entropic barrier. Both schemes are highly automated and empirically perform better than existing methods for sampling from metastable distributions. Last, a complete Bayesian workflow distinguishes itself from a one-shot data analysis by its enthusiasm for multiple model fittings, and open-mindedness to model misspecification. I take the idea of stacking from the point estimation literature and generalize to the combination of Bayesian predictive distributions. Using importance sampling based leave-one-out approximation, stacking is computationally efficient. I compare stacking, Bayesian model averaging, and several variants in a decision theory framework. I further apply the stacking strategy to multimodal sampling in which Markov chain Monte Carlo algorithms can have difficulty moving between modes. The result from stacking is not necessarily equivalent, even asymptotically, to fully Bayesian inference, but it serves many of the same goals. Under misspecified models, stacking can give better predictive performance than full Bayesian inference, hence the multimodality can be considered a blessing rather than a curse. Furthermore, I show that stacking is most effective when the model predictive performance is heterogeneous in inputs, such that it can be further improved by hierarchical modeling. To this end, I develop hierarchical stacking, in which the model weights are input-varying yet partially-pooled, and further generalize this method to incorporate discrete and continuous inputs, other structured priors, and time-series and longitudinal data—big data need big models, and big models need big model evaluation, and big model evaluation itself needs extra data collection and model building

Atomistic modelling of precipitation in Ni-base superalloys

The presence of the ordered $\gamma^{\prime}$ phase ($\text{Ni}_{3}\text{Al}$) in Ni-base superalloys is fundamental to the performance of engineering components such as turbine disks and blades which operate at high temperatures and loads. Hence for these alloys it is important to optimize their microstructure and phase composition. This is typically done by varying their chemistry and heat treatment to achieve an appropriate balance between $\gamma^{\prime}$ content and other constituents such as carbides, borides, oxides and topologically close packed phases. In this work we have set out to investigate the onset of $\gamma^{\prime}$ ordering in Ni-Al single crystals and in Ni-Al bicrystals containing coincidence site lattice grain boundaries (GBs) and we do this at high temperatures, which are representative of typical heat treatment schedules including quenching and annealing. For this we use the atomistic simulation methods of molecular dynamics (MD) and density functional theory (DFT). In the first part of this work we develop robust Bayesian classifiers to identify the $\gamma^{\prime}$ phase in large scale simulation boxes at high temperatures around 1500 K. We observe significant \gamma^{\prime} ordering in the simulations in the form of clusters of $\gamma^{\prime}$-like ordered atoms embedded in a $\gamma$ host solid solution and this happens within 100 ns. Single crystals are found to exhibit the expected homogeneous ordering with slight indications of chemical composition change and a positive correlation between the Al concentration and the concentration of $\gamma^{\prime}$ phase. In general, the ordering is found to take place faster in systems with GBs and preferentially adjacent to the GBs. The sole exception to this is the $\Sigma3 \left(111\right)$ tilt GB, which is a coherent twin. An analysis of the ensemble and time lag average displacements of the GBs reveals mostly `anomalous diffusion' behaviour. Increasing the Al content from pure Ni to Ni 20 at.% Al was found to either consistently increase or decrease the mobility of the GB as seen from the changing slope of the time lag displacement average. The movement of the GB can then be characterized as either `super' or `sub-diffusive' and is interpreted in terms of diffusion induced grain boundary migration, which is posited as a possible precursor to the appearance of serrated edge grain boundaries. In the second part of this work we develop a method for the training of empirical interatomic potentials to capture more elements in the alloy system. We focus on the embedded atom method (EAM) and use the Ni-Al system as a test case. Recently, empirical potentials have been developed based on results from DFT which utilize energies and forces, but neglect the electron densities, which are also available. Noting the importance of electron densities, we propose a route to include them into the training of EAM-type potentials via Bayesian linear regression. Electron density models obtained for structures with a range of bonding types are shown to accurately reproduce the electron densities from DFT. Also, the resulting empirical potentials accurately reproduce DFT energies and forces of all the phases considered within the Ni-Al system. Properties not included in the training process, such as stacking fault energies, are sometimes not reproduced with the desired accuracy and the reasons for this are discussed. General regression issues, known to the machine learning community, are identified as the main difficulty facing further development of empirical potentials using this approach.EPSRC, Rolls-Royc

Advances in approximate Bayesian computation and trans-dimensional sampling methodology

Bayesian statistical models continue to grow in complexity, driven in part by a few key factors: the massive computational resources now available to statisticians; the substantial gains made in sampling methodology and algorithms such as Markov chain Monte Carlo (MCMC), trans-dimensional MCMC (TDMCMC), sequential Monte Carlo (SMC), adaptive algorithms and stochastic approximation methods and approximate Bayesian computation (ABC); and development of more realistic models for real world phenomena as demonstrated in this thesis for financial models and telecommunications engineering. Sophisticated statistical models are increasingly proposed for practical solutions to real world problems in order to better capture salient features of increasingly more complex data. With sophistication comes a parallel requirement for more advanced and automated statistical computational methodologies. The key focus of this thesis revolves around innovation related to the following three significant Bayesian research questions. 1. How can one develop practically useful Bayesian models and corresponding computationally efficient sampling methodology, when the likelihood model is intractable? 2. How can one develop methodology in order to automate Markov chain Monte Carlo sampling approaches to efficiently explore the support of a posterior distribution, defined across multiple Bayesian statistical models? 3. How can these sophisticated Bayesian modelling frameworks and sampling methodologies be utilized to solve practically relevant and important problems in the research fields of financial risk modeling and telecommunications engineering ? This thesis is split into three bodies of work represented in three parts. Each part contains journal papers with novel statistical model and sampling methodological development. The coherent link between each part involves the novel sampling methodologies developed in Part I and utilized in Part II and Part III. Papers contained in each part make progress at addressing the core research questions posed. Part I of this thesis presents generally applicable key statistical sampling methodologies that will be utilized and extended in the subsequent two parts. In particular it presents novel developments in statistical methodology pertaining to likelihood-free or ABC and TDMCMC methodology. The TDMCMC methodology focuses on several aspects of automation in the between model proposal construction, including approximation of the optimal between model proposal kernel via a conditional path sampling density estimator. Then this methodology is explored for several novel Bayesian model selection applications including cointegrated vector autoregressions (CVAR) models and mixture models in which there is an unknown number of mixture components. The second area relates to development of ABC methodology with particular focus on SMC Samplers methodology in an ABC context via Partial Rejection Control (PRC). In addition to novel algorithmic development, key theoretical properties are also studied for the classes of algorithms developed. Then this methodology is developed for a highly challenging practically significant application relating to multivariate Bayesian $\alpha$-stable models. Then Part II focuses on novel statistical model development in the areas of financial risk and non-life insurance claims reserving. In each of the papers in this part the focus is on two aspects: foremost the development of novel statistical models to improve the modeling of risk and insurance; and then the associated problem of how to fit and sample from such statistical models efficiently. In particular novel statistical models are developed for Operational Risk (OpRisk) under a Loss Distributional Approach (LDA) and for claims reserving in Actuarial non-life insurance modelling. In each case the models developed include an additional level of complexity which adds flexibility to the model in order to better capture salient features observed in real data. The consequence of the additional complexity comes at the cost that standard fitting and sampling methodologies are generally not applicable, as a result one is required to develop and apply the methodology from Part I. Part III focuses on novel statistical model development in the area of statistical signal processing for wireless communications engineering. Statistical models will be developed or extended for two general classes of wireless communications problem: the first relates to detection of transmitted symbols and joint channel estimation in Multiple Input Multiple Output (MIMO) systems coupled with Orthogonal Frequency Division Multiplexing (OFDM); the second relates to co-operative wireless communications relay systems in which the key focus is on detection of transmitted symbols. Both these areas will require advanced sampling methodology developed in Part I to find solutions to these real world engineering problems

Detection of clinical depression in adolescents' using acoustic speech analysis

Clinical depression is a major risk factor in suicides and is associated with high mortality rates, therefore making it one of the leading causes of death worldwide every year. Symptoms of depression often first appear during adolescence at a time when the voice is changing, in both males and females, suggesting that specific studies of these phenomena in adolescent populations are warranted. The properties of acoustic speech have previously been investigated as possible cues for depression in adults. However, these studies were restricted to small populations of patients and the speech recordings were made during patient’s clinical interviews or fixed-text reading sessions. A collaborative effort with the Oregon research institute (ORI), USA allowed the development of a new speech corpus consisting of a large sample size of 139 adolescents (46 males and 93 females) that were divided into two groups (68 clinically depressed and 71 controls). The speech recordings were made during naturalistic interactions between adolescents and parents. Instead of covering a plethora of acoustic features in the investigation, this study takes the knowledge based from speech science and groups the acoustic features into five categories that relate to the physiological and perceptual areas of the speech production mechanism. These five acoustic feature categories consisted of the prosodic, cepstral, spectral, glottal and Teager energy operator (TEO) based features. The effectiveness in applying these acoustic feature categories in detecting adolescent’s depression was measured. The salient feature categories were determined by testing the feature categories and their combinations within a binary classification framework. In consistency with previous studies, it was observed that: - there are strong gender related differences in classification accuracy; - the glottal features provide an important enhancement of the classification accuracy when combined with other types of features; An important new contribution provided by this thesis was to observe that the TEO based features significantly outperformed prosodic, cepstral, spectral, glottal features and their combinations. An investigation into the possible reasons of such strong performance of the TEO features pointed into the importance of nonlinear mechanisms associated with the glottal flow formation as possible cues for depression