Single atom imaging with time-resolved electron microscopy

Developments in scanning transmission electron microscopy (STEM) have opened up new possibilities for time-resolved imaging at the atomic scale. However, rapid imaging of single atom dynamics brings with it a new set of challenges, particularly regarding noise and the interaction between the electron beam and the specimen. This thesis develops a set of analytical tools for capturing atomic motion and analyzing the dynamic behaviour of materials at the atomic scale. Machine learning is increasingly playing an important role in the analysis of electron microscopy data. In this light, new unsupervised learning tools are developed here for noise removal under low-dose imaging conditions and for identifying the motion of surface atoms. The scope for real-time processing and analysis is also explored, which is of rising importance as electron microscopy datasets grow in size and complexity. These advances in image processing and analysis are combined with computational modelling to uncover new chemical and physical insights into the motion of atoms adsorbed onto surfaces. Of particular interest are systems for heterogeneous catalysis, where the catalytic activity can depend intimately on the atomic environment. The study of Cu atoms on a graphene oxide support reveals that the atoms undergo anomalous diffusion as a result of spatial and energetic disorder present in the substrate. The investigation is extended to examine the structure and stability of small Cu clusters on graphene oxide, with atomistic modelling used to understand the significant role played by the substrate. Finally, the analytical methods are used to study the surface reconstruction of silicon alongside the electron beam-induced motion of adatoms on the surface. Taken together, these studies demonstrate the materials insights that can be obtained with time-resolved STEM imaging, and highlight the importance of combining state-ofthe- art imaging with computational analysis and atomistic modelling to quantitatively characterize the behaviour of materials with atomic resolution.The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007–2013)/ERC grant agreement 291522–3DIMAGE, as well as from the European Union Seventh Framework Programme under Grant Agreement 312483-ESTEEM2 (Integrated Infrastructure Initiative -I3)

Estimation of missing air pollutant data using a spatiotemporal convolutional autoencoder

A key challenge in building machine learning models for time series prediction is the incompleteness of the datasets. Missing data can arise for a variety of reasons, including sensor failure and network outages, resulting in datasets that can be missing significant periods of measurements. Models built using these datasets can therefore be biased. Although various methods have been proposed to handle missing data in many application areas, more air quality missing data prediction requires additional investigation. This study proposes an autoencoder model with spatiotemporal considerations to estimate missing values in air quality data. The model consists of one-dimensional convolution layers, making it flexible to cover spatial and temporal behaviours of air contaminants. This model exploits data from nearby stations to enhance predictions at the target station with missing data. This method does not require additional external features, such as weather and climate data. The results show that the proposed method effectively imputes missing data for discontinuous and long-interval interrupted datasets. Compared to univariate imputation techniques (most frequent, median and mean imputations), our model achieves up to 65% RMSE improvement and 20–40% against multivariate imputation techniques (decision tree, extra-trees, k-nearest neighbours and Bayesian ridge regressors). Imputation performance degrades when neighbouring stations are negatively correlated or weakly correlated

Addressing training data sparsity and interpretability challenges in AI based cellular networks

To meet the diverse and stringent communication requirements for emerging networks use cases, zero-touch arti cial intelligence (AI) based deep automation in cellular networks is envisioned. However, the full potential of AI in cellular networks remains hindered by two key challenges: (i) training data is not as freely available in cellular networks as in other fields where AI has made a profound impact and (ii) current AI models tend to have black box behavior making operators reluctant to entrust the operation of multibillion mission critical networks to a black box AI engine, which allow little insights and discovery of relationships between the configuration and optimization parameters and key performance indicators. This dissertation systematically addresses and proposes solutions to these two key problems faced by emerging networks. A framework towards addressing the training data sparsity challenge in cellular networks is developed, that can assist network operators and researchers in choosing the optimal data enrichment technique for different network scenarios, based on the available information. The framework encompasses classical interpolation techniques, like inverse distance weighted and kriging to more advanced ML-based methods, like transfer learning and generative adversarial networks, several new techniques, such as matrix completion theory and leveraging different types of network geometries, and simulators and testbeds, among others. The proposed framework will lead to more accurate ML models, that rely on sufficient amount of representative training data. Moreover, solutions are proposed to address the data sparsity challenge specifically in Minimization of drive test (MDT) based automation approaches. MDT allows coverage to be estimated at the base station by exploiting measurement reports gathered by the user equipment without the need for drive tests. Thus, MDT is a key enabling feature for data and artificial intelligence driven autonomous operation and optimization in current and emerging cellular networks. However, to date, the utility of MDT feature remains thwarted by issues such as sparsity of user reports and user positioning inaccuracy. For the first time, this dissertation reveals the existence of an optimal bin width for coverage estimation in the presence of inaccurate user positioning, scarcity of user reports and quantization error. The presented framework can enable network operators to configure the bin size for given positioning accuracy and user density that results in the most accurate MDT based coverage estimation. The lack of interpretability in AI-enabled networks is addressed by proposing a first of its kind novel neural network architecture leveraging analytical modeling, domain knowledge, big data and machine learning to turn black box machine learning models into more interpretable models. The proposed approach combines analytical modeling and domain knowledge to custom design machine learning models with the aim of moving towards interpretable machine learning models, that not only require a lesser training time, but can also deal with issues such as sparsity of training data and determination of model hyperparameters. The approach is tested using both simulated data and real data and results show that the proposed approach outperforms existing mathematical models, while also remaining interpretable when compared with black-box ML models. Thus, the proposed approach can be used to derive better mathematical models of complex systems. The findings from this dissertation can help solve the challenges in emerging AI-based cellular networks and thus aid in their design, operation and optimization

Compressive phase retrieval

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2013.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (p. 129-138).Recovering a full description of a wave from limited intensity measurements remains a central problem in optics. Optical waves oscillate too fast for detectors to measure anything but time{averaged intensities. This is unfortunate since the phase can reveal important information about the object. When the light is partially coherent, a complete description of the phase requires knowledge about the statistical correlations for each pair of points in space. Recovery of the correlation function is a much more challenging problem since the number of pairs grows much more rapidly than the number of points. In this thesis, quantitative phase imaging techniques that works for partially coherent illuminations are investigated. In order to recover the phase information with few measurements, the sparsity in each underly problem and ecient inversion methods are explored under the framework of compressed sensing. In each phase retrieval technique under study, diffraction during spatial propagation is exploited as an effective and convenient mechanism to uniformly distribute the information about the unknown signal into the measurement space. Holography is useful to record the scattered field from a sparse distribution of particles; the ability of localizing each particles using compressive reconstruction method is studied. When a thin sample is illuminated with partially coherent waves, the transport of intensity phase retrieval method is shown to be eective to recover the optical path length of the sample and remove the eect of the illumination. This technique is particularly suitable for X-ray phase imaging since it does not require a coherent source or any optical components. Compressive tomographic reconstruction, which makes full use of the priors that the sample consists of piecewise constant refractive indices, are demonstrated to make up missing data. The third technique, known as the phase space tomography (PST), addresses the correlation function recovery problem. Implementing the PST involves measuring many intensity images under spatial propagation. Experimental demonstration of a compressive reconstruction method, which finds the sparse solution by decomposing the correlation function into a few mutually uncorrelated coherent modes, is presented to produce accurate reconstruction even when the measurement suers from the 'missing cone' problem in the Fourier domain.by Lei Tian.Ph.D

Efficient Model-Based Reconstruction for Dynamic MRI

Dynamic magnetic resonance imaging (MRI) has important clinical and neuro- science applications (e.g., cardiac disease diagnosis, neurological behavior studies). It captures an object in motion by acquiring data across time, then reconstructing a sequence of images from them. This dissertation considers efficient dynamic MRI reconstruction using handcrafted models, to achieve fast imaging with high spatial and temporal resolution. Our modeling framework considers data acquisition process, image properties, and artifact correction. The reconstruction model expressed as a large-scale inverse problem requires optimization algorithms to solve, and we consider efficient implementations that make use of underlying problem structures. In the context of dynamic MRI reconstruction, we investigate efficient updates in two frameworks of algorithms for solving a nonsmooth composite convex optimization problem for the low-rank plus sparse (L+S) model. In the proximal gradient framework, current algorithms for the L+S model involve the classical iterative soft thresholding algorithm (ISTA); we consider two accelerated alternatives, one based on the fast iterative shrinkage-thresholding algorithm (FISTA), and the other with the recent proximal optimized gradient method (POGM). In the augmented Lagrangian (AL) framework, we propose an efficient variable splitting scheme based on the form of the data acquisition operator, leading to simpler computation than the conjugate gradient (CG) approach required by existing AL methods. Numerical results suggest faster convergence of our efficient implementations in both frameworks, with POGM providing the fastest convergence overall and the practical benefit of being free of algorithm tuning parameters. In the context of magnetic field inhomogeneity correction, we present an efficient algorithm for a regularized field inhomogeneity estimation problem. Most existing minimization techniques are computationally or memory intensive for 3D datasets, and are designed for single-coil MRI. We consider 3D MRI with optional consideration of coil sensitivity and a generalized expression that addresses both multi-echo field map estimation and water-fat imaging. Our efficient algorithm uses a preconditioned nonlinear conjugate gradient method based on an incomplete Cholesky factorization of the Hessian of the cost function, along with a monotonic line search. Numerical experiments show the computational advantage of the proposed algorithm over state- of-the-art methods with similar memory requirements. In the context of task-based functional MRI (fMRI) reconstruction, we introduce a space-time model that represents an fMRI timeseries as a sum of task-correlated signal and non-task background. Our model consists of a spatiotemporal decomposition based on assumptions of the activation waveform shape, with spatial and temporal smoothness regularization on the magnitude and phase of the timeseries. Compared with two contemporary task fMRI decomposition models, our proposed model yields better timeseries and activation maps on simulated and human subject fMRI datasets with multiple tasks. The above examples are part of a larger framework for model-based dynamic MRI reconstruction. This dissertation concludes by presenting a general framework with flexibility on model assumptions and artifact compensation options (e.g., field inhomogeneity, head motion), and proposing future work ideas on both the framework and its connection to data acquisition.PHDApplied and Interdisciplinary MathematicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/168081/1/yilinlin_1.pd

Bayesian Variational Regularisation for Dark Matter Reconstruction with Uncertainty Quantification

Despite the great wealth of cosmological knowledge accumulated since the early 20th century, the nature of dark-matter, which accounts for ~85% of the matter content of the universe, remains illusive. Unfortunately, though dark-matter is scientifically interesting, with implications for our fundamental understanding of the Universe, it cannot be directly observed. Instead, dark-matter may be inferred from e.g. the optical distortion (lensing) of distant galaxies which, at linear order, manifests as a perturbation to the apparent magnitude (convergence) and ellipticity (shearing). Ensemble observations of the shear are collected and leveraged to construct estimates of the convergence, which can directly be related to the universal dark-matter distribution. Imminent stage IV surveys are forecast to accrue an unprecedented quantity of cosmological information; a discriminative partition of which is accessible through the convergence, and is disproportionately concentrated at high angular resolutions, where the echoes of cosmological evolution under gravity are most apparent. Capitalising on advances in probability concentration theory, this thesis merges the paradigms of Bayesian inference and optimisation to develop hybrid convergence inference techniques which are scalable, statistically principled, and operate over the Euclidean plane, celestial sphere, and 3-dimensional ball. Such techniques can quantify the plausibility of inferences at one-millionth the computational overhead of competing sampling methods. These Bayesian techniques are applied to the hotly debated Abell-520 merging cluster, concluding that observational catalogues contain insufficient information to determine the existence of dark-matter self-interactions. Further, these techniques were applied to all public lensing catalogues, recovering the then largest global dark-matter mass-map. The primary methodological contributions of this thesis depend only on posterior log-concavity, paving the way towards a, potentially revolutionary, complete hybridisation with artificial intelligence techniques. These next-generation techniques are the first to operate over the full 3-dimensional ball, laying the foundations for statistically principled universal dark-matter cartography, and the cosmological insights such advances may provide

International Conference on Continuous Optimization (ICCOPT) 2019 Conference Book

The Sixth International Conference on Continuous Optimization took place on the campus of the Technical University of Berlin, August 3-8, 2019. The ICCOPT is a flagship conference of the Mathematical Optimization Society (MOS), organized every three years. ICCOPT 2019 was hosted by the Weierstrass Institute for Applied Analysis and Stochastics (WIAS) Berlin. It included a Summer School and a Conference with a series of plenary and semi-plenary talks, organized and contributed sessions, and poster sessions. This book comprises the full conference program. It contains, in particular, the scientific program in survey style as well as with all details, and information on the social program, the venue, special meetings, and more

Patterns and drivers of tetrapod diversity and biogeography in the late Palaeozoic and early Mesozoic

Tetrapods (four-limbed vertebrates) invaded the land more than 370 million years ago and began to diversify into a spectacular range of morphologies and life modes, rapidly achieving a global distribution. However, due to the inherent temporal and spatial bias of the fossil record, global patterns of tetrapod diversity and biogeography during critical intervals of the group’s evolution remain unresolved. This thesis focuses on examining the patterns and drivers of tetrapod diversity during two of these key intervals. Firstly, advanced statistical, phylogenetic, and modelling approaches were used to examine the impact of major environmental change on the first tetrapods to emerge onto land during the late Palaeozoic (358–272 million years ago). Next, these approaches were combined with palaeoclimatic reconstructions to examine the influence of climate on tetrapod diversity during the early Mesozoic (237–174 million years ago), when modern vertebrate groups, including the dinosaurs, were originating. Together, the results provide a comprehensive assessment of the impact of sampling biases on estimates of past diversity, as well as providing greater insights into the role of environmental and climate change on tetrapod diversity and biogeography

LIPIcs, Volume 251, ITCS 2023, Complete Volume

LIPIcs, Volume 251, ITCS 2023, Complete Volum