Partially Coherent Ptychography by Gradient Decomposition of the Probe

Coherent ptychographic imaging experiments often discard over 99.9 % of the flux from a light source to define the coherence of an illumination. Even when coherent flux is sufficient, the stability required during an exposure is another important limiting factor. Partial coherence analysis can considerably reduce these limitations. A partially coherent illumination can often be written as the superposition of a single coherent illumination convolved with a separable translational kernel. In this paper we propose the Gradient Decomposition of the Probe (GDP), a model that exploits translational kernel separability, coupling the variances of the kernel with the transverse coherence. We describe an efficient first-order splitting algorithm GDP-ADMM to solve the proposed nonlinear optimization problem. Numerical experiments demonstrate the effectiveness of the proposed method with Gaussian and binary kernel functions in fly-scan measurements. Remarkably, GDP-ADMM produces satisfactory results even when the ratio between kernel width and beam size is more than one, or when the distance between successive acquisitions is twice as large as the beam width.Comment: 11 pages, 9 figure

New Algorithms in Computational Microscopy

Microscopy plays an important role in providing tools to microscopically observe objects and their surrounding areas with much higher resolution ranging from the scale between molecular machineries (angstrom) and individual cells (micrometer). Under microscopes, illumination, such as visible light and electron-magnetic radiation/electron beam, interacts with samples, then they are scattered to a plane and are recorded. Computational microscopy corresponds to image reconstruction from these measurements as well as improving quality of the images. Along with the evolution of microscopy, new studies are discovered and algorithms need development not only to provide high-resolution imaging but also to decipher new and advanced research. In this dissertation, we focus on algorithm development for inverse problems in microscopy, specifically phase retrieval and tomography, and the application of these techniques to machine learning. The four studies in this dissertation demonstrates the use of optimization and calculus of variation in imaging science and other different disciplines.Study 1 focuses on coherent diffractive imaging (CDI) or phase retrieval, a non-linear inverse problem that aims to recover 2D image from it Fourier transforms in modulus taking into account that extra information provided by oversampling as a second constraint. To solve this two-constraint minimization, we proceed from Hamilton-Jacobi partial differential equation (HJ-PDE) and its Hopf-Lax formula. Introducing generalized Bregman distance to the HJ-PDE and applying Legendre transform, we derive our generalized proximal smoothing (GPS) algorithm under the form of primal-dual hybrid gradient (PDHG). While the reflection operator, known as extrapolating momentum, helps overcome local minima, the smoothing by the generalized Bregman distance is adjusted to improve convergence and consistency of phase retrieval.Study 2 focuses on electron tomography, 3D image reconstruction from a set of 2D projections obtained from a transmission electron microscope (TEM) or X-ray microscope. Notice that current tomography algorithms limit to a single tilt axis and fail to work with fully or partially missing data. In the light of calculus of variations and Fourier slice theorem (FST), we develop a highly accurate tomography iterative algorithm that can provide higher resolution imaging and work with missing data as well as has capability to perform multiple-tilt-axis tomography. The algorithm is further developed to work with non-isolated objects and partially-blocked projections which have become more popular in experiment. The success of real space iterative reconstruction engine (RESIRE) opens a new era to the study of tomography in material science and magnetic structures (vector Tomography).Study 3 and 4 are applications of our algorithms to machine learning. Study 3 develops a backward Euler method in a stochastic manner to solve K-mean clustering, a well-known non-convex optimization problem. The algorithm has been shown to improve minimums and consistency, providing a new powerful tool to the class of classification techniques. Study 4 is a direct application of GPS to deep learning gradient descent algorithms. Linearizing the Hopf-Lax formula derived in GPS, we derive our method Laplacian smoothing gradient descent (LSGD), simply known as gradient smoothing. Our experiment shows that LSGD has the ability to search for better and flatter minimums, reduce variation, and obtain higher accuracy and consistency

Interactive analogical retrieval: practice, theory and technology

Analogy is ubiquitous in human cognition. One of the important questions related to understanding the situated nature of analogy-making is how people retrieve source analogues via their interactions with external environments. This dissertation studies interactive analogical retrieval in the context of biologically inspired design (BID). BID involves creative use of analogies to biological systems to develop solutions for complex design problems (e.g., designing a device for acquiring water in desert environments based on the analogous fog-harvesting abilities of the Namibian Beetle). Finding the right biological analogues is one of the critical first steps in BID. Designers routinely search online in order to find their biological sources of inspiration. But this task of online bio-inspiration seeking represents an instance of interactive analogical retrieval that is extremely time consuming and challenging to accomplish. This dissertation focuses on understanding and supporting the task of online bio-inspiration seeking. Through a series of field studies, this dissertation uncovered the salient characteristics and challenges of online bio-inspiration seeking. An information-processing model of interactive analogical retrieval was developed in order to explain those challenges and to identify the underlying causes. A set of measures were put forth to ameliorate those challenges by targeting the identified causes. These measures were then implemented in an online information-seeking technology designed to specifically support the task of online bio-inspiration seeking. Finally, the validity of the proposed measures was investigated through a series of experimental studies and a deployment study. The trends are encouraging and suggest that the proposed measures has the potential to change the dynamics of online bio-inspiration seeking in favor of ameliorating the identified challenges of online bio-inspiration seeking.PhDCommittee Chair: Goel, Ashok; Committee Member: Kolodner, Janet; Committee Member: Maher, Mary Lou; Committee Member: Nersessian, Nancy; Committee Member: Yen, Jeannett

Source Code Retrieval from Large Software Libraries for Automatic Bug Localization

This dissertation advances the state-of-the-art in information retrieval (IR) based approaches to automatic bug localization in software. In an IR-based approach, one first creates a search engine using a probabilistic or a deterministic model for the files in a software library. Subsequently, a bug report is treated as a query to the search engine for retrieving the files relevant to the bug. With regard to the new work presented, we first demonstrate the importance of taking version histories of the files into account for achieving significant improvements in the precision with which the files related to a bug are located. This is motivated by the realization that the files that have not changed in a long time are likely to have ``stabilized and are therefore less likely to contain bugs. Subsequently, we look at the difficulties created by the fact that developers frequently use abbreviations and concatenations that are not likely to be familiar to someone trying to locate the files related to a bug. We show how an initial query can be automatically reformulated to include the relevant actual terms in the files by an analysis of the files retrieved in response to the original query for terms that are proximal to the original query terms. The last part of this dissertation generalizes our term-proximity based work by using Markov Random Fields (MRF) to model the inter-term dependencies in a query vis-a-vis the files. Our MRF work redresses one of the major defects of the most commonly used modeling approaches in IR, which is the loss of all inter-term relationships in the documents

Content-based Information Retrieval via Nearest Neighbor Search

Content-based information retrieval (CBIR) has attracted significant interest in the past few years. When given a search query, the search engine will compare the query with all the stored information in the database through nearest neighbor search. Finally, the system will return the most similar items. We contribute to the CBIR research the following: firstly, Distance Metric Learning (DML) is studied to improve retrieval accuracy of nearest neighbor search. Additionally, Hash Function Learning (HFL) is considered to accelerate the retrieval process. On one hand, a new local metric learning framework is proposed - Reduced-Rank Local Metric Learning (R2LML). By considering a conical combination of Mahalanobis metrics, the proposed method is able to better capture information like data\u27s similarity and location. A regularization to suppress the noise and avoid over-fitting is also incorporated into the formulation. Based on the different methods to infer the weights for the local metric, we considered two frameworks: Transductive Reduced-Rank Local Metric Learning (T-R2LML), which utilizes transductive learning, while Efficient Reduced-Rank Local Metric Learning (E-R2LML)employs a simpler and faster approximated method. Besides, we study the convergence property of the proposed block coordinate descent algorithms for both our frameworks. The extensive experiments show the superiority of our approaches. On the other hand, *Supervised Hash Learning (*SHL), which could be used in supervised, semi-supervised and unsupervised learning scenarios, was proposed in the dissertation. By considering several codewords which could be learned from the data, the proposed method naturally derives to several Support Vector Machine (SVM) problems. After providing an efficient training algorithm, we also study the theoretical generalization bound of the new hashing framework. In the final experiments, *SHL outperforms many other popular hash function learning methods. Additionally, in order to cope with large data sets, we also conducted experiments running on big data using a parallel computing software package, namely LIBSKYLARK

A graph-based approach for the retrieval of multi-modality medical images

Medical imaging has revolutionised modern medicine and is now an integral aspect of diagnosis and patient monitoring. The development of new imaging devices for a wide variety of clinical cases has spurred an increase in the data volume acquired in hospitals. These large data collections offer opportunities for search-based applications in evidence-based diagnosis, education, and biomedical research. However, conventional search methods that operate upon manual annotations are not feasible for this data volume. Content-based image retrieval (CBIR) is an image search technique that uses automatically derived visual features as search criteria and has demonstrable clinical benefits. However, very few studies have investigated the CBIR of multi-modality medical images, which are making a monumental impact in healthcare, e.g., combined positron emission tomography and computed tomography (PET-CT) for cancer diagnosis. In this thesis, we propose a new graph-based method for the CBIR of multi-modality medical images. We derive a graph representation that emphasises the spatial relationships between modalities by structurally constraining the graph based on image features, e.g., spatial proximity of tumours and organs. We also introduce a graph similarity calculation algorithm that prioritises the relationships between tumours and related organs. To enable effective human interpretation of retrieved multi-modality images, we also present a user interface that displays graph abstractions alongside complex multi-modality images. Our results demonstrated that our method achieved a high precision when retrieving images on the basis of tumour location within organs. The evaluation of our proposed UI design by user surveys revealed that it improved the ability of users to interpret and understand the similarity between retrieved PET-CT images. The work in this thesis advances the state-of-the-art by enabling a novel approach for the retrieval of multi-modality medical images