SHIRAZ: an automated histology image annotation system for zebrafish phenomics

Histological characterization is used in clinical and research contexts as a highly sensitive method for detecting the morphological features of disease and abnormal gene function. Histology has recently been accepted as a phenotyping method for the forthcoming Zebrafish Phenome Project, a large-scale community effort to characterize the morphological, physiological, and behavioral phenotypes resulting from the mutations in all known genes in the zebrafish genome. In support of this project, we present a novel content-based image retrieval system for the automated annotation of images containing histological abnormalities in the developing eye of the larval zebrafish

Multiresolution Rotational Symmetry Detection via Radius-Based Frieze-Expansion

Rotational symmetry is important for many applications in computer graphics, vision, and image processing. However, it remains difficult to design an effective algorithm for automatic symmetry recognition. In this paper, we present a rotational symmetry detection algorithm, which is easy to use and can determine both the center and the radius of the rotational symmetry supporting region without human interaction. Our algorithm is derived from frieze-expansions approach and improved through a radius-based expansion idea. Multiresolution pyramid is used to accelerate this detection process. We also discuss a solution to deal with rotational symmetry detection under slight affine transformation. Experimental results show that the method is effective for most nature images with rotational symmetry

Nonconvex Recovery of Low-complexity Models

Today we are living in the era of big data, there is a pressing need for efficient, scalable and robust optimization methods to analyze the data we create and collect. Although Convex methods offer tractable solutions with global optimality, heuristic nonconvex methods are often more attractive in practice due to their superior efficiency and scalability. Moreover, for better representations of the data, the mathematical model we are building today are much more complicated, which often results in highly nonlinear and nonconvex optimizations problems. Both of these challenges require us to go beyond convex optimization. While nonconvex optimization is extraordinarily successful in practice, unlike convex optimization, guaranteeing the correctness of nonconvex methods is notoriously difficult. In theory, even finding a local minimum of a general nonconvex function is NP-hard – nevermind the global minimum. This thesis aims to bridge the gap between practice and theory of nonconvex optimization, by developing global optimality guarantees for nonconvex problems arising in real-world engineering applications, and provable, efficient nonconvex optimization algorithms. First, this thesis reveals that for certain nonconvex problems we can construct a model specialized initialization that is close to the optimal solution, so that simple and efficient methods provably converge to the global solution with linear rate. These problem include sparse basis learning and convolutional phase retrieval. In addition, the work has led to the discovery of a broader class of nonconvex problems – the so-called ridable saddle functions. Those problems possess characteristic structures, in which (i) all local minima are global, (ii) the energy landscape does not have any ''flat'' saddle points. More interestingly, when data are large and random, this thesis reveals that many problems in the real world are indeed ridable saddle, those problems include complete dictionary learning and generalized phase retrieval. For each of the aforementioned problems, the benign geometric structure allows us to obtain global recovery guarantees by using efficient optimization methods with arbitrary initialization