Homological Region Adjacency Tree for a 3D Binary Digital Image via HSF Model

Given a 3D binary digital image I, we define and compute an edge-weighted tree, called Homological Region Tree (or Hom-Tree, for short). It coincides, as unweighted graph, with the classical Region Adjacency Tree of black 6-connected components (CCs) and white 26- connected components of I. In addition, we define the weight of an edge (R, S) as the number of tunnels that the CCs R and S “share”. The Hom-Tree structure is still an isotopic invariant of I. Thus, it provides information about how the different homology groups interact between them, while preserving the duality of black and white CCs. An experimentation with a set of synthetic images showing different shapes and different complexity of connected component nesting is performed for numerically validating the method.Ministerio de Economía y Competitividad MTM2016-81030-

Computing the Component-Labeling and the Adjacency Tree of a Binary Digital Image in Near Logarithmic-Time

Connected component labeling (CCL) of binary images is one of the fundamental operations in real time applications. The adjacency tree (AdjT) of the connected components offers a region-based representation where each node represents a region which is surrounded by another region of the opposite color. In this paper, a fully parallel algorithm for computing the CCL and AdjT of a binary digital image is described and implemented, without the need of using any geometric information. The time complexity order for an image of m × n pixels under the assumption that a processing element exists for each pixel is near O(log(m+ n)). Results for a multicore processor show a very good scalability until the so-called memory bandwidth bottleneck is reached. The inherent parallelism of our approach points to the direction that even better results will be obtained in other less classical computing architectures.Ministerio de Economía y Competitividad MTM2016-81030-PMinisterio de Economía y Competitividad TEC2012-37868-C04-0

Parallel Image Processing Using a Pure Topological Framework

Image processing is a fundamental operation in many real time applications, where lots of parallelism can be extracted. Segmenting the image into different connected components is the most known operations, but there are many others like extracting the region adjacency graph (RAG) of these regions, or searching for features points, being invariant to rotations, scales, brilliant changes, etc. Most of these algorithms part from the basis of Tracing-type approaches or scan/raster methods. This fact necessarily implies a data dependence between the processing of one pixel and the previous one, which prevents using a pure parallel approach. In terms of time complexity, this means that linear order O(N) (N being the number of pixels) cannot be cut down. In this paper, we describe a novel approach based on the building of a pure Topological framework, which allows to implement fully parallel algorithms. Concerning topological analysis, a first stage is computed in parallel for every pixel, thus conveying the local neighboring conditions. Then, they are extended in a second parallel stage to the necessary global relations (e.g. to join all the pixels of a connected component). This combinatorial optimization process can be seen as the compression of the whole image to just one pixel. Using this final representation, every region can be related with the rest, which yields to pure topological construction of other image operations. Besides, complex data structures can be avoided: all the processing can be done using matrixes (with the same indexation as the original image) and element-wise operations. The time complexity order of our topological approach for a m×n pixel image is near O(log(m+n)), under the assumption that a processing element exists for each pixel. Results for a multicore processor show very good scalability until the memory bandwidth bottleneck is reached, both for bigger images and for much optimized implementations. The inherent parallelism of our approach points to the direction that even better results will be obtained in other less classical computing architectures.1Ministerio de Economía y Competitividad (España) TEC2012-37868-C04-02AEI/FEDER (UE) MTM2016-81030-PVPPI of the University of Sevill

A Parallel Implementation for Computing the Region-Adjacency-Tree of a Segmentation of a 2D Digital Image

A design and implementation of a parallel algorithm for computing the Region-Adjacency Tree of a given segmentation of a 2D digital image is given. The technique is based on a suitable distributed use of the algorithm for computing a Homological Spanning Forest (HSF) structure for each connected region of the segmentation and a classical geometric algorithm for determining inclusion between regions. The results show that this technique scales very well when executed in a multicore processor.Ministerio de Ciencia e Innovación TEC2012-37868-C04-02Universidad de Sevilla 2014/75

Hyperspectral-Augmented Target Tracking

With the global war on terrorism, the nature of military warfare has changed significantly. The United States Air Force is at the forefront of research and development in the field of intelligence, surveillance, and reconnaissance that provides American forces on the ground and in the air with the capability to seek, monitor, and destroy mobile terrorist targets in hostile territory. One such capability recognizes and persistently tracks multiple moving vehicles in complex, highly ambiguous urban environments. The thesis investigates the feasibility of augmenting a multiple-target tracking system with hyperspectral imagery. The research effort evaluates hyperspectral data classification using fuzzy c-means and the self-organizing map clustering algorithms for remote identification of moving vehicles. Results demonstrate a resounding 29.33% gain in performance from the baseline kinematic-only tracking to the hyperspectral-augmented tracking. Through a novel methodology, the hyperspectral observations are integrated in the MTT paradigm. Furthermore, several novel ideas are developed and implemented—spectral gating of hyperspectral observations, a cost function for hyperspectral observation-to-track association, and a self-organizing map filtering method. It appears that relatively little work in the target tracking and hyperspectral image classification literature exists that addresses these areas. Finally, two hyperspectral sensor modes are evaluated—Pushbroom and Region-of-Interest. Both modes are based on realistic technologies, and investigating their performance is the goal of performance-driven sensing. Performance comparison of the two modes can drive future design of hyperspectral sensors

Computational analysis of genetic interaction network structures and gene properties

University of Minnesota Ph.D. dissertation. July 2017. Major: Computer Science. Advisor: Chad Myers. 1 computer file (PDF); viii, 155 pages.Cellular systems are responsible for many complex tasks, such as carrying out cell cycle phases, responding to intra- and extra-cellular conditions, and resolving errors. Through analysis of biological networks, researchers have begun to describe how cells coordinate these processes by means of modularity and between-process connections. However, descriptions of this network-based cellular organization often do not incorporate the diverse characteristics and individual behaviors of the genes that compose it. Knowledge of gene properties and their relationships with biological network evolution is crucial for a complete understanding of cellular function, and investigation in this area can lead to general principles of biology that apply to many species. This dissertation will describe analyses of the Saccharomyces cerevisiae (baker’s yeast) genetic interaction network that connect gene topological behavior with various physical, functional, and evolutionary properties of genes. Genetic interactions occur between paired genes whose simultaneous mutations produce unexpected double-mutant phenotypes, which are indicative of a range of functional relationships. Because genetic interactions can be identified genome-wide in high-throughput experiments, their networks are comprehensive and unbiased representations of function to which we can apply computational methods that search for structure-function relationships. We begin by exploring the association between a set of gene properties and gene genetic interaction (GI) degree. Here, we build a decision tree model that sorts genes based on a set of properties, each of which has a correlation with GI degree, and accurately predicts GI degree. We show that our model, trained on S. cerevisiae, is also accurate for a very distant yeast species, Schizosaccharomyces pombe, demonstrating that the rules governing gene connectivity are well conserved. Finally, we used predictions from the model to identify gene modules that differ between the two yeast species. Next, we further characterize hub genes through an investigation of pleiotropy, the phenomenon of a single genetic locus with multiple phenotypic effects. Pleiotropy has typically been described by counting organism-level phenotypes, but a characterization based on genetic interactions can capture details about cellular processes that are buffered by the cell and never manifest in single mutant cellular phenotypes. For this analysis, we use frequent item set mining to discover GI modules, which we annotate with high-level processes, and use entropy to measure the functional diversity of each gene’s set of containing modules, thus distinguishing between genes whose functional influence is limited to very few bioprocesses and those whose roles are important for varied cellular functions. We identified a number of gene and protein characteristics that differed between genes with high and low pleiotropy and discuss the implications of these results regarding the nature and evolution of pleiotropy

Two and three dimensional segmentation of multimodal imagery

The role of segmentation in the realms of image understanding/analysis, computer vision, pattern recognition, remote sensing and medical imaging in recent years has been significantly augmented due to accelerated scientific advances made in the acquisition of image data. This low-level analysis protocol is critical to numerous applications, with the primary goal of expediting and improving the effectiveness of subsequent high-level operations by providing a condensed and pertinent representation of image information. In this research, we propose a novel unsupervised segmentation framework for facilitating meaningful segregation of 2-D/3-D image data across multiple modalities (color, remote-sensing and biomedical imaging) into non-overlapping partitions using several spatial-spectral attributes. Initially, our framework exploits the information obtained from detecting edges inherent in the data. To this effect, by using a vector gradient detection technique, pixels without edges are grouped and individually labeled to partition some initial portion of the input image content. Pixels that contain higher gradient densities are included by the dynamic generation of segments as the algorithm progresses to generate an initial region map. Subsequently, texture modeling is performed and the obtained gradient, texture and intensity information along with the aforementioned initial partition map are used to perform a multivariate refinement procedure, to fuse groups with similar characteristics yielding the final output segmentation. Experimental results obtained in comparison to published/state-of the-art segmentation techniques for color as well as multi/hyperspectral imagery, demonstrate the advantages of the proposed method. Furthermore, for the purpose of achieving improved computational efficiency we propose an extension of the aforestated methodology in a multi-resolution framework, demonstrated on color images. Finally, this research also encompasses a 3-D extension of the aforementioned algorithm demonstrated on medical (Magnetic Resonance Imaging / Computed Tomography) volumes