Online parameter estimation in dynamic Markov Random Fields for image sequence analysis

pre-printMarkov Random Fields (MRF) have proven to be extremely useful models for efficient and accurate image segmentation.Recent literature points to an increased effort towards incorporating useful priors (shape, geometry, context) in a MRF framework. However, topological priors, considered extremely crucial in biological and natural image sequences have been less explored. This work proposes a strategy wherein free parameters of the MRF are used to make it topology aware using a semantic graphical model working in conjunction with the MRF. Estimation of free parameters is constrained by prior knowledge of an object's topological dynamics encoded by the graphical model. Maximizing a regional conformance measure yields parameters for the frame under consideration. The application motivating this work is the tracing of neuronal structures across 3D serial section Transmission Electron Micrograph (ssTEM) stacks. Applicability of the proposed method is demonstrated by tracing 3D structures in ssTEM stacks

Properties of Healthcare Teaming Networks as a Function of Network Construction Algorithms

Network models of healthcare systems can be used to examine how providers collaborate, communicate, refer patients to each other. Most healthcare service network models have been constructed from patient claims data, using billing claims to link patients with providers. The data sets can be quite large, making standard methods for network construction computationally challenging and thus requiring the use of alternate construction algorithms. While these alternate methods have seen increasing use in generating healthcare networks, there is little to no literature comparing the differences in the structural properties of the generated networks. To address this issue, we compared the properties of healthcare networks constructed using different algorithms and the 2013 Medicare Part B outpatient claims data. Three different algorithms were compared: binning, sliding frame, and trace-route. Unipartite networks linking either providers or healthcare organizations by shared patients were built using each method. We found that each algorithm produced networks with substantially different topological properties. Provider networks adhered to a power law, and organization networks to a power law with exponential cutoff. Censoring networks to exclude edges with less than 11 shared patients, a common de-identification practice for healthcare network data, markedly reduced edge numbers and greatly altered measures of vertex prominence such as the betweenness centrality. We identified patterns in the distance patients travel between network providers, and most strikingly between providers in the Northeast United States and Florida. We conclude that the choice of network construction algorithm is critical for healthcare network analysis, and discuss the implications for selecting the algorithm best suited to the type of analysis to be performed.Comment: With links to comprehensive, high resolution figures and networks via figshare.co

A Testing Environment for Continuous Colormaps

Many computer science disciplines (e.g., combinatorial optimization, natural language processing, and information retrieval) use standard or established test suites for evaluating algorithms. In visualization, similar approaches have been adopted in some areas (e.g., volume visualization), while user testimonies and empirical studies have been the dominant means of evaluation in most other areas, such as designing colormaps. In this paper, we propose to establish a test suite for evaluating the design of colormaps. With such a suite, the users can observe the effects when different continuous colormaps are applied to planar scalar fields that may exhibit various characteristic features, such as jumps, local extrema, ridge or valley lines, different distributions of scalar values, different gradients, different signal frequencies, different levels of noise, and so on. The suite also includes an expansible collection of real-world data sets including the most popular data for colormap testing in the visualization literature. The test suite has been integrated into a web-based application for creating continuous colormaps (https://ccctool.com/), facilitating close inter-operation between design and evaluation processes. This new facility complements traditional evaluation methods such as user testimonies and empirical studies

A Raster-Based Neighborhood Model for Evaluating Complexity in Dynamic Maps

ABSTRACT: The cartographic community has taken a renewed interest in evaluating the effectiveness of automated map displays, given their increasing prevalence among general map users. The changing values of the mapped area from frame to frame in a dynamic thematic map constitute its main element of visual complexity, while many of the peripheral map components often change little (titles) or not at all (scale bars, color ramps). Building on recent research into visual complexity as it relates to dynamic thematic mapping, this study developed a raster-based GIS model for evaluating the graphical variability between sequences of choropleth maps as they would appear as scenes in a dynamic map. The evaluation of visual complexity is based on two previously established metrics, Basic Magnitude of Change (BMOC) and Magnitude of Rank Change (MORC), for describing the variability and average class 'jump' for enumeration units across map scenes. The model presented in this paper uses a neighborhood focal operator that sequentially moves across the entire map, replicating the user's viewing perspective as it divides the scene to instantaneously focus only on the part of the map within the foveal viewing area, a zone of enhanced visual-cognitive acuity. This model accepts a single vector map, uses its class membership attribute data as inputs, computes the BMOC and MORC variability, and writes the value to the focus. The model output is two smoothed map images depicting relative visual complexity values for the sequence of maps. While the neighborhood paradigm can theoretically be used to quantify change on either a vector or raster map, the raster-based approach suggests several improvements over one based on vector polygons. These include a potentially higher degree of accuracy in modeling the user's perspective, especially if enumeration units vary widely in size within the foveal area and map itself, plus the ability to use (with minimal customization) existing image-processing software such as ERDAS Imagine, ArcGIS Spatial Analyst and ENVI to perform analysis of dynamic map complexity

An Evolutionary Approach to Adaptive Image Analysis for Retrieving and Long-term Monitoring Historical Land Use from Spatiotemporally Heterogeneous Map Sources

Land use changes have become a major contributor to the anthropogenic global change. The ongoing dispersion and concentration of the human species, being at their orders unprecedented, have indisputably altered Earth’s surface and atmosphere. The effects are so salient and irreversible that a new geological epoch, following the interglacial Holocene, has been announced: the Anthropocene. While its onset is by some scholars dated back to the Neolithic revolution, it is commonly referred to the late 18th century. The rapid development since the industrial revolution and its implications gave rise to an increasing awareness of the extensive anthropogenic land change and led to an urgent need for sustainable strategies for land use and land management. By preserving of landscape and settlement patterns at discrete points in time, archival geospatial data sources such as remote sensing imagery and historical geotopographic maps, in particular, could give evidence of the dynamic land use change during this crucial period. In this context, this thesis set out to explore the potentials of retrospective geoinformation for monitoring, communicating, modeling and eventually understanding the complex and gradually evolving processes of land cover and land use change. Currently, large amounts of geospatial data sources such as archival maps are being worldwide made online accessible by libraries and national mapping agencies. Despite their abundance and relevance, the usage of historical land use and land cover information in research is still often hindered by the laborious visual interpretation, limiting the temporal and spatial coverage of studies. Thus, the core of the thesis is dedicated to the computational acquisition of geoinformation from archival map sources by means of digital image analysis. Based on a comprehensive review of literature as well as the data and proposed algorithms, two major challenges for long-term retrospective information acquisition and change detection were identified: first, the diversity of geographical entity representations over space and time, and second, the uncertainty inherent to both the data source itself and its utilization for land change detection. To address the former challenge, image segmentation is considered a global non-linear optimization problem. The segmentation methods and parameters are adjusted using a metaheuristic, evolutionary approach. For preserving adaptability in high level image analysis, a hybrid model- and data-driven strategy, combining a knowledge-based and a neural net classifier, is recommended. To address the second challenge, a probabilistic object- and field-based change detection approach for modeling the positional, thematic, and temporal uncertainty adherent to both data and processing, is developed. Experimental results indicate the suitability of the methodology in support of land change monitoring. In conclusion, potentials of application and directions for further research are given

Multimodal image analysis of the human brain

Gedurende de laatste decennia heeft de snelle ontwikkeling van multi-modale en niet-invasieve hersenbeeldvorming technologieën een revolutie teweeg gebracht in de mogelijkheid om de structuur en functionaliteit van de hersens te bestuderen. Er is grote vooruitgang geboekt in het beoordelen van hersenschade door gebruik te maken van Magnetic Reconance Imaging (MRI), terwijl Elektroencefalografie (EEG) beschouwd wordt als de gouden standaard voor diagnose van neurologische afwijkingen. In deze thesis focussen we op de ontwikkeling van nieuwe technieken voor multi-modale beeldanalyse van het menselijke brein, waaronder MRI segmentatie en EEG bronlokalisatie. Hierdoor voegen we theorie en praktijk samen waarbij we focussen op twee medische applicaties: (1) automatische 3D MRI segmentatie van de volwassen hersens en (2) multi-modale EEG-MRI data analyse van de hersens van een pasgeborene met perinatale hersenschade. We besteden veel aandacht aan de verbetering en ontwikkeling van nieuwe methoden voor accurate en ruisrobuuste beeldsegmentatie, dewelke daarna succesvol gebruikt worden voor de segmentatie van hersens in MRI van zowel volwassen als pasgeborenen. Daarenboven ontwikkelden we een geïntegreerd multi-modaal methode voor de EEG bronlokalisatie in de hersenen van een pasgeborene. Deze lokalisatie wordt gebruikt voor de vergelijkende studie tussen een EEG aanval bij pasgeborenen en acute perinatale hersenletsels zichtbaar in MRI

Anomaly Detection, Rule Adaptation and Rule Induction Methodologies in the Context of Automated Sports Video Annotation.

Automated video annotation is a topic of considerable interest in computer vision due to its applications in video search, object based video encoding and enhanced broadcast content. The domain of sport broadcasting is, in particular, the subject of current research attention due to its fixed, rule governed, content. This research work aims to develop, analyze and demonstrate novel methodologies that can be useful in the context of adaptive and automated video annotation systems. In this thesis, we present methodologies for addressing the problems of anomaly detection, rule adaptation and rule induction for court based sports such as tennis and badminton. We first introduce an HMM induction strategy for a court-model based method that uses the court structure in the form of a lattice for two related modalities of singles and doubles tennis to tackle the problems of anomaly detection and rectification. We also introduce another anomaly detection methodology that is based on the disparity between the low-level vision based classifiers and the high-level contextual classifier. Another approach to address the problem of rule adaptation is also proposed that employs Convex hulling of the anomalous states. We also investigate a number of novel hierarchical HMM generating methods for stochastic induction of game rules. These methodologies include, Cartesian product Label-based Hierarchical Bottom-up Clustering (CLHBC) that employs prior information within the label structures. A new constrained variant of the classical Chinese Restaurant Process (CRP) is also introduced that is relevant to sports games. We also propose two hybrid methodologies in this context and a comparative analysis is made against the flat Markov model. We also show that these methods are also generalizable to other rule based environments