Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 558

Search results for: imaging pathway visualization

558 Visualizing Imaging Pathways after Anatomy-Specific Follow-Up Imaging Recommendations

Authors: Thusitha Mabotuwana, Christopher S. Hall

Abstract:

Radiologists routinely make follow-up imaging recommendations, usually based on established clinical practice guidelines, such as the Fleischner Society guidelines for managing lung nodules. In order to ensure optimal care, it is important to make guideline-compliant recommendations, and also for patients to follow-up on these imaging recommendations in a timely manner. However, determining such compliance rates after a specific finding has been observed usually requires many time-consuming manual steps. To address some of these limitations with current approaches, in this paper we discuss a methodology to automatically detect finding-specific follow-up recommendations from radiology reports and create a visualization for relevant subsequent exams showing the modality transitions. Nearly 5% of patients who had a lung related follow-up recommendation continued to have at least eight subsequent outpatient CT exams during a seven year period following the recommendation. Radiologist and section chiefs can use the proposed tool to better understand how a specific patient population is being managed, identify possible deviations from established guideline recommendations and have a patient-specific graphical representation of the imaging pathways for an abstract view of the overall treatment path thus far.

Keywords: Follow-up recommendations, care pathways, imaging pathway visualization, follow-up tracking.

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557 Real-Time Visualization Using GPU-Accelerated Filtering of LiDAR Data

Authors: Sašo Pečnik, Borut Žalik

Abstract:

This paper presents a real-time visualization technique and filtering of classified LiDAR point clouds. The visualization is capable of displaying filtered information organized in layers by the classification attribute saved within LiDAR datasets. We explain the used data structure and data management, which enables real-time presentation of layered LiDAR data. Real-time visualization is achieved with LOD optimization based on the distance from the observer without loss of quality. The filtering process is done in two steps and is entirely executed on the GPU and implemented using programmable shaders.

Keywords: Filtering, graphics, level-of-details, LiDAR, realtime visualization.

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556 Efficient CT Image Volume Rendering for Diagnosis

Authors: HaeNa Lee, Sun K. Yoo

Abstract:

Volume rendering is widely used in medical CT image visualization. Applying 3D image visualization to diagnosis application can require accurate volume rendering with high resolution. Interpolation is important in medical image processing applications such as image compression or volume resampling. However, it can distort the original image data because of edge blurring or blocking effects when image enhancement procedures were applied. In this paper, we proposed adaptive tension control method exploiting gradient information to achieve high resolution medical image enhancement in volume visualization, where restored images are similar to original images as much as possible. The experimental results show that the proposed method can improve image quality associated with the adaptive tension control efficacy.

Keywords: Tension control, Interpolation, Ray-casting, Medical imaging analysis.

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555 Metabolomics Profile Recognition for Cancer Diagnostics

Authors: Valentina L. Kouznetsova, Jonathan W. Wang, Igor F. Tsigelny

Abstract:

Metabolomics has become a rising field of research for various diseases, particularly cancer. Increases or decreases in metabolite concentrations in the human body are indicative of various cancers. Further elucidation of metabolic pathways and their significance in cancer research may greatly spur medicinal discovery. We analyzed the metabolomics profiles of lung cancer. Thirty-three metabolites were selected as significant. These metabolites are involved in 37 metabolic pathways delivered by MetaboAnalyst software. The top pathways are glyoxylate and dicarboxylate pathway (its hubs are formic acid and glyoxylic acid) along with Citrate cycle pathway followed by Taurine and hypotaurine pathway (the hubs in the latter are taurine and sulfoacetaldehyde) and Glycine, serine, and threonine pathway (the hubs are glycine and L-serine). We studied interactions of the metabolites with the proteins involved in cancer-related signaling networks, and developed an approach to metabolomics biomarker use in cancer diagnostics. Our analysis showed that a significant part of lung-cancer-related metabolites interacts with main cancer-related signaling pathways present in this network: PI3K–mTOR–AKT pathway, RAS–RAF–ERK1/2 pathway, and NFKB pathway. These results can be employed for use of metabolomics profiles in elucidation of the related cancer proteins signaling networks.

Keywords: Cancer, metabolites, metabolic pathway, signaling pathway.

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554 New Findings on the User’s Preferences about Data Visualization of Online Reviews

Authors: Elizabeth Simão Carvalho, Marcirio Silveira Chaves

Abstract:

The information visualization is still a knowledge field that lacks from a solid theory to support it and there is a myriad of existing methodologies and taxonomies that can be combined and adopted as guidelines. In this context, it is necessary to pre-evaluate as much as possible all the assumptions that are considered for its design and development. We present an exploratory study (n = 123) to detect the graphical preferences of travelers using accommodation portals of Web 2.0 (e.g. tripadvisor.com). We took into account some of the most relevant ground rules applied in the field to map visually data and design end-user interaction. Moreover, the evaluation process was completely data visualization oriented. We found out that people tend to refuse more advanced types of visualization and that a hybrid combination between radial graphs and stacked bars should be explored. In sum, this paper introduces new findings about the visual model and the cognitive response of users of accommodation booking websites.

Keywords: Information visualization, Data visualization, Visualization evaluation, Online reviews, Booking portal, Hotel booking.

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553 An Interactive Ontology Visualization Approach for the Networked Home Environment

Authors: Ilkka Niskanen, Jarmo Kalaoja, Julia Kantorovitch, Toni Piirainen

Abstract:

Ontologies are broadly used in the context of networked home environments. With ontologies it is possible to define and store context information, as well as to model different kinds of physical environments. Ontologies are central to networked home environments as they carry the meaning. However, ontologies and the OWL language is complex. Several ontology visualization approaches have been developed to enhance the understanding of ontologies. The domain of networked home environments sets some special requirements for the ontology visualization approach. The visualization tool presented here, visualizes ontologies in a domain-specific way. It represents effectively the physical structures and spatial relationships of networked home environments. In addition, it provides extensive interaction possibilities for editing and manipulating the visualization. The tool shortens the gap from beginner to intermediate OWL ontology reader by visualizing instances in their actual locations and making OWL ontologies more interesting and concrete, and above all easier to comprehend.

Keywords: Ontologies, visualization, interaction.

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552 Angular-Coordinate Driven Radial Tree Drawing

Authors: Farshad Ghassemi Toosi, Nikola S. Nikolov

Abstract:

We present a visualization technique for radial drawing of trees consisting of two slightly different algorithms. Both of them make use of node-link diagrams for visual encoding. This visualization creates clear drawings without edge crossing. One of the algorithms is suitable for real-time visualization of large trees, as it requires minimal recalculation of the layout if leaves are inserted or removed from the tree; while the other algorithm makes better utilization of the drawing space. The algorithms are very similar and follow almost the same procedure but with different parameters. Both algorithms assign angular coordinates for all nodes which are then converted into 2D Cartesian coordinates for visualization. We present both algorithms and discuss how they compare to each other.

Keywords: Radial Tree Drawing, Real-Time Visualization, Angular Coordinates, Large Trees.

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551 Medical Imaging Techniques in Clinical Medicine

Authors: Sharan Badiger, Prema T. Akkasaligar

Abstract:

Medical imaging technology has experienced a dramatic change in the last few years. Medical imaging refers to the techniques and processes used to create images of the human body (or parts thereof) for various clinical purposes such as medical procedures and diagnosis or medical science including the study of normal anatomy and function. With the growth of computers and image technology, medical imaging has greatly influenced the medical field. The diagnosis of a health problem is now highly dependent on the quality and the credibility of the image analysis. This paper deals with the various aspects and types of medical imaging.

Keywords: Computed Tomography, Echocardiography, Medical Imaging, Magnetic Resonance, Ultrasound Imaging.

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550 NFκB Pathway Modeling for Optimal Drug Combination Therapy on Multiple Myeloma

Authors: Huiming Peng, Jianguo Wen, Hongwei Li, Jeff Chang, Xiaobo Zhou

Abstract:

NFκB activation plays a crucial role in anti-apoptotic responses in response to the apoptotic signaling during tumor necrosis factor (TNFa) stimulation in Multiple Myeloma (MM). Although several drugs have been found effective for the treatment of MM by mainly inhibiting NFκB pathway, there are no any quantitative or qualitative results of comparison assessment on inhibition effect between different single drugs or drug combinations. Computational modeling is becoming increasingly indispensable for applied biological research mainly because it can provide strong quantitative predicting power. In this study, a novel computational pathway modeling approach is employed to comparably assess the inhibition effects of specific single drugs and drug combinations on the NFκB pathway in MM, especially the prediction of synergistic drug combinations.

Keywords: Computational modeling, drug combination, inhibition effect, multiple myeloma, NFkB pathway.

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549 Automatic Visualization Pipeline Formation for Medical Datasets on Grid Computing Environment

Authors: Aboamama Atahar Ahmed, Muhammad Shafie Abd Latiff, Kamalrulnizam Abu Bakar, Zainul AhmadRajion

Abstract:

Distance visualization of large datasets often takes the direction of remote viewing and zooming techniques of stored static images. However, the continuous increase in the size of datasets and visualization operation causes insufficient performance with traditional desktop computers. Additionally, the visualization techniques such as Isosurface depend on the available resources of the running machine and the size of datasets. Moreover, the continuous demand for powerful computing powers and continuous increase in the size of datasets results an urgent need for a grid computing infrastructure. However, some issues arise in current grid such as resources availability at the client machines which are not sufficient enough to process large datasets. On top of that, different output devices and different network bandwidth between the visualization pipeline components often result output suitable for one machine and not suitable for another. In this paper we investigate how the grid services could be used to support remote visualization of large datasets and to break the constraint of physical co-location of the resources by applying the grid computing technologies. We show our grid enabled architecture to visualize large medical datasets (circa 5 million polygons) for remote interactive visualization on modest resources clients.

Keywords: Visualization, Grid computing, Medical datasets, visualization techniques, thin clients, Globus toolkit, VTK.

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548 Research on IBR-Driven Distributed Collaborative Visualization System

Authors: Yin Runmin, Song Changfeng

Abstract:

Image-based Rendering(IBR) techniques recently reached in broad fields which leads to a critical challenge to build up IBR-Driven visualization platform where meets requirement of high performance, large bounds of distributed visualization resource aggregation and concentration, multiple operators deploying and CSCW design employing. This paper presents an unique IBR-based visualization dataflow model refer to specific characters of IBR techniques and then discusses prominent feature of IBR-Driven distributed collaborative visualization (DCV) system before finally proposing an novel prototype. The prototype provides a well-defined three level modules especially work as Central Visualization Server, Local Proxy Server and Visualization Aid Environment, by which data and control for collaboration move through them followed the previous dataflow model. With aid of this triple hierarchy architecture of that, IBR oriented application construction turns to be easy. The employed augmented collaboration strategy not only achieve convenient multiple users synchronous control and stable processing management, but also is extendable and scalable.

Keywords: Image-Based Rendering, Distributed CollaborativeVisualization, Computer Supported Cooperative Work, Model andSimulation, Modular Visualization Environment.

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547 Use of Visualization Techniques for Active Learning Engagement in Environmental Science Engineering Courses

Authors: Srinivasan Latha, M. R. Christhu Raj, Rajeev Sukumaran

Abstract:

Active learning strategies have completely rewritten the concept of teaching and learning. Academicians have clocked back to Socratic approaches of questioning. Educators have started implementing active learning strategies for effective learning with the help of tools and technology. As Generation-Y learners are mostly visual, engaging them using visualization techniques play a vital role in their learning process. The facilitator has an important role in intrinsically motivating the learners using different approaches to create self-learning interests. Different visualization techniques were used along with lectures to help students understand and appreciate the concepts. Anonymous feedback was collected from learners. The consolidated report shows that majority of learners accepted the usage of visualization techniques was helpful in understanding concepts as well as create interest in learning the course. This study helps to understand, how the use of visualization techniques help the facilitator to engage learners effectively as well create and intrinsic motivation for their learning.

Keywords: Visualization techniques, concept maps, mind maps, argument maps, flowchart, tree diagram, problem solving.

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546 Automated Stereophotogrammetry Data Cleansing

Authors: Stuart Henry, Philip Morrow, John Winder, Bryan Scotney

Abstract:

The stereophotogrammetry modality is gaining more widespread use in the clinical setting. Registration and visualization of this data, in conjunction with conventional 3D volumetric image modalities, provides virtual human data with textured soft tissue and internal anatomical and structural information. In this investigation computed tomography (CT) and stereophotogrammetry data is acquired from 4 anatomical phantoms and registered using the trimmed iterative closest point (TrICP) algorithm. This paper fully addresses the issue of imaging artifacts around the stereophotogrammetry surface edge using the registered CT data as a reference. Several iterative algorithms are implemented to automatically identify and remove stereophotogrammetry surface edge outliers, improving the overall visualization of the combined stereophotogrammetry and CT data. This paper shows that outliers at the surface edge of stereophotogrammetry data can be successfully removed automatically.

Keywords: Data cleansing, stereophotogrammetry.

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545 Visualization of Code Clone Detection Results and the Implementation with Structured Data

Authors: Kazuaki Maeda

Abstract:

This paper describes a code clone visualization method, called FC graph, and the implementation issues. Code clone detection tools usually show the results in a textual representation. If the results are large, it makes a problem to software maintainers with understanding them. One of the approaches to overcome the situation is visualization of code clone detection results. A scatter plot is a popular approach to the visualization. However, it represents only one-to-one correspondence and it is difficult to find correspondence of code clones over multiple files. FC graph represents correspondence among files, code clones and packages in Java. All nodes in FC graph are positioned using force-directed graph layout, which is dynami- cally calculated to adjust the distances of nodes until stabilizing them. We applied FC graph to some open source programs and visualized the results. In the author’s experience, FC graph is helpful to grasp correspondence of code clones over multiple files and also code clones with in a file.

Keywords: code clone detection, program comprehension, software maintenance, visualization

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544 Intelligent Control of Robotized Workcell by Augmented Reality Application

Authors: L. Novakova-Marcincinova, J. Novak-Marcincin, M. Janak

Abstract:

The computer aided for design, analysis, control, visualization and simulation of robotized workcells is very interesting in this time. Computer Aided Robot Control (CARC) is a subsystem of the system CIM including the computer aided systems of all activities connected with visualization and working of robotized workcells. There are three basic ideas: current CAD/CAM/CAE systems for design and 3D visualization, special PC based control and simulation systems and Augmented Reality Aided Manufacturing (ARAM) systems. This paper describes example of Open Source software application that can to be utilized at planning of the robotized workcells, visualization and off-line programming the automated processes realized by authors.

Keywords: Intelligent control, augmented reality, robot.

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543 Visualization of Searching and Sorting Algorithms

Authors: Bremananth R, Radhika.V, Thenmozhi.S

Abstract:

Sequences of execution of algorithms in an interactive manner using multimedia tools are employed in this paper. It helps to realize the concept of fundamentals of algorithms such as searching and sorting method in a simple manner. Visualization gains more attention than theoretical study and it is an easy way of learning process. We propose methods for finding runtime sequence of each algorithm in an interactive way and aims to overcome the drawbacks of the existing character systems. System illustrates each and every step clearly using text and animation. Comparisons of its time complexity have been carried out and results show that our approach provides better perceptive of algorithms.

Keywords: Algorithms, Searching, Sorting, Visualization.

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542 Contrast-Enhanced Multispectal Upconversion Fluorescence Analysis for High-Resolution in-vivo Deep Tissue Imaging

Authors: Lijiang Wang, Wei Wang, Yuhong Xu

Abstract:

Lanthanide-doped upconversion nanoparticles which can convert near-infrared lights to visible lights have attracted growing interest because of their great potentials in fluorescence imaging. Upconversion fluorescence imaging technique with excitation in the near-infrared (NIR) region has been used for imaging of biological cells and tissues. However, improving the detection sensitivity and decreasing the absorption and scattering in biological tissues are as yet unresolved problems. In this present study, a novel NIR-reflected multispectral imaging system was developed for upconversion fluorescent imaging in small animals. Based on this system, we have obtained the high contrast images without the autofluorescence when biocompatible UCPs were injected near the body surface or deeply into the tissue. Furthermore, we have extracted respective spectra of the upconversion fluorescence and relatively quantify the fluorescence intensity with the multispectral analysis. To our knowledge, this is the first time to analyze and quantify the upconversion fluorescence in the small animal imaging.

Keywords: Multispectral imaging, near-infrared, upconversion fluorescence imaging, upconversion nanoparticles.

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541 Automated 3D Segmentation System for Detecting Tumor and Its Heterogeneity in Patients with High Grade Ovarian Epithelial Cancer

Authors: D. A. Binas, M. Konidari, C. Bourgioti, L. Angela Moulopoulou, T. L. Economopoulos, G. K. Matsopoulos

Abstract:

High grade ovarian epithelial cancer (OEC) is the most fatal gynecological cancer and poor prognosis of this entity is closely related to considerable intratumoral genetic heterogeneity. By examining imaging data, it is possible to assess the heterogeneity of tumorous tissue. This study presents a methodology for aligning, segmenting and finally visualizing information from various magnetic resonance imaging series, in order to construct 3D models of heterogeneity maps from the same tumor in OEC patients. The proposed system may be used as an adjunct digital tool by health professionals for personalized medicine, as it allows for an easy visual assessment of the heterogeneity of the examined tumor.

Keywords: K-means segmentation, ovarian epithelial cancer, quantitative characteristics, registration, tumor visualization.

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540 Visual Text Analytics Technologies for Real-Time Big Data: Chronological Evolution and Issues

Authors: Siti Azrina B. A. Aziz, Siti Hafizah A. Hamid

Abstract:

New approaches to analyze and visualize data stream in real-time basis is important in making a prompt decision by the decision maker. Financial market trading and surveillance, large-scale emergency response and crowd control are some example scenarios that require real-time analytic and data visualization. This situation has led to the development of techniques and tools that support humans in analyzing the source data. With the emergence of Big Data and social media, new techniques and tools are required in order to process the streaming data. Today, ranges of tools which implement some of these functionalities are available. In this paper, we present chronological evolution evaluation of technologies for supporting of real-time analytic and visualization of the data stream. Based on the past research papers published from 2002 to 2014, we gathered the general information, main techniques, challenges and open issues. The techniques for streaming text visualization are identified based on Text Visualization Browser in chronological order. This paper aims to review the evolution of streaming text visualization techniques and tools, as well as to discuss the problems and challenges for each of identified tools.

Keywords: Information visualization, visual analytics, text mining, visual text analytics tools, big data visualization.

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539 3-D Visualization and Optimization for SISO Linear Systems Using Parametrization of Two-Stage Compensator Design

Authors: Kazuyoshi Mori, Keisuke Hashimoto

Abstract:

In this paper, we consider the two-stage compensator designs of SISO plants. As an investigation of the characteristics of the two-stage compensator designs, which is not well investigated yet, of SISO plants, we implement three dimensional visualization systems of output signals and optimization system for SISO plants by the parametrization of stabilizing controllers based on the two-stage compensator design. The system runs on Mathematica by using “Three Dimensional Surface Plots,” so that the visualization can be interactively manipulated by users. In this paper, we use the discrete-time LTI system model. Even so, our approach is the factorization approach, so that the result can be applied to many linear models.

Keywords: Linear systems, visualization, optimization, two-Stage compensator design, Mathematica.

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538 Simulation Data Summarization Based on Spatial Histograms

Authors: Jing Zhao, Yoshiharu Ishikawa, Chuan Xiao, Kento Sugiura

Abstract:

In order to analyze large-scale scientific data, research on data exploration and visualization has gained popularity. In this paper, we focus on the exploration and visualization of scientific simulation data, and define a spatial V-Optimal histogram for data summarization. We propose histogram construction algorithms based on a general binary hierarchical partitioning as well as a more specific one, the l-grid partitioning. For effective data summarization and efficient data visualization in scientific data analysis, we propose an optimal algorithm as well as a heuristic algorithm for histogram construction. To verify the effectiveness and efficiency of the proposed methods, we conduct experiments on the massive evacuation simulation data.

Keywords: Simulation data, data summarization, spatial histograms, exploration and visualization.

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537 Transmit Sub-aperture Optimization in MSTA Ultrasound Imaging Method

Authors: YuriyTasinkevych, Ihor Trots, AndrzejNowicki, Marcin Lewandowski

Abstract:

The paper presents the optimization problem for the multi-element synthetic transmit aperture method (MSTA) in ultrasound imaging applications. The optimal choice of the transmit aperture size is performed as a trade-off between the lateral resolution, penetration depth and the frame rate. Results of the analysis obtained by a developed optimization algorithm are presented. Maximum penetration depth and the best lateral resolution at given depths are chosen as the optimization criteria. The optimization algorithm was tested using synthetic aperture data of point reflectors simulated by Filed II program for Matlab® for the case of 5MHz 128-element linear transducer array with 0.48 mm pitch are presented. The visualization of experimentally obtained synthetic aperture data of a tissue mimicking phantom and in vitro measurements of the beef liver are also shown. The data were obtained using the SonixTOUCH Research systemequipped with a linear 4MHz 128 element transducerwith 0.3 mm element pitch, 0.28 mm element width and 70% fractional bandwidth was excited by one sine cycle pulse burst of transducer's center frequency.

Keywords: synthetic aperture method, ultrasound imaging, beamforming.

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536 Visualization of Conway Polyhedron Notation

Authors: Hidetoshi Nonaka

Abstract:

This paper presents an interactive modeling system of polyhedra using the isomorphic graphs. Especially, Conway polyhedron notation is implemented. The notation can be observed as interactive animation.

Keywords: Conway polyhedron notation, Polyhedral graph, Visualization.

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535 A Proposed Framework for Visualization to Teach Computer Science

Authors: Muhammed Yousoof, Mohd Sapiyan, Khaja Kamaluddin

Abstract:

Computer programming is considered a very difficult course by many computer science students. The reasons for the difficulties include cognitive load involved in programming, different learning styles of students, instructional methodology and the choice of the programming languages. To reduce the difficulties the following have been tried: pair programming, program visualization, different learning styles etc. However, these efforts have produced limited success. This paper reviews the problem and proposes a framework to help students overcome the difficulties involved.

Keywords: Cognitive Load, Instructional Models, LearningStyles, Program Visualization.

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534 Automatic Map Simplification for Visualization on Mobile Devices

Authors: Hang Yu

Abstract:

The visualization of geographic information on mobile devices has become popular as the widespread use of mobile Internet. The mobility of these devices brings about much convenience to people-s life. By the add-on location-based services of the devices, people can have an access to timely information relevant to their tasks. However, visual analysis of geographic data on mobile devices presents several challenges due to the small display and restricted computing resources. These limitations on the screen size and resources may impair the usability aspects of the visualization applications. In this paper, a variable-scale visualization method is proposed to handle the challenge of small mobile display. By merging multiple scales of information into a single image, the viewer is able to focus on the interesting region, while having a good grasp of the surrounding context. This is essentially visualizing the map through a fisheye lens. However, the fisheye lens induces undesirable geometric distortion in the peripheral, which renders the information meaningless. The proposed solution is to apply map generalization that removes excessive information around the peripheral and an automatic smoothing process to correct the distortion while keeping the local topology consistent. The proposed method is applied on both artificial and real geographical data for evaluation.

Keywords: Map simplification, visualization, mobile devices.

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533 Improved Lung Nodule Visualization on Chest Radiographs using Digital Filtering and Contrast Enhancement

Authors: Benjamin Y. M. Kwan, Hon Keung Kwan

Abstract:

Early detection of lung cancer through chest radiography is a widely used method due to its relatively affordable cost. In this paper, an approach to improve lung nodule visualization on chest radiographs is presented. The approach makes use of linear phase high-frequency emphasis filter for digital filtering and histogram equalization for contrast enhancement to achieve improvements. Results obtained indicate that a filtered image can reveal sharper edges and provide more details. Also, contrast enhancement offers a way to further enhance the global (or local) visualization by equalizing the histogram of the pixel values within the whole image (or a region of interest). The work aims to improve lung nodule visualization of chest radiographs to aid detection of lung cancer which is currently the leading cause of cancer deaths worldwide.

Keywords: Chest radiographs, Contrast enhancement, Digital filtering, Lung nodule detection

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532 Metaphor in Terminology: Visualization as a Way to Term Perception

Authors: Jeļena Tretjakova

Abstract:

Metaphor has recently gained extensive interest most probably due to developments in cognitive sciences and the study of language as the reflection of humans- world perception. Metaphor is no longer reckoned as solely literary expressive means. Nowadays it is studied in a whole number of discourses, such as politics, law, medicine, sports, etc. with the purpose of the analysis and determining its role. The scientific language is not an exception. It might seem that metaphor cannot suit it; we would dare to draw a hypothesis that metaphor has indeed found its stable place in terminology. In comprehension of metaphorically represented terms the stage of visualization plays a significant role. We proceeded on the assumption that this stage is the main in provision of better term comprehension and would try to exemplify it with metaphoricallyoriented terms.

Keywords: Comprehension, metaphor, terminology, visualization.

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531 Application of KL Divergence for Estimation of Each Metabolic Pathway Genes

Authors: Shohei Maruyama, Yasuo Matsuyama, Sachiyo Aburatani

Abstract:

Development of a method to estimate gene functions is an important task in bioinformatics. One of the approaches for the annotation is the identification of the metabolic pathway that genes are involved in. Since gene expression data reflect various intracellular phenomena, those data are considered to be related with genes’ functions. However, it has been difficult to estimate the gene function with high accuracy. It is considered that the low accuracy of the estimation is caused by the difficulty of accurately measuring a gene expression. Even though they are measured under the same condition, the gene expressions will vary usually. In this study, we proposed a feature extraction method focusing on the variability of gene expressions to estimate the genes' metabolic pathway accurately. First, we estimated the distribution of each gene expression from replicate data. Next, we calculated the similarity between all gene pairs by KL divergence, which is a method for calculating the similarity between distributions. Finally, we utilized the similarity vectors as feature vectors and trained the multiclass SVM for identifying the genes' metabolic pathway. To evaluate our developed method, we applied the method to budding yeast and trained the multiclass SVM for identifying the seven metabolic pathways. As a result, the accuracy that calculated by our developed method was higher than the one that calculated from the raw gene expression data. Thus, our developed method combined with KL divergence is useful for identifying the genes' metabolic pathway.

Keywords: Metabolic pathways, gene expression data, microarray, Kullback–Leibler divergence, KL divergence, support vector machines, SVM, machine learning.

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530 Numerical and Infrared Mapping of Temperature in Heat Affected Zone during Plasma Arc Cutting of Mild Steel

Authors: Dalvir Singh, Somnath Chattopadhyaya

Abstract:

During welding or flame cutting of metals, the prediction of heat affected zone (HAZ) is critical. There is need to develop a simple mathematical model to calculate the temperature variation in HAZ and derivative analysis can be used for this purpose. This study presents analytical solution for heat transfer through conduction in mild steel plate. The homogeneous and nonhomogeneous boundary conditions are single variables. The full field analytical solutions of temperature measurement, subjected to local heating source, are derived first by method of separation of variables followed with the experimental visualization using infrared imaging. Based on the present work, it is suggested that appropriate heat input characteristics controls the temperature distribution in and around HAZ.

Keywords: Conduction Heat Transfer, Heat Affected Zone (HAZ), Infra-Red Imaging, Numerical Method, Orthogonal Function, Plasma Arc Cutting, Separation of Variables, Temperature Measurement.

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529 Multidimensional Visualization Tools for Analysis of Expression Data

Authors: Urska Cvek, Marjan Trutschl, Randolph Stone II, Zanobia Syed, John L. Clifford, Anita L. Sabichi

Abstract:

Expression data analysis is based mostly on the statistical approaches that are indispensable for the study of biological systems. Large amounts of multidimensional data resulting from the high-throughput technologies are not completely served by biostatistical techniques and are usually complemented with visual, knowledge discovery and other computational tools. In many cases, in biological systems we only speculate on the processes that are causing the changes, and it is the visual explorative analysis of data during which a hypothesis is formed. We would like to show the usability of multidimensional visualization tools and promote their use in life sciences. We survey and show some of the multidimensional visualization tools in the process of data exploration, such as parallel coordinates and radviz and we extend them by combining them with the self-organizing map algorithm. We use a time course data set of transitional cell carcinoma of the bladder in our examples. Analysis of data with these tools has the potential to uncover additional relationships and non-trivial structures.

Keywords: microarrays, visualization, parallel coordinates, radviz, self-organizing maps.

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