42451139
Visualizing scientific paradigms: An introduction
This special topic issue includes a collection of seven articles on visualizing scientific paradigms. All articles in this special issue reflect the influence of Thomas Kuhn’s structure of scientific revolutions on our understanding of the growth of scientific knowledge. On the other hand, each article represents a unique perspective of how one may pursue the quest for transforming something as intangible and empirically evasive as invisible colleges and competing paradigms into something that is more accessible and traceable to scholars and professions of various disciplines, ranging from historians, philosophers, and educators to scientists and engineers. The opening article is Henry Small’s personal account of the endeavor in probing scientific paradigms using science mapping. His article, entitled “Paradigms, Citations and Maps of Science: A Personal History,” provides a valuable introduction to the key issues involved in this area and reveals an overview of promising avenues as well as challenging routes. He identifies an emerging trend that reflects and redefines Kuhn’s paradigms and emphasizes the empirical viability of research methodologies in understanding the growth of scientific knowledge. He suggests that revolutionary and normal science should be seen as extremes on a continuum of rates of change rather than, as Kuhn originally asserted, as an all-or-none proposition. The second and third articles take a prominent historical perspective in depicting the evolution of scientific citations. Eugene Garfield and his collaborators’ article is entitled “Why Do We Need Algorithmic Historiography?” They explain the rationale for creating HistCite, their new program that produces historiographs of scholarly topics. These historiographs help analysts and historians identify key events, people, and journals in a particular field. Scholars can evaluate the evolution of a scientific paradigm by studying the genealogic profile of such evolution. The third article is entitled “Timeline Visualization of Research Fronts.” Steven Morris and his colleagues focus on temporal changes in research fronts and explain the power of timeline visualizations. They first cluster documents into research fronts based on bibliographic coupling and then visualize research fronts using horizontal timeline tracks. Documents from research fronts are plotted along corresponding timeline tracks. Because time line visualizations can reveal temporal relations among research fronts and their member documents, time lines are potentially useful tools in identifying new research fronts as well as existing research expertise and research excellence. Although both the fourth and fifth articles have connections to Pathfinder networks, they address different topics. Howard White’s article, entitled “Pathfinder Networks and Author Cocitation Analysis: A Remapping of Paradigmatic Information Scientists,” clarifies an important methodological issue, whereas Chen and Kuljis focus on a general framework for visualizing scientific paradigms in their article. Author Cocitation Analysis (ACA) is a long established methodology for studying intellectual structures. Researchers have routinely used Pearson correlation coefficients rather than raw cocitation counts as the measure of similarity between author pairs. Howard White compellingly demonstrates the advantages of using raw cocitation counts in Pathfinder network visualizations of author cocitation structures. He compares Pathfinder networks of the information scientists derived from raw cocitation counts and Pearson correlation coefficients, respectively. In the fifth article “The Rising Landscape: A Visual Exploration of Superstring Revolutions in Physics,” Chen and Kuljis introduce a general framework for visualizing the growth of scientific paradigms based on Kuhn’s theory on scientific revolutions. They illustrate the use of this framework in a case study of superstring revolutions in physics. The evolution of cocitation networks is depicted and explained through animated visualizations of citations and cocitation links. Visual-spatial properties as well as structural patterns associated with superstring revolutions are identified. The sixth and seventh articles deal with heterogeneous data sources. In their article entitled “Indicator-Assisted Evaluation and Funding of Research: Visualizing the Influ© 2003 Wiley Periodicals, Inc.
45076304
Spatial Semantic Virtual Worlds: The Structural Duality and Beyond
15424500
Semantically modified diffusion limited aggregation for visualizing large-scale networks
Diffusion-limited aggregation (DLA) is a model of fractal growth. Computer models can simulate the fast aggregation of millions of particles. We propose a modified version of DLA, called semantically modified DLA (SM-DLA), for visualizing large-scale networks. SM-DLA introduces similarity measures between particles so that instead of attaching to the nearest particle in the aggregation, a new particle is stochastically directed to attach to particles that are similar to it. The results of our initial experiment with a co-citation network using SM-DLA are encouraging, suggesting that the algorithm has the potential as an alternative paradigm for visualizing large-scale networks. Further studies in this direction are recommended.
206109439
How did university departments interweave the Web: A study of connectivity and underlying factors
This paper presents two studies of the use of the WWW in Scottish universities and American land-grant universities. First, we investigated the relationship between the organisational profile of a university department in Scotland and its structural connectivity on the WWW. A Spearman rank order correlation analysis revealed a number of strong correlation relationships between structural connectivity measures and the organisational profile based on research assessment exercise ratings, teaching quality assessments, student‐staff ratios and funding levels. Linkage patterns from 13 Scottish academic sites to commercial sites in Britain and America highlighted the impact of culture and the appropriateness of information technologies on the acceptance of the WWW. The second study is a content survey of WWW-based education activities in American land-grant universities to investigate successful applications of these enabling techniques in education. The two studies together highlighted cultural, political and technological interactions in the use of the WWW. q 1998 Elsevier Science B.V. All rights reserved
45097070
Spatial ability and visual navigation: an Empirical Study
Abstract In this paper, we describe an empirical study of individuals' spatial navigation strategies and a number of performance and preference measures with regard to the design of a novel 3D visualisation. The underlying semantic space of the user interface consists of a collection of papers from the three most recent ACM SIGCHI conference proceedings, visualised as a virtual reality network. This network was automatically constructed based on semantic similarities derived from latent semantic analysis. We studied die search strategies and general preferences of eleven subjects who used this system to find papers on various topics. The study has led to a number of interesting findings, which should be valuable for designers and evaluators of 3D user interfaces. The results highlight the importance of structural elements in the design of a semantically based user interface, because search strategies of users relied heavily on these mechanisms in the design. The results of this study also demonstrate that...
46129433
Behavioural Patterns of Collaborative Writing with Hypertext - A State Transition Approach
This study investigates behavioural patterns of collaborative writing with a hypertext system by using a state-transition approach. State-transition models are empirically developed for capturing the dynamic nature of collaborative writing. Users were frequently engaged in tasks such as exploration, organization, and editing, whereas the use of collaborative support functions was transient in nature. The study shows that state-transition analysis is an important approach to task analysis, requirements engineering, and human-computer interaction studies. This study has produced some valuable experiences and lessons for researchers and practitioners in collaborative writing.
2887282
Rat Genome Database (RGD): mapping disease onto the genome
The Rat Genome Database (RGD, http://rgd.mcw.edu) is an NIH-funded project whose stated mission is 'to collect, consolidate and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community'. In a collaboration between the Bioinformatics Research Center at the Medical College of Wisconsin, the Jackson Laboratory and the National Center for Biotechnology Information, RGD has been created to meet these stated aims. The rat is uniquely suited to its role as a model of human disease and the primary focus of RGD is to aid researchers in their study of the rat and in applying their results to studies in a wider context. In support of this we have integrated a large amount of rat genetic and genomic resources in RGD and these are constantly being expanded through ongoing literature and bulk dataset curation. RGD version 2.0, released in June 2001, includes curated data on rat genes, quantitative trait loci (QTL), microsatellite markers and rat strains used in genetic and genomic research. VCMap, a dynamic sequence-based homology tool was introduced, and allows researchers of rat, mouse and human to view mapped genes and sequences and their locations in the other two organisms, an essential tool for comparative genomics. In addition, RGD provides tools for gene prediction, radiation hybrid mapping, polymorphic marker selection and more. Future developments will include the introduction of disease-based curation expanding the curated information to cover popular disease systems studied in the rat. This will be integrated with the emerging rat genomic sequence and annotation pipelines to provide a high-quality disease-centric resource, applicable to human and mouse via comparative tools such as VCMap. RGD has a defined community outreach focus with a Visiting Scientist program and the Rat Community Forum, a web-based forum for rat researchers and others interested in using the rat as an experimental model. Thus, RGD is not only a valuable resource for those working with the rat but also for researchers in other model organisms wishing to harness the existing genetic and physiological data available in the rat to complement their own work.
14219803
A new method to measure the semantic similarity of GO terms
MOTIVATION
Although controlled biochemical or biological vocabularies, such as Gene Ontology (GO) (http://www.geneontology.org), address the need for consistent descriptions of genes in different data sources, there is still no effective method to determine the functional similarities of genes based on gene annotation information from heterogeneous data sources.


RESULTS
To address this critical need, we proposed a novel method to encode a GO term's semantics (biological meanings) into a numeric value by aggregating the semantic contributions of their ancestor terms (including this specific term) in the GO graph and, in turn, designed an algorithm to measure the semantic similarity of GO terms. Based on the semantic similarities of GO terms used for gene annotation, we designed a new algorithm to measure the functional similarity of genes. The results of using our algorithm to measure the functional similarities of genes in pathways retrieved from the saccharomyces genome database (SGD), and the outcomes of clustering these genes based on the similarity values obtained by our algorithm are shown to be consistent with human perspectives. Furthermore, we developed a set of online tools for gene similarity measurement and knowledge discovery.


AVAILABILITY
The online tools are available at: http://bioinformatics.clemson.edu/G-SESAME.


SUPPLEMENTARY INFORMATION
http://bioinformatics.clemson.edu/Publication/Supplement/gsp.htm.
19946044
On edge-Hamiltonian property of Cayley graphs
Abstract Let G be a group generated by X . A Cayley graph over G is defined as a graph G ( X ) whose vertex set is G and whose edge set consists of all unordered pairs [ a,b ] with a , b ϵ G and a -1 b ϵ X ∩ X -1 , where X -1 denotes the set { x -1 ∣ x ϵ X }. When X is a minimal generating set or each element of X is of even order, it can be shown that G ( X ) is Hamiltonian if it is edge-Hamiltonian. Hence every Cayley graph of order a power of 2 is edge-Hamiltonian.
17555851
Sensor Transforms for Invariant Image Enhancement
The invariant image [1,2]formed from an RGB image taken under light that can be approximated as Planckian solves the colour constancy problem at a single pixel. The invariant is a very useful tool for possible use in a large number of computer vision problems,such as removal of shadows from images [3].This image is formed by projecting log-log chromaticity coordinates into a 1D direction determined by a calibration of the imaging camera. The invariant can be formed whether or not gammacorrection is applied to images and thus can work for ordinary webcam images,for example,once a self-calibration is carried out [3].As such,the invariant image is an important new mechanism for image understanding.Since the resulting greyscale image is approximately independent of illumination,it is impervious to lighting change and hence to the presence of shadows.However,in forming the invariant image,it can sometimes happen that shadows are not completely removed.Here,we consider the problem of simple matrixing of sensor values so that the resulting invariant image is improved.To do so,we consider the calibration images and apply an optimization routine for establishing a 3 x 3 matrix to apply to the sensors, prior to forming the invariant,with an eye to improving lighting invariance.We find that an optimization does indeed improve the invariant.The resulting image generally has smaller entropy value because the invariant value is smoothed out across former shadow boundaries;thus the new invariant more smoothly captures the underlying intrinsic reflectance properties in the scene.
15112267
Evaluation of 3D face analysis and synthesis techniques
The reconstruction of 3D face models is mostly achieved by using 2D images. We compare the strengths and weaknesses of different image processing techniques for 3D face generation. It is anticipated that the optimal solution will be applied in the future for 3D face analysis and synthesis. As approaches to 3D face modelling, the paper presents: binocular stereo, using a stereo correspondence algorithm or manual triangulation; orthogonal views; photometric stereo. Photometric stereo and orthogonal views seem to provide the best rendering while keeping a reasonable time efficiency, implementation difficulty and cumbersomeness. However, 3D face acquisition techniques have not closed the gap between accuracy and cumbersomeness