Pub Date : 2016-04-19DOI: 10.1109/PACIFICVIS.2016.7465282
Chien-Hsin Hsueh, J. Chu, K. Ma, Joyce Ma, Jennifer Frazier
We share our challenges and lessons learned in designing our exhibit prototype that encourages museum visitors to learn about marine animal behaviors through interactive visualization and data exploration. Our intent is to have visitors draw comparisons between animal behaviors, similarly to how scientists would, to make insights and discoveries. In our efforts, we have designed a set of visual encodings around the Tagging of Pelagic Predator (TOPP) data set to create the appropriate abstractions of this rich and complex field data. We have incorporated Multiple External Representations (MERs) and tangible user interfaces (TUIs) to provide a complementary representation of the data and promote self-learning. Through the formative evaluation, we can identify a few strengths and weaknesses of our prototype design. Our evaluation results suggest that we are progressing in the right direction - we observed the public making some comparisons and inferences - but still require further design iterations to improve our visualization exhibit.
我们在设计展览原型时分享我们的挑战和经验教训，鼓励博物馆游客通过交互式可视化和数据探索了解海洋动物的行为。我们的目的是让参观者对动物的行为进行比较，就像科学家一样，从而获得见解和发现。在我们的努力下，我们设计了一套可视化编码，围绕着标签的远洋捕食者(TOPP)数据集来创建这个丰富而复杂的领域数据的适当抽象。我们整合了多个外部表示(Multiple External representation, MERs)和有形用户界面(tangible user interface, tui)，以提供数据的补充表示并促进自我学习。通过形成性评估，我们可以识别出原型设计的一些优点和缺点。我们的评估结果表明，我们正朝着正确的方向前进——我们观察到公众做出了一些比较和推断——但仍需要进一步的设计迭代来改进我们的可视化展示。
{"title":"Fostering comparisons: Designing an interactive exhibit that visualizes marine animal behaviors","authors":"Chien-Hsin Hsueh, J. Chu, K. Ma, Joyce Ma, Jennifer Frazier","doi":"10.1109/PACIFICVIS.2016.7465282","DOIUrl":"https://doi.org/10.1109/PACIFICVIS.2016.7465282","url":null,"abstract":"We share our challenges and lessons learned in designing our exhibit prototype that encourages museum visitors to learn about marine animal behaviors through interactive visualization and data exploration. Our intent is to have visitors draw comparisons between animal behaviors, similarly to how scientists would, to make insights and discoveries. In our efforts, we have designed a set of visual encodings around the Tagging of Pelagic Predator (TOPP) data set to create the appropriate abstractions of this rich and complex field data. We have incorporated Multiple External Representations (MERs) and tangible user interfaces (TUIs) to provide a complementary representation of the data and promote self-learning. Through the formative evaluation, we can identify a few strengths and weaknesses of our prototype design. Our evaluation results suggest that we are progressing in the right direction - we observed the public making some comparisons and inferences - but still require further design iterations to improve our visualization exhibit.","PeriodicalId":129600,"journal":{"name":"2016 IEEE Pacific Visualization Symposium (PacificVis)","volume":"192 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121072800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-19DOI: 10.1109/PACIFICVIS.2016.7465274
Chien-Hsin Hsueh, Jia-Kai Chou, K. Ma
While the assessment of using motion in visualizations has been polarized, we conjecture that motion may be more effective in comparative visualizations if applied properly, especially when dealing with large amounts of multi-dimensional data. We have designed visualizations to represent driver behaviors. A series of user studies have been conducted to verify if adding motion to the static visualization can help users make comparisons and separate drastically different behaviors. Results show that adding motion indeed leads to shorter completion time and less cognitive workload.
{"title":"A study of using motion for comparative visualization","authors":"Chien-Hsin Hsueh, Jia-Kai Chou, K. Ma","doi":"10.1109/PACIFICVIS.2016.7465274","DOIUrl":"https://doi.org/10.1109/PACIFICVIS.2016.7465274","url":null,"abstract":"While the assessment of using motion in visualizations has been polarized, we conjecture that motion may be more effective in comparative visualizations if applied properly, especially when dealing with large amounts of multi-dimensional data. We have designed visualizations to represent driver behaviors. A series of user studies have been conducted to verify if adding motion to the static visualization can help users make comparisons and separate drastically different behaviors. Results show that adding motion indeed leads to shorter completion time and less cognitive workload.","PeriodicalId":129600,"journal":{"name":"2016 IEEE Pacific Visualization Symposium (PacificVis)","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125049488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-19DOI: 10.1109/PACIFICVIS.2016.7465250
A. Preston, Ramyar Ghods, Jingrong Xie, F. Sauer, Nick Leaf, K. Ma, Esteban Rangel, E. Kovacs, K. Heitmann, S. Habib
Cosmological simulations produce a multitude of data types whose large scale makes them difficult to thoroughly explore in an interactive setting. One aspect of particular interest to scientists is the evolution of groups of dark matter particles, or "halos," described by merger trees. However, in order to fully understand subtleties in the merger trees, other data types derived from the simulation must be incorporated as well. In this work, we develop a novel interactive linked-view visualization system that focuses on simultaneously exploring dark matter halos, their hierarchical evolution, corresponding particle data, and other quantitative information. We employ a parallel remote renderer and a local merger tree selection tool so that users can analyze large data sets interactively. This allows scientists to assess their simulation code, understand inconsistencies in extracted data, and intuitively understand simulation behavior on all scales. We demonstrate the effectiveness of our system through a set of case studies on large-scale cosmological data from the HACC (Hardware/Hybrid Accelerated Cosmology Code) simulation framework.
{"title":"An integrated visualization system for interactive analysis of large, heterogeneous cosmology data","authors":"A. Preston, Ramyar Ghods, Jingrong Xie, F. Sauer, Nick Leaf, K. Ma, Esteban Rangel, E. Kovacs, K. Heitmann, S. Habib","doi":"10.1109/PACIFICVIS.2016.7465250","DOIUrl":"https://doi.org/10.1109/PACIFICVIS.2016.7465250","url":null,"abstract":"Cosmological simulations produce a multitude of data types whose large scale makes them difficult to thoroughly explore in an interactive setting. One aspect of particular interest to scientists is the evolution of groups of dark matter particles, or \"halos,\" described by merger trees. However, in order to fully understand subtleties in the merger trees, other data types derived from the simulation must be incorporated as well. In this work, we develop a novel interactive linked-view visualization system that focuses on simultaneously exploring dark matter halos, their hierarchical evolution, corresponding particle data, and other quantitative information. We employ a parallel remote renderer and a local merger tree selection tool so that users can analyze large data sets interactively. This allows scientists to assess their simulation code, understand inconsistencies in extracted data, and intuitively understand simulation behavior on all scales. We demonstrate the effectiveness of our system through a set of case studies on large-scale cosmological data from the HACC (Hardware/Hybrid Accelerated Cosmology Code) simulation framework.","PeriodicalId":129600,"journal":{"name":"2016 IEEE Pacific Visualization Symposium (PacificVis)","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131518004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-19DOI: 10.1109/PACIFICVIS.2016.7465249
Rickard Englund, S. Kottravel, T. Ropinski
User evaluations have gained increasing importance in visualization research over the past years, as in many cases these evaluations are the only way to support the claims made by visualization researchers. Unfortunately, recent literature reviews show that in comparison to algorithmic performance evaluations, the number of user evaluations is still very low. Reasons for this are the required amount of time to conduct such studies together with the difficulties involved in participant recruitment and result reporting. While it could be shown that the quality of evaluation results and the simplified participant recruitment of crowdsourcing platforms makes this technology a viable alternative to lab experiments when evaluating visualizations, the time for conducting and reporting such evaluations is still very high. In this paper, we propose a software system, which integrates the conduction, the analysis and the reporting of crowdsourced user evaluations directly into the scientific visualization development process. With the proposed system, researchers can conduct and analyze quantitative evaluations on a large scale through an evaluation-centric user interface with only a few mouse clicks. Thus, it becomes possible to perform iterative evaluations during algorithm design, which potentially leads to better results, as compared to the time consuming user evaluations traditionally conducted at the end of the design process. Furthermore, the system is built around a centralized database, which supports an easy reuse of old evaluation designs and the reproduction of old evaluations with new or additional stimuli, which are both driving challenges in scientific visualization research. We will describe the system's design and the considerations made during the design process, and demonstrate the system by conducting three user evaluations, all of which have been published before in the visualization literature.
{"title":"A crowdsourcing system for integrated and reproducible evaluation in scientific visualization","authors":"Rickard Englund, S. Kottravel, T. Ropinski","doi":"10.1109/PACIFICVIS.2016.7465249","DOIUrl":"https://doi.org/10.1109/PACIFICVIS.2016.7465249","url":null,"abstract":"User evaluations have gained increasing importance in visualization research over the past years, as in many cases these evaluations are the only way to support the claims made by visualization researchers. Unfortunately, recent literature reviews show that in comparison to algorithmic performance evaluations, the number of user evaluations is still very low. Reasons for this are the required amount of time to conduct such studies together with the difficulties involved in participant recruitment and result reporting. While it could be shown that the quality of evaluation results and the simplified participant recruitment of crowdsourcing platforms makes this technology a viable alternative to lab experiments when evaluating visualizations, the time for conducting and reporting such evaluations is still very high. In this paper, we propose a software system, which integrates the conduction, the analysis and the reporting of crowdsourced user evaluations directly into the scientific visualization development process. With the proposed system, researchers can conduct and analyze quantitative evaluations on a large scale through an evaluation-centric user interface with only a few mouse clicks. Thus, it becomes possible to perform iterative evaluations during algorithm design, which potentially leads to better results, as compared to the time consuming user evaluations traditionally conducted at the end of the design process. Furthermore, the system is built around a centralized database, which supports an easy reuse of old evaluation designs and the reproduction of old evaluations with new or additional stimuli, which are both driving challenges in scientific visualization research. We will describe the system's design and the considerations made during the design process, and demonstrate the system by conducting three user evaluations, all of which have been published before in the visualization literature.","PeriodicalId":129600,"journal":{"name":"2016 IEEE Pacific Visualization Symposium (PacificVis)","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116922094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-19DOI: 10.1109/PACIFICVIS.2016.7465279
Tsai-Ling Fung, Jia-Kai Chou, K. Ma
This paper presents a comparative study on personal visualizations of bibliographic data. We consider three designs for egocentric visualization: node-link diagrams, adjacency matrices, and botanical trees to depict one's academic career in terms of his/her publication records. Case studies are conducted to compare the effectiveness of resulting visualizations for conveying particular aspect of a researcher's bibliographic records. Based on our study, we find that node-link diagrams are better at revealing the overall distribution of certain attributes; adjacency matrices can convey more information with less clutter; and botanical trees are visually attractive and provide the best at a glance characterization of the mapped data, but mapping data to tree features must be carefully done to derive expressive visualization.
{"title":"A design study of personal bibliographic data visualization","authors":"Tsai-Ling Fung, Jia-Kai Chou, K. Ma","doi":"10.1109/PACIFICVIS.2016.7465279","DOIUrl":"https://doi.org/10.1109/PACIFICVIS.2016.7465279","url":null,"abstract":"This paper presents a comparative study on personal visualizations of bibliographic data. We consider three designs for egocentric visualization: node-link diagrams, adjacency matrices, and botanical trees to depict one's academic career in terms of his/her publication records. Case studies are conducted to compare the effectiveness of resulting visualizations for conveying particular aspect of a researcher's bibliographic records. Based on our study, we find that node-link diagrams are better at revealing the overall distribution of certain attributes; adjacency matrices can convey more information with less clutter; and botanical trees are visually attractive and provide the best at a glance characterization of the mapped data, but mapping data to tree features must be carefully done to derive expressive visualization.","PeriodicalId":129600,"journal":{"name":"2016 IEEE Pacific Visualization Symposium (PacificVis)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122362893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-19DOI: 10.1109/PACIFICVIS.2016.7465255
A. Brambilla, Paolo Angelelli, Ø. Andreassen, H. Hauser
Comparing time surfaces at different integration time points, or from different seeding areas, can provide valuable insight into transport phenomena of fluid flows. Such a comparative study is challenging due to the often convoluted shapes of these surfaces. We propose a new approach for comparative flow visualization based on time surfaces, which exploits the idea of embedding the surfaces in a carefully designed, reformed 2D visualization space. Such an embedding enables new opportunities for comparative flow visualization. We present three different strategies for comparative flow visualization that take advantage of the reformation. By reforming the time surfaces, we not only mitigate occlusion issues, but we can devote also the third dimension of the visualization space to the comparative aspects of the visualization. Our approach is effective in a variety of flow study cases. The direct comparison of individual time surfaces reveals small scale differences and fine details about the fluid's motion. The concurrent study of multiple surface families enables the identification and the comparison of the most prominent motion patterns. This work was developed in close collaboration with an expert in fluid dynamics, who assessed the potential usefulness of this approach in his field.
{"title":"Comparative visualization of multiple time surfaces by planar surface reformation","authors":"A. Brambilla, Paolo Angelelli, Ø. Andreassen, H. Hauser","doi":"10.1109/PACIFICVIS.2016.7465255","DOIUrl":"https://doi.org/10.1109/PACIFICVIS.2016.7465255","url":null,"abstract":"Comparing time surfaces at different integration time points, or from different seeding areas, can provide valuable insight into transport phenomena of fluid flows. Such a comparative study is challenging due to the often convoluted shapes of these surfaces. We propose a new approach for comparative flow visualization based on time surfaces, which exploits the idea of embedding the surfaces in a carefully designed, reformed 2D visualization space. Such an embedding enables new opportunities for comparative flow visualization. We present three different strategies for comparative flow visualization that take advantage of the reformation. By reforming the time surfaces, we not only mitigate occlusion issues, but we can devote also the third dimension of the visualization space to the comparative aspects of the visualization. Our approach is effective in a variety of flow study cases. The direct comparison of individual time surfaces reveals small scale differences and fine details about the fluid's motion. The concurrent study of multiple surface families enables the identification and the comparison of the most prominent motion patterns. This work was developed in close collaboration with an expert in fluid dynamics, who assessed the potential usefulness of this approach in his field.","PeriodicalId":129600,"journal":{"name":"2016 IEEE Pacific Visualization Symposium (PacificVis)","volume":"106 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123329517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-19DOI: 10.1109/PACIFICVIS.2016.7465263
Paul van der Corput, J. V. Wijk
We present a new approach for the analysis of large image collections. We argue that categorization plays an important role in this process, not only to label images as end result, but also during exploration. Furthermore, to increase the effectiveness and efficiency of the categorization process we enable the use of all available metadata, treated as multivariate data. We identified images, attributes, and categories as important aspects and integrated these in a system called ICLIC. The system consists of four views that are connected by the selection of images, which is a central action in the approach. By using a minimalist interface with only standard metaphors, users are enabled to use the system in short time. The system enables complex queries in a natural way, and it can deal with collections containing more than 100,000 images and more than 1,000 metadata attributes. This was confirmed by two evaluation cycles with domain experts.
{"title":"ICLIC: Interactive categorization of large image collections","authors":"Paul van der Corput, J. V. Wijk","doi":"10.1109/PACIFICVIS.2016.7465263","DOIUrl":"https://doi.org/10.1109/PACIFICVIS.2016.7465263","url":null,"abstract":"We present a new approach for the analysis of large image collections. We argue that categorization plays an important role in this process, not only to label images as end result, but also during exploration. Furthermore, to increase the effectiveness and efficiency of the categorization process we enable the use of all available metadata, treated as multivariate data. We identified images, attributes, and categories as important aspects and integrated these in a system called ICLIC. The system consists of four views that are connected by the selection of images, which is a central action in the approach. By using a minimalist interface with only standard metaphors, users are enabled to use the system in short time. The system enables complex queries in a natural way, and it can deal with collections containing more than 100,000 images and more than 1,000 metadata attributes. This was confirmed by two evaluation cycles with domain experts.","PeriodicalId":129600,"journal":{"name":"2016 IEEE Pacific Visualization Symposium (PacificVis)","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122605581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-19DOI: 10.1109/PACIFICVIS.2016.7465248
Panpan Xu, Nan Cao, Huamin Qu, J. Stasko
A bipartite graph models the relation between two different types of entities. It is applicable, for example, to describe persons' affiliations to different social groups or their association with subjects such as topics of interest. In these applications, it is important to understand the connectivity patterns among the entities in the bipartite graph. For the example of a bipartite relation between persons and their topics of interest, people may form groups based on their common interests, and the topics also can be grouped or categorized based on the interested audiences. Co-clustering methods can identify such connectivity patterns and find clusters within the two types of entities simultaneously. In this paper, we propose an interactive visualization design that incorporates co-clustering methods to facilitate the identification of node clusters formed by their common connections in a bipartite graph. Besides highlighting the automatically detected node clusters and the connections among them, the visual interface also provides visual cues for evaluating the homogeneity of the bipartite connections in a cluster, identifying potential outliers, and analyzing the correlation of node attributes with the cluster structure. The interactive visual interface allows users to flexibly adjust the node grouping to incorporate their prior knowledge of the domain, either by direct manipulation (i.e., splitting and merging the clusters), or by providing explicit feedback on the cluster quality, based on which the system will learn a parametrization of the co-clustering algorithm to better align with the users' notion of node similarity. To demonstrate the utility of the system, we present two example usage scenarios on real world datasets.
{"title":"Interactive visual co-cluster analysis of bipartite graphs","authors":"Panpan Xu, Nan Cao, Huamin Qu, J. Stasko","doi":"10.1109/PACIFICVIS.2016.7465248","DOIUrl":"https://doi.org/10.1109/PACIFICVIS.2016.7465248","url":null,"abstract":"A bipartite graph models the relation between two different types of entities. It is applicable, for example, to describe persons' affiliations to different social groups or their association with subjects such as topics of interest. In these applications, it is important to understand the connectivity patterns among the entities in the bipartite graph. For the example of a bipartite relation between persons and their topics of interest, people may form groups based on their common interests, and the topics also can be grouped or categorized based on the interested audiences. Co-clustering methods can identify such connectivity patterns and find clusters within the two types of entities simultaneously. In this paper, we propose an interactive visualization design that incorporates co-clustering methods to facilitate the identification of node clusters formed by their common connections in a bipartite graph. Besides highlighting the automatically detected node clusters and the connections among them, the visual interface also provides visual cues for evaluating the homogeneity of the bipartite connections in a cluster, identifying potential outliers, and analyzing the correlation of node attributes with the cluster structure. The interactive visual interface allows users to flexibly adjust the node grouping to incorporate their prior knowledge of the domain, either by direct manipulation (i.e., splitting and merging the clusters), or by providing explicit feedback on the cluster quality, based on which the system will learn a parametrization of the co-clustering algorithm to better align with the users' notion of node similarity. To demonstrate the utility of the system, we present two example usage scenarios on real world datasets.","PeriodicalId":129600,"journal":{"name":"2016 IEEE Pacific Visualization Symposium (PacificVis)","volume":"70 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122624835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-19DOI: 10.1109/PACIFICVIS.2016.7465257
Talha Bin Masood, V. Natarajan
Study of cavities and channels in molecular structure is a crucial step in understanding the function of biomolecules. Current tools and techniques for extracting these structural features are sensitive to uncertainties in atomic position and radii. In this paper, we study the problem of cavity extraction in biomolecules while taking into account such uncertainties. We propose an approach that connects user-specified cavities by computing an optimal conduit within the region occupied by the molecule. The conduit is computed using a topological representation of the occupied and empty regions and is guaranteed to satisfy well defined geometric optimality criteria. Visualization of the set of all cavities with multiple linked views serves as a useful interface for interactive extraction of stable cavities. We demonstrate the utility of the proposed method in successfully identifying biologically significant pathways between molecular cavities using several case studies.
{"title":"An integrated geometric and topological approach to connecting cavities in biomolecules","authors":"Talha Bin Masood, V. Natarajan","doi":"10.1109/PACIFICVIS.2016.7465257","DOIUrl":"https://doi.org/10.1109/PACIFICVIS.2016.7465257","url":null,"abstract":"Study of cavities and channels in molecular structure is a crucial step in understanding the function of biomolecules. Current tools and techniques for extracting these structural features are sensitive to uncertainties in atomic position and radii. In this paper, we study the problem of cavity extraction in biomolecules while taking into account such uncertainties. We propose an approach that connects user-specified cavities by computing an optimal conduit within the region occupied by the molecule. The conduit is computed using a topological representation of the occupied and empty regions and is guaranteed to satisfy well defined geometric optimality criteria. Visualization of the set of all cavities with multiple linked views serves as a useful interface for interactive extraction of stable cavities. We demonstrate the utility of the proposed method in successfully identifying biologically significant pathways between molecular cavities using several case studies.","PeriodicalId":129600,"journal":{"name":"2016 IEEE Pacific Visualization Symposium (PacificVis)","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115293546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-19DOI: 10.1109/PACIFICVIS.2016.7465247
Hui Zhang, Yiwen Zhong, Jade Jiang
In this paper we present a mathematical knot/braid diagram interface that exploits 3D computer graphics, interactive visualization, and multi-touch technology to enhance one's intuitive experience with mathematical theory of knots. Our interaction model is based on the clever but simple geometric construction named the Reidemeister moves, which allows 3D topological manipulations using rather simple 2D moves. Multi-touch interfaces can provide a natural way for us to interact with the extra degrees of freedom that characterize knots' mathematical, physical, and arithmetic properties. Relative to a specialized mouse-driven interface, the proposed multi-touch interface is easier and more intuitive to learn, and our pilot study shows that knot and braid manipulation with multi-touch is much faster and more efficient. All these combine to show that interactive computer graphics methods and computer interfaces can be used to construct virtual manipulatives and meet the challenge of exploring abstract mathematical worlds.
{"title":"Visualizing knots and braids with touchable 3D manipulatives","authors":"Hui Zhang, Yiwen Zhong, Jade Jiang","doi":"10.1109/PACIFICVIS.2016.7465247","DOIUrl":"https://doi.org/10.1109/PACIFICVIS.2016.7465247","url":null,"abstract":"In this paper we present a mathematical knot/braid diagram interface that exploits 3D computer graphics, interactive visualization, and multi-touch technology to enhance one's intuitive experience with mathematical theory of knots. Our interaction model is based on the clever but simple geometric construction named the Reidemeister moves, which allows 3D topological manipulations using rather simple 2D moves. Multi-touch interfaces can provide a natural way for us to interact with the extra degrees of freedom that characterize knots' mathematical, physical, and arithmetic properties. Relative to a specialized mouse-driven interface, the proposed multi-touch interface is easier and more intuitive to learn, and our pilot study shows that knot and braid manipulation with multi-touch is much faster and more efficient. All these combine to show that interactive computer graphics methods and computer interfaces can be used to construct virtual manipulatives and meet the challenge of exploring abstract mathematical worlds.","PeriodicalId":129600,"journal":{"name":"2016 IEEE Pacific Visualization Symposium (PacificVis)","volume":"100 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130671543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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