Matching Items (458)
Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval
Description
Background
Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.
Results
In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.
Conclusions
We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.
Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.
Results
In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.
Conclusions
We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.
ContributorsYuan, Lei (Author) / Woodard, Alexander (Author) / Ji, Shuiwang (Author) / Jiang, Yuan (Author) / Zhou, Zhi-Hua (Author) / Kumar, Sudhir (Author) / Ye, Jieping (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / Ira A. Fulton Schools of Engineering (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2012-05-23
ContributorsMayer, Gary R. (Author) / Sarjoughian, Hessam S. (Author) / Allen, Eowyn K. (Author) / Falconer, Steven E. (Author) / Barton, C. Michael (Author)
Created2006
Description
Invited presentation for "Next Generation Simulations of Human-Environmental Interactions" sponsored by the Santa Fe Institute and the University of Arizona, Tucson, 12-14 December, 2005.
ContributorsSarjoughian, Hessam S. (Author)
Created2005
Description
Invited paper presented at the Workshop on Aspects of Social and Socio-Environmental Dynamics, Arizona State University, January 2007.
ContributorsSarjoughian, Hessam S. (Author) / Barton, C. Michael (Author)
Created2007
Description
Invited presentation for "Next Generation Simulations of Human-Environmental Interactions," sponsored by the Santa Fe Institute and the University of Arizona, Tucson, 12-14 December, 2005.
ContributorsBarton, C. Michael (Author) / Sarjoughian, Hessam S. (Author) / Falconer, Steven E. (Contributor)
Created2005
ContributorsBergin, Sean M. (Author) / Ullah, Isaac I. T., 1979- (Author) / Barton, C. Michael (Author) / Mayer, Gary R. (Author) / Sarjoughian, Hessam S. (Author)
Created2010
ContributorsBarton, C. Michael (Author) / Ullah, Isaac I. T., 1979- (Author) / Mayer, Gary R. (Author) / Sarjoughian, Hessam S. (Author) / Bergin, Sean M. (Author) / Miller, Alexandra E. (Author) / Mitasova, H. (Author)
Created2010
Description
Internet of Things (IoT) is emerging as part of the infrastructures for advancing a large variety of applications involving connections of many intelligent devices, leading to smart communities. Due to the severe limitation of the computing resources of IoT devices, it is common to offload tasks of various applications requiring substantial computing resources to computing systems with sufficient computing resources, such as servers, cloud systems, and/or data centers for processing. However, this offloading method suffers from both high latency and network congestion in the IoT infrastructures.
Recently edge computing has emerged to reduce the negative impacts of tasks offloading to remote computing systems. As edge computing is in close proximity to IoT devices, it can reduce the latency of task offloading and reduce network congestion. Yet, edge computing has its drawbacks, such as the limited computing resources of some edge computing devices and the unbalanced loads among these devices. In order to effectively explore the potential of edge computing to support IoT applications, it is necessary to have efficient task management and load balancing in edge computing networks.
In this dissertation research, an approach is presented to periodically distributing tasks within the edge computing network while satisfying the quality-of-service (QoS) requirements of tasks. The QoS requirements include task completion deadline and security requirement. The approach aims to maximize the number of tasks that can be accommodated in the edge computing network, with consideration of tasks’ priorities. The goal is achieved through the joint optimization of the computing resource allocation and network bandwidth provisioning. Evaluation results show the improvement of the approach in increasing the number of tasks that can be accommodated in the edge computing network and the efficiency in resource utilization.
Recently edge computing has emerged to reduce the negative impacts of tasks offloading to remote computing systems. As edge computing is in close proximity to IoT devices, it can reduce the latency of task offloading and reduce network congestion. Yet, edge computing has its drawbacks, such as the limited computing resources of some edge computing devices and the unbalanced loads among these devices. In order to effectively explore the potential of edge computing to support IoT applications, it is necessary to have efficient task management and load balancing in edge computing networks.
In this dissertation research, an approach is presented to periodically distributing tasks within the edge computing network while satisfying the quality-of-service (QoS) requirements of tasks. The QoS requirements include task completion deadline and security requirement. The approach aims to maximize the number of tasks that can be accommodated in the edge computing network, with consideration of tasks’ priorities. The goal is achieved through the joint optimization of the computing resource allocation and network bandwidth provisioning. Evaluation results show the improvement of the approach in increasing the number of tasks that can be accommodated in the edge computing network and the efficiency in resource utilization.
ContributorsSong, Yaozhong (Author) / Yau, Sik-Sang (Thesis advisor) / Huang, Dijiang (Committee member) / Sarjoughian, Hessam S. (Committee member) / Zhang, Yanchao (Committee member) / Arizona State University (Publisher)
Created2018
Description
In recent years, the food, energy, and water (FEW) nexus has become a topic of considerable importance and has spurred research in many scientific and technical fields. This increased interest stems from the high level, and broad area, of impact that could occur in the long term if the interactions between these complex FEW sectors are incorrectly or only partially defined. For this reason, a significant amount of interdisciplinary collaboration is needed to accurately define these interactions and produce viable solutions to help sustain and secure resources within these sectors. Providing tools that effectively promote interdisciplinary collaboration would allow for the development of a better understanding of FEW nexus interactions, support FEW policy-making under uncertainty, facilitate identification of critical design requirements for FEW visualizations, and encourage proactive FEW visualization design.
The goal of this research will be the completion of 3 primary objectives: (i) specify visualization design requirements relating to the FEW nexus; (ii) develop visualization approaches for the FEW nexus; and (iii) provide a comparison of current FEW visualization approaches against the proposed visualization approach. These objectives will be accomplished by reviewing graph-based visualization, network evolution, and visual analysis of volume data tasks, discussion with domain experts, examination of currently used visualization methods in FEW research, and conduction of a user study. This will provide a more thorough and representative depiction of the FEW nexus, as well as a basis for further research in the area of FEW visualization. This research will enhance collaboration between policymakers and domain experts in an attempt to encourage in-depth nexus research that will help support informed policy-making and promote future resource security.
The goal of this research will be the completion of 3 primary objectives: (i) specify visualization design requirements relating to the FEW nexus; (ii) develop visualization approaches for the FEW nexus; and (iii) provide a comparison of current FEW visualization approaches against the proposed visualization approach. These objectives will be accomplished by reviewing graph-based visualization, network evolution, and visual analysis of volume data tasks, discussion with domain experts, examination of currently used visualization methods in FEW research, and conduction of a user study. This will provide a more thorough and representative depiction of the FEW nexus, as well as a basis for further research in the area of FEW visualization. This research will enhance collaboration between policymakers and domain experts in an attempt to encourage in-depth nexus research that will help support informed policy-making and promote future resource security.
ContributorsMathis, Brandon (Author) / Maciejewski, Ross (Thesis advisor) / Mascaro, Giuseppe (Committee member) / Sarjoughian, Hessam S. (Committee member) / Arizona State University (Publisher)
Created2019
Description
One of the main goals of computer architecture design is to improve performance without much increase in the power consumption. It cannot be achieved by adding increasingly complex intelligent schemes in the hardware, since they will become increasingly less power-efficient. Therefore, parallelism comes up as the solution. In fact, the irrevocable trend of computer design in near future is still to keep increasing the number of cores while reducing the operating frequency. However, it is not easy to scale number of cores. One important challenge is that existing cores consume too much power. Another challenge is that cache-based memory hierarchy poses a serious limitation due to the rapidly increasing demand of area and power for coherence maintenance.
In this dissertation, opportunities to resolve the aforementioned issues were explored in two aspects.
Firstly, the possibility of removing hardware cache altogether, and replacing it with scratchpad memory with software management was explored. Scratchpad memory consumes much less power than caches. However, as data management logic is completely shifted to Software, how to reduce software overhead is challenging. This thesis presents techniques to manage scratchpad memory judiciously by exploiting application semantics and knowledge of data access patterns, thereby enabling optimization of data movement across the memory hierarchy. Experimental results show that the optimization was able to reduce stack data management overhead by 13X, produce better code mapping in more than 80% of the case, and improve performance by 83% in heap management.
Secondly, the possibility of using software branch hinting to replace hardware branch prediction to completely eliminate power consumption on corresponding hardware components was explored. As branch predictor is removed from hardware, software logic is responsible for reducing branch penalty. Techniques to minimize the branch penalty by optimizing branch hint placement were proposed, which can reduce branch penalty by 35.4% over the state-of-the-art.
In this dissertation, opportunities to resolve the aforementioned issues were explored in two aspects.
Firstly, the possibility of removing hardware cache altogether, and replacing it with scratchpad memory with software management was explored. Scratchpad memory consumes much less power than caches. However, as data management logic is completely shifted to Software, how to reduce software overhead is challenging. This thesis presents techniques to manage scratchpad memory judiciously by exploiting application semantics and knowledge of data access patterns, thereby enabling optimization of data movement across the memory hierarchy. Experimental results show that the optimization was able to reduce stack data management overhead by 13X, produce better code mapping in more than 80% of the case, and improve performance by 83% in heap management.
Secondly, the possibility of using software branch hinting to replace hardware branch prediction to completely eliminate power consumption on corresponding hardware components was explored. As branch predictor is removed from hardware, software logic is responsible for reducing branch penalty. Techniques to minimize the branch penalty by optimizing branch hint placement were proposed, which can reduce branch penalty by 35.4% over the state-of-the-art.
ContributorsLu, Jing (Author) / Shrivastava, Aviral (Thesis advisor) / Sarjoughian, Hessam S. (Committee member) / Wu, Carole-Jean (Committee member) / Doupe, Adam (Committee member) / Arizona State University (Publisher)
Created2019