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Articles 121 - 150 of 733
Full-Text Articles in Computer Engineering
Mercury Blastn Biosequence Similarity Search System: Technical Reference Guide, Jeremy Buhler
Mercury Blastn Biosequence Similarity Search System: Technical Reference Guide, Jeremy Buhler
All Computer Science and Engineering Research
This guide documents the operation of the Mercury BLASTN system for hardware-accelerated DNA similarity search. It includes detailed information on the syntax and limitations of the system's component commands, as well as a description of the system's hardware platform suitable for administrators who need to maintain a Mercury BLASTN system. Mercury BLASTN is a product of the High Performance COmputational Biology Group at Washington University.
Efficient Deadlock Avoidance For Streaming Computation With Filtering, Jeremy Buhler, Kunal Agrawal, Peng Li, Roger D. Chamberlain
Efficient Deadlock Avoidance For Streaming Computation With Filtering, Jeremy Buhler, Kunal Agrawal, Peng Li, Roger D. Chamberlain
All Computer Science and Engineering Research
In this report, we show that deadlock avoidance for streaming computations with filtering can be performed efficiently for a large class of DAG topologies. We first give efficient algorithms for dummy interval computation in series-parallel DAGs, then generalize our results to a larger graph family, the CS4DAGs, in which every undirected cycle has exactly one source and one sink. Our results show that, for a large set of application topologies that are both intuitively useful and formalizable, the streaming model with filtering can be implemented safely with reasonable compilation overhead.
Hierarchical Scheduling For Multicores With Multilevel Cache Hierarchies, Kunal Agrawal, Jim Sukha
Hierarchical Scheduling For Multicores With Multilevel Cache Hierarchies, Kunal Agrawal, Jim Sukha
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Cache-locality is an important consideration for the performance in multicore systems. In modern and future multicore systems with multilevel cache hierarchies, caches may be arranged in a tree of caches, where a level k cache is shared between Pk processors, called a processor group, and Pk increases with k. In order to get good performance, as much as possible, subcomputations that share more data should execute on processors which share a lower-level cache. Therefore, the number of cache misses in these systems depends on the scheduling decisions, and a scheduler is responsible for not just achieving good load-balance and low …
Near Optimal Rate Selection For Wireless Control Systems, Abusayeed Saifullah, Chengjie Wu, Paras Babu Tiwari, You Xu, Yong Fu, Chenyang Lu, Yixin Chen
Near Optimal Rate Selection For Wireless Control Systems, Abusayeed Saifullah, Chengjie Wu, Paras Babu Tiwari, You Xu, Yong Fu, Chenyang Lu, Yixin Chen
All Computer Science and Engineering Research
With the advent of industrial standards such as WirelessHART, process industries are now gravitating towards wireless control systems. Due to limited bandwidth in a wireless network shared by multiple control loops, it is critical to optimize the overall control performance. In this paper, we address the scheduling-control co-design problem of determining the optimal sampling rates of feedback control loops sharing a WirelessHART network. The objective is to minimize the overall control cost while ensuring that all data flows meet their end-to-end deadlines. The resulting constrained optimization based on existing delay bounds for WirelessHART networks is challenging since it is non-differentiable, …
Distributed Channel Allocation Algorithms For Wireless Sensor Networks, Abusayeed Saifullah, You Xu, Chenyang Lu, Yixin Chen
Distributed Channel Allocation Algorithms For Wireless Sensor Networks, Abusayeed Saifullah, You Xu, Chenyang Lu, Yixin Chen
All Computer Science and Engineering Research
Interference between concurrent transmissions can cause severe performance degradation in wireless sensor networks (WSNs). While multiple channels available in WSN technology such as IEEE 802.15.4 can be exploited to mitigate interference, channel allocation can have a significant impact on the performance of multi-channel communication. This paper proposes a set of distributed algorithms for near-optimal channel allocation in WSNs with theoretical bounds. We first consider the problem of minimizing the number of channels needed to remove interference in a WSN, and propose both receiver-based and link-based distributed channel allocation protocols. For WSNs with an insufficient number of channels, we formulate a …
Feedback Thermal Control Of Real-Time Systems On Multicore Processors, Yong Fu, Nicholas Kottenstette, Chenyang Lu, Xenofon D. Koutsoukos
Feedback Thermal Control Of Real-Time Systems On Multicore Processors, Yong Fu, Nicholas Kottenstette, Chenyang Lu, Xenofon D. Koutsoukos
All Computer Science and Engineering Research
Real-time systems face significant challenges in thermal management with their adoption of modern multicore processors. While earlier research on feedback thermal control has shown promise in dealing with the uncertainties in the thermal characteristics, multicore processors introduce new challenges that cannot be handled by previous solutions designed for single-core processors. Multicore processors require the temperatures and real-time performance of multiple cores to be controlled simultaneously, leading to multi-input-multi-output (MIMO) control problems with inter-core thermal coupling. Furthermore, current Dynamic Voltage and Frequency Scaling (DVFS) mechanisms only support a finite set of states, leading to discrete control variables that cannot be handled …
Energy-Efficient Low Power Listening For Wireless Sensor Networks In Noisy Environments, Mo Sha, Gregory Hackmann, Chenyang Lu
Energy-Efficient Low Power Listening For Wireless Sensor Networks In Noisy Environments, Mo Sha, Gregory Hackmann, Chenyang Lu
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Low Power Listening (LPL) is a common MAC-layer technique for reducing energy consumption in wireless sensor networks, where nodes periodically wake up to sample the wireless channel to detect activity. However, LPL is highly susceptible to false wakeups caused by environmental noise being detected as activity on the channel, causing nodes to spuriously wake up in order to receive nonexistent transmissions. In empirical studies in residential environments, we observe that the false wakeup problem can significantly increase a node's duty cycle, compromising the benefit of LPL. We also find that the energy-level threshold used by the Clear Channel Assessment (CCA) …
2-Edge-Connectivity And 2-Vertex-Connectivity With Fault Containment, Abusayeed Saifullah
2-Edge-Connectivity And 2-Vertex-Connectivity With Fault Containment, Abusayeed Saifullah
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Self-stabilization for non-masking fault-tolerant distributed system has received considerable research interest over the last decade. In this paper, we propose a self-stabilizing algorithm for 2-edge-connectivity and 2-vertex-connectivity of an asynchronous distributed computer network. It is based on a self-stabilizing depth-first search, and is not a composite algorithm in the sense that it is not composed of a number of self-stabilizing algorithms that run concurrently. The time and space complexities of the algorithm are the same as those of the underlying self-stabilizing depth-first search algorithm.
Implementation And Evaluation Of Mixed-Criticality Scheduling Approaches For Periodic Tasks, Huang-Ming Huang, Christopher Gill, Chenyang Lu
Implementation And Evaluation Of Mixed-Criticality Scheduling Approaches For Periodic Tasks, Huang-Ming Huang, Christopher Gill, Chenyang Lu
All Computer Science and Engineering Research
Traditional fixed-priority scheduling analysis for periodic task sets is based on the assumption that all tasks are equally critical to the correct operation of the system. Therefore, every task has to be schedulable under the scheduling policy, and estimates of tasks’ worst case execution times must be conservative in case a task runs longer than is usual. To address the significant under-utilization of a system’s resources under normal operating conditions that can arise from these assumptions, three main approaches have been proposed: priority assignment, period transformation, and zero-slack scheduling. However, to date there has been no quantitative comparison of system …
Generating Muscle Driven Arm Movements Using Reinforcement Learning, Alex S. Broad
Generating Muscle Driven Arm Movements Using Reinforcement Learning, Alex S. Broad
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This project focuses on using Reinforcement Learning to optimize arm dynamics through muscle control for desired trajectories. The goal of this project was to create a tool that can be used to gain a better understanding of the arm’s muscles and collect information that is useful in many other disciplines such as biomechanics, anthropology, medicine and robotics. I developed biologically realistic models of primate arm's using Stanford’s SimTK software, an open-source tool for modeling musculoskeletal structures. I then made use of Differential Dynamic Programming in order to generate novel movements from first principles and optimize motion over a specified trajectory. …
A Survey On Communication Networks In Emergency Warning Systems, Yan Li
A Survey On Communication Networks In Emergency Warning Systems, Yan Li
All Computer Science and Engineering Research
No abstract provided.
End-To-End Communication Delay Analysis In Wirelesshart Networks, Abusayeed Saifullah, You Xu, Chenyang Lu, Yixin Chen
End-To-End Communication Delay Analysis In Wirelesshart Networks, Abusayeed Saifullah, You Xu, Chenyang Lu, Yixin Chen
All Computer Science and Engineering Research
WirelessHART is a new standard specifically designed for real-time and reliable communication between sensor and actuator devices for industrial process monitoring and control applications. End-to-end communication delay analysis for WirelessHART networks is required to determine the schedulability of real-time data flows from sensors to actuators for the purpose of acceptance test or workload adjustment in response to network dynamics. In this paper, we map the scheduling of real-time periodic data flows in a WirelessHART network to real-time multiprocessor scheduling. We then exploit the response time analysis for multiprocessor scheduling and propose a novel method for the delay analysis that establishes …
Results Of An Observational Study On Sketching, Cindy Grimm
Results Of An Observational Study On Sketching, Cindy Grimm
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We present the results of an observational study on sketching. Artists were asked to sketch a small number of objects and comment on how and why they made the marks they did. We summarize these findings, from low-level details on individual marks through the drawing construction order. Based on these observations we provide suggestions for future research directions in 3D sketching.
Flux Balance Analysis Of Dynamic Metabolism In Shewanella Oneidensis Mr-1 Using A Static Optimization Approach, Xueyang Feng, You Xu, Yixin Chen, Yinjie Tang
Flux Balance Analysis Of Dynamic Metabolism In Shewanella Oneidensis Mr-1 Using A Static Optimization Approach, Xueyang Feng, You Xu, Yixin Chen, Yinjie Tang
All Computer Science and Engineering Research
Shewanella bacteria are facultative anaerobes isolated from aquatic and sedimentary environments (Hau and Gralnick 2007) with a broad capacity for reduction of multiple electron receptors (Pinchuk et al. 2009; Serres and Riley 2006), including Fe(III), Mn(IV), sulfur, nitrate, and fumarate. With the accomplishment of complete genome sequencing of several Shewanella bacteria, the general pictures of the carbon metabolism have been revealed (Serres and Riley 2006). metabolism. One of the most physiological methods to decipher the time-variant metabolic regulation is to determine the dynamic distribution of intracellular metabolic fluxes since it reveals the final response of cellular metabolism to genomic, transcriptional …
Webcam Image Alignment, Matthew Klein
Webcam Image Alignment, Matthew Klein
All Computer Science and Engineering Research
No abstract provided.
Real Time Baseball Augmented Reality, Adam Kraft
Real Time Baseball Augmented Reality, Adam Kraft
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As computer hardware becomes increasingly powerful, there is an ongoing trend towards integrating complex, legacy real-time systems using fewer hosts through virtualization. Especially in embedded systems domains such as avionics and automotive engineerin
Multi-Core Real-Time Scheduling For Generalized Parallel Task Models, Abusayeed Saifullah, Kunal Agrawal, Chenyang Lu, Christopher Gill
Multi-Core Real-Time Scheduling For Generalized Parallel Task Models, Abusayeed Saifullah, Kunal Agrawal, Chenyang Lu, Christopher Gill
All Computer Science and Engineering Research
Multi-core processors over a significant performance increase over single-core processors. Therefore, they have the potential to enable computation-intensive real-time applications with stringent timing constraints that cannot be met on traditional single-core processors. However, most results in traditional multiprocessor real-time scheduling are limited to sequential programming models and ignore intra-task parallelism. In this paper, we address the problem of scheduling periodic parallel tasks with implicit deadlines on multi-core processors. We first consider a synchronous task model where each task consists of segments, each segment having an arbitrary number of parallel threads that synchronize at the end of the segment. We propose …
Optimization Of Gene Prediction Via More Accurate Phylogenetic Substitution Models, Ezekiel Maier, Randall H. Brown, Michael R. Brent
Optimization Of Gene Prediction Via More Accurate Phylogenetic Substitution Models, Ezekiel Maier, Randall H. Brown, Michael R. Brent
All Computer Science and Engineering Research
Determining the beginning and end positions of each exon in each protein coding gene within a genome can be difficult because the DNA patterns that signal a gene’s presence have multiple weakly related alternate forms and the DNA fragments that comprise a gene are generally small in comparison to the size of the genome. In response to this challenge, automated gene predictors were created to generate putative gene structures. N SCAN identifies gene structures in a target DNA sequence and can use conservation patterns learned from alignments between a target and one or more informant DNA sequences. N SCAN uses …
Performance Tuning Of Streaming Applications Via Search-Space Decomposition, Shobana Padmanabhan, Roger D. Chamberlain, Yixin Chen
Performance Tuning Of Streaming Applications Via Search-Space Decomposition, Shobana Padmanabhan, Roger D. Chamberlain, Yixin Chen
All Computer Science and Engineering Research
High-performance streaming applications are typically pipelined and deployed on architecturally diverse (hybrid)systems. Developers of such applications are interested in customizing components used, so as to benefit application performance. We present an efficient and automatic technique for design-space exploration of applications in this problem domain. We solve performance tuning as an optimization problem by formulating cost functions using results from queueing theory. This results in a mixed-integer nonlinear optimization problem which is NP-hard. We reduce the search complexity by decomposing the search space. We have developed a domain-specific decomposition technique using topological information of the application embodied in the queueing network …
Global Constructive Optimization Of Vascular Systems, Manfred Georg, Tobias Preusser, Horst K. Hahn
Global Constructive Optimization Of Vascular Systems, Manfred Georg, Tobias Preusser, Horst K. Hahn
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We present a framework for the construction of vascular systems based on optimality principles of theoretical physiology. Given the position and flow distribution of end points of a vascular system, we construct the topology and positions of internal nodes to complete the vascular system in a realistic manner. Optimization is driven by intravascular volume minimization with constraints derived from physiological principles. Direct optimization of a vascular system, including topological changes, is used instead of simulating vessel growth. A good initial topology is found by extracting key information from a previously optimized model with less detail. This technique is used iteratively …
Sorting As A Streaming Application Executing On Chip Multiprocessors, Roger D. Chamberlain, Greg A. Galloway, Mark A. Franklin
Sorting As A Streaming Application Executing On Chip Multiprocessors, Roger D. Chamberlain, Greg A. Galloway, Mark A. Franklin
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Expressing concurrency in applications has always been a difficult and error-prone endeavor, yet effective utilization of multi-core processors requires that the concurrency in applications be understood. One approach to the expression of concurrency is streaming, which has shown real promise as a safe and effective method for many application classes. Here, we express a classic problem, sorting, in the streaming paradigm and explore the implications of various algorithm and architectural design parameters on the performance of the application.
Priority Assignment For Real-Time Flows In Wirelesshart Sensor-Actuator Networks, Abusayeed Saifullah, You Chenyang, Yixin Chen
Priority Assignment For Real-Time Flows In Wirelesshart Sensor-Actuator Networks, Abusayeed Saifullah, You Chenyang, Yixin Chen
All Computer Science and Engineering Research
Recent years have witnessed the adoption of wireless sensor-actuator networks as a communication infrastructure for process control applications. An important enabling technology for industrial process control is WirelessHART, an open wireless sensor-actuator network standard specifically developed for process industries. A key challenge faced byWirelessHART networks is to meet the stringent real-time communication requirements imposed by feedback control systems in process industries. Fixed priority scheduling, a popular scheduling policy in real-time networks, has recently been shown to be an effective real-time transmission scheduling policy in WirelessHART networks. Priority assignment has a major impact on the schedulability of real-time flows in these …
End-To-End Delay Analysis For Fixed Priority Scheduling In Wirelesshart Networks, Abusayeed Saifullah, You Xu, Chenyang Lu, Yixin Chen
End-To-End Delay Analysis For Fixed Priority Scheduling In Wirelesshart Networks, Abusayeed Saifullah, You Xu, Chenyang Lu, Yixin Chen
All Computer Science and Engineering Research
The WirelessHART standard has been specifically designed for real-time communication between sensor and actuator devices for industrial process monitoring and control. End-to-end communication delay analysis for WirelessHART networks is required for acceptance test of real-time data flows from sensors to actuators and for workload adjustment in response to network dynamics. In this paper, we map the scheduling of real-time periodic data flows in a WirelessHART network to real-time multiprocessor scheduling. We, then, exploit the response time analysis for multiprocessor scheduling and propose a novel method for the end-to-end delay analysis of the real-time flows that are scheduled using a fixed …
Split And Merge Functions For Supporting Multiple Processing Pipelines In Mercury Blastn, Jwalant Ahir, Jeremy Buhler, Roger D. Chamberlain
Split And Merge Functions For Supporting Multiple Processing Pipelines In Mercury Blastn, Jwalant Ahir, Jeremy Buhler, Roger D. Chamberlain
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Biosequence similarity search is an important application in computational biology. Mercury BLASTN, an FPGA-based implementation of BLAST for DNA, is one of the alternatives for fast DNA sequence comparison. The re-design of BLAST into a streaming application combined with a high-throughput hardware pipeline have enabled Mercury BLAST to emerge as one of the fastest implementations of bio-sequence similarity search. This performance can be further enhanced by exploiting the data-level parallelism present within the application. Here we present a multiple FPGA-based Mercury BLASTN design in order to double the speed and throughput of DNA sequence computation. This paper describes a dual …
Toward A Two-Tier Clinical Warning System For Hospitalized Patients, Gregory Hackmann, Minmin Chen, Octav Chipara, Chenyang Lu, Yixin Chen, Marin Kollef, Thomas C. Bailey
Toward A Two-Tier Clinical Warning System For Hospitalized Patients, Gregory Hackmann, Minmin Chen, Octav Chipara, Chenyang Lu, Yixin Chen, Marin Kollef, Thomas C. Bailey
All Computer Science and Engineering Research
Clinical study has found early detection and intervention to be essential for preventing clinical deterioration in patients at general hospital units. In this paper, we envision a two-tiered early warning system designed to identify the signs of clinical deterioration and provide early warning of serious clinical events. The first tier of the system automatically identifies patients at risk of clinical deterioration from existing electronic medical record databases. The second tier performs real-time clinical event detection based on real-time vital sign data collected from on-body wireless sensors attached to those high-risk patients. We employ machine-learning techniques to analyze data from both …
Optimal Design-Space Exploration Of Streaming Applications, Shobana Padmanabhan, Yixin Chen, Roger D. Chamberlain
Optimal Design-Space Exploration Of Streaming Applications, Shobana Padmanabhan, Yixin Chen, Roger D. Chamberlain
All Computer Science and Engineering Research
Many embedded and scientific applications are frequently pipelined asynchronously and deployed on architecturally diverse systems to meet performance requirements and resource constraints. We call such pipelined applications streaming applications. Typically, there are several design parameters in the algorithms and architectures used that, when customized, impact the tradeoff between different metrics of application performance as well as resource utilization. Automatic exploration of this design space is the goal of this research. When using architecturally diverse systems to accelerate streaming applications, the design search space is often complex. We present a global optimization framework comprising a novel domain-specific variation of branch-and-bound that …
An Inexpensive Robot Platform For Teleoperation And Experimentation, Daniel A. Lazewatsky, William D. Smart
An Inexpensive Robot Platform For Teleoperation And Experimentation, Daniel A. Lazewatsky, William D. Smart
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Most commercially-available robots are either aimed at the research community, or are designed with a single purpose in mind. The extensive hobbyist community has tended to focus on the hardware and the low-level software aspects. We claim that there is a need for a low-cost, general-purpose robot, accessible to the hobbyist community, with sufficient computation and sensing to run ``research-grade'' software. In this paper, we describe the design and implementation of such a robot. We explicitly outline our design goals, and show how a capable robot can be assembled from off-the-shelf parts, for a modest cost, by a single person …
Against All Probabilities: A Modeling Paradigm For Streaming Applications That Goes Against Common Notions, Rahav Dor
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Hardware and software design requires the right portion of skills and mental faculties. The design of a good system is an exercise in rational thinking, engineering, and art. The design process is further complicated when we aspire to build systems that exploit parallelism or are targeted to be deployed on architecturally diverse computing devices, FPGAs or GPUs to name just a few. The need to develop systems that can take advantage of computing devices beyond general purpose CPUs is real. There are several application domains and research efforts that will simply not be able to adequately perform or yield answers …
Arch: Practical Channel Hopping For Reliable Home-Area Sensor Networks, Mo Sha, Gregory Hackmann, Chenyang Lu
Arch: Practical Channel Hopping For Reliable Home-Area Sensor Networks, Mo Sha, Gregory Hackmann, Chenyang Lu
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Home area networks (HANs) promise to enable sophisticated home automation applications such as smart energy usage and assisted living. However, recent empirical study of HAN reliability in real-world residential environments revealed significant challenges to achieving reliable performance in the face of significant and variable interference from a multitude of coexisting wireless devices. We propose the Adaptive and Robust Channel Hopping (ARCH) protocol: a lightweight receiveroriented protocol which handles the dynamics of residential environments by reactively channel hopping when channel conditions have degraded. ARCH has several key features. First, ARCH is an adaptive protocol that channel-hops based on changes in channel …
Multi-Channel Reliability And Spectrum Usage In Real Homes: Empirical Studies For Home-Area Sensor Networks, Mo Sha, Gregory Hackmann, Chenyang Lu
Multi-Channel Reliability And Spectrum Usage In Real Homes: Empirical Studies For Home-Area Sensor Networks, Mo Sha, Gregory Hackmann, Chenyang Lu
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Home area networks (HANs) consisting of wireless sensors have emerged as the enabling technology for important applications such as smart energy and assisted living. A key challenge faced by HANs is maintaining reliable operation in real-world residential environments. This paper presents two in-depth empirical studies on the wireless channels in real homes. The spectrum study analyzes the spectrum usage in the 2.4 GHz band where wireless sensor networks based on the IEEE 802.15.4 standard must coexist with existing wireless devices. We characterize the ambient wireless environment in six apartments through passive spectrum analysis across the entire 2.4 GHz band over …