## All Computer Science and Engineering Research

#### Research from 2017

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Decoupling Information and Connectivity in Information-Centric Networking
Hila Ben Abraham, Jyoti Parwatikar, John Dehart, Adam Drescher, and Patrick Crowley
Technical Report

Abstract:

This paper introduces and demonstrates the concept of Information-Centric Transport as a mechanism for cleanly decoupling the information plane from the connectivity plane in Information-Centric Networking (ICN) architectures, such as NDN and CICN. These are coupled in today's incarnations of NDN and CICN through the use of forwarding strategy, which is the architectural component for deciding how to forward packets in the presence of either multiple next-hop options or dynamic feedback. As presently designed, forwarding strategy is not sustainable: application developers can only confidently specify strategy if they understand connectivity... Read More

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Underwater Celestial Navigation Using the Polarization of Light Fields, Samuel Bear Powell

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Pricing and Bidding Strategies for Cloud Computing Spot Instances
Jiayi Song and Roch A. Guérin
Conference Paper

Abstract:

We consider a cloud service based on spot instances and explore bidding and pricing strategies aimed at optimizing users' utility and provider's revenue, respectively. Our focus is on jobs that are heterogeneous in both valuation and sensitivity to execution delay. Of particular interest is the impact of correlation in these two dimensions. We characterize optimal bidding and pricing strategies under some simplifying assumptions, and more importantly highlight the impact of correlation in determining the benefits of a spot service over an on-demand service. We also provide a preliminary assessment of... Read More

#### Research from 2016

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In-Network Retransmissions in Named Data Networking
Hila Ben Abraham and Patrick Crowley
Technical Report

Abstract:

The strategy layer is an important architectural component in both Content-Centric Networking (CCN) and Named Data Networking (NDN). This component introduces a new forwarding model that allows an application to configure its namespace with a forwarding strategy.

A core mechanism in every forwarding strategy is the decision of whether to retransmit an unsatisfied Interest or to wait for an application retransmission. While some applications request control of all retransmissions, others rely on the assumption that the strategy will retransmit an Interest when it is not satisfied. Although an application can... Read More

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MERCATOR (Mapping EnumeRATOR for CUDA) User's Manual
Stephen V. Cole and Jeremy Buhler
Technical Report

Abstract:

Welcome to the MERCATOR user's manual! MERCATOR is a CUDA/C++ system designed to assist you in writing efficient CUDA applications by automatically generating significant portions of the GPU-side application code. We hope you find it helpful; please feel free to contact the authors with any questions or feedback.

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Multipath and Rate Stability
Junjie Liu and Roch A. Guérin
Conference Paper

Abstract:

Originally Published In Proc. IEEE Globecom Conference - CQRM: Communication QoS, Reliability & Modeling Symposium

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Jordyn Maglalang, Sriram Krishnamoorthy, and Kunal Agrawal
Conference Paper

Abstract:

Dynamic task graph schedulers automatically balance work across processor cores by scheduling tasks among available threads while preserving dependences. In this paper, we design NabbitC, a provably efficient dynamic task graph scheduler that accounts for data locality on NUMA systems. NabbitC allows users to assign a color to each task representing the location (e.g., a processor core) that has the most efficient access to data needed during that node’s execution. NabbitC then automatically adjusts the scheduling so as to preferentially execute each node at the location that matches its color—leading... Read More

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Grafalgo - A Library of Graph Algorithms and Supporting Data Structures (revised)
Jonathan Turner
Technical Report

Abstract:

This report provides an (updated) overview of Grafalgo, an open-source library of graph algorithms and the data structures used to implement them. The programs in this library were originally written to support a graduate class in advanced data structures and algorithms at Washington University. Because the code's primary purpose was pedagogical, it was written to be as straightforward as possible, while still being highly efficient. Grafalgo is implemented in C++ and incorporates some features of C++11. The library is available on an open-source basis and may be downloaded from https://code.google.com/p/grafalgo/.... Read More

#### Research from 2015

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WOODSTOCC: Extracting Latent Parallelism from a DNA Sequence Aligner on a GPU
Stephen V. Cole, Jacob R. Gardner, and Jeremy D. Buhler
Technical Report

Abstract:

An exponential increase in the speed of DNA sequencing over the past decade has driven demand for fast, space-efficient algorithms to process the resultant data. The first step in processing is alignment of many short DNA sequences, or reads, against a large reference sequence. This work presents WOODSTOCC, an implementation of short-read alignment designed for Graphics Processing Unit (GPU) architectures. WOODSTOCC translates a novel CPU implementation of gapped short-read alignment, which has guaranteed optimal and complete results, to the GPU. Our implementation combines an irregular trie search with dynamic programming... Read More

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Faster Maximium Priority Matchings in Bipartite Graphs
Jonathan Turner
Technical Report

Abstract:

A maximum priority matching is a matching in an undirected graph that maximizes a priority score defined with respect to given vertex priorities. An earlier paper showed how to find maximum priority matchings in unweighted graphs. This paper describes an algorithm for bipartite graphs that is faster when the number of distinct priority classes is limited. For graphs with k distinct priority classes it runs in O(kmn1/2) time, where n is the number of vertices in the graph and m is the number of edges.

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Grafalgo - A Library of Graph Algorithms and Supporting Data Structures
Jonathan Turner
Technical Report

Abstract:

This report provides an overview of Grafalgo, an open-source library of graph algorithms and the data structures used to implement them. The programs in this library were originally written to support a graduate class in advanced data structures and algorithms at Washington University. Because the code's primary purpose was pedagogical, it was written to be as straightforward as possible, while still being highly efficient. Grafalgo is implemented in C++ and incorporates some features of C++11.

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Maximum Priority Matchings
Jonathan Turner
Technical Report

Abstract:

Let G=(V,E) be an undirected graph with n vertices and m edges, in which each vertex u is assigned an integer priority in [1,n], with 1 being the highest'' priority. Let M be a matching of G. We define the priority score of M to be an n-ary integer in which the i-th most-significant digit is the number of vertices with priority i that are incident to an edge in M. We describe a variation of the augmenting path method (Edmonds' algorithm) that finds a matching with maximum priority score... Read More

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The Bounded Edge Coloring Problem and Offline Crossbar Scheduling
Jonathan Turner
Technical Report

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This paper introduces a variant of the classical edge coloring problem in graphs that can be applied to an offline scheduling problem for crossbar switches. We show that the problem is NP-complete, develop three lower bounds bounds on the optimal solution value and evaluate the performance of several approximation algorithms, both analytically and experimentally. We show how to approximate an optimal solution with a worst-case performance ratio of 3/2 and our experimental results demonstrate that the best algorithms produce results that very closely track a lower bound.

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The Edge Group Coloring Problem with Applications to Multicast Switching
Jonathan Turner
Technical Report

Abstract:

This paper introduces a natural generalization of the classical edge coloring problem in graphs that provides a useful abstraction for two well-known problems in multicast switching. We show that the problem is {\sl NP}-hard and evaluate the performance of several approximation algorithms, both analytically and experimentally. We find that for random $\chi$-colorable graphs, the number of colors used by the best algorithms falls within a small constant factor of $\chi$, where the constant factor is mainly a function of the ratio of the number of outputs to inputs. When this... Read More

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Maximizing Network Lifetime of Wireless Sensor-Actuator Networks under Graph Routing
Chengjie Wu, Dolvara Gunatilaka, Abusayeed Saifullah, Mo Sha, Paras Tiwari, Chenyang Lu, and Yixin Chen
Technical Report

Abstract:

Process industries are adopting wireless sensor-actuator networks (WSANs) as the communication infrastructure. The dynamics of industrial environments and stringent reliability requirements necessitate high degrees of fault tolerance in routing. WirelessHART is an open industrial standard for WSANs that have seen world-wide deployments. WirelessHART employs graph routing schemes to achieve network reliability through multiple paths. Since many industrial devices operate on batteries in harsh environments where changing batteries are prohibitively labor-intensive, WSANs need to achieve long network lifetime. To meet industrial demand for long-term reliable communication, this paper studies the problem... Read More

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Conflict-Aware Real-Time Routing for Industrial Wireless Sensor-Actuator Networks
Chengjie Wu, Dolvara Gunatilaka, Mo Sha, and Chenyang Lu
Technical Report

Abstract:

Process industries are adopting wireless sensor-actuator networks (WSANs) as the communication infrastructure. WirelessHART is an open industrial standard for WSANs that have seen world-wide deployments. Real-time scheduling and delay analysis have been studied for WSAN extensively. End-to-end delay in WSANs highly depends on routing, which is still open problem. This paper presents the first real-time routing design for WSAN. We first discuss end-to-end delays of WSANs, then present our real-time routing design. We have implemented and experimented our routing designs on a wireless testbed of 69 nodes. Both experimental results... Read More

#### Research from 2014

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Exploring User-Provided Connectivity
Mohammad H. Afrasiabi and Roch Guerin
Technical Report

Abstract:

Network services often exhibit positive and negative externalities that affect users' adoption decisions. One such service is "user-provided connectivity" or UPC. The service offers an alternative to traditional infrastructure-based communication services by allowing users to share their "home base" connectivity with other users, thereby increasing their access to connectivity. More users mean more connectivity alternatives, i.e., a positive externality, but also greater odds of having to share one's own connectivity, i.e., a negative externality. The tug of war between positive and negative externalities together with the fact that they often... Read More

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Data Transport System
Rahav Dor
MS Project Report

Abstract:

To facilitate the WU Smart Home research [21] we built a system that collects data from sensors and uploads the data to the cloud. The system supports data collection from multiple locations (typically apartments) that are independent from each other, endowing the system with two benefit: distributed data collection and alleviating privacy concerns. Each location is managed by a local micro-server (μServer) that is responsible for receiving data packets from sensors and managing their transient storage. Periodically the μServer triggers a data transport process that moves the data to a... Read More

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CloudPowerCap: Integrating Power Budget and Resource Management across a Virtualized Server Cluster
Yong Fu, Anne Holler, and Chenyang Lu
Technical Report

Abstract:

In many datacenters, server racks are highly underutilized. Rack slots are left empty to keep the sum of the server nameplate maximum power below the power provisioned to the rack. And the servers that are placed in the rack cannot make full use of available rack power. The root cause of this rack underutilization is that the server nameplate power is often much higher than can be reached in practice. To address rack underutilization, server vendors are shipping support for per-host power caps, which provide a server-enforced limit on the... Read More

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Performance Modeling of Virtualized Custom Logic Computations
Michael J. Hall and Roger D. Chamberlain
Technical Report

Abstract:

Virtualization of custom logic computations (i.e., by sharing a fixed function across distinct data streams) provides a means of reusing hardware resources, particularly when resources are limited. This is common practice in traditional processors where more than one user can share processor resources. In this paper, we virtualize a custom logic block using C-slow techniques to support fine-grain context-switching. We then develop and present an analytic model for several performance measures (throughput, latency, input queue occupancy) for both fine-grained and coarse-grained context switching (to a secondary memory). Next, we calibrate... Read More

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Federated Scheduling for Stochastic Parallel Real-time Tasks
Jing Li, Kunal Agrawal, Christopher Gill, and Chenyang Lu
Technical Report

Abstract:

Federated scheduling is a strategy to schedule parallel real-time tasks: It allocates a dedicated cluster of cores to high-utilization task (utilization >1); It uses a multiprocessor scheduling algorithm to schedule and execute all low-utilization tasks sequentially, on a shared cluster of the remaining cores. Prior work has shown that federated scheduling has the best known capacity augmentation bound of 2 for parallel tasks with implicit deadlines. In this paper, we explore the soft real-time performance of federated scheduling and address the average-case workloads instead of the worst-case values. In particular,... Read More

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Capacity Augmentation Bound of Federated Scheduling for Parallel DAG Tasks
Jing Li, Abusayeed Saifullah, Kunal Agrawal, and Christopher Gill
Technical Report

Abstract:

We present a novel federated scheduling approach for parallel real-time tasks under a general directed acyclic graph (DAG) model. We provide a capacity augmentation bound of 2 for hard real-time scheduling; here we use the worst-case execution time and critical-path length of tasks to determine schedulability. This is the best known capacity augmentation bound for parallel tasks. By constructing example task sets, we further show that the lower bound on capacity augmentation of federated scheduling is also 2 for any m > 2. Hence, the gap is closed and bound... Read More

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Streaming Computations with Precise Control
Peng Li, Kunal Agrawal, Jeremy Buhler, and Roger Chamberlain
Technical Report

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Migrating to IPv6 - The Role of Basic Coordination
Mehdi Nikkhah and Roch Guerin
Conference Paper

Abstract:

The need for a larger Internet address space was acknowledged early on, and a solution (IPv6) standardized years ago. Its adoption has, however, been anything but easy and still faces significant challenges. The situation begs the questions of "why has it been so difficult?" and "what could have been (or still be) done to facilitate this migration?" There has been significant recent interest in those questions, and the paper builds on a line of work based on technology adoption models to explore them. The results confirm the impact of several... Read More

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Software Defined Application Delivery Networking, Subharthi Paul

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Real-Time Wireless Sensor-Actuator Networks for Cyber-Physical Systems, Abusayeed Saifullah

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Inferring Memory Map Instructions
Paul T. Scheid, Ari J. Spilo, and Ron K. Cytron
MS Project Report

Abstract:

We describe the problem of inferring a set of memory map instructions from a reference trace, with the goal of minimizing the number of such instructions as well as the number of unreferenced but mapped storage locations. We prove the related decision problem NP-complete. We then present and compare the results of two heuristic approaches on some actual traces.

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On the Analysis of DNA Methylation, Michael Stevens

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RT-OpenStack: a Real-Time Cloud Management System
Sisu Xi, Chong Li, Chenyang Lu, Christopher D. Gill, Meng Xu, Linh T.X. Phan, Insup Lee, and Oleg Sokolsky
Technical Report

Abstract:

Clouds have become appealing platforms for running not only general-purpose applications but also real-time applications. However, current clouds cannot provide real-time performance for virtual machines (VM) for two reasons: (1) the lack of a real-time virtual machine monitor (VMM) scheduler on a single host, and (2) the lack of a real-time aware VM placement scheme by the cloud manager. While real-time VM schedulers do exist, prior solutions employ either heuristics-based approaches that cannot always achieve predictable latency or apply real-time scheduling theory that may result in low CPU utilization. We... Read More

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#### Research from 2013

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Simple Analytic Performance Models for Streaming Data Applications Deployed on Diverse Architectures
Jonathan C. Beard, Roger D. Chamberlain, and Mark A. Franklin
Technical Report

Abstract:

Modern hardware is inherently heterogeneous. With heterogeneity comes multiple abstraction layers that hide underlying complex systems. While hidden, this complexity makes quantitative performance modeling a difficult task. Designers of high-performance streaming applications for heterogeneous systems must contend with unpredictable and often non-generalizable models to predict performance of a particular application and hardware mapping. This paper outlines a computationally simple approach that can be used to model the overall throughput and buffering needs of a streaming application on heterogeneous hardware. The model presented is based upon a hybrid maximum flow and... Read More

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Delivering Consistent Network Performance in Multi-tenant Data Centers, Mart Albert Haitjema

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Kernel Density Metric Learning
Yujie He, Wenlin Chen, and Yixin Chen
Technical Report

Abstract:

This paper introduces a supervised metric learning algorithm, called kernel density metric learning (KDML), which is easy to use and provides nonlinear, probability-based distance measures. KDML constructs a direct nonlinear mapping from the original input space into a feature space based on kernel density estimation. The nonlinear mapping in KDML embodies established distance measures between probability density functions, and leads to correct classification on datasets for which linear metric learning methods would fail. Existing metric learning algorithms, such as large margin nearest neighbors (LMNN), can then be applied to the... Read More

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Adding Data Parallelism to Streaming Pipelines for Throughput Optimization
Peng Li, Kunal Agrawal, Jeremy Buhler, and Roger D. Chamberlain
Technical Report

Abstract:

The streaming model is a popular model for writing high-throughput parallel applications. A streaming application is represented by a graph of computation stages that communicate with each other via FIFO channels. In this report, we consider the problem of mapping streaming pipelines — streaming applications where the graph is a linear chain — in order to maximize throughput. In a parallel setting, subsets of stages, called components can be mapped onto different computing resources. The through-put of an application is determined by the throughput of the slowest component. Therefore, if... Read More

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Efficient Parallel Real-Time Upsampling of Ultrasound Vectors
William D. Richard Ph.D.
Technical Report

Abstract:

Upsampling is required prior to the summation step in most receive digital beamforming implementations to produce an accurate summed RF line or vector. This is true in both annular and linear array systems where receive echos are digitized first and then time delayed in the digital domain to achieve proper signal alignment. The efficient, parallel, real-time upsampling circuit presented here produces M upsampled values per ADC clock, where M is the desired upsampling factor. A circuit implementation that upsamples by a factor of M=4 is presented as an example of... Read More

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Parallel Real-Time Scheduling of DAGs
Abusayeed Saifullah, David Ferry, Jing Li, Kunal Agrawal, Chenyang Lu, and Christopher Gill
Technical Report

Abstract:

Recently, multi-core processors have become mainstream in processor design. To take full advantage of multi-core processing, computation-intensive real-time systems must exploit intra-task parallelism. In this paper, we address the open problem of real-time scheduling for a general model of deterministic parallel tasks, where each task is represented as a directed acyclic graph (DAG) with nodes having arbitrary execution requirements. We prove processor-speed augmentation bounds for both preemptive and non-preemptive real-time scheduling for general DAG tasks on multi-core processors. We first decompose each DAG into sequential tasks with their own release... Read More

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Self-Adapting MAC Layer for Wireless Sensor Networks
Mo Sha, Meng Xu, Chenyang Lu, Linh T.X. Phan, Tae-Suk Kim, and Taerim Park
Technical Report

Abstract:

The integration of wireless sensors with mobile phones is gaining momentum as an enabling platform for numerous emerging applications. These mobile systems face dynamic environments where both application requirements and ambient wireless conditions change frequently. Despite the existence of many MAC protocols however, none can provide optimal performance along multiple dimensions, in particular when the conditions are frequently changing. Instead of pursuing a one-MAC-fit all approach we present a Self-Adapting MAC Layer (SAML) comprising (1) a Reconfigurable MAC Architecture (RMA) that can switch to different MAC protocols at run time... Read More

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Automated Color Calibration of Display Devices
Andrew Shulman
Technical Report

Abstract:

If you compare two identical images on two different monitors, they will likely appear different. Every display device is supposed to adhere to a particular set of standards regulating the color and intensity of the image it outputs. However, in practice, very few do. Color calibration is the practice of modifying the signal path such that the colors produced more closely match reference standards. This is essential for graphics professionals who are mastering original content. They must ensure that the source material appears correct when viewed on a reference monitor.... Read More

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EWA Model with Recency Effect and Limited Memory
Hang Xie
Technical Report

Abstract:

Game theory is an important field in economics; it studies how people make decisions amid conflict and cooperation. Various experiments have been carried to study the way people play those games, and economists study those data for various purposes. There has been a rise of need for using artificial agents to simulate the game, since we could save the cost of hiring human subjects for the experiments, and we could gain more control over the experiment settings.

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Real-Time Multi-Core Virtual Machine Scheduling in Xen
Sisu Xi, Meng Xu, Chenyang Lu, Linh T.X. Phan, Christopher Gill, Olga Sokolsky, and Insup Lee
Technical Report

Abstract:

Recent years have witnessed two major trends in the development of complex real-time systems. First, to reduce cost and enhance flexibility, multiple systems are sharing common computing platforms via virtualization technology, instead of being deployed separately on physically isolated hosts. Second, multicore processors are increasingly being used in real-time systems. The integration of real-time systems as virtual machines (VMs) atop common multicore platforms raises significant new research challenges in meeting the real-time performance requirements of multiple systems.

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Scanner: An Efficient and Accurate Trimming Tool for Illumina Next Generation Sequencing Reads
Xiang Zhou
Technical Report

Abstract:

Recent advances in High-Throughput Sequencing (HTS) technology have greatly facilitated the researches in bioinformatics field. With the ultra-high sequencing speed and improved base-calling accuracy, Illumina Genome Analyzer is currently the most widely used platform in the field. To use the raw reads generated from the sequencing machine, the 3’ adapter sequence attached to the real read in the process of ligation needs to be correctly trimmed. This is often done by some inhouse scripts or different packages with various parameters. They either use the Smith-Waterman algorithm or search for an... Read More

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#### Research from 2012

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Common DMA Engine Interface
Roger Alessi
Technical Report

Abstract:

Circuit boards with Field Programmable Gate Arrays (FPGAs) have a historically diverse set of standards for communicating with other devices. This provides a challenge for developers creating FPGA applications and makes migration of applications from one board or FPGA to another difficult. Many board manufacturers, including Xilinx and GiDEL, create boards with Peripheral Component Interconnect Express (PCIe) buses. PCIe provides a low-level standard for transferring data between a Central Processing Unit (CPU) and an FPGA, and these manufacturers have designed Direct Memory Access (DMA) engines to implement the standard. However,... Read More

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Kinect Hand Recognition and Tracking
Alex Drake
Technical Report

Abstract:

he goal of this research project was to be able to identify and track a hand using the depth image from a Microsoft Kinect. The ability to do this would have uses in sign language recognition, rehabilitation, and gesture recognition amongst others. The Microsoft Kinect is currently capable of identifying and tracking whole bodies. Our approach was to follow the method that Microsoft used but apply it to detailed hand recognition instead of the body. The basic strategy they used was to take a large amount of labeled depth data... Read More

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Abstract:

Cerebral palsy is a group of neurological disorders that impair body movement, muscle coordination, hearing, vision, and cognitive function. Symptoms vary but can include muscle weakness, muscle and joint tightness, abnormal or unsteady gait, seizures, learning disabilities, speech problems, as well as hearing or vision problems [1]. Although cerebral palsy cannot be cured, treatments such as physical and occupational therapy can greatly help affected children develop motor skills needed to increase mobility and foster independence [2]. Computer based therapy games have shown promise in helping stroke survivors recover from stroke... Read More

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Implementation of Real-Time Calibration of Polarization Imaging Sensors
Collin Foster
Technical Report

Abstract:

Recent breakthroughs in nanofabrication techniques have led to development of sophisticated Division-of-Focal-Plane (DoFP) polarization imaging sensors. One such technique allows the fabrication of nanowire filters fabricated directly on the imaging sensor itself. This technique can be used to fabricate robust DoFP polarization imaging sensors. However, the polarization information captured by the imagers can be degraded due to imperfections in the fabrication of the nanowire filters on the imaging sensor. Polarization information can also be degraded from other sources including crosstalk between pixels. To compensate for these undesired effects, a calibration... Read More

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Reading Your Own Mind: Dynamic Visualization of Real-Time Neural Signals, Zachary V. Freudenburg

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Just Draw It! A 3D Sketching System
Cindy Grimm and Pushkar Joshi
Technical Report

Abstract:

We present a system for sketching in 2D to create 3D curves. The interface is light-weight, pen-based, and based on observations of how artists sketch on paper.

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Practical Approaches to Biological Network Discovery, Brian Haynes

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MCFlow: Middleware for Mixed-Criticality Distributed Real-Time Systems, Huang-Ming Huang

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Building a Skeleton of a Human Hand Using Microsoft Kinect
Jed Jackoway
Technical Report

Abstract:

The goal of the project was to reconstruct the skeleton of a Microsoft Kinect user’s hand. Out of the box, Kinect reconstruct the skeleton of users’ bodies, but it only does large joints, such that the hand is given a location on the general skeleton, but the specifics of the fingers and fist are not actually calculated.

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RIDE: A Mixed-Mode Control Interface for Mobile Robot Teams
Erik Karulf, Marshall Strother, Parker Dunton, and William D. Smart
Technical Report

Abstract:

There is a growing need for robot control interfaces that allow a single user to effectively control a large number of mostly-autonomous robots. The challenges in controlling such a collection of robots are very similar to the challenges of controlling characters in some genres of video games. In this paper, we argue that interfaces based on elements from computer video games are effective tools for the control of large robot teams. We present RIDE, the Robot Interactive Display Environment, an example of such an interface, and give the results of... Read More

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The Clear Channel Prior
Devorah Langsam
Technical Report

Abstract:

Capturing imagery from outdoor cameras provides a large amount of information about a scene. The true surface appearances of elements in a scene, however, are often incorrectly represented in images. To get a better representation of the scene it is necessary to separate the effects of the underlying reflectance, illumination, and fog in the image. The goal of the dark channel prior is to eliminate the effects of haze in outdoor images and recover the true surface reflectance image for the scene.

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Data collection and performance monitoring of real-time parallel systems
Technical Report

Abstract:

Instrumentation and log data monitoring are important features present in many different applications today that are used in analysis of a system behaviour. They are largely used in collection of key information from the system which might allow us to describe or establish certain facts about the behavior of the system. Instrumentation in any application usually comes along with its overheads. In some cases , code for instrumentation might become more expensive on the underlying resources than the application itself. For many applications, especially real-time applications , this overhead can... Read More

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A Memory Access Model for Highly-threaded Many-core Architectures
Lin Ma, Kunal Agrawal, and Roger D. Chamberlain
Technical Report

Abstract:

Many-core architectures are excellent in hiding memory-access latency by low-overhead context switching among a large number of threads. The speedup of algorithms carried out on these machines depends on how well the latency is hidden. If the number of threads were infinite, then theoretically these machines should provide the performance predicted by the PRAM analysis of the programs. However, the number of allowable threads per processor is not infinite. In this paper, we introduce the Threaded Many-core Memory (TMM) model which is meant to capture the important characteristics of these... Read More

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An Integrated Data Mining Approach to Real-time Clinical Monitoring and Deterioration Warning
Yi Mao, Wenlin Chen, Yixin Chen, and Chenyang Lu
Technical Report

Abstract:

Clinical study found that early detection and intervention are essential for preventing clinical deterioration in patients, for patients both in intensive care units (ICU) as well as in general wards but under real-time data sensing (RDS). In this paper, we develop an integrated data mining approach to give early deterioration warnings for patients under real-time monitoring in ICU and RDS. Existing work on mining real-time clinical data often focus on certain single vital sign and specific disease. In this paper, we consider an integrated data mining approach for general sudden... Read More

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A 3D Selection & Query Tool for the GeneAtlas Project
Donald McCurdy
Technical Report

Abstract:

In this project, I present an application to view, interact with, and search 3D medical volumes as part of the GeneAtlas project.

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Youpon
Garrison Prinslow
Technical Report

Abstract:

This project was motivated by two related ideas: what can be learned about the unique issues involved with developing cloud-based mobile applications; and, what application could be developed to evaluate these characteristics that would also be innovative and provide value to users. After vetting ideas for the latter objective, it was clear that a new digital coupon system could offer value and apply interesting technologies to computer science problems, such as shortest path calculation, position-aware authentication, game theory, and statistical reasoning. A brief summary of the motivation for developing the... Read More

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Self-Stabilization in the Distributed Systems of Finite State Machines
Abusayeed Saifullah
Technical Report

Abstract:

The notion of self-stabilization was first proposed by Dijkstra in 1974 in his classic paper. The paper defines a system as self-stabilizing if, starting at any, possibly illegitimate, state the system can automatically adjust itself to eventually converge to a legitimate state in finite amount of time and once in a legitimate state it will remain so unless it incurs a subsequent transient fault. Dijkstra limited his attention to a ring of finite-state machines and provided its solution for self-stabilization. In the years following his introduction, very few papers were... Read More

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Studying Network Optimization in the Context of Self-Stabilization
Abusayeed Saifullah
Technical Report

Abstract:

Self-stabilization is a theoretical framework of non-masking fault-tolerance for distributed networks. A self-stabilizing system is capable of tolerating any unexpected transient fault without outside intervention and, regardless of the initial state, it can converge to a legitimate global state, a predefined vector of local states, in finite time. Self-stabilization has rendered a good problem solving paradigm of networks over the last decade. In this paper, we survey the self-stabilizing solutions for various network optimization problems such as network flow, load balancing, load and resource distribution, routing, file distribution, shortest paths... Read More

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Correction of an Augmentation Bound Analysis for Parallel Real-Time Tasks
Abusayeed Saifullah, Kunal Agrawal, Chenyang Lu, and Christopher Gill
Technical Report

Abstract:

This paper proposes some significant corrections in a recent work of Lakshmanan et al on parallel task scheduling. Lakshmanan et al have proposed a transformation of parallel tasks into sequential tasks, and have claimed a resource augmentation bound of 3:42 for partitioned deadline monotonic (DM) scheduling of the transformed tasks. We demonstrate that their analysis for resource augmentation bound is incorrect. We propose a different technique for task transformation that requires a resource augmentation bound of 5 for partitioned DM scheduling.

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Real-Time Scheduling of Parallel Tasks under a General DAG Model
Abusayeed Saifullah, David Ferry, Chenyang Lu, and Christopher Gill
Technical Report

Abstract:

Due to their potential to deliver increased performance over single-core processors, multi-core processors have become mainstream in processor design. Computation-intensive real-time systems must exploit intra-task parallelism to take full advantage of multi-core processing. However, existing results in real-time scheduling of parallel tasks focus on restrictive task models such as the synchronous model where a task is a sequence of alternating parallel and sequential segments, and parallel segments have threads of execution that are of equal length. In this paper, we address a general model for deterministic parallel tasks, where a... Read More

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Accounting for Failures in Delay Analysis for WirelessHART Networks
Abusayeed Saifullah, Paras Babu Tiwari, Bo Li, and Chenyang Lu lu@wustl.edu
Technical Report

Abstract:

WirelessHART networks are gaining ground as a real-time communication infrastructure in industrial wireless control systems. Because wireless communication is often susceptible to transmission failures in industrial environments, it is essential to account for failures in the delay analysis for realtime flows between sensors and actuators in process control. WirelessHART networks handle transmission failures through retransmissions using dedicated and shared time slots through different paths in the routing graphs. While these mechanisms for handling transmission failures are critical for process control requiring reliable communication, they introduce substantial challenges to worst-case end-to-end... Read More

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Foveon F13 Camera
David Shelley
Technical Report

Abstract:

Most high-fidelity digital cameras currently available obtain their images using technology where individual pixels can only acquire a single color. Since the acquisition of multiple colors is necessary to capture a full colored image, picture resolution is lost due to difficulties in interpolation between non-adjacent, same color pixels. The resulting unsharp images create the need to find a new way to obtain these images without requiring interpolation between adjacent pixels. An innovative method to capture images with individual pixel cells consisting of three layers of photodetectors stacked vertically upon one... Read More

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Modeling Surfaces from Volume Data Using Nonparallel Contours, Ross Taylor Sowell

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Specializing Interfaces for Citizen Science Segmentation of Volumetric Data
Michelle Vaughan, Cindy Grimm, Ruth Sowell, Robert Pless, and Stephen Kobourov
Technical Report

Abstract:

Segmentation of 3D and time-varying volumetric (4D) image data is considered a time and resource intensive bottleneck in scientific endeavors. Automatic methods are becoming more reliable, but many data sets still require manual intervention. This can mainly be attributed to the characteristics of the image data not being amenable to automated methods, the existence of variations in or poor image quality, or the need for an expert to review and edit results from an automatic technique. Manually segmenting volumetric data is a challenge even for those more experienced. Understanding the... Read More

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Limitations and Solutions for Real-Time Local Inter-Domain Communication in Xen
Sisu Xi, Chong Li, Chenyang Lu, and Christopher Gill
Technical Report

Abstract:

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 engineering, this kind of system integration can greatly reduce system weight, cost, and power requirements. When systems are integrated in this manner, network communication may become local inter-domain communication (IDC) within the same host. This paper examines the limitations of inter-domain communication in Xen, a widely used open-source virtual machine monitor (VMM) that recently has been extended to... Read More

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Early Warning System: Relay Sensor Deployment & Network Reliability Analysis
Zhicheng Yang
Technical Report

Abstract:

In this project, we continued Dr. Chipara's study, which developed an early warning system (EWS) to detect the vital signs of patients in order to help doctors to intervene in time [1]. Since the number of wards increased, the environment our system faced with became more complicated and our network became more sensitive. This project focused on finding reasons on the relays that didn't work and doing a reliability analysis on the network in one ward our study covered.

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Delaunay-restricted Optimal Triangulation of 3D Polygons
Ming Zou, Tao Ju, and Nathan Carr
Technical Report

Abstract:

Triangulation of 3D polygons is a well studied topic of research. Existing methods for finding triangulations that minimize given metrics (e.g., sum of triangle areas or dihedral angles) run in a costly O(n4) time [BS95,BDE96], while the triangulations are not guaranteed to be free of intersections. To address these limitations, we restrict our search to the space of triangles in the Delaunay tetrahedralization of the polygon. The restriction allows us to reduce the running time down to O(n2) in practice (O(n3) worst case) while guaranteeing that the solutions are intersection... Read More

#### Research from 2011

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Hierarchical Scheduling for Multicores with Multilevel Cache Hierarchies
Kunal Agrawal and Jim Sukha
Technical Report

Abstract:

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... Read More

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Generating Muscle Driven Arm Movements Using Reinforcement Learning
Technical Report

Abstract:

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... Read More

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Mercury BLASTN Biosequence Similarity Search System: Technical Reference Guide
Jeremy Buhler
Technical Report

Abstract:

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.

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Efficient Deadlock Avoidance for Streaming Computation with Filtering
Jeremy Buhler, Kunal Agrawal, Peng Li, and Roger D. Chamberlain
Technical Report

Abstract:

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.

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Clinical Interpretation of Novel Copy Number Variations, Clifton Carey

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Flux Balance Analysis of Dynamic Metabolism in Shewanella oneidensis MR-1 Using a Static Optimization Approach
Xueyang Feng, You Xu, Yixin Chen, and Yinjie Tang
Technical Report

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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... Read More

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Feedback Thermal Control of Real-time Systems on Multicore Processors
Yong Fu, Nicholas Kottenstette, Chenyang Lu, and Xenofon D. Koutsoukos
Technical Report

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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... Read More

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Results of an observational study on sketching
Cindy Grimm
Technical Report

Abstract:

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.

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Practical and Robust Power Management for Wireless Sensor Networks, Gregory Hackmann

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Implementation and Evaluation of Mixed-Criticality Scheduling Approaches for Periodic Tasks
Huang-Ming Huang, Christopher Gill, and Chenyang Lu
Technical Report

Abstract:

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,... Read More

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Efficient Automated Planning with New Formulations, Ruoyun Huang

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Mixed-Mode Control Interfaces of Mobile Robot Teams, Erik Karulf

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Webcam Image Alignment
Matthew Klein
Technical Report

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Real Time Baseball Augmented Reality
Technical Report

Abstract:

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

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Low-Impact Profiling of Streaming, Heterogeneous Applications, Joseph Lancaster

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A Survey on Communication Networks in Emergency Warning Systems
Yan Li
Technical Report

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Optimization of Gene Prediction via More Accurate Phylogenetic Substitution Models
Ezekiel Maier, Randall H. Brown, and Michael R. Brent
Technical Report

Abstract:

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... Read More

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