Technical Reports and MS Project Reports

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

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.

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.

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

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.

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

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

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

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

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

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

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

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.

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

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

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

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

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

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.

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

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

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

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.

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.

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

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

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.

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

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

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

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.

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 ...Read More

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 ...Read More

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 ...Read More

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 ...Read More

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 ...Read More

Forest is an overlay network designed for large real-time distributed systems. In particular, we’re interested in virtual worlds that provide high-quality interaction over a constantly changing pattern of communication. Forest is suitable for applications in which many entities send data to a large set of constantly changing entities. By using tree-structured channels, we can create logically isolated private networks which support both unicast and multicast routing. In this paper, we will discuss the core components of Forest and measure the performance of the control elements of the network. We will ...Read More

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 ...Read More

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.

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 ...Read More

Partially-Observable Markov Decision Processes (POMDPs) are typically solved by finding an approximate global solution to a corresponding belief-MDP. In this paper, we offer a new planning algorithm for POMDPs with continuous state, action and observation spaces. Since such domains have an inherent notion of locality, we can find an approximate solution using local optimization methods. We parameterize the belief distribution as a Gaussian mixture, and use the Extended Kalman Filter (EKF) to approximate the belief update. Since the EKF is a first-order filter, we can marginalize over the observations analytically. ...Read More

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 ...Read More

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 ...Read More

Modern computer architectures have evolved from uni-processor platforms to multi-processor and multi-core plat- forms, but traditional real-time distributed middleware such as RT-CORBA has not kept pace with that evolution. To address those issues, this paper describes the design and implementation of MCFlow, a new real-time distributed middleware for dependent task graphs running on multi-core platforms. MCFlow provides the following contributions to the state of the art in real-time middleware: (1) it provides an efficient C++ based component model through which computations can be configured flexibly for execution within a single ...Read More

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 ...Read More

Graph search has been employed by many AI techniques and applications. A natural way to improve the efficiency of search is to utilize ad- vanced, more powerful computing platforms. However, expensive computing infrastructures, such as supercomputers and large-scale clusters, are traditionally available to only a limited number of projects and researchers. As a results, most AI applications, with access to only commodity com- puters and clusters, cannot benefit from the efficiency improvements of high-performance parallel search algorithms. Cloud computing provides an attractive, highly accessible alternative to other traditional high- performance ...Read More

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 ...Read More

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 ...Read More