All Computer Science and Engineering Research

We introduce the integral-pixel camera model, where measurements integrate over large and potentially overlapping parts of the visual field. This models a wide variety of novel camera designs, including omnidirectional cameras, compressive sensing cameras, and novel programmable-pixel imaging chips. We explore the relationship of integral-pixel measurements with image motion and find (a) that direct motion estimation using integral-pixels is possible and in some cases quite good, (b) standard compressive-sensing reconstructions are not good for estimating motion, and (c) when we design image reconstruction algorithms that explicitly reason about image motion,... Read More

Skeleton descriptors are commonly used to represent, understand and process shapes. While existing methods produce skeletons at a fixed dimension, such as surface or curve skeletons for a 3D object, often times objects are better described using skeleton geometry at a mixture of dimensions. In this paper we present a novel algorithm for computing mixed-dimensional skeletons. Our method is guided by a continuous analogue that extends the classical grassfire erosion. This analogue allows us to identify medial geometry at multiple dimensions, and to formulate a measure that captures how well... Read More

Networking research funding agencies in the USA, Europe, Japan, and other countries are encouraging research on revolutionary networking architectures that may or may not be bound by the restrictions of the current TCP/IP based Internet. We present a comprehensive survey of such research projects and activities. The topics covered include various testbeds for experimentations for new architectures, new security mechanisms, content delivery mechanisms, management and control frameworks, service architectures, and routing mechanisms. Delay/Disruption tolerant networks, which allow communications even when complete end-to-end path is not available, are also discussed.

The single best-effort service of the Internet struggles to accommodate divergent needs of different distributed applications. Numerous alternative network architectures have been proposed to offer diversified network services. These innovative solutions failed to gain wide deployment primarily due to economic and legacy issues rather than technical shortcomings. Our paper presents a new simple paradigm for network service differentiation that accounts explicitly for the multiplicity of Internet service providers and users as well as their economic interests in environments with partly deployed new services. Our key idea is to base the... Read More

A high profile internet server is always a target of denial-of-service attacks. In this paper, we propose a novel technique for protecting an internet server from distributed denial-of-service attacks. The defense mechanism is based on a distributed algorithm that performs weight-fair throttling at the upstream routers. The throttling is weight-fair because the traffics destined for the server are controlled increased or decreased ) by the leaky-buckets at the routers based on the number of users connected, directly or through other routers, to each router. To the best of our knowledge,... Read More

Vertex-connectivity and edge-connectivity represent the extent to which a graph is connected. Study of these key properties of graphs plays an important role in varieties of computer science applications. Recent years have witnessed a number of linear time 3-edge-connectivity algorithms - with increasing simplicity. In contrast, the state-of-the-art algorithm for 3-vertex-connectivity due to Hopcroft and Tarjan lacks the simplicity in the sense of ease of implementation as well as the number of passes over the graph although its time and space complexity is theoretically linear. In this paper, we propose... Read More

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 in deploying robust wireless sensor networks (WSNs) for home automation applications is the need to provide long-term, reliable operation in the face of the varied sources of interference found in typical residential settings. To better understand the channel dynamics in these environments, we performed an in-depth empirical study of the performance of HANs in ten real-life apartments. Our empirical study leads to... Read More

Recent advances in surface reconstruction algorithms allow surfaces to be built from contours lying on non-parallel planes. Such algorithms allow users to construct surfaces of similar quality more efficiently by using a small set of oblique contours, rather than many parallel contours. However, current medical imaging systems do not provide tools for sketching contours on oblique planes. In this paper, we take the first steps towards bridging the gap between the new surface reconstruction technologies and putting those methods to use in practice. We develop a novel interface for modeling... Read More

Workflows, widely used on the Internet today, typically consist of a graph-like structure that defines the orchestration rules for executing a set of tasks, each of which is matched at run-rime to a corresponding service. The graph is static, specialized directories enable the discovery of services, and the wired infrastructure supports routing of results among tasks. In this paper we introduce a radically new paradigm for workflow construction and execution called open workflow. It is motivated by the growing reliance on wireless ad hoc networks in settings such as emergency... Read More

Workflow middleware executes tasks orchestrated by rules defined in a carefully handcrafted static graph. Workflow management systems have proved effective for service-oriented business automation in stable, wired infrastructures. We introduce a radically new paradigm for workflow construction and execution called open workflow to support goal-directed coordination among physically mobile people and devices that form a transient community over an ad hoc wireless network. The quintessential feature of the open workflow paradigm is dynamic construction of custom, context-specific workflows in response to unpredictable and evolving circumstances by exploiting the knowledge and... Read More

Existing workflow middleware executes tasks orchestrated by rules defined in a carefully handcrafted static graph. Workflow management systems have proved effective for service-oriented business automation in stable, wired infrastructures. We introduce a radically new paradigm for workflow construction and execution called open workflow to support goal-directed coordination among physically mobile people and devices that form a transient community over an ad hoc wireless network. The quintessential feature of the open workflow paradigm is dynamic construction and execution of custom, context-specific workflows in response to unpredictable and evolving circumstances by exploiting... Read More

The Least Occupied Output First (LOOFA) scheduler is one of several unbuffered crossbar schedulers that provides strong performance guarantees when operated with a speedup of 2 or more. Because LOOFA requires the computation of a maximal matching, it has been considered too slow for use in systems with link rates of 10 Gb/s or more. This paper studies an approximate variant of LOOFA described briefly in [16]. We introduce a general family of schedulers that allows for partial sorting and that includes the LOOFA scheduler as a special case. We... Read More

This report describes the Supercharged Planetlab Platform (SPP), a system designed as a prototype of an internet-scale overlay hosting platform. Overlay networks have become an important vehicle for delivering Internet applications. Overlay network nodes are typically implemented using general purpose servers or clusters. The SPP offers a more integrated architecture, combining general-purpose servers with high performance Network Processor (NP) subsystems. SPP nodes have recently been deployed as part of the Global Environment for Network Innovation (GENI) and are available for use by research users.

Real-time systems on non-preemptive platforms require a means of bounding the execution time of programs for admission purposes. Worst-Case Execution Time (WCET) is most commonly used to bound program execution time. While bounding a program’s WCET statically is possible, computing its true WCET is difficult.We present a new technique we call partial program admission, a means of statically enforcing an otherwise untrusted assertion of WCET without adding runtime overhead, by means of code duplication. We apply this technique to real programs from the virtual networking arena and present the results.

Virtualized network infrastructures are currently deployed in both research and commercial contexts. The complexity of the virtualization layer varies greatly in different deployments, ranging from cloud computing environments, to carrier Ethernet applications using stacked VLANs, to networking testbeds. In all of these cases, there are many users sharing the resources of one provider, where each user expects their resources to be isolated from all other users. Our work in this area is focused on network testbeds. In particular, we present the design of the latest version of the Open Network... Read More

Network testbeds such as Emulab and the Open Network Laboratory use virtualization to enable users to define end user virtual networks within a shared substrate. This involves mapping users' virtual network nodes onto distinct substrate components and mapping virtual network links onto substrate paths. The mappings guarantee that different users' activities can not interfere with one another. The problem of mapping virtual networks onto a shared substrate is a variant of the general graph embedding problem, long known to be NP-hard. In this paper, we focus on a more general... Read More

In the last few years, there has been active research on aggregating advanced statistical measures in multidimensional data cubes from partitioned subsets of data. In this paper, we propose an online compression and aggregation scheme to support Bayesian estimations in data cubes based on the asymptotic properties of Bayesian statistics. In the proposed approach, we compress each data segment by retaining only the model parameters and a small amount of auxiliary measures. We then develop an aggregation formula that allows us to reconstruct the Bayesian estimation from partitioned segments with... Read More

Partial order based reduction (POR) has recently attracted research in planning. POR algorithms reduce search space by recognizing interchangable orders between actions and expanding only a subset of all possible orders during the search. POR has been extensively studied in model checking and proved to be an enabling technique for reducing the search space and costs. Recently, two POR algorithms, including the expansion core (EC) and stratified planning (SP) algorithms, have been proposed. Being orthogonal to the development of accurate heuristic functions, these reduction methods show great potential to improve... Read More

We present a novel constraint-partitioning approach for solving continuous nonlinear optimization based on augmented Lagrange method. In contrast to previous work, our approach is based on a new constraint partitioning theory and can handle global constraints. We employ a hyper-graph partitioning method to recognize the problem structure. We prove global convergence under assumptions that are much more relaxed than previous work and solve problems as large as 40,000 variables that other solvers such as IPOPT [11] cannot solve.

With the fast development of wireless sensor network (WSN) technologies, WSNs have widely shifted from a specialized platform for a single application to an integrated infrastructure supporting multiple applications. It is hence a critical problem to allocate multiple applications to multiple sensors in order to maximize user utility subject to various resource constraints. The resulting constrained optimization problem is difficult since it is discrete, nonlinear, and not in closed-form. In this report, we develop an efficient optimization algorithm with rigorous approximation bounds for submodular monotonic optimization with multiple knapsack constraints.... Read More

Traditional AI search methods, such as BFS, DFS, and A*, look for a path from a starting state to the goal in a state space most typically modelled as a directed graph. Prohibitively large sizes of the state space graphs make optimal search difficult. A key observation, as manifested by the SAS+ formalism for planning, is that most commonly a state-space graph is well structured as the Cartesian product of several small subgraphs. This paper proposes novel search algorithms that exploit such structure. The results reveal that standard search algorithms... Read More

Real-time patient monitoring is critical to early detection of clinical patient deterioration in general hospital wards. A key challenge in such applications is to reliably deliver sensor data from mobile patients. We present an empirical analysis on the reliability of data collection from wireless pulse oximeters attached to users. We observe that most packet loss occur from mobile users to their first-hop relays. Based on this insight we developed the Dynamic Relay Association Protocol (DRAP), a simple and effective mechanism for dynamically discovering the right relays for wireless sensors attached... Read More

This paper presents Servilla, a highly flexible service provisioning framework for heterogeneous wireless sensor networks. Its service-oriented programming model and middleware enable developers to construct platform-independent applications over a dynamic set of devices with diverse computational resources and sensors. A salient feature of Servilla is its support for dynamic discovery and binding to local and remote services, which enables flexible and energy-efficient in-network collaboration among heterogeneous devices. Furthermore, Servilla provides a modular middleware architecture that can be easily tailored for devices with a wide range of resources, allowing even resource-limited... Read More

Open soft real-time systems, such as mobile robots, experience unpredictable interactions with their environments and yet must respond both adaptively and with reasonable temporal predictability. New scheduling approaches are needed to address the demands of such systems, in which many of the assumptions made by traditional real-time scheduling theory do not hold. In previous work we established foundations for a scheduling policy design and verification approach for open soft real-time systems, that can use different decision models, e.g., a Markov Decision Process (MDP), to capture the nuances of their scheduling... Read More

We introduce the concept of local neighborhoods, a generalization of the one-ring on a mesh to unlabeled 3D data points arising from sampling a 2D surface embedded in 3D. The local neighborhood supports both local shape classification and robust normal estimation. In particular, local neighborhoods out-perform traditional approaches in unevenly sampled, curved regions. We show that the local neighborhood can be used in place of a full mesh structure for applications such as smoothing, moving least-squares reconstruction, and parameterization. Longer version of paper submitted to CAGD

Wireless sensor networks (WSNs) have become an increasingly compelling platform for Structural Health Monitoring (SHM) applications, since they can be installed relatively inexpensively onto existing infrastructure. Existing approaches to SHM in WSNs typically address computing system issues or structural engineering techniques, but not both in conjunction. In this paper, we propose a holistic approach to SHM that integrates a decentralized computing architecture with the Damage Localization Assurance Criterion algorithm. In contrast to centralized approaches that require transporting large amounts of sensor data to a base station, our system pushes the... Read More

Component based middleware helps to facilitate software reuse by separating application-specific concerns into modular components that are shielded from the concerns of other components and from the common concerns addressed by underlying middleware services. In real-time systems, concerns such as invocation rates, execution latencies, deadlines, and concurrency semantics cross-cut multiple component and middleware abstractions. Thus, the verification of these systems must consider features of the application components (e.g., their execution latencies and relative invocation rates) and of the supporting middleware (e.g., concurrency and scheduling) together. However, existing approaches only address... Read More

Component-based software architectures enable reuse by separating application-specific concerns into modular components that are shielded from each other and from common concerns addressed by underlying services. Even so, concerns such as invocation rates, execution latencies, deadlines, and concurrency and scheduling semantics still cross-cut component boundaries in many real-time systems. Verification of these systems therefore must consider how composition of components relates to timing, resource utilization, and other properties. However, existing approaches only address a sub-set of the concerns that must be modeled in component-based distributed real-time systems, and a new... Read More

Operational Type Theory (OpTT) can be used to construct and check proofs related to programs, but the development of these proofs can be somewhat tedious. An algorithm is presented that can be used to automatically generate proofs of equality in OpTT. The algorithm takes as input a set of ground equations and two terms that should be tested for joinability modulo the supplied ground equations. The algorithm will equate the terms if and only if there exists an OpTT proof that can equate the two terms using only the proof... Read More

Low Level Verification (LLV) is a user-driven software verification system focused on proving properties of C-style computer programs. The system is introduced in multiple parts, starting with a through description of the syntax and operational semantics of LLV code. The LLV execution language is presented as a simplified version of C/C++, in which data types and object constructs have been removed. The machine level implementation of LLV is not specified within the scope of this paper. Instead, the conceptual operation of the execution environment is described in a way that... Read More

Continued rapid improvements in the hardware capabilities of mobile computing devices is driving a parallel need for a paradigm shift in software design for such devices with the aim of ushering in new classes of software applications for devices of the future. One such class of software application is collaborative applications that seem to reduce the burden and overhead of collaborations on human users by providing automated computational support for the more mundane and mechanical aspects of a cooperative effort. This dissertation addresses the research and software engineering questions associated... Read More

Computational finance relies heavily on the use of Monte Carlo simulation techniques. However, Monte Carlo simulation is computationally very demanding. We demonstrate the use of architecturally diverse systems to accelerate the performance of these simulations, exploiting both graphics processing units and field-programmable gate arrays. Performance results include a speedup of 74× relative to an 8 core multiprocessor system (180× relative to a single processor core).

Scheduling the execution of multiple concurrent tasks on shared resources such as CPUs and network links is essential to ensuring the reliable operation of many autonomic systems. Well known techniques such as rate-monotonic scheduling can offer rigorous timing and preemption guarantees, but only under assumptions (i.e., a fixed set of tasks with well-known execution times and invocation rates) that do not hold in many autonomic systems. New hierarchical scheduling techniques are better suited to enforce the more flexible execution constraints and enforcement mechanisms that are required for autonomic systems, but... Read More

As technology continues to advance, robots are more likely to make their way into everyday life. As these robots gradually take on more complicated everyday jobs that they require working with humans directly, the study of Human-Robot Integration (HRI) will gain more importance. The task of studying human-robot interaction must combine a wide array of subjects ranging from computer science to performance. This dissertation describes a collaborative effort between the Media & Machines Lab and the Performing Arts Department at Washington University in Saint Louis to study the relationship between... Read More

Real-time systems on non-preemptive platforms require a means of bounding the execution time of programs for admission purposes. Worst-Case Execution Time (WCET) is most commonly used to bound program execution time. While bounding a program's WCET statically is possible, computing its true WCET is difficult without significant semantic knowledge. We present an algorithm for partial program admission, suited for non-preemptive platforms, using dynamic programming to perform explicit enumeration of program paths. Paths - possible or not - are bounded by the available execution time and admitted on a path-by-path basis... Read More

An increasing number of distributed real-time applications are running on multicore platforms. However, existing real-time middleware (e.g., Real-Time CORBA) lacks support for scheduling soft real-time tasks on multicore platforms while guaranteeing their time constraints will be satisfied. This paper makes three contributions to the state of the art in real-time system software for multicore platforms. First, it offers what is to our knowledge the first experimental analysis of real-time performance for vanilla Linux primitives on multicore platforms. Second, it presents MC-ORB, the first real-time object request broker (ORB), designed to... Read More

Different distributed cyber-physical systems must handle aperiodic and periodic events with diverse requirements. While existing real-time middleware such as Real-Time CORBA has shown promise as a platform for distributed systems with time constraints, it lacks flexible configuration mechanisms needed to manage end-to-end timing easily for a wide range of different cyber-physical systems with both aperiodic and periodic events. The primary contribution of this work is the design, implementation and performance evaluation of the first configurable component middleware services for admission control and load balancing of aperiodic and periodic event handling... Read More

Existing off-line schedulability analysis for real-time systems can only handle periodic or sporadic tasks with known minimum inter-arrival times. Modeling sporadic tasks with fixed minimum inter-arrival times is a poor approximation for systems in which tasks arrive in bursts, but have longer intervals between the bursts. In such cases, schedulability analysis based on the existing sporadic task model is pessimistic and seriously overestimates the task's time demand. In this paper, we propose a generalized sporadic task model that characterizes arrival times more precisely than the traditional sporadic task model, and... Read More

Existing off-line schedulability analysis for real-time systems can only handle periodic or sporadic tasks with known minimum inter-arrival times. Modeling sporadic tasks with fixed minimum inter-arrival times is a poor approximation for systems in which tasks arrive in bursts, but have longer intervals between the bursts. In such cases, schedulability analysis based on the existing sporadic task model is pessimistic and seriously overestimates the task's time demand. In this paper, we propose a generalized sporadic task model that characterizes arrival times more precisely than the traditional sporadic task model, and... Read More

More recent evidence has shown that access of animal microRNAs (miRNAs) to their complementary sites in target mRNAs is determined by more sequence-specific determinants than the seed regions in the 5' end of miRNAs. Although these factors have been shown to be related to the repressive power of miRNAs and used, in separate programs, to predict the efficacy of miRNA complementary sites, it remains unclear whether these factors can help to improve miRNA target prediction. We develop a new miRNA target prediction algorithm, called Hitsensor, by incorporating more sequence-specific features... Read More

Determining protein structure is an important problem for structural biologists, which has received a significant amount of attention in the recent years. In this thesis, we describe a novel, shape-modeling approach as an intermediate step towards recovering 3D protein structures from volumetric images. The input to our method is a sequence of alpha-helices that make up a protein, and a low-resolution volumetric image of the protein where possible locations of alpha-helices have been detected. Our task is to identify the correspondence between the two sets of helices, which will shed... Read More

Humanoid robots have the potential to become a part of everyday life as their hardware and software challenges are being solved. In this paper we present a system that gets as input a motion trajectory in the form of motion capture data, and produces a controller that controls a humanoid robot in real-time to achieve a motion trajectory that is similar to the input motion data. The controller expects the input motion data not to be dynamically feasible for the robot and employs a combined controller with corrective components to... Read More

Multi-robot systems require efficient and accurate planning in order to perform mission-critical tasks. However, algorithms that find the optimal solution are usually computationally expensive and may require a large number of messages between the robots as the robots need to be aware of the global spatiotemporal information. In this paper, we introduce an emergent task allocation approach for mobile robots. Each robot uses only the information obtained from its immediate neighbors in its decision. Our technique is general enough to be applicable to any task allocation scheme as long as... Read More

Connectivity is an important requirement for wireless sensor networks especially in real-time monitoring and data transfer applications. However, node movements and failures change the topology of the initial deployed network, which can result in partitioning of the communication graph. In this paper, we present a method for maintaining and repairing the communication network of a dynamic mobile wireless sensor network. We assume that we cannot control the motion of wireless sensor nodes, but there are robots whose motion can be controlled by the wireless sensor nodes to maintain and repair... Read More

The relationship between color and perceived depth for realistic, colored objects with varying shading was explored. Background: Studies have shown that warm-colored stimuli tend to appear nearer in depth than cool-colored stimuli. The majority of these studies asked human observers to view physically equidistant, colored stimuli and compare them for relative depth. However, in most cases, the stimuli presented were rather simple: straight colored lines, uniform color patches, point light sources, or symmetrical objects with uniform shading. Additionally, the colors were typically highly saturated. Although such stimuli are useful for... Read More

Many emergent distributed sensing applications need to keep track of mobile entities across multiple sensor networks connected via an IP network. To simplify the realization of such applications, we present MLDS, a Multi-resolution Location Directory Service for tiered sensor networks. MLDS provides a rich set of spatial query services ranging from simple queries about entity location, to complex nearest neighbor queries. Furthermore, MLDS supports multiple query granularities which allow an application to achieve the desired tradeoff between query accuracy and communication cost. We implemented MLDS on Agimone, a unified middleware... Read More

In this dissertation we describe a system that uses a low dimensional input derived from electromyography and electrocorticography data to control a robot. The work involves creating a system that allows signals recorded directly from a human body to allow control of a small robot arm. We compare direct joystick control with electromyogram (EMG) input to determine if one input system is superior, or if the quality of control between them is comparable. We also verify the system that is used to record the electromyogram signals is adaptable to other... Read More

The goal of the Fingerspell Visualization Project is to research methods to improve learning of reading skills through sign language. The techniques are centered on Fingerspelling as the method to bridge stages of skill development. Visualization of a string of text in images of a hand performing the letters of the alphabet in standardized fingerspell sign language positions provide Full Motion Learning as opposed to learning from single pictures.

This report describes a hashing scheme for a dictionary of short bit strings. The scheme, which we call near-perfect hashing, was designed as part of the construction of Mercury BLAST, an FPGA-based accelerator for the BLAST family of biosequence comparison algorithms. Near-perfect hashing is a heuristic variant of the well-known displacement hashing approach to building perfect hash functions. It uses a family of hash functions composed from linear transformations on bit vectors and lookups in small precomputed tables, both of which are especially appropriate for implementation in ardware logic. We... Read More

Many distributed real-time systems face the challenge of dynamically maximizing system utility in response to fluctuations in system workload. We present the MultiParametric Rate Adaptation (MPRA) algorithm for discrete rate adaptation in distributed real-time systems with end-to-end tasks. The key novelty and advantage of MPRA is that it can efficiently produce optimal solutions in response to workload changes such as dynamic task arrivals. Through oline preprocessing MPRA transforms a NP-hard utility optimization problem to a set of simple linear functions in different regions expressed in term of CPU utilization changes... Read More

Many distributed real-time systems face the challenge of dynamically maximizing system utility in response to fluctuations in system workload. We present the MultiParametric Rate Adaptation (MPRA) algorithm for discrete rate adaptation in distributed real-time systems with end-to-end tasks. The key novelty and advantage of MPRA is that it can efficiently produce optimal solutions in response to workload variations such as dynamic task arrivals. Through offline preprocessing MPRA transforms an NP-hard utility optimization problem to the evaluation of a piecewise linear function of the CPU utilization. At run time MPRA produces... Read More

Duality is an important notion for constrained optimization which provides a theoretical foundation for a number of constraint decomposition schemes such as separable programming and for deriving lower bounds in space decomposition algorithms such as branch and bound. However, the conventional duality theory has the fundamental limit that it leads to duality gaps for nonconvex optimization problems, especially discrete and mixed-integer problems where the feasible sets are nonconvex. In this paper, we propose a novel extended duality theory for nonlinear optimization that overcomes some limitations of previous dual methods. Based... Read More

Recent years have seen the emergence of wireless sensor network (WSN) systems that require high data rate real-time communication. This paper proposes Real-Time Query Scheduling (RTQS), a novel approach to conflict-free transmission scheduling for real-time queries in WSNs. We show that there is an inherent trade-off between prioritization and throughput in conflict-free query scheduling. RTQS provides three new real-time scheduling algorithms. The non-preemptive query scheduling algorithm achieves high throughput while introducing priority inversions. The preemptive query scheduling algorithm eliminates priority inversion at the cost of reduced throughput. The slack stealing... Read More

High-performance document clustering systems enable similar documents to automatically self-organize into groups. In the past, the large amount of computational time needed to cluster documents prevented practical use of such systems with a large number of documents. A full hardware implementation of K-means clustering has been designed and implemented in reconfigurable hardware that rapidly clusters a half million documents. Documents and concepts are represented as vectors with 4000 dimensions. The circuit was implemented in Field Programmable Gate Array (FPGA) logic and uses four parallel cosine distance metrics to cluster document... Read More

Since the advent of the Java programming language and the development of real-time garbage collection, Java has become an option for implementing real-time applications. The memory management choices provided by real-time garbage collection allow for real-time eJava developers to spend more of their time implementing real-time solutions. Unfortunately, the real-time community is not convinced that real-time garbage collection works in managing memory for Java applications deployed in a real-time context. Consequently, the Real-Time for Java Expert Group formulated the Real-Time Specification for Java (RTSJ) standards to make Java a real-time... Read More

Various languages and tools supporting advanced separation of concerns (such as aspect-oriented programming) provide a software developer with the ability to separate functional and non-functional programmatic intentions. Once these separate pieces of the software have been specified, the tools automatically handle interaction points between separate modules, relieving the developer of this chore and permitting more understandable, maintainable code. Many approaches have left traditional compiler analysis and optimization until after the composition has been performed; unfortunately, analyses performed after composition cannot make use of the logical separation present in the original... Read More

The publish-subscribe communication paradigm is enjoying increasing popularity thanks to its ability to simplify the development of complex distributed applications. However, existing solutions in the publish-subscribe domain address only part of the challenges associated with the development of applications in dynamic scenarios such as mobile ad hoc networks. Mobile applications must be able to assist users in a variety of situations, responding not only to their inputs but also to the characteristics of the environment in which they operate. In this paper, we address these challenges by extending the publish-subscribe... Read More

This dissertation presents a technique for comparing local shape properties for similar three-dimensional objects represented by meshes. Our novel shape representation, the curvature map, describes shape as a function of surface curvature in the region around a point. A multi-pass approach is applied to the curvature map to detect features at different scales. The feature detection step does not require user input or parameter tuning. We use features ordered by strength, the similarity of pairs of features, and pruning based on geometric consistency to efficiently determine key corresponding locations on... Read More

Fair Queuing (FQ) algorithms provide isolation between packet flows, allowing max-min fair sharing of a link even when flows misbehave. However, fairness comes at the expense of per-flow state. To keep the memory requirement independent of the flow count, the router can isolate aggregates of flows, rather than individual flows. We investigate the feasibility of protecting individual flows under such aggregate isolation in the context of Multiple Queue Fair Queuing (MQFQ), where the router maintains a fixed number of queues and associates multiple queues with each flow. MQFQ places packets... Read More

A computer network serves distributed applications by communicating messages between their remote ends. Many such applications desire minimal delay for their messages. Beside this efficiency objective, allocation of the network capacity is also subject to the fairness constraint of not shutting off communication for any individual message. Processor Sharing (PS) is a de facto standard of fairness but provides significantly higher average delay than Shortest Remaining Processing Time (SRPT), which is an optimally efficient but unfair algorithm. In this paper, we explore efficient fair algorithms for message communication where fairness... Read More

The widespread deployment of mobile devices like PDAs and mobile phones has created a vast computation and communication platform for pervasive computing applications. However, these devices feature an array of incompatible hardware and software architectures, discouraging ad-hoc interactions among devices. The Business Process Execution Language (BPEL) allows users in wired computing settings to model applications of significant complexity, leveraging Web standards to guarantee interoperability. However, BPEL's inflexible communication model effectively prohibits its deployment on the kinds of dynamic wireless networks used by most pervasive computing devices. This paper presents extensions... Read More

The ability to effectively model the interaction between proteins is an important and open problem. In molecular biology it is well accepted that from sequence arises form and from form arises function but relating structure to function remains a challenge. The function of a given protein is defined by its interactions. Likewise a malfunction or a change in protein-protein interactions is a hallmark of many diseases. Many researchers are studying the mechanisms of protein-protein interactions and one of the overarching goals of the community is to predict whether two proteins... Read More

Elastic applications are primarily interested in minimal delay achievable for their messages under current network load. In this paper, we investigate how to transmit such messages over a bottleneck link efficiently and fairly. While SRPT (Shortest Remaining Processing Time) is an optimally efficient algorithm that minimizes average delay of messages, large messages might starve under SRPT in heavy load conditions. PS (Processor Sharing) and ViFi (Virtual Finish Time First) are fair but yield higher average delays than under SRPT. We explore the class of fair algorithms further and prove that... Read More

Radio power management is of paramount concern in wireless sensor networks that must achieve long lifetimes on scarce amounts of energy. While a multitude of power management protocols have been proposed in the past, the lack of system support for flexibly integrating them with a diverse set of applications and network platforms has made them difficult to use. Instead of proposing yet another power management protocol, this thesis focuses on providing link layer support towards realizing a Unified Power Management Architecture (UPMA) for flexible radio power management in wireless sensor... Read More

In this dissertation we discuss methologies for estimating the performance of applications on hybrid architectures, systems that include various types of computing resources (e.g. traditional general-purpose processors, chip multiprocessors, reconfigurable hardware). A common use of hybrid architectures will be to deploy coarse pipeline stages of application on "suitable" compute units with communication path for transferring data. The first problem we focus on relates to the sizing the data queues between the different processing elements of an hybrid system. Much of the discussion centers on our analytical models that can be... Read More

The importance of network security has grown tremendously and a collection of devices have been introduced, which can improve the security of a network. Network intrusion detection systems (NIDS) are among the most widely deployed such system; popular NIDS use a collection of signatures of known security threats and viruses, which are used to scan each packet's payload. Today, signatures are often specified as regular expressions; thus the core of the NIDS comprises of a regular expressions parser, such parsers are traditionally implemented as finite automata. Deterministic Finite Automata (DFA)... Read More

Directed graphs with edge labels are used in packet processing algorithms for a variety of network applications. In this paper we present a novel representation for such graph that significantly reduces the memory required for such graphs. This approach called History-based Encoding, eXecution and Addressing (HEXA) challenges the conventional assumption that graph data structures must store pointers of log2n bits to identify successor nodes. HEXA takes advantage of implict information to reduce the information that must be stored explicitly. We demonstrate that the binary tries used for IP route lookup... Read More

Massive amounts of data are passed over public networks. There is a need for network administrators to analyze this traffic, but it was not previously possible to analyze live network data at high speed. It has been shown that streaming computation and deep packet analysis are possible at very high rates through the use of hardware acceleration. This work provides analysis for a larger project that involves digesting large amounts of network traffic. In this system, we process the traffic using hardware that has constraints. The workings of the system... Read More

The Work-In-Progress session of the 13th IEEE Real-Time and Embedded Technology and Applications Symposium (RTAS'07) presents papers describing contributions both to state of the art and state of the practice in the broad field of real-time and embedded systems. The 17 accepted papers were selected from 19 submissions. This proceedings is also available as Washington University in St. Louis Technical Report WUCSE-2007-17, at http://www.cse.seas.wustl.edu/Research/FileDownload.asp?733. Special thanks go to the General Chairs – Steve Goddard and Steve Liu and Program Chairs - Scott Brandt and Frank Mueller for their support and... Read More

In a diversified internet, meta-networks (“metanets?for short) share a common substrate and offer value-added services to millions of users around the globe. Therefore, configuring low-cost metanets with links having enough bandwidth to accommodate all anticipated user traffic is critical to the success of the metanets. In this paper, we propose a novel pruning algorithm that configures metanets on any given substrate in a cost-efficient way. In contrast to other testbed configuration systems, we solve the metanet configuration problem from a higher level specification and produces a network that is dimensioned... Read More

Web Services that provide mission-critical functionality must be replicated to guarantee correct execution and high availability in spite of arbitrary (Byzantine) faults. Existing approaches for Byzantine fault-tolerant execution of Web Services are inadequate to guarantee correct execution due to several major limitations. Some approaches do not support interoperability between replicated Web Services. Other approaches do not provide fault isolation guarantees that are strong enough to prevent cascading failures across organizational and application boundaries. Moreover, existing approaches place impractical limitations on application development by not supporting long-running active threads of computation,... Read More

Modern distributed applications rely upon the functionality of services from multiple providers. Mission-critical services, possibly shared by multiple applications, must be replicated to guarantee correct execution and availability in spite of arbitrary (Byzantine) faults. Furthermore, shared services must enforce strict fault isolation policies to prevent cascading failures across organizational and application boundaries. Most existing protocols for Byzantine fault-tolerant execution do not support interoperability between replicated services while others provide poor fault isolation. Moreover, existing protocols place impractical limitations on application development by disallowing long-running threads of computation, asynchronous operation invocation,... Read More

Explicit and delay-driven congestion control protocols strive to preclude overflow of link buffers by reducing transmission upon incipient congestion. In this paper, we explore fundamental limitations of any congestion control with respect to minimum queuing and loss achievable at highly multiplexed links. We present and evaluate an idealized protocol where all flows always transmit at equal rates. The ideally smooth congestion control causes link queuing only due to asynchrony of flow arrivals, which is intrinsic to computer networks. With overprovisioned buffers, our analysis and simulations for different smooth distributions of... Read More

The ability of TCP (Transmission Control Protocol) or alternative congestion control algorithms to operate successfully in networks with small link buffers has recently become a subject of intensive research. In this paper, we investigate fundamental limitations on minimum buffer requirements for any congestion control. We present an idealized protocol where all flows always transmit at their fair rates. The ideally smooth congestion control causes link queuing only due to asynchrony of flow arrivals, which is intrinsic to computer networks. Our analysis and simulations for different distributions of flow interarrival times... Read More

Lung transplantation is the treatment of choice for end-stage pulmonary diseases. A limited donor supply has resulted in 4000 patients on the waiting list. Currently, 10-20% of donor organs offered for transplantation are deemed suitable under the selection criteria, of which 15-25% fails due to primary graft dysfunction (PGD). This has resulted in increased efforts to search for alternative donor lungs selection criteria. In this study, we attempt to further our understanding of PGD by observing the changes in gene expression across donor lungs that developed PGD versus those that... Read More

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder currently with no cure. Understanding the pathogenesis in the early stages of late-onset AD can help gain important mechanistic insights into this disease as well as aid in effective drug development. The analysis of incipient AD is steeped in difficulties due to its slight pathological and genetic differences from normal ageing. The difficulty also lies in the choice of analysis techniques as statistical power to analyse incipient AD with a small sample size, as is common in pilot studies, can be low... Read More

Understanding the pathogenesis in the early stages of late-onset Alzheimer's disease (LOAD) can help in gaining important mechanistic insights into this devastating neurodegenerative disorder. Alzheimer's disease (AD) is characterised by extensive cell death with disease progression. In this paper laser capture microdissection (LCM) based gene expression profiling, which is able to profile gene expression in a single cell type, is employed to analyse the gene expression regulation of incipient AD. Our analysis shows that LCM based gene expression profiling of neurons has a critical advantage over the conventional gene expression... Read More

When multiple participants work on a workflow that represents a large, collaborative activity, it is important to have a well defined process to determine the portions of the workflow that each participant is responsible for executing. In this paper, we describe a process and related algorithms required to assign tasks in a workflow, to hosts that are willing to carry out the execution of these tasks, and thereby contributing to the completion of the activity. This problem is a stylized form of the multi-processor scheduling algorithm which has been shown... Read More

Fine-grained hardware protection could provide a powerful and effective means for isolating untrusted code. However, previous techniques for providing fine-grained protection in hardware have lead to poor performance. Legba has been proposed as a new caching architecture, designed to reduce the granularity of protection, without slowing down the processor. Unfortunately, the designers of Legba have not attempted an implementation. Instead, all of their analysis is based purely on simulations. We present an implementation of the Legba design on a MIPS Core Processor, along with an analysis of our observations and... Read More

Recent advancements in FPGA technology have allowed manufacturers to place general-purpose processors alongside user-configurable logic gates on a single chip. At first glance, these integrated devices would seem to be the ideal deployment platform for hardware-software co-designed systems, but some issues, such as incompatibility across vendors and confusion over which bus interfaces to support, have impeded adoption of these platforms. This thesis describes the design and operation of Splice, a software-based code generation tool intended to address these types of issues by providing a bus-independent structure that allows end-users to... Read More

Recent advancements in FPGA technology have allowed manufacturers to place general-purpose processors alongside user-configurable logic gates on a single chip. At first glance, these integrated devices would seem to be the ideal deployment platform for hardware-software co-designed systems, but some issues, such as incompatibility across vendors and confusion over which bus interfaces to support, have impeded adoption of these platforms. This thesis describes the design and operation of Splice, a software-based code generation tool intended to address these types of issues by providing a bus-independent structure that allows end-users to... Read More

Distributed real-time and embedded (DRE) systems have stringent constraints on timeliness and other properties whose assurance is crucial to correct system behavior. Our previous research has shown that detailed models of essential middleware mechanisms can be developed, composed, and for constrained examples verified tractably, using state of the art timed automata model checkers. However, to apply model checking to a wider range of real-time systems, particularly those involving more general forms of preemptive concurrency, new techniques are needed to address decidability and tractability concerns. This paper makes three contributions to... Read More

Crossbar-based switches are commonly used to implement routers with throughputs up to about 1 Tb/s. The advent of crossbar scheduling algorithms that provide strong performance guarantees now makes it possible to engineer systems that perform well, even under extreme traffic conditions. Until recently, such performance guarantees have only been developed for crossbars that switch cells rather than variable length packets. Cell-based crossbars incur a worst-case bandwidth penalty of up to a factor of two, since they must fragment variable length packets into fixed length cells. In addition, schedulers for cell-based... Read More

There is a growing interest in virtualized network infrastructures as a means to enable experimental evaluation of new network architectures on a realistic scale. The National Science Foundation's GENI initiative seeks to develop a national experimental facility that would include virtualized network platforms that can support many concurrent experimental networks. Some researchers seek to make virtualization a central architectural component of a future Internet, so that new network architectures can be introduced at any time, without the barriers to entry that currently make this difficult. This paper focuses on how... Read More

Modern high performance routers rely on sophisticated interconnection networks to meet ever increasing demands on capacity. Regulating the flow of packets through these interconnects is critical to providing good performance, particularly in the presence of extreme traffic patterns that result in sustained overload at output ports. Previous studies have used a combination of analysis and idealized simulations to show that coarse-grained scheduling of traffic flows can be effective in preventing congestion, while ensuring high utilization. In this paper, we study the performance of a coarse-grained scheduler in a real router... Read More

Many distributed real-time applications must handle mixed periodic and aperiodic tasks with diverse requirements. However, existing middleware lacks flexible configuration mechanisms needed to manage end-to-end timing easily for a wide range of different applications with both periodic and aperiodic tasks. The primary contribution of this work is the design, implementation and performance evaluation of the first configurable component middleware services for admission control and load balancing of aperiodic and periodic tasks in distributed real-time systems. Empirical results demonstrate the need for and effectiveness of our configurable component middleware approach in... Read More

Many distributed real-time applications must handle mixed aperiodic and periodic tasks with diverse requirements. However, existing middleware lacks flexible configuration mechanisms needed to manage end-to-end timing easily for a wide range of different applications with both aperiodic and periodic tasks. The primary contribution of this work is the design, implementation and performance evaluation of the first configurable component middleware services for admission control and load balancing of aperiodic and periodic tasks in distributed real-time systems. Empirical results demonstrate the need for, and the effectiveness of, our configurable component middleware approach... Read More

Current methods for high-throughput automatic annotation of newly sequenced genomes are largely limited to tools which predict only one transcript per gene locus. Evidence suggests that 20-50% of genes in higher eukariotic organisms are alternatively spliced. This leaves the remainder of the transcripts to be annotated by hand, an expensive time-consuming process. Genomes are being sequenced at a much higher rate than they can be annotated. We present three methods for using the alignments of inexpensive Expressed Sequence Tags in combination with HMM-based gene prediction with N-SCAN EST to recreate... Read More

In this paper, we propose a new approach to wireless sensor network assisted navigation while avoiding moving dangers. Our approach relies on an embedded roadmap in the sensor network that always contains safe paths. The roadmap is adaptive, i.e., it adapts its topology to changing dangers. The mobile robots in the environment uses the roadmap to reach their destinations. We evaluated the performance of embedded roadmap both in simulations using realistic conditions and with real hardware. Our results show that the proposed navigation algorithm is better suited for sensor networks... Read More