@conference {15269,
	title = {A cooperative combinatorial Particle Swarm Optimization algorithm for side-chain packing},
	booktitle = {IEEE Swarm Intelligence Symposium, 2009. SIS {\textquoteright}09},
	year = {2009},
	month = {2009/04/30/March},
	pages = {22 - 29},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {Particle Swarm Optimization (PSO) is a well-known, competitive technique for numerical optimization with real-parameter representation. This paper introduces CCPSO, a new Cooperative Particle Swarm Optimization algorithm for combinatorial problems. The cooperative strategy is achieved by splitting the candidate solution vector into components, where each component is optimized by a particle. Particles move throughout a continuous space, their movements based on the influences exerted by static particles that then get feedback based on the fitness of the candidate solution. Here, the application of this technique to side-chain packing (a proteomics optimization problem) is investigated. To verify the efficiency of the proposed CCPSO algorithm, we test our algorithm on three side-chain packing problems and compare our results with the provably optimal result. Computational results show that the proposed algorithm is very competitive, obtaining a conformation with an energy value within 1\% of the provably optimal solution in many proteins.},
	keywords = {Algorithm design and analysis, Amino acids, combinatorial mathematics, cooperative combinatorial particle swarm optimization algorithm, Design optimization, Encoding, Feedback, numerical optimization, Optimization methods, particle swarm optimisation, Particle swarm optimization, Partitioning algorithms, Proteins, proteomics, proteomics optimization, Robustness, side-chain packing},
	isbn = {978-1-4244-2762-8},
	doi = {10.1109/SIS.2009.4937840},
	author = {Lapizco-Encinas,G. and Kingsford, Carl and Reggia, James A.}
}
@conference {17162,
	title = {Finding comparable temporal categorical records: A similarity measure with an interactive visualization},
	booktitle = {IEEE Symposium on Visual Analytics Science and Technology, 2009. VAST 2009},
	year = {2009},
	month = {2009/10/12/13},
	pages = {27 - 34},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {An increasing number of temporal categorical databases are being collected: Electronic Health Records in healthcare organizations, traffic incident logs in transportation systems, or student records in universities. Finding similar records within these large databases requires effective similarity measures that capture the searcher{\textquoteright}s intent. Many similarity measures exist for numerical time series, but temporal categorical records are different. We propose a temporal categorical similarity measure, the M\&M (Match \& Mismatch) measure, which is based on the concept of aligning records by sentinel events, then matching events between the target and the compared records. The M\&M measure combines the time differences between pairs of events and the number of mismatches. To accom-modate customization of parameters in the M\&M measure and results interpretation, we implemented Similan, an interactive search and visualization tool for temporal categorical records. A usability study with 8 participants demonstrated that Similan was easy to learn and enabled them to find similar records, but users had difficulty understanding the M\&M measure. The usability study feedback, led to an improved version with a continuous timeline, which was tested in a pilot study with 5 participants.},
	keywords = {data visualisation, Educational institutions, Feedback, Information retrieval, interactive search tool, interactive systems, interactive visualization tool, large databases, M\&M Measure, Match \& Mismatch measure, Medical services, numerical time series, parameters customization, Particle measurements, Similan, similarity measure, Similarity Search, temporal categorical databases, Temporal Categorical Records, temporal databases, Testing, Time measurement, time series, transportation, usability, very large databases, visual databases, Visualization},
	isbn = {978-1-4244-5283-5},
	doi = {10.1109/VAST.2009.5332595},
	author = {Wongsuphasawat,K. and Shneiderman, Ben}
}
@conference {15469,
	title = {Using GUI Run-Time State as Feedback to Generate Test Cases},
	booktitle = {Software Engineering, 2007. ICSE 2007. 29th International Conference on},
	year = {2007},
	month = {2007/05//},
	pages = {396 - 405},
	abstract = {This paper presents a new automated model-driven technique to generate test cases by using feedback from the execution of a "seed test suite" on an application under test (AUT). The test cases in the seed suite are designed to be generated automatically and executed very quickly. During their execution, feedback obtained from the AUT{\textquoteright}s run-time state is used to generate new, "improved" test cases. The new test cases subsequently become part of the seed suite. This "anytime technique" continues iteratively, generating and executing additional test cases until resources are exhausted or testing goals have been met. The feedback-based technique is demonstrated for automated testing of graphical user interfaces (GUIs). An existing abstract model of the GUI is used to automatically generate the seed test suite. It is executed; during its execution, state changes in the GUI pinpoint important relationships between GUI events, which evolve the model and help to generate new test cases. Together with a reverse- engineering algorithm used to obtain the initial model and seed suite, the feedback-based technique yields a fully automatic, end-to-end GUI testing process. A feasibility study on four large fielded open-source software (OSS) applications demonstrates that this process is able to significantly improve existing techniques and help identify/report serious problems in the OSS. In response, these problems have been fixed by the developers of the OSS in subsequent versions.},
	keywords = {application under test, automated test case generation, Feedback, feedback-based technique, Graphical user interfaces, GUI run-time state, model-driven technique, open-source software, program testing, public domain software, reverse engineering, reverse-engineering algorithm, seed test suite},
	doi = {10.1109/ICSE.2007.94},
	author = {Xun Yuan and Memon, Atif M.}
}
@article {17258,
	title = {Interactive sonification of choropleth maps},
	journal = {IEEE Multimedia},
	volume = {12},
	year = {2005},
	month = {2005/06//April},
	pages = {26 - 35},
	abstract = {Auditory information is an important channel for the visually impaired. Effective sonification (the use of non-speech audio to convey information) promotes equal working opportunities for people with vision impairments by helping them explore data collections for problem solving and decision making. Interactive sonification systems can make georeferenced data accessible to people with vision impairments. The authors compare methods for using sound to encode georeferenced data patterns and for navigating maps.},
	keywords = {audio signal processing, audio user interfaces, Auditory (non-speech) feedback, auditory information, cartography, choropleth maps, data collections, decision making, Evaluation, Feedback, georeferenced data, Guidelines, handicapped aids, Hardware, HUMANS, information resources, interaction style, Interactive sonification, interactive systems, Navigation, nonspeech audio, problem solving, Problem-solving, sound, universal usability, US Government, User interfaces, vision impairments, World Wide Web},
	isbn = {1070-986X},
	doi = {10.1109/MMUL.2005.28},
	author = {Zhao,Haixia and Smith,B. K and Norman,K. and Plaisant, Catherine and Shneiderman, Ben}
}
@conference {13192,
	title = {Pedestrian classification from moving platforms using cyclic motion pattern},
	booktitle = {Image Processing, 2005. ICIP 2005. IEEE International Conference on},
	volume = {2},
	year = {2005},
	month = {2005/09//},
	pages = {II - 854-7 - II - 854-7},
	abstract = {This paper describes an efficient pedestrian detection system for videos acquired from moving platforms. Given a detected and tracked object as a sequence of images within a bounding box, we describe the periodic signature of its motion pattern using a twin-pendulum model. Then a principle gait angle is extracted in every frame providing gait phase information. By estimating the periodicity from the phase data using a digital phase locked loop (dPLL), we quantify the cyclic pattern of the object, which helps us to continuously classify it as a pedestrian. Past approaches have used shape detectors applied to a single image or classifiers based on human body pixel oscillations, but ours is the first to integrate a global cyclic motion model and periodicity analysis. Novel contributions of this paper include: i) development of a compact shape representation of cyclic motion as a signature for a pedestrian, ii) estimation of gait period via a feedback loop module, and iii) implementation of a fast online pedestrian classification system which operates on videos acquired from moving platforms.},
	keywords = {analysis;, angle;, body, classification;, compact, cyclic, DETECTION, detection;, digital, Feedback, Gait, human, image, information;, locked, loop, loop;, loops;, module;, MOTION, object, oscillations;, pattern;, pedestrian, phase, Pixel, principle, representation;, sequence;, sequences;, SHAPE, system;},
	doi = {10.1109/ICIP.2005.1530190},
	author = {Yang Ran and Qinfen Zheng and Weiss, I. and Davis, Larry S. and Abd-Almageed, Wael and Liang Zhao}
}
@article {12682,
	title = {Visual tracking and recognition using appearance-adaptive models in particle filters},
	journal = {IEEE Transactions on Image Processing},
	volume = {13},
	year = {2004},
	month = {2004/11//},
	pages = {1491 - 1506},
	abstract = {We present an approach that incorporates appearance-adaptive models in a particle filter to realize robust visual tracking and recognition algorithms. Tracking needs modeling interframe motion and appearance changes, whereas recognition needs modeling appearance changes between frames and gallery images. In conventional tracking algorithms, the appearance model is either fixed or rapidly changing, and the motion model is simply a random walk with fixed noise variance. Also, the number of particles is typically fixed. All these factors make the visual tracker unstable. To stabilize the tracker, we propose the following modifications: an observation model arising from an adaptive appearance model, an adaptive velocity motion model with adaptive noise variance, and an adaptive number of particles. The adaptive-velocity model is derived using a first-order linear predictor based on the appearance difference between the incoming observation and the previous particle configuration. Occlusion analysis is implemented using robust statistics. Experimental results on tracking visual objects in long outdoor and indoor video sequences demonstrate the effectiveness and robustness of our tracking algorithm. We then perform simultaneous tracking and recognition by embedding them in a particle filter. For recognition purposes, we model the appearance changes between frames and gallery images by constructing the intra- and extrapersonal spaces. Accurate recognition is achieved when confronted by pose and view variations.},
	keywords = {adaptive filters, adaptive noise variance, algorithms, appearance-adaptive model, Artificial intelligence, Cluster Analysis, Computer Graphics, Computer simulation, Feedback, Filtering, first-order linear predictor, hidden feature removal, HUMANS, Image Enhancement, Image Interpretation, Computer-Assisted, image recognition, Information Storage and Retrieval, Kinematics, Laboratories, Male, Models, Biological, Models, Statistical, MOTION, Movement, Noise robustness, Numerical Analysis, Computer-Assisted, occlusion analysis, Particle filters, Particle tracking, Pattern Recognition, Automated, Predictive models, Reproducibility of results, robust statistics, Sensitivity and Specificity, Signal Processing, Computer-Assisted, State estimation, statistical analysis, Subtraction Technique, tracking, Training data, visual recognition, visual tracking},
	isbn = {1057-7149},
	doi = {10.1109/TIP.2004.836152},
	author = {Zhou,Shaohua Kevin and Chellapa, Rama and Moghaddam, B.}
}
@article {14804,
	title = {Modeling and evaluating design alternatives for an on-line instrumentation system: a case study},
	journal = {IEEE Transactions on Software Engineering},
	volume = {24},
	year = {1998},
	month = {1998/06//},
	pages = {451 - 470},
	abstract = {This paper demonstrates the use of a model-based evaluation approach for instrumentation systems (ISs). The overall objective of this study is to provide early feedback to tool developers regarding IS overhead and performance; such feedback helps developers make appropriate design decisions about alternative system configurations and task scheduling policies. We consider three types of system architectures: network of workstations (NOW), symmetric multiprocessors (SMP), and massively parallel processing (MPP) systems. We develop a Resource OCCupancy (ROCC) model for an on-line IS for an existing tool and parameterize it for an IBM SP-2 platform. This model is simulated to answer several {\textquotedblleft}what if{\textquotedblright} questions regarding two policies to schedule instrumentation data forwarding: collect-and-forward (CF) and batch-and-forward (BF). In addition, this study investigates two alternatives for forwarding the instrumentation data: direct and binary tree forwarding for an MPP system. Simulation results indicate that the BF policy can significantly reduce the overhead and that the tree forwarding configuration exhibits desirable scalability characteristics for MPP systems. Initial measurement-based testing results indicate more than 60 percent reduction in the direct IS overhead when the BF policy was added to Paradyn parallel performance measurement tool},
	keywords = {alternative system configurations, Application software, batch-and-forward, collect-and-forward, Computer aided software engineering, design alternatives, design decisions, Feedback, IBM SP-2 platform, Instruments, massively parallel processing, model-based evaluation approach, Monitoring, multiprocessing programs, on-line instrumentation system, Paradyn parallel performance measurement tool, PARALLEL PROCESSING, Real time systems, scalability characteristics, software metrics, software tools, Space technology, symmetric multiprocessors, system architectures, system monitoring, System testing, task scheduling policies, tool developers, tree forwarding configuration, Workstations},
	isbn = {0098-5589},
	doi = {10.1109/32.689402},
	author = {Waheed, A. and Rover, D. T and Hollingsworth, Jeffrey K}
}
@conference {17056,
	title = {Design and evaluation of incremental data structures and algorithms for dynamic query interfaces},
	booktitle = {IEEE Symposium on Information Visualization, 1997. Proceedings},
	year = {1997},
	month = {1997/10/21/21},
	pages = {81 - 86},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {A dynamic query interface (DQI) is a database access mechanism that provides continuous real-time feedback to the user during query formulation. Previous work shows that DQIs are elegant and powerful interfaces to small databases. Unfortunately, when applied to large databases, previous DQI algorithms slow to a crawl. We present a new incremental approach to DQI algorithms and display updates that work well with large databases, both in theory and in practice.},
	keywords = {Algorithm design and analysis, Bars, Computer science, continuous real-time feedback, Data structures, data visualisation, Data visualization, database access mechanism, Displays, DQI algorithms, dynamic query interfaces, Feedback, Graphical user interfaces, Heuristic algorithms, incremental data structures, Information Visualization, large databases, Manipulator dynamics, NASA, query formulation, query languages, Query processing, real-time systems, small databases, User interfaces, very large databases, visual databases, visual languages},
	isbn = {0-8186-8189-6},
	doi = {10.1109/INFVIS.1997.636790},
	author = {Tanin,E. and Beigel,R. and Shneiderman, Ben}
}
@conference {14787,
	title = {Modeling, Evaluation, and Testing of Paradyn Instrumentation System},
	booktitle = {Proceedings of the 1996 ACM/IEEE Conference on Supercomputing, 1996},
	year = {1996},
	month = {1996///},
	pages = {18 - 18},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {This paper presents a case study of modeling, evaluating, and testing the data collection services (called an instrumentation system) of the Paradyn parallel performance measurement tool using well-known performance evaluation and experiment design techniques. The overall objective of the study is to use modeling- and simulation-based evaluation to provide feedback to the tool developers to help them choose system configurations and task scheduling policies that can significantly reduce the data collection overheads. We develop and parameterize a resource occupancy model for the Paradyn instrumentation system (IS) for an IBM SP-2 platform. This model is parameterized with a measurement-based workload characterization and subsequently used to answer several "what if" questions regarding configuration options and two policies to schedule instrumentation system tasks: collect-and-forward (CF) and batch-and-forward (BF) policies. Simulation results indicate that the BF policy can significantly reduce the overheads. Based on this feedback, the BF policy was implemented in the Paradyn IS as an option to manage the data collection. Measurement-based testing results obtained from this enhanced version of the Paradyn IS are reported in this paper and indicate more than 60\% reduction in the direct IS overheads when the BF policy is used.},
	keywords = {Distributed control, Feedback, High performance computing, Instruments, Monitoring, Real time systems, Software measurement, Software systems, Software testing, System testing},
	isbn = {0-89791-854-1},
	doi = {10.1109/SUPERC.1996.183524},
	author = {Waheed, A. and Rover, D. T and Hollingsworth, Jeffrey K}
}
@conference {17438,
	title = {Tree-maps: a space-filling approach to the visualization of hierarchical information structures},
	booktitle = {, IEEE Conference on Visualization, 1991. Visualization {\textquoteright}91, Proceedings},
	year = {1991},
	month = {1991/10/22/25},
	pages = {284 - 291},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {A method for visualizing hierarchically structured information is described. The tree-map visualization technique makes 100\% use of the available display space, mapping the full hierarchy onto a rectangular region in a space-filling manner. This efficient use of space allows very large hierarchies to be displayed in their entirety and facilitates the presentation of semantic information. Tree-maps can depict both the structure and content of the hierarchy. However, the approach is best suited to hierarchies in which the content of the leaf nodes and the structure of the hierarchy are of primary importance, and the content information associated with internal nodes is largely derived from their children},
	keywords = {Computer displays, Computer Graphics, Computer science, Data analysis, display space, Educational institutions, Feedback, hierarchical information structures, HUMANS, Laboratories, Libraries, Marine vehicles, rectangular region, semantic information, space-filling approach, tree-map visualization technique, trees (mathematics), Two dimensional displays, Visualization},
	isbn = {0-8186-2245-8},
	doi = {10.1109/VISUAL.1991.175815},
	author = {Johnson,B. and Shneiderman, Ben}
}
