@conference {12986,
	title = {Computing the Tree of Life: Leveraging the Power of Desktop and Service Grids},
	booktitle = {Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on},
	year = {2011},
	month = {2011/05//},
	pages = {1896 - 1902},
	abstract = {The trend in life sciences research, particularly in molecular evolutionary systematics, is toward larger data sets and ever-more detailed evolutionary models, which can generate substantial computational loads. Over the past several years we have developed a grid computing system aimed at providing researchers the computational power needed to complete such analyses in a timely manner. Our grid system, known as The Lattice Project, was the first to combine two models of grid computing - the service model, which mainly federates large institutional HPC resources, and the desktop model, which harnesses the power of PCs volunteered by the general public. Recently we have developed a "science portal" style web interface that makes it easier than ever for phylogenetic analyses to be completed using GARLI, a popular program that uses a maximum likelihood method to infer the evolutionary history of organisms on the basis of genetic sequence data. This paper describes our approach to scheduling thousands of GARLI jobs with diverse requirements to heterogeneous grid resources, which include volunteer computers running BOINC software. A key component of this system provides a priori GARLI runtime estimates using machine learning with random forests.},
	keywords = {(artificial, (mathematics);user, analysis;science, BOINC, computation;grid, computational, computing, computing;information, computing;machine, data;grid, estimation;portals;trees, evolutionary, Grid, grids;service, handling;evolutionary, history;evolutionary, intelligence);maximum, interface;computational, interfaces;, jobs;HPC, learning;maximum, likelihood, load;Internet;data, method;molecular, model;genetic, model;substantial, portal;service, power;data, project;life, resource;lattice, resource;Web, sequence, services;learning, sets;evolutionary, software;GARLI, system;heterogeneous, systematics;phylogenetic, tree},
	doi = {10.1109/IPDPS.2011.344},
	author = {Bazinet,A. L and Cummings, Michael P.}
}
@conference {14389,
	title = {Characterizing RNA Secondary-Structure Features and Their Effects on Splice-Site Prediction},
	booktitle = {Data Mining Workshops, 2007. ICDM Workshops 2007. Seventh IEEE International Conference on},
	year = {2007},
	month = {2007/10//},
	pages = {89 - 94},
	abstract = {RNA molecules are distinguished by their sequence composition and by their three-dimensional shape, called the secondary structure. The secondary structure of a pre-mRNA sequence may have a strong influence on gene splicing. In our previous work, we showed that a splice-site model employing sequence features built using our feature generation algorithm was very effective in predicting splice sites. The generated sequence features also contained biologically relevant features. In this paper, we extend the feature generation algorithm to construct secondary-structure features. These features capture the nucleotide pairing tendency in the splice-site neighborhood. We extend the splice-site model to include both pre-mRNA sequence and structure characteristics. The new model significantly outperforms the sequence-based features model. The identified secondary-structure features capture biologically relevant signals such as splicing silencers. We also found these signals to prefer specific regions around the splice-site neighborhood and we detail their preference.},
	keywords = {algorithm;gene, biophysics;molecular, composition;splice-site, compounds;sequences;, computing;genetics;macromolecules;molecular, configurations;organic, features;feature, generation, model;splice-site, molecules;RNA, neighborhood;three-dimensional, pairing, RNA, secondary-structure, sequence, shape;biology, splicing;nucleotide, tendency;pre-mRNA},
	doi = {10.1109/ICDMW.2007.119},
	author = {Dogan,R. I and Getoor, Lise and Wilbur,W. J}
}
@conference {12583,
	title = {From Videos to Verbs: Mining Videos for Activities using a Cascade of Dynamical Systems},
	booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on},
	year = {2007},
	month = {2007/06//},
	pages = {1 - 8},
	abstract = {Clustering video sequences in order to infer and extract activities from a single video stream is an extremely important problem and has significant potential in video indexing, surveillance, activity discovery and event recognition. Clustering a video sequence into activities requires one to simultaneously recognize activity boundaries (activity consistent subsequences) and cluster these activity subsequences. In order to do this, we build a generative model for activities (in video) using a cascade of dynamical systems and show that this model is able to capture and represent a diverse class of activities. We then derive algorithms to learn the model parameters from a video stream and also show how a single video sequence may be clustered into different clusters where each cluster represents an activity. We also propose a novel technique to build affine, view, rate invariance of the activity into the distance metric for clustering. Experiments show that the clusters found by the algorithm correspond to semantically meaningful activities.},
	keywords = {activities, clustering;image, clustering;video, extraction;dynamical, mining;video, processing;, sequence, sequences;pattern, signal, stream;video, systems;single, video},
	doi = {10.1109/CVPR.2007.383170},
	author = {Turaga, P.K. and Veeraraghavan,A. and Chellapa, Rama}
}
@conference {18279,
	title = {Security Issues in Cooperative Communications: Tracing Adversarial Relays},
	booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on},
	volume = {4},
	year = {2006},
	month = {2006/05//},
	pages = {IV - IV},
	abstract = {Cooperative communication system explores a new dimension of diversity in wireless communications to combat unfriendly wireless environment through strategic relays. While this emerging technology is promising in improving communication quality, some security problems inherent to cooperative relay also arise. In this paper we investigate the security issues in cooperative communications that consist of multiple relay nodes using decode-and-forward strategy. In particular, we consider the situation where one of the relay nodes is adversarial and tries to corrupt the communications by sending garbled signals. We show that the conventional physical-layer signal detection will not be effective in such a scenario, and the application-layer cryptography alone is not sufficient to identify the adversarial relay. To combat adversarial relay, we propose a cross-layer scheme that uses pseudo-random tracing symbols, with an adaptive signal detection rule at the physical layer, and direct sequence spread spectrum symbol construction at the application layer for tracing and identifying adversarial relay. Our experimental simulations show that the proposed tracing scheme is effective and efficient},
	keywords = {adaptive, Communication, communications;adaptive, construction;multiple, detection;adversarial, detection;decoding;radiocommunication;telecommunication, issues;strategic, nodes;pseudo-random, relay, relay;decode-and-forward, relays;cooperative, relays;wireless, security;, sequence, signal, spectrum, spread, strategy;direct, symbol, symbols;security, system;cooperative, tracing},
	doi = {10.1109/ICASSP.2006.1660907},
	author = {Mao,Yinian and M. Wu}
}
@article {12752,
	title = {A generic approach to simultaneous tracking and verification in video},
	journal = {Image Processing, IEEE Transactions on},
	volume = {11},
	year = {2002},
	month = {2002/05//},
	pages = {530 - 544},
	abstract = {A generic approach to simultaneous tracking and verification in video data is presented. The approach is based on posterior density estimation using sequential Monte Carlo methods. Visual tracking, which is in essence a temporal correspondence problem, is solved through probability density propagation, with the density being defined over a proper state space characterizing the object configuration. Verification is realized through hypothesis testing using the estimated posterior density. In its most basic form, verification can be performed as follows. Given a measurement vector Z and two hypotheses H<sub>1</sub> and H0, we first estimate posterior probabilities P(H<sub>0</sub>|Z) and P(H<sub>1</sub>|Z), and then choose the one with the larger posterior probability as the true hypothesis. Several applications of the approach are illustrated by experiments devised to evaluate its performance. The idea is first tested on synthetic data, and then experiments with real video sequences are presented, illustrating vehicle tracking and verification, human (face) tracking and verification, facial feature tracking, and image sequence stabilization.},
	keywords = {approach;, Carlo, configuration;, correspondence, data;, density, density;, estimated, estimation;, evaluation;, extraction;, Face, facial, feature, generic, human, hypothesis, image, measurement, methods;, Monte, object, performance, posterior, probability, probability;, problem;, processing;, propagation;, recognition;, road, sequence, sequences;, sequential, signal, space;, stabilization;, state, synthetic, temporal, testing;, tracking;, vector;, vehicle, vehicles;, verification;, video, visual},
	isbn = {1057-7149},
	doi = {10.1109/TIP.2002.1006400},
	author = {Li,Baoxin and Chellapa, Rama}
}
