Significance Of inter-species matches when evolutionary rate varies
We develop techniques to estimate the statistical significance of gap-free alignments between two genomic DNA sequences, using human-mouse alignments as an example. The sequences are assumed to be sufficiently similar that some but not all of the neutrally evolving regions (i.e., those under no evolutionary constraint) can be reliably aligned. Our goal is to model the situation in which the neutral rate of evolution, and hence the extent of the aligning intervals, varies across the genome. In some cases, this permits the weaker of two matches to be judged as less likely to have arisen by chance, provided it lies in a genomic interval with a high level of background divergence. We employ a Hidden Markov Model to capture variations in divergence rates, and assign probability values to gap-free alignments using techniques related to those used for the same purpose by Blast. Our methods are illustrated in detail using a 1.49 Mb genomic region. Preliminary results using all of human chromosome 22 indicate that these techniques will work for the entire human genome.

title: On Zador's entropy-constrained quantization theorem
abstract: Zador's classic result for the asymptotic high-rate behavior of entropy-constrained vector quantization is recast in a Lagrangian form which better matches the Lloyd algorithm used to optimize such quantizers. A proof that the result holds for a general class of distributions is sketched.

title: Unsupervised Multiresolution Segmentation for Images with Low Depth of Field
abstract: Unsupervised segmentation of images with low depth of field (DOF) is highly useful in various applications. This paper describes a novel multiresolution image segmentation algorithm for low DOF images. The algorithm is designed to separate a sharply focused object-of-interest from other foreground or background objects. The algorithm is fully automatic in that all parameters are image independent. A multi-scale approach based on high frequency wavelet coefficients and their statistics is used to perform context-dependent classification of individual blocks of the image. Unlike other edge-based approaches, our algorithm does not rely on the process of connecting object boundaries. The algorithm has achieved high accuracy when tested on more than 100 low DOF images, many with inhomogeneous foreground or background distractions. Compared with he state of the art algorithms, this new algorithm provides better accuracy at higher speed.

title: Asymptotic Performance of Vector Quantizers with a Perceptual Distortion Measure
abstract: Gersho's (1979) bounds on the asymptotic performance of vector quantizers are valid for vector distortions which are powers of the Euclidean norm. Yamada, Tazaki, and Gray (1980) generalized the results to distortion measures that are increasing functions of the norm of their argument. In both cases, the distortion is uniquely determined by the vector quantization error, i.e., the Euclidean difference between the original vector and the codeword into which it is quantized. We generalize these asymptotic bounds to input-weighted quadratic distortion measures and measures that are approximately output-weighted-quadratic when the distortion is small, a class of distortion measures often claimed to be perceptually meaningful. An approximation of the asymptotic distortion based on Gersho's conjecture is derived as well. We also consider the problem of source mismatch, where the quantizer is designed using a probability density different from the true source density. The resulting asymptotic performance in terms of distortion increase in decibels is shown to be linear in the relative entropy between the true and estimated probability densities.

title: A source coding approach to classification by vector quantization and the principle of minimum description length
abstract: An algorithm for supervised classification using vector quantization and entropy coding is presented. The classification rule is formed from a set of training data {(X/sub i/, Y/sub i/)}/sub i=1//sup n/, which are independent samples from a joint distribution P/sub XY/. Based on the principle of minimum description length (MDL), a statistical model that approximates the distribution P/sub XY/ ought to enable efficient coding of X and Y. On the other hand, we expect a system that encodes (X, Y) efficiently to provide ample information on the distribution P/sub XY/. This information can then be used to classify X, i.e., to predict the corresponding Y based on X. To encode both X and Y, a two-stage vector quantizer is applied to X and a Huffman code is formed for Y conditioned on each quantized value of X. The optimization of the encoder is equivalent to the design of a vector quantizer with an objective function reflecting the joint penalty of quantization error and misclassification rate. This vector quantizer provides an estimation of the conditional distribution of Y given X, which in turn yields an approximation to the Bayes classification rule. This algorithm, namely discriminant vector quantization (DVQ), is compared with learning vector quantization (LVQ) and CART/sup R/ on a number of data sets. DVQ outperforms the other two on several data sets. The relation between DVQ, density estimation, and regression is also discussed.

title: Real-Time Computerized Annotation of Pictures
abstract: Developing effective methods for automated annotation of digital pictures continues to challenge computer scientists. The capability of annotating pictures by computers can lead to breakthroughs in a wide range of applications, including Web image search, online picture-sharing communities, and scientific experiments. In this work, the authors developed new optimization and estimation techniques to address two fundamental problems in machine learning. These new techniques serve as the basis for the automatic linguistic indexing of pictures - real time (ALIPR) system of fully automatic and high-speed annotation for online pictures. In particular, the D2-clustering method, in the same spirit as K-Means for vectors, is developed to group objects represented by bags of weighted vectors. Moreover, a generalized mixture modeling technique (kernel smoothing as a special case) for nonvector data is developed using the novel concept of hypothetical local mapping (HLM). ALIPR has been tested by thousands of pictures from an Internet photo-sharing site, unrelated to the source of those pictures used in the training process. Its performance has also been studied at an online demonstration site, where arbitrary users provide pictures of their choices and indicate the correctness of each annotation word. The experimental results show that a single computer processor can suggest annotation terms in real time and with good accuracy.

title: Grid Resource Discovery Using Semantic Communities
abstract: Grid technologies enable the sharing and collaborating of a wide variety of resources. To fully utilize these resources, effective resource discovery mechanisms are necessities. However, the complicated and dynamic characteristics of the grid resources make sharing and discovering them a challenging issue. In this paper, we propose a semantic community approach to assisting the efficient resource discovery and query in grids. Semantic community is a natural arrangement of distributed systems. It prunes the searching space and reduces the cost of searching. Moreover, it exhibits many desirable properties, including being fully decentralized and supporting complex queries. Our simulation results show how searching the girds can take advantage of semantic communities to reduce the searching cost and improve the quality of search results.

title: Construct robust rule sets for classification
abstract: We study the problem of computing classification rule sets from relational databases so that accurate predictions can be made on test data with missing attribute values. Traditional classifiers perform badly when test data are not as complete as the training data because they tailor a training database too much. We introduce the concept of one rule set being more robust than another, that is, able to make more accurate predictions on test data with missing attribute values. We show that the optimal class association rule set is as robust as the complete class association rule set. We then introduce the k-optimal rule set, which provides predictions exactly the same as the optimal class association rule set on test data with up to k missing attribute values. This leads to a hierarchy of k-optimal rule sets in which decreasing size corresponds to decreasing robustness, and they all more robust than a traditional classification rule set. We introduce two methods to find k-optimal rule sets, i.e. an optimal association rule mining approach and a heuristic approximate approach. We show experimentally that a k-optimal rule set generated by the optimal association rule mining approach performs better than that by the heuristic approximate approach and both rule sets perform significantly better than a typical classification rule set (C4.5Rules) on incomplete test data.

title: Enhanced smart-card based license management
abstract: In many e-commerce (electronic commerce) situations, the owner of a digital object wants to enforce policies on the object after the object is in the customer's hands. The object can be thought of as being software, because data is often protected by forcing access to it to take place through a particular authorized software (e.g., a "reader" for an encrypted media file, in which case a license to view the movie is, in some sense, a "software license"). One of the ways that were proposed for such policy enforcement is the use of smart cards. We describe an enhanced solution to software license management based on tamper-resistant smart cards. Our public-key protocols for binding software licenses to smart cards improve on previous schemes in that they support flexible and partial transfers of licenses between cards. The license is verified by checking the presence of the associated card. The user can therefore have several software licenses all of which are bound to one card, to avoid juggling several cards in and out of the card reader.

title: Modeling the effects of elevation data resolution on the performance of topography-based watershed runoff simulation
abstract: The spatial uncertainty of a topography based rainfall runoff model (TOPMODEL) is addressed in this study to assess its variability in simulating watershed hydrologic response with regards to the change of digital elevation model (DEM) resolution. Twelve DEM realizations of different grid sizes ranging from 30m to 3000m for each of two case watersheds are used for comparative examinations. The study shows that DEM grid size has significant influence on the topographic index distribution which represents the effect of topography on watershed hydrology in TOPMODEL. The smoothing effect of grid size increase may result in deteriorated topographic index distributions at coarse resolutions as the ratio of grid cell area to watershed area gets larger. The simulated discharges and model efficiencies using a same set of TOPMODEL parameters are sensitive to DEM grid size especially at coarse resolutions. This sensitivity, however, can be moderated by parameter calibrations as the optimization runs show that fairly equal efficiencies can be preserved by the compensation effect of transmissivity parameter T"0 within a large extent of DEM resolution for each watershed. The interaction between T"0 and the topographic index distribution with respect to TOPMDOEL model performance is also examined. It is found that both study watersheds demonstrate a similar pattern of change in model performance along with the increase of the grid-to-watershed ratio. The analysis reveals that the ratio poses an important factor in controlling the effect of DEM grid size on TOPMODEL performance. A ratio of less than 5% is suggested in DEM resolution selection for TOPMODEL applications based on the results of this study.

title: Finite element analysis for a nonlinear diffusion model in image processing
abstract: The optimal error estimate O ( h k +1 ) for a popular nonlinear diffusion model widely used in image processing is proved for the standard k th -order ( k ≥ 1) conforming tensor-product finite elements in the L 2 -norm. The optimal L 2 -estimate is obtained by the integral identity technique [1–3] without using the classic Nitsche duality argument [4].