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2000


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Knowledge Discovery in Databases: An Information Retrieval Perspective

Ong, CS.

Malaysian Journal of Computer Science, 13(2):54-63, December 2000 (article)

Abstract
The current trend of increasing capabilities in data generation and collection has resulted in an urgent need for data mining applications, also called knowledge discovery in databases. This paper identifies and examines the issues involved in extracting useful grains of knowledge from large amounts of data. It describes a framework to categorise data mining systems. The author also gives an overview of the issues pertaining to data pre processing, as well as various information gathering methodologies and techniques. The paper covers some popular tools such as classification, clustering, and generalisation. A summary of statistical and machine learning techniques used currently is also provided.

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PDF [BibTex]

2000


PDF [BibTex]


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A Simple Iterative Approach to Parameter Optimization

Zien, A., Zimmer, R., Lengauer, T.

Journal of Computational Biology, 7(3,4):483-501, November 2000 (article)

Abstract
Various bioinformatics problems require optimizing several different properties simultaneously. For example, in the protein threading problem, a scoring function combines the values for different parameters of possible sequence-to-structure alignments into a single score to allow for unambiguous optimization. In this context, an essential question is how each property should be weighted. As the native structures are known for some sequences, a partial ordering on optimal alignments to other structures, e.g., derived from structural comparisons, may be used to adjust the weights. To resolve the arising interdependence of weights and computed solutions, we propose a heuristic approach: iterating the computation of solutions (here, threading alignments) given the weights and the estimation of optimal weights of the scoring function given these solutions via systematic calibration methods. For our application (i.e., threading), this iterative approach results in structurally meaningful weights that significantly improve performance on both the training and the test data sets. In addition, the optimized parameters show significant improvements on the recognition rate for a grossly enlarged comprehensive benchmark, a modified recognition protocol as well as modified alignment types (local instead of global and profiles instead of single sequences). These results show the general validity of the optimized weights for the given threading program and the associated scoring contributions.

ei

Web [BibTex]

Web [BibTex]


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Identification of Drug Target Proteins

Zien, A., Küffner, R., Mevissen, T., Zimmer, R., Lengauer, T.

ERCIM News, 43, pages: 16-17, October 2000 (article)

ei

Web [BibTex]

Web [BibTex]


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Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites

Zien, A., Rätsch, G., Mika, S., Schölkopf, B., Lengauer, T., Müller, K.

Bioinformatics, 16(9):799-807, September 2000 (article)

Abstract
Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS). Results: The task of finding TIS can be modeled as a classification problem. We demonstrate the applicability of support vector machines for this task, and show how to incorporate prior biological knowledge by engineering an appropriate kernel function. With the described techniques the recognition performance can be improved by 26% over leading existing approaches. We provide evidence that existing related methods (e.g. ESTScan) could profit from advanced TIS recognition.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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A Meanfield Approach to the Thermodynamics of a Protein-Solvent System with Application to the Oligomerization of the Tumour Suppressor p53.

Noolandi, J., Davison, TS., Vokel, A., Nie, F., Kay, C., Arrowsmith, C.

Proceedings of the National Academy of Sciences of the United States of America, 97(18):9955-9960, August 2000 (article)

ei

Web [BibTex]

Web [BibTex]


Probabilistic detection and tracking of motion boundaries
Probabilistic detection and tracking of motion boundaries

Black, M. J., Fleet, D. J.

Int. J. of Computer Vision, 38(3):231-245, July 2000 (article)

Abstract
We propose a Bayesian framework for representing and recognizing local image motion in terms of two basic models: translational motion and motion boundaries. Motion boundaries are represented using a non-linear generative model that explicitly encodes the orientation of the boundary, the velocities on either side, the motion of the occluding edge over time, and the appearance/disappearance of pixels at the boundary. We represent the posterior probability distribution over the model parameters given the image data using discrete samples. This distribution is propagated over time using a particle filtering algorithm. To efficiently represent such a high-dimensional space we initialize samples using the responses of a low-level motion discontinuity detector. The formulation and computational model provide a general probabilistic framework for motion estimation with multiple, non-linear, models.

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pdf pdf from publisher Video [BibTex]

pdf pdf from publisher Video [BibTex]


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New Support Vector Algorithms

Schölkopf, B., Smola, A., Williamson, R., Bartlett, P.

Neural Computation, 12(5):1207-1245, May 2000 (article)

Abstract
We propose a new class of support vector algorithms for regression and classification. In these algorithms, a parameter {nu} lets one effectively control the number of support vectors. While this can be useful in its own right, the parameterization has the additional benefit of enabling us to eliminate one of the other free parameters of the algorithm: the accuracy parameter {epsilon} in the regression case, and the regularization constant C in the classification case. We describe the algorithms, give some theoretical results concerning the meaning and the choice of {nu}, and report experimental results.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Bounds on Error Expectation for Support Vector Machines

Vapnik, V., Chapelle, O.

Neural Computation, 12(9):2013-2036, 2000 (article)

Abstract
We introduce the concept of span of support vectors (SV) and show that the generalization ability of support vector machines (SVM) depends on this new geometrical concept. We prove that the value of the span is always smaller (and can be much smaller) than the diameter of the smallest sphere containing th e support vectors, used in previous bounds. We also demonstate experimentally that the prediction of the test error given by the span is very accurate and has direct application in model selection (choice of the optimal parameters of the SVM)

ei

GZIP [BibTex]

GZIP [BibTex]


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Two-dimensional fine particle positioning under an optical microscope using a piezoresistive cantilever as a manipulator

Sitti, M., Hashimoto, H.

journal of Micromechatronics, 1(1):25-48, Brill, 2000 (article)

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[BibTex]


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Investigation of Virtual Reality Interface for AFM-based Nano Manipulation

Horiguchi, S., Sitti, M., Hashimoto, H.

IEEJ Transactions on Electronics, Information and Systems, 120(12):1948-1956, The Institute of Electrical Engineers of Japan, 2000 (article)

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[BibTex]

[BibTex]


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Macro to Nano Tele-Manipulation Towards Nanoelectromec hanical Systems

Sitti, M., Hashimoto, H.

Journal of Robotics and Mechatronics, 12(3):209-217, FUJI TECHNOLOGY PRESS LTD., 2000 (article)

pi

[BibTex]

[BibTex]


Design and use of linear models for image motion analysis
Design and use of linear models for image motion analysis

Fleet, D. J., Black, M. J., Yacoob, Y., Jepson, A. D.

Int. J. of Computer Vision, 36(3):171-193, 2000 (article)

Abstract
Linear parameterized models of optical flow, particularly affine models, have become widespread in image motion analysis. The linear model coefficients are straightforward to estimate, and they provide reliable estimates of the optical flow of smooth surfaces. Here we explore the use of parameterized motion models that represent much more varied and complex motions. Our goals are threefold: to construct linear bases for complex motion phenomena; to estimate the coefficients of these linear models; and to recognize or classify image motions from the estimated coefficients. We consider two broad classes of motions: i) generic “motion features” such as motion discontinuities and moving bars; and ii) non-rigid, object-specific, motions such as the motion of human mouths. For motion features we construct a basis of steerable flow fields that approximate the motion features. For object-specific motions we construct basis flow fields from example motions using principal component analysis. In both cases, the model coefficients can be estimated directly from spatiotemporal image derivatives with a robust, multi-resolution scheme. Finally, we show how these model coefficients can be use to detect and recognize specific motions such as occlusion boundaries and facial expressions.

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pdf [BibTex]

pdf [BibTex]


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Controlled pushing of nanoparticles: modeling and experiments

Sitti, M., Hashimoto, H.

IEEE/ASME transactions on mechatronics, 5(2):199-211, IEEE, 2000 (article)

pi

[BibTex]

[BibTex]


Robustly estimating changes in image appearance
Robustly estimating changes in image appearance

Black, M. J., Fleet, D. J., Yacoob, Y.

Computer Vision and Image Understanding, 78(1):8-31, 2000 (article)

Abstract
We propose a generalized model of image “appearance change” in which brightness variation over time is represented as a probabilistic mixture of different causes. We define four generative models of appearance change due to (1) object or camera motion; (2) illumination phenomena; (3) specular reflections; and (4) “iconic changes” which are specific to the objects being viewed. These iconic changes include complex occlusion events and changes in the material properties of the objects. We develop a robust statistical framework for recovering these appearance changes in image sequences. This approach generalizes previous work on optical flow to provide a richer description of image events and more reliable estimates of image motion in the presence of shadows and specular reflections.

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pdf pdf from publisher DOI [BibTex]

pdf pdf from publisher DOI [BibTex]