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PubMed2006

Oriented wavelet transform for image compression and denoising.

In this paper, we introduce a new transform for image processing, based on wavelets and the lifting paradigm. The lifting steps of a unidimensional wavelet are applied along a local orientation defined on a quincunx sampling grid. To maximize energy compaction, the orientation minimizing the prediction error is chosen adaptively. A fine-grained multiscale analysis is provided by iterating the decomposition on the low-frequency band. In the context of image compression, the multiresolution orientation map is coded using a quad tree. The rate allocation between the orientation map and wavelet coefficients is jointly optimized in a rate-distortion sense. For image denoising, a Markov model is used to extract the orientations from the noisy image. As long as the map is sufficiently homogeneous, interesting properties of the original wavelet are preserved such as regularity and orthogonality. Perfect reconstruction is ensured by the reversibility of the lifting scheme. The mutual information between the wavelet coefficients is studied and compared to the one observed with a separable wavelet transform. The rate-distortion performance of this new transform is evaluated for image coding using state-of-the-art subband coders. Its performance in a denoising application is also assessed against the performance obtained with other transforms or denoising methods.

Algorithms↗
PubMed2004

Online recognition of Chinese characters: the state-of-the-art.

Online handwriting recognition is gaining renewed interest owing to the increase of pen computing applications and new pen input devices. The recognition of Chinese characters is different from western handwriting recognition and poses a special challenge. To provide an overview of the technical status and inspire future research, this paper reviews the advances in online Chinese character recognition (OLCCR), with emphasis on the research works from the 1990s. Compared to the research in the 1980s, the research efforts in the 1990s aimed to further relax the constraints of handwriting, namely, the adherence to standard stroke orders and stroke numbers and the restriction of recognition to isolated characters only. The target of recognition has shifted from regular script to fluent script in order to better meet the requirements of practical applications. The research works are reviewed in terms of pattern representation, character classification, learning/adaptation, and contextual processing. We compare important results and discuss possible directions of future research.

Algorithms↗
PubMed2004

The writer independent online handwriting recognition system frog on hand and cluster generative statistical dynamic time warping.

In this paper, we give a comprehensive description of our writer-independent online handwriting recognition system frog on hand. The focus of this work concerns the presentation of the classification/training approach, which we call cluster generative statistical dynamic time warping (CSDTW). CSDTW is a general, scalable, HMM-based method for variable-sized, sequential data that holistically combines cluster analysis and statistical sequence modeling. It can handle general classification problems that rely on this sequential type of data, e.g., speech recognition, genome processing, robotics, etc. Contrary to previous attempts, clustering and statistical sequence modeling are embedded in a single feature space and use a closely related distance measure. We show character recognition experiments of frog on hand using CSDTW on the UNIPEN online handwriting database. The recognition accuracy is significantly higher than reported results of other handwriting recognition systems. Finally, we describe the real-time implementation of frog on hand on a Linux Compaq iPAQ embedded device.

Algorithms↗
PubMed2004

Machine printed text and handwriting identification in noisy document images.

In this paper, we address the problem of the identification of text in noisy document images. We are especially focused on segmenting and identifying between handwriting and machine printed text because: 1) Handwriting in a document often indicates corrections, additions, or other supplemental information that should be treated differently from the main content and 2) the segmentation and recognition techniques requested for machine printed and handwritten text are significantly different. A novel aspect of our approach is that we treat noise as a separate class and model noise based on selected features. Trained Fisher classifiers are used to identify machine printed text and handwriting from noise and we further exploit context to refine the classification. A Markov Random Field-based (MRF) approach is used to model the geometrical structure of the printed text, handwriting, and noise to rectify misclassifications. Experimental results show that our approach is robust and can significantly improve page segmentation in noisy document collections.

Algorithms↗
PubMed2004

Estimating degradation model parameters using neighborhood pattern distributions: an optimization approach.

Noise models are crucial for designing image restoration algorithms, generating synthetic training data, and predicting algorithm performance. There are two related but distinct estimation scenarios. The first is model calibration, where it is assumed that the input ideal bitmap and the output of the degradation process are both known. The second is the general estimation problem, where only the image from the output of the degradation process is given. While researchers have addressed the problem of calibration of models, issues with the general estimation problems have not been addressed in the literature. In this paper, we describe a parameter estimation algorithm for a morphological, binary, page-level image degradation model. The inputs to the estimation algorithm are 1) the degraded image and 2) information regarding the font type (italic, bold, serif, sans serif). We simulate degraded images using our model and search for the optimal parameter by looking for a parameter value for which the local neighborhood pattern distributions in the simulated image and the given degraded image are most similar. The parameter space is searched using a direct search optimization algorithm. We use the p-value of the Kolmogorov-Smirnov test as the measure of similarity between the two neighborhood pattern distributions. We show results of our algorithm on degraded document images.

Algorithms↗
PubMed2005

Fast SVM training algorithm with decomposition on very large data sets.

Training a support vector machine on a data set of huge size with thousands of classes is a challenging problem. This paper proposes an efficient algorithm to solve this problem. The key idea is to introduce a parallel optimization step to quickly remove most of the nonsupport vectors, where block diagonal matrices are used to approximate the original kernel matrix so that the original problem can be split into hundreds of subproblems which can be solved more efficiently. In addition, some effective strategies such as kernel caching and efficient computation of kernel matrix are integrated to speed up the training process. Our analysis of the proposed algorithm shows that its time complexity grows linearly with the number of classes and size of the data set. In the experiments, many appealing properties of the proposed algorithm have been investigated and the results show that the proposed algorithm has a much better scaling capability than Libsvm, SVMlight, and SVMTorch. Moreover, the good generalization performances on several large databases have also been achieved.

Algorithms↗
PubMed2006

Symbol recognition with kernel density matching.

We propose a novel approach to similarity assessment for graphic symbols. Symbols are represented as 2D kernel densities and their similarity is measured by the Kullback-Leibler divergence. Symbol orientation is found by gradient-based angle searching or independent component analysis. Experimental results show the outstanding performance of this approach in various situations.

Algorithms↗
PubMed2006

Metric learning for text documents.

Many algorithms in machine learning rely on being given a good distance metric over the input space. Rather than using a default metric such as the Euclidean metric, it is desirable to obtain a metric based on the provided data. We consider the problem of learning a Riemannian metric associated with a given differentiable manifold and a set of points. Our approach to the problem involves choosing a metric from a parametric family that is based on maximizing the inverse volume of a given data set of points. From a statistical perspective, it is related to maximum likelihood under a model that assigns probabilities inversely proportional to the Riemannian volume element. We discuss in detail learning a metric on the multinomial simplex where the metric candidates are pull-back metrics of the Fisher information under a Lie group of transformations. When applied to text document classification the resulting geodesic distance resemble, but outperform, the tfidf cosine similarity measure.

Algorithms↗
PubMed2005

Recognition of merged characters based on forepart prediction, necessity-sufficiency matching, and character-adaptive masking.

Merged characters are the major cause of recognition errors. We classify the merging relationship between two involved characters into three types: "linear," "nonlinear," and "overlapped." Most segmentation methods handle the first type well, however, their capabilities of handling the other two types are limited. The weakness of handling the nonlinear and overlapped types results from character segmentation by linear, usually vertical, cuts assumed in these methods. This paper proposes a novel merged character segmentation and recognition method based on forepart prediction, necessity-sufficiency matching and character-adaptive masking. This method utilizes the information obtained from the forepart of merged characters to predict candidates for the leftmost character, and then applies character-adaptive masking and character recognition to verifying the prediction. Therefore, the arbitrary-shaped cutting path will follow the right shape of the leftmost character so as to preserve the shape of the next character. This method handles the first two types well and greatly improves the segmentation accuracy of the overlapped type. The experimental results and the performance comparisons with other methods demonstrate the effectiveness of the proposed method.

Algorithms↗
PubMedDate not supplied

Drawing directed graphs using quadratic programming.

We describe a new method for visualization of directed graphs. The method combines constraint programming techniques with a high performance force-directed placement (FDP) algorithm. The resulting placements highlight hierarchy in directed graphs while retaining useful properties of FDP; such as emphasis of symmetries and preservation of proximity relations. Our algorithm automatically identifies those parts of the digraph that contain hierarchical information and draws them accordingly. Additionally, those parts that do not contain hierarchy are drawn at the same quality expected from a nonhierarchical, undirected layout algorithm. Our experiments show that this new approach is better able to convey the structure of large digraphs than the most widely used hierarchical graph-drawing method. An interesting application of our algorithm is directional multidimensional scaling (DMDS). DMDS deals with low-dimensional embedding of multivariate data where we want to emphasize the overall flow in the data (e.g., chronological progress) along one of the axes.

Computer Graphics↗
PubMed2006

Locating previously unknown patterns in data-mining results: a dual data- and knowledge-mining method.

BACKGROUND: Data mining can be utilized to automate analysis of substantial amounts of data produced in many organizations. However, data mining produces large numbers of rules and patterns, many of which are not useful. Existing methods for pruning uninteresting patterns have only begun to automate the knowledge acquisition step (which is required for subjective measures of interestingness), hence leaving a serious bottleneck. In this paper we propose a method for automatically acquiring knowledge to shorten the pattern list by locating the novel and interesting ones. METHODS: The dual-mining method is based on automatically comparing the strength of patterns mined from a database with the strength of equivalent patterns mined from a relevant knowledgebase. When these two estimates of pattern strength do not match, a high "surprise score" is assigned to the pattern, identifying the pattern as potentially interesting. The surprise score captures the degree of novelty or interestingness of the mined pattern. In addition, we show how to compute p values for each surprise score, thus filtering out noise and attaching statistical significance. RESULTS: We have implemented the dual-mining method using scripts written in Perl and R. We applied the method to a large patient database and a biomedical literature citation knowledgebase. The system estimated association scores for 50,000 patterns, composed of disease entities and lab results, by querying the database and the knowledgebase. It then computed the surprise scores by comparing the pairs of association scores. Finally, the system estimated statistical significance of the scores. CONCLUSION: The dual-mining method eliminates more than 90% of patterns with strong associations, thus identifying them as uninteresting. We found that the pruning of patterns using the surprise score matched the biomedical evidence in the 100 cases that were examined by hand. The method automates the acquisition of knowledge, thus reducing dependence on the knowledge elicited from human expert, which is usually a rate-limiting step.

Algorithms↗
PubMed2004

Simultaneous storage of medical images in the spatial and frequency domain: a comparative study.

BACKGROUND: Digital watermarking is a technique of hiding specific identification data for copyright authentication. This technique is adapted here for interleaving patient information with medical images, to reduce storage and transmission overheads. METHODS: The patient information is encrypted before interleaving with images to ensure greater security. The bio-signals are compressed and subsequently interleaved with the image. This interleaving is carried out in the spatial domain and Frequency domain. The performance of interleaving in the spatial, Discrete Fourier Transform (DFT), Discrete Cosine Transform (DCT) and Discrete Wavelet Transform (DWT) coefficients is studied. Differential pulse code modulation (DPCM) is employed for data compression as well as encryption and results are tabulated for a specific example. RESULTS: It can be seen from results, the process does not affect the picture quality. This is attributed to the fact that the change in LSB of a pixel changes its brightness by 1 part in 256. Spatial and DFT domain interleaving gave very less %NRMSE as compared to DCT and DWT domain. CONCLUSION: The Results show that spatial domain the interleaving, the %NRMSE was less than 0.25% for 8-bit encoded pixel intensity. Among the frequency domain interleaving methods, DFT was found to be very efficient.

Algorithms↗
PubMed1992

The application of quality filters in searching the clinical literature: some possible heuristics.

Experienced searchers can help their patrons find the "best" by employing any of several techniques which might filter search results. Using a sample search on Alzheimer's Disease, this article describes and illustrates the following five objective indicators which might be considered signs of quality: methodological rigor, document attributes, peer review, journal reputation, and filtering at input. Sample techniques and results are presented for six databases: MEDLINE, CINAHL, EMBASE, SAMM, CCML, and JWAT. Understanding of the patron's need and knowledge of the structure and contents of the database will determine when each should be applied to search results.

Alzheimer Disease↗
PubMed2005

ITER- International Toxicity Estimates for Risk, new TOXNET database.

ITER, the International Toxicity Estimates for Risk database, joined the TOXNET system in the winter of 2004. ITER features international comparisons of environmental health risk assessment information and contains over 620 chemical records. ITER includes data from the EPA, Health Canada, the National Institute of Public Health and the Environment of the Netherlands, and other organizations that provide risk values that have been peer-reviewed.

Data Display↗
PubMed2006

Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*.

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) has emerged as the leading fully public repository for gene expression data. This chapter describes how to use Web-based interfaces, applications, and graphics to effectively explore, visualize, and interpret the hundreds of microarray studies and millions of gene expression patterns stored in GEO. Data can be examined from both experiment-centric and gene-centric perspectives using user-friendly tools that do not require specialized expertise in microarray analysis or time-consuming download of massive data sets. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

Algorithms↗
PubMed2001

RepGene: a spreadsheet template for the management of reporter gene assays.

One of the most powerful techniques in molecular biology is the controlled expression of specific proteins by transfection of eukaryotic cells. This method has become feasible and highly sensitive and, thus, suitable for high-throughput reporter gene assays in basic and applied research. Moreover, the limiting factors are neither the transfection efficiency nor the functional analysis, but rather the ability to manage complex experimental protocols when multiple genes are co-transfected and/or when the effects of several chemical compounds are investigated within the same experiment. Here, we describe an easy-to-use and highly flexible spreadsheet template intended to rationalize and expedite the organization and data management of multi-step reporter gene assays. The objectives of this spreadsheet template are the design of the transfection protocol, the coordination of the administration of test compounds, and the graphical presentation and statistical analysis of the results.

Data Display↗