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At least 595 records · Page 33Linked to original sources
PubMed1997

Quantitative coronary angiography with deformable spline models.

Although current edge-following schemes can be very efficient in determining coronary boundaries, they may fail when the feature to be followed is disconnected (and the scheme is unable to bridge the discontinuity) or branch points exist where the best path to follow is indeterminate. In this paper, we present new deformable spline algorithms for determining vessel boundaries, and enhancing their centerline features. A bank of even and odd S-Gabor filter pairs of different orientations are convolved with vascular images in order to create an external snake energy field. Each filter pair will give maximum response to the segment of vessel having the same orientation as the filters. The resulting responses across filters of different orientations are combined to create an external energy field for snake optimization. Vessels are represented by B-Spline snakes, and are optimized on filter outputs with dynamic programming. The points of minimal constriction and the percent-diameter stenosis are determined from a computed vessel centerline. The system has been statistically validated using fixed stenosis and flexible-tube phantoms. It has also been validated on 20 coronary lesions with two independent operators, and has been tested for interoperator and intraoperator variability and reproducibility. The system has been found to be specially robust in complex images involving vessel branchings and incomplete contrast filling.

Algorithms↗
PubMed1998

Model-guided labeling of coronary structure.

Assigning anatomic labels to coronary arteries in X-ray angiograms is an important task in medical imaging, motivated by the desire to standardize the assessment of coronary artery disease and to facilitate the three-dimensional (3-D) reconstruction and visualization of the coronary vasculature. However, automatic labeling poses a number of significant challenges, including the presence of noise, artifacts, competing structures, misleading visual cues, and other difficulties associated with a dynamic and inherently complex structure. We have developed a model-guided approach that addresses these challenges and automatically labels the vascular structure in coronary angiographic images. The approach consists of two models: 1) a symbolic model, represented through a directed acyclic graph, that captures vascular tree hierarchies and branch interrelationships and 2) a generalized 3-D model that captures spatial and geometric relationships. Importantly, the approach detects ambiguities (such as vessel overlaps) that may be found in a frame of a ciné sequence, and resolves these ambiguities by considering the information derived from other (unambiguous) frames in the temporal sequence, employing dynamic programming methods to match the image features found in the different (ambiguous and unambiguous) frames. This paper presents this model-guided labeling algorithm and discusses the experimental results obtained from implementing and applying the resulting labeling system to a variety of clinical images. The results indicate the feasibility of achieving robust and consistently accurate image labeling through this model-guided, temporal disambiguation method.

Coronary Angiography↗
PubMed2001

Automatic lung segmentation for accurate quantitation of volumetric X-ray CT images.

Segmentation of pulmonary X-ray computed tomography (CT) images is a precursor to most pulmonary image analysis applications. This paper presents a fully automatic method for identifying the lungs in three-dimensional (3-D) pulmonary X-ray CT images. The method has three main steps. First, the lung region is extracted from the CT images by gray-level thresholding. Then, the left and right lungs are separated by identifying the anterior and posterior junctions by dynamic programming. Finally, a sequence of morphological operations is used to smooth the irregular boundary along the mediastinum in order to obtain results consistent with those obtained by manual analysis, in which only the most central pulmonary arteries are excluded from the lung region. The method has been tested by processing 3-D CT data sets from eight normal subjects, each imaged three times at biweekly intervals with lungs at 90% vital capacity. We present results by comparing our automatic method to manually traced borders from two image analysts. Averaged over all volumes, the root mean square difference between the computer and human analysis is 0.8 pixels (0.54 mm). The mean intrasubject change in tissue content over the three scans was 2.75% +/- 2.29% (mean +/- standard deviation).

Algorithms↗
PubMed1999

Optimal control of walking with functional electrical stimulation: a computer simulation study.

Bipedal locomotion was simulated to generate a pattern of activating muscles for walking using electrical stimulation in persons with spinal cord injury (SCI) or stroke. The simulation presented in this study starts from a model of the body determined with user-specific parameters, individualized with respect to the lengths, masses, inertia, muscle and joint properties. The trajectory used for simulation was recorded from an able-bodied subject while walking with ankle-foot orthoses. A discrete mathematical model and dynamic programming were used to determine the optimal control. A cost function was selected as the sum of the squares of the tracking errors from the desired trajectories, and the weighted sum of the squares of agonist and antagonist activations of the muscle groups acting around the hip and knee joints. The aim of the simulation was to study plausible trajectories keeping in mind the limitations imposed by the spinal cord injury or stroke (e.g., spasticity, decreased range of movements in some joints, limited strength of paralyzed, externally activated muscles). If the muscles were capable of generating the movements required and the trajectory was achieved, then the simulation provided two kinds of information: 1) timing of the onset and offset of muscle activations with respect to the various gait events and 2) patterns of activation with respect to the maximum activation. These results are important for synthesizing a rule-based controller.

Algorithms↗
PubMed2004

Separation of ion types in tandem mass spectrometry data interpretation -- a graph-theoretic approach.

Mass spectrometry is one of the most popular analytical techniques for identification of individual proteins in a protein mixture, one of the basic problems in proteomics. It identifies a protein through identifying its unique mass spectral pattern. While the problem is theoretically solvable, it remains a challenging problem computationally. One of the key challenges comes from the difficulty in distinguishing the N- and C-terminus ions, mostly b- and y-ions respectively. In this paper, we present a graph algorithm for solving the problem of separating bfrom y-ions in a set of mass spectra. We represent each spectral peak as a node and consider two types of edges: a type-1 edge connects two peaks possibly of the same ion types and a type-2 edge connects two peaks possibly of different ion types, predicted based on local information. The ion-separation problem is then formulated and solved as a graph partition problem, which is to partition the graph into three subgraphs, namely b-, y-ions and others respectively, so to maximize the total weight of type-1 edges while minimizing the total weight of type-2 edges within each subgraph. We have developed a dynamic programming algorithm for rigorously solving this graph partition problem and implemented it as a computer program PRIME. We have tested PRIME on 18 data sets of high accurate FT-ICR tandem mass spectra and found that it achieved ~90% accuracy for separation of b- and y- ions.

Algorithms↗
PubMed2005

TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree.

We present TreeRefiner, a tool for refining multiple alignments of biological sequences. Given a multiple alignment, a phylogenetic tree, and scoring parameters as input, TreeRefiner optimizes the sum-of-pairs function in a restricted three-dimensional space around the alignment. At each internal node of the unrooted tree, the multiple alignment is projected to the sub-alignments corresponding to the three neighboring nodes, and three-dimensional dynamic programming is performed within a user-specified radius r around the original alignment. We test TreeRefiner on simulated sequences aligned by several popular tools, and demonstrate substantial improvements in the percentage of correctly aligned positions.

Algorithms↗
PubMed2005

Optimal H infinity insulin injection control for blood glucose regulation in diabetic patients.

The theory of H infinity optimal control has the feature of minimizing the worst-case gain of an unknown disturbance input. When appropriately modified, the theory can be used to design a "switching" controller that can be applied to insulin injection for blood glucose (BG) regulation. The "switching" controller is defined by a collection of basic insulin rates and a rule that switches the insulin rates from one value to another. The rule employed an estimation of BG from noisy measurements, and the subsequent optimization of a performance index that involves the solution of a "jump" Riccati differential equation and a discrete-time dynamic programming equation. With an appropriate patient model, simulation studies have shown that the controller could correct BG deviation using clinically acceptable insulin delivery rates.

Algorithms↗
PubMed2006

Optimized structured treatment interruption for HIV therapy and its performance analysis on controllability.

This paper presents dynamic programming therapy to reduce medication and establish long-term immune response against HIV-infection. Understanding HIV-related immune system control enables better HIV therapy without using full-treatments. Discrete regimen and continuous regimen characteristics are compared. Controllability of HIV-related immune system is analyzed for better understanding of optimal control in HIV therapy. Using optimal control provides more effective therapy than the full treatment without interruption in terms of controllability analysis. Case studies indicated the proposed therapy induces long-term nonprogression while preserving high CD4 T-helper cell count and low virus load in HIV-infected patients.

Algorithms↗
PubMed2006

Automated left ventricular segmentation in cardiac MRI.

We present an automated left ventricular (LV) myocardial boundary extraction method. Automatic localization of the LV is achieved using a motion map and an expectation maximization algorithm. The myocardial region is then segmented using an intensity-based fuzzy affinity map and the myocardial contours are extracted by cost minimization through a dynamic programming approach. The results from the automated algorithm compared against the experienced radiologists using Bland and Altman analysis were found to have consistent mean bias of 7% and limits of agreement comparable to the inter-observer variability inherent in the manual method.

Adult↗
PubMedDate not supplied

Counting all possible ancestral configurations of sample sequences in population genetics.

Given a set D of input sequences, a genealogy for D can be constructed backward in time using such evolutionary events as mutation, coalescent, and recombination. An ancestral configuration (AC) can be regarded as the multiset of all sequences present at a particular point in time in a possible genealogy for D. The complexity of computing the likelihood of observing D depends heavily on the total number of distinct ACs of D and, therefore, it is of interest to estimate that number. For D consisting of binary sequences of finite length, we consider the problem of enumerating exactly all distinct ACs. We assume that the root sequence type is known and that the mutation process is governed by the infinite-sites model. When there is no recombination, we construct a general method of obtaining closed-form formulas for the total number of ACs. The enumeration problem becomes much more complicated when recombination is involved. In that case, we devise a method of enumeration based on counting contingency tables and construct a dynamic programming algorithm for the approach. Last, we describe a method of counting the number of ACs that can appear in genealogies with less than or equal to a given number R of recombinations. Of particular interest is the case in which R is close to the minimum number of recombinations for D.

Biological Evolution↗
PubMed2004

Optimal context quantization in lossless compression of image data sequences.

In image compression context-based entropy coding is commonly used. A critical issue to the performance of context-based image coding is how to resolve the conflict of a desire for large templates to model high-order statistic dependency of the pixels and the problem of context dilution due to insufficient sample statistics of a given input image. We consider the problem of finding the optimal quantizer Q that quantizes the K-dimensional causal context Ct = (Xt-t1,Xt-t2,...,X t-tK) of a source symbol Xt into one of a set of conditioning states. The optimality of context quantization is defined to be the minimum static or minimum adaptive code length of given a data set. For a binary source alphabet an optimal context quantizer can be computed exactly by a fast dynamic programming algorithm. Faster approximation solutions are also proposed. In case of m-ary source alphabet a random variable can be decomposed into a sequence of binary decisions, each of which is coded using optimal context quantization designed for the corresponding binary random variable. This optimized coding scheme is applied to digital maps and alpha-plane sequences. The proposed optimal context quantization technique can also be used to establish a lower bound on the achievable code length, and hence is a useful tool to evaluate the performance of existing heuristic context quantizers.

Algorithms↗
PubMed2005

Mutual information-based analysis of JPEG2000 contexts.

Context-based arithmetic coding has been widely adopted in image and video compression and is a key component of the new JPEG2000 image compression standard. In this paper, the contexts used in JPEG2000 are analyzed using the mutual information, which is closely related to the compression performance. We first show that, when combining the contexts, the mutual information between the contexts and the encoded data will decrease unless the conditional probability distributions of the combined contexts are the same. Given I, the initial number of contexts, and F, the final desired number of contexts, there are S(I, F) possible context classification schemes where S(I, F) is called the Stirling number of the second kind. The optimal classification scheme is the one that gives the maximum mutual information. Instead of using an exhaustive search, the optimal classification scheme can be obtained through a modified generalized Lloyd algorithm with the relative entropy as the distortion metric. For binary arithmetic coding, the search complexity can be reduced by using dynamic programming. Our experimental results show that the JPEG2000 contexts capture the correlations among the wavelet coefficients very well. At the same time, the number of contexts used as part of the standard can be reduced without loss in the coding performance.

Algorithms↗
PubMed2005

Rate-distortion optimal video summary generation.

The need for video summarization originates primarily from a viewing time constraint. A shorter version of the original video sequence is desirable in a number of applications. Clearly, a shorter version is also necessary in applications where storage, communication bandwidth, and/or power are limited. The summarization process inevitably introduces distortion. The amount of summarization distortion is related to its "conciseness," or the number of frames available in the summary. If there are m frames in the original sequence and n frames in the summary, we define the summarization rate as m/n, to characterize this "conciseness". We also develop a new summarization distortion metric and formulate the summarization problem as a rate-distortion optimization problem. Optimal algorithms based on dynamic programming are presented and compared experimentally with heuristic algorithms. Practical constraints, like the maximum number of frames that can be skipped, are also considered in the formulation and solution of the problem.

Algorithms↗
PubMed2006

Context quantization by kernel Fisher discriminant.

Optimal context quantizers for minimum conditional entropy can be constructed by dynamic programming in the probability simplex space. The main difficulty, operationally, is the resulting complex quantizer mapping function in the context space, in which the conditional entropy coding is conducted. To overcome this difficulty, we propose new algorithms for designing context quantizers in the context space based on the multiclass Fisher discriminant and the kernel Fisher discriminant (KFD). In particular, the KFD can describe linearly nonseparable quantizer cells by projecting input context vectors onto a high-dimensional curve, in which these cells become better separable. The new algorithms outperform the previous linear Fisher discriminant method for context quantization. They approach the minimum empirical conditional entropy context quantizer designed in the probability simplex space, but with a practical implementation that employs a simple scalar quantizer mapping function rather than a large lookup table.

Algorithms↗
PubMed2006

Optimal requantization of deep grayscale images and Lloyd-Max quantization.

The classic signal quantization problem was introduced by Lloyd. We formulate another, similar problem: The optimal mapping of digital fine grayscale images (such as 9-13 bits-per-pixel medical images) to a coarser scale (e.g., 8 bits per pixel on conventional computer monitors). While the former problem is defined basically in the real signal domain with smoothly distributed noise, the latter refers to an essentially digital domain. As we show in this paper, it is this difference that makes the classic quantization methods virtually inapplicable in typical cases of requantization of the already digitized images. We found experimentally that an algorithm based on dynamic programming provides significantly better results than Lloyd's method.

Algorithms↗
PubMed2006

Joint source-channel coding for wireless object-based video communications utilizing data hiding.

In recent years, joint source-channel coding for multimedia communications has gained increased popularity. However, very limited work has been conducted to address the problem of joint source-channel coding for object-based video. In this paper, we propose a data hiding scheme that improves the error resilience of object-based video by adaptively embedding the shape and motion information into the texture data. Within a rate-distortion theoretical framework, the source coding, channel coding, data embedding, and decoder error concealment are jointly optimized based on knowledge of the transmission channel conditions. Our goal is to achieve the best video quality as expressed by the minimum total expected distortion. The optimization problem is solved using Lagrangian relaxation and dynamic programming. The performance of the proposed scheme is tested using simulations of a Rayleigh-fading wireless channel, and the algorithm is implemented based on the MPEG-4 verification model. Experimental results indicate that the proposed hybrid source-channel coding scheme significantly outperforms methods without data hiding or unequal error protection.

Algorithms↗
PubMed2006

Robust contour matching via the order-preserving assignment problem.

A common approach to determining corresponding points on two shapes is to compute the cost of each possible pairing of points and solve the assignment problem (weighted bipartite matching) for the resulting cost matrix. We consider the problem of solving for point correspondences when the shapes of interest are each defined by a single, closed contour. A modification of the standard assignment problem is proposed whereby the correspondences are required to preserve the ordering of the points induced from the shapes' contours. Enforcement of this constraint leads to significantly improved correspondences. Robustness with respect to outliers and shape irregularity is obtained by required only a fraction of feature points to be matched. Furthermore, the minimum matching size may be specified in advance. We present efficient dynamic programming algorithms to solve the proposed optimization problem. Experiments on the Brown and MPEG-7 shape databases demonstrate the effectiveness of the proposed method relative to the standard assignment problem.

Algorithms↗
PubMed2003

Estimating coronary artery lumen area with optimization-based contour detection.

A modified optimization-based contour detection method was presented to compute the lumen area of the coronary artery from intravascular ultrasound (IVUS) video images. First, the search range for the artery inner wall was determined based on the continuity of IVUS video frames. Next, the internal and external energy were calculated to describe the smoothness of the arterial wall and the grayscale variation of ultrasound images, respectively. Here, a novel form of the external energy which combines the gradient and variance of the intensity of image in the radial direction was used. Finally, the minimal energy path based on the optimum contour of the artery wall was obtained using circular dynamic programming (DP). By the comparison with the typical DP procedure using the traditional external energy form, based only on the image gradient, the reliability of this modified method is considerably improved in the measurement of coronary artery lumen area.

Algorithms↗