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At least 613 records · Page 34Linked to original sources
PubMed2006

Unwrapping of MR phase images using a Markov random field model.

Phase unwrapping is an important problem in many magnetic resonance imaging applications, such as field mapping and flow imaging. The challenge in two-dimensional phase unwrapping lies in distinguishing jumps due to phase wrapping from those due to noise and/or abrupt variations in the actual function. This paper addresses this problem using a Markov random field to model the true phase function, whose parameters are determined by maximizing the a posteriori probability. To reduce the computational complexity of the optimization procedure, an efficient algorithm is also proposed for parameter estimation using a series of dynamic programming connected by the iterated conditional modes. The proposed method has been tested with both simulated and experimental data, yielding better results than some of the state-of-the-art method (e.g., the popular least-squares method) in handling noisy phase images with rapid phase variations.

Algorithms↗
PubMed2006

Generalized Haar DWT and transformations between decision trees and neural networks.

The core contribution of this paper is a three-fold improvement of the Haar discrete wavelet transform (DWT). It is modified to efficiently transform a multiclass- (rather than numerical-) valued function over a multidimensional (rather than low dimensional) domain, or transform a multiclass-valued decision tree into another useful representation. We prove that this multidimensional, multiclass DWT uses dynamic programming to minimize (within its framework) the number of nontrivial wavelet coefficients needed to summarize a training set or decision tree. It is a spatially localized algorithm that takes linear time in the number of training samples, after a sort. Convergence of the DWT to benchmark training sets seems to degrade with rising dimension in this test of high dimensional wavelets, which have been seen as difficult to implement. This multiclass multidimensional DWT has tightly coupled applications from learning "dyadic" decision trees directly from training data, rebalancing or converting preexisting decision trees to fixed depth boolean or threshold neural networks (in effect parallelizing the evaluation of the trees), or learning rule/exception sets represented as a new form of tree called an "E-tree", which could greatly help interpretation/visualization of a dataset.

Journal Article↗
PubMed2006

One-class-at-a-time removal sequence planning method for multiclass classification problems.

Using dynamic programming, this work develops a one-class-at-a-time removal sequence planning method to decompose a multiclass classification problem into a series of two-class problems. Compared with previous decomposition methods, the approach has the following distinct features. First, under the one-class-at-a-time framework, the approach guarantees the optimality of the decomposition. Second, for a K-class problem, the number of binary classifiers required by the method is only K-1. Third, to achieve higher classification accuracy, the approach can easily be adapted to form a committee machine. A drawback of the approach is that its computational burden increases rapidly with the number of classes. To resolve this difficulty, a partial decomposition technique is introduced that reduces the computational cost by generating a suboptimal solution. Experimental results demonstrate that the proposed approach consistently outperforms two conventional decomposition methods.

Algorithms↗
PubMed2004

Error-tolerant sign retrieval using visual features and maximum a posteriori estimation.

This paper proposes an efficient error-tolerant approach to retrieving sign words from a Taiwanese Sign Language (TSL) database. This database is tagged with visual gesture features and organized as a multilist code tree. These features are defined in terms of the visual characteristics of sign gestures by which they are indexed for sign retrieval and displayed using an anthropomorphic interface. The maximum a posteriori estimation is exploited to retrieve the most likely sign word given the input feature sequence. An error-tolerant mechanism based on mutual information criterion is proposed to retrieve a sign word of interest efficiently and robustly. A user-friendly anthropomorphic interface is also developed to assist learning TSL. Several experiments were performed in an educational environment to investigate the system's retrieval accuracy. Our proposed approach outperformed a dynamic programming algorithm in its task and shows tolerance to user input errors.

Algorithms↗
PubMed2004

Panoramic appearance-based recognition of video contents using matching graphs.

This paper proposes a general scheme for recognizing the contents of a video using a set of panoramas recorded in a database. In essence, a panorama inherently records the appearances of an omni-directional scene from its central point to arbitrary viewing directions and, thus, can serve as a compact representation of an environment. In particular, this paper emphasizes the use of a sequence of successive frames in a video taken with a video camera, instead of a single frame, for visual recognition. The associated recognition task is formulated as a shortest-path searching problem, and a dynamic-programming technique is used to solve it. Experimental results show that our method can effectively recognize a video.

Algorithms↗
PubMed2004

Finding relevant sequences in time series containing crisp, interval, and fuzzy interval data.

Finding similar sequences in time series has received much attention and is a widely studied topic. Most existing approaches in the time series area focus on the efficiency of algorithms but seldom provide a means to handle imprecise data. In this paper, a more general approach is proposed to measure the distance of time sequences containing crisp values, intervals, and fuzzy intervals as well. The concept of distance measurement and its associated dynamic-programming-based algorithms are described. In addition to finding the sequences with similar evolving trends, a means of finding the sequences with opposite evolving tendencies is also proposed, which is usually omitted in current related research but could be of great interest to many users.

Algorithms↗
PubMed2005

A fuzzy reinforcement learning approach to power control in wireless transmitters.

We address the issue of power-controlled shared channel access in wireless networks supporting packetized data traffic. We formulate this problem using the dynamic programming framework and present a new distributed fuzzy reinforcement learning algorithm (ACFRL-2) capable of adequately solving a class of problems to which the power control problem belongs. Our experimental results show that the algorithm converges almost deterministically to a neighborhood of optimal parameter values, as opposed to a very noisy stochastic convergence of earlier algorithms. The main tradeoff facing a transmitter is to balance its current power level with future backlog in the presence of stochastically changing interference. Simulation experiments demonstrate that the ACFRL-2 algorithm achieves significant performance gains over the standard power control approach used in CDMA2000. Such a large improvement is explained by the fact that ACFRL-2 allows transmitters to learn implicit coordination policies, which back off under stressful channel conditions as opposed to engaging in escalating "power wars."

Algorithms↗
PubMed2004

Alignment of protein sequences by their profiles.

The accuracy of an alignment between two protein sequences can be improved by including other detectably related sequences in the comparison. We optimize and benchmark such an approach that relies on aligning two multiple sequence alignments, each one including one of the two protein sequences. Thirteen different protocols for creating and comparing profiles corresponding to the multiple sequence alignments are implemented in the SALIGN command of MODELLER. A test set of 200 pairwise, structure-based alignments with sequence identities below 40% is used to benchmark the 13 protocols as well as a number of previously described sequence alignment methods, including heuristic pairwise sequence alignment by BLAST, pairwise sequence alignment by global dynamic programming with an affine gap penalty function by the ALIGN command of MODELLER, sequence-profile alignment by PSI-BLAST, Hidden Markov Model methods implemented in SAM and LOBSTER, pairwise sequence alignment relying on predicted local structure by SEA, and multiple sequence alignment by CLUSTALW and COMPASS. The alignment accuracies of the best new protocols were significantly better than those of the other tested methods. For example, the fraction of the correctly aligned residues relative to the structure-based alignment by the best protocol is 56%, which can be compared with the accuracies of 26%, 42%, 43%, 48%, 50%, 49%, 43%, and 43% for the other methods, respectively. The new method is currently applied to large-scale comparative protein structure modeling of all known sequences.

Algorithms↗
PubMed2005

A novel approach to structural alignment using realistic structural and environmental information.

In the era of structural genomics, it is necessary to generate accurate structural alignments in order to build good templates for homology modeling. Although a great number of structural alignment algorithms have been developed, most of them ignore intermolecular interactions during the alignment procedure. Therefore, structures in different oligomeric states are barely distinguishable, and it is very challenging to find correct alignment in coil regions. Here we present a novel approach to structural alignment using a clique finding algorithm and environmental information (SAUCE). In this approach, we build the alignment based on not only structural coordinate information but also realistic environmental information extracted from biological unit files provided by the Protein Data Bank (PDB). At first, we eliminate all environmentally unfavorable pairings of residues. Then we identify alignments in core regions via a maximal clique finding algorithm. Two extreme value distribution (EVD) form statistics have been developed to evaluate core region alignments. With an optional extension step, global alignment can be derived based on environment-based dynamic programming linking. We show that our method is able to differentiate three-dimensional structures in different oligomeric states, and is able to find flexible alignments between multidomain structures without predetermined hinge regions. The overall performance is also evaluated on a large scale by comparisons to current structural classification databases as well as to other alignment methods.

Algorithms↗
PubMed2001

Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor.

A method based on neural networks is trained and tested on a nonredundant set of beta-barrel membrane proteins known at atomic resolution with a jackknife procedure. The method predicts the topography of transmembrane beta strands with residue accuracy as high as 78% when evolutionary information is used as input to the network. Of the transmembrane beta-strands included in the training set, 93% are correctly assigned. The predictor includes an algorithm of model optimization, based on dynamic programming, that correctly models eight out of the 11 proteins present in the training/testing set. In addition, protein topology is assigned on the basis of the location of the longest loops in the models. We propose this as a general method to fill the gap of the prediction of beta-barrel membrane proteins.

Algorithms↗
PubMed1999

Feasibility in the inverse protein folding protocol.

Methods for protein structure (3D)-sequence (1D) compatibility evaluation (threading) have been developed during the past decade. The protocol in which a sequence can recognize its compatible structure in the structural library (i.e., the fold recognition or the forward-folding search) is available for the structure prediction of new proteins. However, the reverse protocol, in which a structure recognizes its homologous sequences among a sequence database, named the inverse-folding search, is a more difficult application. In this study, we have investigated the feasibility of the latter approach. A structural library, composed of about 400 well-resolved structures with mutually dissimilar sequences, was prepared, and 163 of them had remote homologs in the library. We examined whether they could correctly seek their homologs by both forward- and inverse-folding searches. The results showed that the inverse-folding protocol is more effective than the forward-folding protocol, once the reference states of the compatibility functions are appropriately adjusted. This adjustment only slightly affects the ability of the forward-folding search. We noticed that the scoring, in which a given sequence is re-mounted onto a structure according to the 3D-1D alignment determined by the dynamic programming method, is only effective in the forward-folding protocol and not in the inverse-folding protocol. Namely, the inverse-folding search works significantly better with the score given by the 3D-1D alignment per se, rather than that obtained by the re-mounting. The implications of these results are discussed.

Algorithms↗
PubMed2000

Multiple-changepoint testing for an alternating segments model of a binary sequence.

A binary sequence may give the appearance of being composed of alternating segments with relatively high and relatively low probability of success. Determining whether such an alternating pattern is significant is a multiple-changepoint problem where the number of segments and their success probabilities are unknown, with the added constraint of segment alternation. A dynamic programming method for determining the optimal segmentation into a given number of segments is provided. Given this, a variation on the simulation method of Venter and Steel (1996, Computational Statistics and Data Analysis 22, 481-504) may be employed to test the null hypothesis of a homogeneous sequence as well as to estimate the number and location of changepoints. A sample application, the assessment of the possibility of genetic recombination in HIV sequences, is presented.

Base Sequence↗
PubMedDate not supplied

Comparative and phylogenetic analysis of developmental sequences.

Event pairing has been proposed for the optimization of developmental sequences (event sequences) on a given phylogenetic hypothesis (cladogram) to determine instances of sequence heterochrony. Here, we show that event pairing is faulty, leading to the optimization of impossible hypothetical ancestors, the underestimation of the lengths of the developmental sequences on the tree, and the proposition of synapomorphies that are not supported by the data. When used for phylogenetic analysis, event pairing can even produce cladograms that are inconsistent with the data. These errors are caused by the fact that event pairing treats dependent features as if they were independent. We present a new method for comparative and phylogenetic analysis of developmental sequences that does not exhibit these errors. Our method applies Search-based character optimization and treats the entire developmental sequence as a single character that is then analyzed by using an edit cost function, which specifies the transformation cost between pairs of observed and unobserved character states, and dynamic programming. In other words, the developmental sequence is directly optimized on the tree. We used event pairing as an edit cost function, but others are possible.

Animals↗
PubMed2004

Numerical estimation of blood damage in artificial organs.

The aim of this study was to determine a method for the numerical estimation of blood damage. Normally, human or animal blood is used for in vitro evaluation of lysis by artificial organs. However, blood has some disadvantages: large biological variability and different initial test conditions lead to nonreproducible test results. For that reason, it would be an advantage to have a numerical method for blood damage estimation. This proposed method is based on the calculation of an integrated hemolysis and platelet lysis index along the path line in the flow field of the artificial organ. The time-dependent shear stress related lysis is based on known experimental data. In order to calibrate these data, the method was first applied to blood circulation in the human body. The results showed that the known data overestimate hemolysis by a factor of approximately 25. Next, the method was applied to a standard Björk-Shiley valve. The flow through a valve was simulated with the computational fluid dynamics program FLUENT. The calculation of lysis was added into FLUENT and done automatically. The results showed that the Björk-Shiley valve increased the hemolysis index by 7% if implanted in the human body circulation.

Algorithms↗
PubMed2006

Characterization of an artificial valve flow using the numerical dye washout visualization technique: application to the monoleaflet valve with purged flow.

Until today, no ideal heart valve prosthesis for the replacement of a diseased natural valve or for use in ventricular assist devices exists. Valves still cause thromboembolic complications originating from thrombus formations in the valve's stagnant zones. Optimization of valve design involves avoiding stagnation zones and zones of high shear stresses. This requires detailed flow field investigations. Usually, the regions which are more prone to thrombus formation can be estimated using a dye washout experiment. The method allows an assessment of regions with a high or low residence time that may in turn predict regions with a corresponding thrombus risk. This successful experimental method was simulated using numerical methods with a combination of the computational fluid dynamics program FLUENT (Fluent Inc., Lebanon, NH, USA) and of the visualization tool AMIRA (TGS Inc., San Diego, CA, USA). The numerical dye washout visualization was applied to four monoleaflet valves with varying valve housing geometries. The results show a significant difference in the washout processes of the examined valves. The dye washout was characterized by a time course of the gray value averaged over a defined region of interest. Finally, these curves were quantified by a half dye time. The half dye time in the best optimized valve was only 0.2753 s. The same time in the original valve was 0.6834 s. This study shows that the proposed numerical method of dye washout visualization can be used as an additional tool of the flow characterization in artificial organs.

Dye Dilution Technique↗
PubMedDate not supplied

Dynamic optimal ground water remediation including fixed and operation costs.

In time-varying ground water remediation, the lack of an optimal control algorithm to simultaneously consider fixed costs and time-varying operating costs makes it nearly impossible to obtain an optimal solution. This study presents a novel algorithm that integrates a genetic algorithm (GA) and constrained differential dynamic programming (CDDP) to solve this time-varying ground water remediation problem. A GA can easily incorporate the fixed costs associated with the installation of wells. However, using a GA to solve for time-varying policies would dramatically increase the computational resources required. Therefore, the CDDP is used to handle the subproblems associated with time-varying operating costs. A hypothetical case study that incorporates fixed and time-varying operating costs is presented to demonstrate the effectiveness of the proposed algorithm. Simulation results indicate that the fixed costs can significantly influence the number and locations of wells, and a notable total cost savings can be realized by applying the novel algorithm herein.

Algorithms↗
PubMed1985

Numerical experiments with a new differentiation filter.

A dynamic programming filter which provides estimates of the first and second derivative of empirical displacement data is investigated numerically. This filter uses a weighted least squares criteria in estimating the derivatives. The filter equations are presented together with several numerical examples. These examples are taken from references that proposed other techniques.

Biomechanical Phenomena↗