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PubMed2006

Hybridization-ligation versus parallel overlap assembly: an experimental comparison of initial pool generation for direct-proportional length-based DNA computing.

Previously, direct-proportional length-based DNA computing (DPLB-DNAC) for solving weighted graph problems has been reported. The proposed DPLB-DNAC has been successfully applied to solve the shortest path problem, which is an instance of weighted graph problems. The design and development of DPLB-DNAC is important in order to extend the capability of DNA computing for solving numerical optimization problem. According to DPLB-DNAC, after the initial pool generation, the initial solution is subjected to amplification by polymerase chain reaction and, finally, the output of the computation is visualized by gel electrophoresis. In this paper, however, we give more attention to the initial pool generation of DPLB-DNAC. For this purpose, two kinds of initial pool generation methods, which are generally used for solving weighted graph problems, are evaluated. Those methods are hybridization-ligation and parallel overlap assembly (POA). It is found that for DPLB-DNAC, POA is better than that of the hybridization-ligation method, in terms of population size, generation time, material usage, and efficiency, as supported by the results of actual experiments.

Base Sequence↗
PubMed2004

Multiview registration of 3D scenes by minimizing error between coordinate frames.

This paper addresses the problem of large-scale multiview registration of range images captured from unknown viewing directions. To reduce the computational burden, we separate the local problem of pairwise registration on neighboring views from the global problem of distribution of accumulated errors. We define the global problem as an optimization over the graph of neighboring views, and we show how the graph can be decomposed into a set of cycles such that the optimal transformation parameters for each cycle can be solved in closed form. We then describe an iterative procedure that can be used to integrate the solutions for the set of cycles across the graph of views. This method for error distribution does not require point correspondences between views, and can be used to integrate any method of pairwise registration or robot odometry.

Algorithms↗
PubMed2005

Building k edge-disjoint spanning trees of minimum total length for isometric data embedding.

Isometric data embedding requires construction of a neighborhood graph that spans all data points so that geodesic distance between any pair of data points could be estimated by distance along the shortest path between the pair on the graph. This paper presents an approach for constructing k-edge-connected neighborhood graphs. It works by finding k edge-disjoint spanning trees the sum of whose total lengths is a minimum. Experiments show that it outperforms the nearest neighbor approach for geodesic distance estimation.

Algorithms↗
PubMed2006

Graphical models and point pattern matching.

This paper describes a novel solution to the rigid point pattern matching problem in Euclidean spaces of any dimension. Although we assume rigid motion, jitter is allowed. We present a noniterative, polynomial time algorithm that is guaranteed to find an optimal solution for the noiseless case. First, we model point pattern matching as a weighted graph matching problem, where weights correspond to Euclidean distances between nodes. We then formulate graph matching as a problem of finding a maximum probability configuration in a graphical model. By using graph rigidity arguments, we prove that a sparse graphical model yields equivalent results to the fully connected model in the noiseless case. This allows us to obtain an algorithm that runs in polynomial time and is provably optimal for exact matching between noiseless point sets. For inexact matching, we can still apply the same algorithm to find approximately optimal solutions. Experimental results obtained by our approach show improvements in accuracy over current methods, particularly when matching patterns of different sizes.

Algorithms↗
PubMed2006

Dense photometric stereo: a Markov random field approach.

We address the problem of robust normal reconstruction by dense photometric stereo, in the presence of complex geometry, shadows, highlight, transparencies, variable attenuation in light intensities, and inaccurate estimation in light directions. The input is a dense set of noisy photometric images, conveniently captured by using a very simple set-up consisting of a digital video camera, a reflective mirror sphere, and a handheld spotlight. We formulate the dense photometric stereo problem as a Markov network and investigate two important inference algorithms for Markov Random Fields (MRFs)--graph cuts and belief propagation--to optimize for the most likely setting for each node in the network. In the graph cut algorithm, the MRF formulation is translated into one of energy minimization. A discontinuity-preserving metric is introduced as the compatibility function, which allows alpha-expansion to efficiently perform the maximum a posteriori (MAP) estimation. Using the identical dense input and the same MRF formulation, our tensor belief propagation algorithm recovers faithful normal directions, preserves underlying discontinuities, improves the normal estimation from one of discrete to continuous, and drastically reduces the storage requirement and running time. Both algorithms produce comparable and very faithful normals for complex scenes. Although the discontinuity-preserving metric in graph cuts permits efficient inference of optimal discrete labels with a theoretical guarantee, our estimation algorithm using tensor belief propagation converges to comparable results, but runs faster because very compact messages are passed and combined. We present very encouraging results on normal reconstruction. A simple algorithm is proposed to reconstruct a surface from a normal map recovered by our method. With the reconstructed surface, an inverse process, known as relighting in computer graphics, is proposed to synthesize novel images of the given scene under user-specified light source and direction. The synthesis is made to run in real time by exploiting the state-of-the-art graphics processing unit (GPU). Our method offers many unique advantages over previous relighting methods and can handle a wide range of novel light sources and directions.

Algorithms↗
PubMed2004

On a multimode test sequencing problem.

Test sequencing is a binary identification problem wherein one needs to develop a minimal expected cost test procedure to determine which one of a finite number of possible failure states, if any, is present. In this paper, we consider a multimode test sequencing (MMTS) problem, in which tests are distributed among multiple modes and additional transition costs will be incurred if a test sequence involves mode changes. The multimode test sequencing problem can be solved optimally via dynamic programming or AND/OR graph search methods. However, for large systems, the associated computation with dynamic programming or AND/OR graph search methods is substantial due to the rapidly increasing number of OR nodes (denoting ambiguity states and current modes) and AND nodes (denoting next modes and tests) in the search graph. In order to overcome the computational explosion, we propose to apply three heuristic algorithms based on information gain: information gain heuristic (IG), mode capability evaluation (MC), and mode capability evaluation with limited exploration of depth and degree of mode Isolation (MCLEI). We also propose to apply rollout strategies, which are guaranteed to improve the performance of heuristics, as long as the heuristics are sequentially improving. We show computational results, which suggest that the information-heuristic based rollout policies are significantly better than traditional information gain heuristic. We also show that among the three information heuristics proposed, MCLEI achieves the best tradeoff between optimality and computational complexity.

Algorithms↗
PubMed2005

A region dissimilarity relation that combines feature-space and spatial information for color image segmentation.

This paper proposes a methodology that incorporates principles from cluster analysis and graph representation to achieve efficient image segmentation results. More specifically, a feature-based, inter-region dissimilarity relation is considered here in order to determine the dissimilarity matrix in a graph-based segmentation scheme. The calculation of the dissimilarity function between adjacent elementary image regions is based on the proximity of each region's feature vector to the main clusters that are formed by the image samples in the feature space. In contrast to typical segmentation approaches of the literature, the global feature space information is included in the spatial graph representation that was derived from the initial Watershed partitioning. A region grouping process is applied next to form the final segmentation results. The proposed approach was also compared to approaches that use feature-based, or spatial information exclusively, to indicate its effectiveness.

Algorithms↗
PubMed2006

A note on the spread of worms in scale-free networks.

This paper considers the spread of worms in computer networks using insights from epidemiology and percolation theory. We provide three new results. The first result refines previous work showing that epidemics occur in scale-free graphs more easily because of their structure. We argue, using recent results from random graph theory that for scaling factors between 0 and approximately 3.4875, any computer worm infection of a scale-free network will become an epidemic. Our second result uses this insight to provide a mathematical explanation for the empirical results of Chen and Carley, who demonstrate that the Countermeasure Competing strategy can be more effective for immunizing networks to viruses or worms than traditional approaches. Our third result uses random graph theory to contradict the current supposition that, for very large networks, monocultures are necessarily more susceptible than diverse networks to worm infections.

Computer Communication Networks↗
PubMedDate not supplied

Non-Euclidean spring embedders.

We present a conceptually simple approach to generalizing force-directed methods for graph layout from Euclidean geometry to Riemannian geometries. Unlike previous work on non-Euclidean force-directed methods, ours is not limited to special classes of graphs, but can be applied to arbitrary graphs. The method relies on extending the Euclidean notions of distance, angle, and force-interactions to smooth non-Euclidean geometries via projections to and from appropriately chosen tangent spaces. In particular, we formally describe the calculations needed to extend such algorithms to hyperbolic and spherical geometries. We also study the theoretical and practical considerations that arise when working with non-Euclidean geometries.

Algorithms↗
PubMed1996

Visual effect of partogram designs on the management and outcome of labour.

A prospective study of 3 partogram designs was performed in 990 women in labour with singleton pregnancy. Partogram A, B and C showed a progressively flatter steepness of the curve of labour progression. Oxytocin was administered in 35.1% of partogram-A users, 45.9% of partogram-B users (p = 0.001) and 44.1% of partogram-C users (p = 0.035). Significantly fewer patients among the partogram-A users (10.2%) were administered oxytocin too early compared to 18.6% of partogram-B users and 20.5% of partogram-C users. Of those with spontaneous onset of labour, a significantly smaller total dose of oxytocin was administered to the partogram-A users compared to the other 2 groups. Ominous electrocardiotocographic fetal heart patterns were detected less frequently during the first stage of labour in partogram A users (0.4%) compare to partogram-B users (1.1%) and partogram-C users (3.0%). Significantly fewer infants born to partogram-A users had depressed Apgar scores at 1 and 5 minutes. Partograms displaying a flat graph, compared to a steep graph, were more often considered to have a slow progress of labour. Adoption of partograms showing a steep graph of progress of cervical dilatation is recommended.

Cervix Uteri↗
PubMed2004

Bioelectric impedance vector distribution in peritoneal dialysis patients with different hydration status.

BACKGROUND: In continuous ambulatory peritoneal dialysis (CAPD), total body water (TBW) is estimated by functions of body weight, and by equations of bioelectric impedance analysis (BIA). These procedures may be biased with abnormal tissue hydration. We validated vector BIA (BIVA) patterns of hydration in CAPD patients, based on direct measurements of resistance (R) and reactance (Xc) (RXc graph) without knowledge of the body weight. METHODS: Cross-sectional study in 200 adult CAPD patients from two groups: 149 patients (77 males and 72 females) without edema (BMI 24.3 kg/m2), and 51 (29 males and 22 females) with pitting edema (BMI 24.6 kg/m2). Single frequency (50 kHz), whole-body impedance vector was measured with both empty and filled peritoneal cavity. Vector distribution was compared with that from 726 healthy subjects, 1116 hemodialysis patients, and 50 nephrotic patients, all with a same BMI. The performance of BIVA was compared with indications of four anthropometry and four conventional BIA equations for TBW. RESULTS: TBW estimates from anthropometry (Watson, Hume and Weyers, Chertow, and Johansson formulas) were misleading, indicating the same hydration in edema. TBW estimates from BIA equations indicated a 10% excess TBW in edema. BIVA were very sensitive to fluid overload, as both R (by 10%) and Xc (by 40%) were reduced in patients with edema (regardless of peritoneal filling). The vector distribution of individual CAPD patients without edema was superposable to that of the healthy, gender-specific, reference population (50%, 75%, and 95% tolerance ellipses, RXc graph) and close to the hemodialysis, presession distribution. Vectors from patients with edema were displaced downward on the RXc graph, out of the 75% ellipse (88% sensitivity and 87% specificity), and close to vectors from nephrotic patients. CONCLUSION: CAPD prescription would keep or bring vectors of patients back into the 75% reference ellipse (border for progression from latent to apparent overhydration across the lower pole) regardless of body weight. Whether CAPD patients with vector within the target ellipse have better outcome needs longitudinal evaluation.

Adolescent↗
PubMed1985

Relationship of mean platelet volume to platelet count in morphologic evaluation of thrombopoiesis.

A graph of the relationship between mean platelet volume (MPV) and platelet count (TPK) was constructed out of 158 haematologically normal individuals, 19 patients with thrombocytopenia and 63 patients with thrombocytosis. Patients with thrombocytopenia and thrombocytosis whose bone marrows were found to show adequate or increased, morphologically normal, thrombopoiesis were included in the graph. The graph was found to exhibit the previously known inverse relationship between TPK and MPV extended into thrombocytopenic values and is thought to represent an intact marrow function capable of meeting the increased demands of thrombopoiesis. On the other hand, 15 patients whose bone marrows were showing evidence of hypoplastic thrombopoiesis fell outside the region representing intact marrow function. The position of an individual's values of MPV vs TPK in a coordinate system with these variables on the axes correlates well with the morphologic evaluation of thrombopoietic function and seems to be clinically useful.

Blood Platelets↗
PubMed2004

Fast and robust computation of colon centerline in CT colonography.

Although several methods for generating the centerline of a colon from CT colonographic scans have been proposed, in general they are time-consuming and do not take into account that the images of the colon may be of nonoptimal quality, with collapsed regions, and stool within the colon. Furthermore, the colonic lumen or wall, which is often used as a basis for computation of a centerline, is not always precisely segmented. In this study, we have developed an algorithm for computation of a colon centerline that is fast compared to the centerline algorithms presented in the reviewed literature, and that relies little on a complete colon segments identification. The proposed algorithm first extracts local maxima in a distance map of a segmented colonic lumen. The maxima are considered to be nodes in a set of graphs, and are iteratively linked together, based on a set of connection criteria, giving a minimum distance spanning tree. The connection criteria are computed from the distance from object boundary, the Euclidean distance between nodes and the voxel values on the pathway between pairs of nodes. After the last iteration, redundant branches are removed and end segments are recovered for each remaining graph. A subset of the initial maxima is used for distinguishing between the colon and noncolonic centerline segments among the set of graphs, giving the final centerline representation. A phantom study showed that, with respect to phantom variations, the algorithm achieved nearly constant computation time (2.3-2.9 s) except for the most extreme setting (20.2 s). The algorithm successfully found all, or most of, the centerline (93% - 100%). Displacement from optimum varied with colon diameter (1.2-6.6 mm). By use of 40 CT colonographic scans, the computer-generated centerlines were compared with the centerlines generated by three radiologists. The similarity was measured based on percent coverage and average displacement. The computer-generated centerlines, when compared with human-generated centerlines, had approximately the same displacement as when the human-generated centerlines were compared among each other (3.8 mm versus 4.0 mm). The coverage of the computer-generated centerlines was slightly less than that of the human-generated centerlines (92% versus 94%). The 40 centerlines were, on average, computed in 10.5 seconds, including computation time for the distance transform, with an Intel Pentium-based 800 MHz computer, as compared with 12-17 seconds or more (excluding computation time for the distance transform needed) per centerline as reported in other studies.

Algorithms↗
PubMed2001

Monitoring and evaluating the UK National Health Service Breast Screening Programme: evaluating the variation in radiological performance between individual programmes using PPV-referral diagrams.

A high quality breast cancer screening programme can be defined as one offering both a high cancer detection rate and a low referral rate of women for further investigation. Such a programme will have as few women as possible undergoing further investigations who do not have a final diagnosis of breast cancer--that is, a high positive predictive value of referral for further investigation. This paper introduces a graphical technique to illustrate individual programme performance. The graph plots positive predictive value of referral against referral rate, with the cancer detection rate expressed as "isobars" on the graph. Confidence limits can be expressed as "boxes" on the diagram. The graph not only illustrates programme performance but also enables suggestions to be made to improve performance. The definition of high quality screening is seen to have a subjective element as well as an objective element, as radiologists have to balance screening sensitivity with specificity. The technique is illustrated using data from the individual screening programmes in the UK National Health Service Breast Screening Programme for the screening year 1 April 1998 to 31 March 1999. The methodology could also be applied to other national screening programmes.

Breast Neoplasms↗
PubMed2004

Diagnosis of bacterial vaginosis: need for validation of microscopic image area used for scoring bacterial morphotypes.

BACKGROUND: The diagnosis of bacterial vaginosis (BV) is often made according to Nugent's classification, a scoring system based on bacterial counting of Gram stained slides of vaginal secretion. However as the image area of the microscope field will influence the number of morphotypes seen there is a need to standardise the area. METHODS: A graph intended for recalculation of number of bacterial morphotypes seen by the observer using 1000 x magnification from various microscope set-ups was constructed and applied to data sets typical for scoring BV. The graph was used in recalculation of Nugent scores, which were also compared with the Ison/Hay scores to evaluate the consequences for the diagnosis of BV. RESULTS: The observed image area differed by 300% among the investigated microscope set-ups. In two different data sets, one treatment study and one screening study, a considerable change in the number of women classified as intermediate was seen when the graph was used to standardise the image area. The recalculated numbers were also compared to the Ison/Hay classification. Weighted kappa indexes between the different methods were 0.84, 0.88, and 0.90, indicating that the methods are comparable. CONCLUSION: Because of the considerable differences among image areas covered by different microscope set-ups used in Nugent and Ison/Hay scoring, there is a need to standardise the area in order to reach comparable scores reflecting the diagnosis of BV in different laboratories. The differences in the intermediate group will have a considerable effect on the results from both treatment and prevalence studies, even though the kappa indexes indicate very good agreement between the methods used.

Calibration↗
PubMed1993

How many times per day should peak expiratory flow rates be assessed when investigating occupational asthma?

BACKGROUND: Serial peak expiratory flow rate (PEF) recording has been advocated as a sensitive and specific means of confirming work related asthma. The optimum number of recordings per day to achieve the best between-reader and within-reader reproducibility and sensitivity/specificity ratio compared with the final diagnosis determined by specific inhalation challenges is unknown. METHODS: PEF recording was carried out every two hours in 74 subjects referred for possible occupational asthma. Specific inhalation challenges performed in a hospital laboratory or at the workplace (positive in 33 subjects and negative in 41) were considered the gold standard. The duration of monitoring at work and away from work was at least two weeks each. Graphs of PEF recordings were generated in four different ways: every two hours, four times/day, three times/day, and every morning and evening. The graphs were assessed by three readers in three different centres in a blind manner. Furthermore, one third of each type of graph was read blind by the same reader one week after the initial interpretation. RESULTS: Agreement between the three readers was a little more frequent (82%) in the case of the every two hour readings than for the other types of readings (70% v 77%). Agreement between at least two of the three readers occurred in 73% of positive challenges (sensitivity) and in 78% of negative challenges (specificity) for every two hour readings. The figures varied from 61% to 70% for positive challenges and from 78% to 88% for negative challenges for the other types of readings. Within-subject reproducibility from one reading to the next (one week apart) was excellent (83% to 100%). CONCLUSIONS: Recording PEF every two hours results in a slightly more satisfactory agreement between readers and in concordance in terms of sensitivity/specificity than less frequent PEF readings, although the four times a day assessment is almost as satisfactory.

Asthma↗
PubMed2004

An annealed chaotic maximum neural network for bipartite subgraph problem.

In this paper, based on maximum neural network, we propose a new parallel algorithm that can help the maximum neural network escape from local minima by including a transient chaotic neurodynamics for bipartite subgraph problem. The goal of the bipartite subgraph problem, which is an NP- complete problem, is to remove the minimum number of edges in a given graph such that the remaining graph is a bipartite graph. Lee et al. presented a parallel algorithm using the maximum neural model (winner-take-all neuron model) for this NP- complete problem. The maximum neural model always guarantees a valid solution and greatly reduces the search space without a burden on the parameter-tuning. However, the model has a tendency to converge to a local minimum easily because it is based on the steepest descent method. By adding a negative self-feedback to the maximum neural network, we proposed a new parallel algorithm that introduces richer and more flexible chaotic dynamics and can prevent the network from getting stuck at local minima. After the chaotic dynamics vanishes, the proposed algorithm is then fundamentally reined by the gradient descent dynamics and usually converges to a stable equilibrium point. The proposed algorithm has the advantages of both the maximum neural network and the chaotic neurodynamics. A large number of instances have been simulated to verify the proposed algorithm. The simulation results show that our algorithm finds the optimum or near-optimum solution for the bipartite subgraph problem superior to that of the best existing parallel algorithms.

Algorithms↗
PubMed2003

Two notes on genome rearrangement.

A central problem in genome rearrangement is finding a most parsimonious rearrangement scenario using certain rearrangement operations. An important problem of this type is sorting a signed genome by reversals and translocations (SBRT). Hannenhalli and Pevzner presented a duality theorem for SBRT which leads to a polynomial time algorithm for sorting a multi-chromosomal genome using a minimum number of reversals and translocations. However, there is one case for which their theorem and algorithm fail. We describe that case and suggest a correction to the theorem and the polynomial algorithm. The solution of SBRT uses a reduction to the problem of sorting a signed permutation by reversals (SBR). The best extant algorithms for SBR require quadratic time. The common approach to solve SBR is by finding a safe reversal using the overlap graph or the interleaving graph of a permutation. We describe a family of signed permutations which proves a quadratic lower bound on the number of affected vertices in the overlap/interleaving graph during any optimal sorting scenario. This implies, in particular, an Omega(n3) lower bound for Bergeron's algorithm.

Algorithms↗