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At least 469 records · Page 26Linked to original sources

PubMed1992

An approach based on two-dimensional graph theory for structural cluster detection and its histopathological application.

An approach based on graph theory is described for detecting clusters of cells in tissue specimens (two-dimensional space). With a set of discrete basic elements (cell nuclei) having several measurable features (area, surface, main and minor axis of best-fitting ellipses) a graph is defined as having attributes associated with edges. Different minimum spanning trees (MSTs) can be constructed using different weight functions on the attributes (attributed MST). Analysis of the MST and of an attributed MST by use of a decomposition function allows detection of image areas with similar local properties. These clusters, which are then clusters of the tree, describe, for example, partial growth in different directions in a case of a human fibrosarcoma assuming that tumour cell nuclei are homogeneous with respect to their configuration and size. The model allows the separation of clusters of tumour cells growing in different directions and the approximation of the different growth angles. This decomposition also allows us to create new (higher) orders of structure (cluster tree).

Algorithms↗

PubMed1999

The RXc graph in evaluating and monitoring fluid balance in patients with liver cirrhosis.

A recent study, using height-standardized resistance (R/H) and reactance (Xc/H) and assuming a bivariate distribution, has proposed the "RXc graph". We applied this new approach for patients with chronic liver disease in differentiating various degrees of fluid unbalance. Our data showed that a 95% confidence ellipse of patients with chronic hepatitis (CH) overlapped that of healthy control subjects (CONTR), while those of patients with liver cirrhosis (CIR), patients with cirrhosis and ascites (ACIR), and patients with cirrhosis, edemas, and ascites (AECIR) were clearly different for both genders. A progressively shorter mean impedance vector proportional to the stage of liver disease and to the degree of fluid unbalance was found. The lower half of the 50% tolerance ellipse for the healthy population proved to be a threshold for cirrhotics, while almost all the subjects with clinically detectable edema fell outside this limit. The RXc graph was shown to be useful in monitoring the treatment of fluid unbalance and for the immediate selection of patients in whom BIA can precisely assess body composition.

Adolescent↗

PubMed1982

Numbers of receptor sites from Scatchard graphs: facts and fantasies.

Data for ligand and receptor binding presented in the format of a Scatchard graph are compared with the same data shown as bound ligand plotted against the logarithm of free ligand. From this comparison it is apparent that extrapolations in the Scatchard graph to yield total number of receptor sites are generally not correct.

Kinetics↗

PubMed2004

Graph theoretical characterization and tracking of the effective neural connectivity during episodes of mesial temporal epileptic seizure.

Via a detailed case study of mesial temporal lobe epilepsy, we show that a method of determining the direction of information flow among signals is able to provide focal localization via the simultaneous analysis of multiple EEG channels. This determination is accomplished by representing information flow direction via directed graphs, where focal electrodes are associated with high observed rates of pertinence to strongly connected subgraphs. Further clinical support to this finding is provided by results for an additional 9 cases of focal epilepsy cases. The graph theoretical approach is a tool for describing and analyzing the effective connectivity dynamics behind epileptic seizures and may provide a common language for studying other complex dynamic relationships between neural structures.

Electroencephalography↗

PubMed1987

Solvent flow in osmosis and hydraulics: network thermodynamics and representation by bond graphs.

A tutorial introduction to network thermodynamics and bond graphs as a modeling technique for any physiochemical system is presented with a particular emphasis on reaction diffusion systems. It combines the generality of nonequilibrium thermodynamics with the advantages of a graph theory. It is applied to the representation of osmotic and hydraulic flows across a semipermeable membrane on the basis of the solvent diffusion theory of osmosis. This theory allows for an easy derivation of the van't Hoff law of osmotic pressure from the Fick law of diffusion. Molar flows and volume flows are transformed into one another by transducers, the modulus of which is the partial molar volume of water, in such a way that power is conserved by a reciprocal transformation between the chemical potential and the pressure. Osmotic and hydraulic resistances are calculated, and their dependence on pore size is estimated.

Diffusion↗

PubMed1997

Image analysis based grading of bladder carcinoma. Comparison of object, texture and graph based methods and their reproducibility.

The possibility that computerized image analysis could increase the reproducibility of grading of bladder carcinoma as compared to conventional subjective grading made by pathologists was investigated. Object, texture and graph based analysis were carried out from Feulgen stained histological tissue sections. The object based features were extracted from gray scale images, binary images obtained by thresholding the nuclei and several other images derived through image processing operations. The textural features were based on the spatial gray-tone co-occurrence probability matrices and the graph based features were extracted from the minimum spanning trees connecting all nuclei. The large numbers of extracted features were evaluated in relation to subjective grading and to factors related to prognosis using multivariate statistical methods and multilayer backpropagation neural networks. All the methods were originally developed and tested on material from one patient and then tested for reproducibility on entirely different patient material. The results indicate reasonably good reproducibility for the best sets of features. In addition, image analysis based grading showed almost identical correlation to mitotic density and expression of p53 protein as subjective grading. It should thus be possible to use this kind of image analysis as a prognostic tool for bladder carcinoma.

Humans↗

PubMed2000

A signal-flow-graph approach to on-line gradient calculation.

A large class of nonlinear dynamic adaptive systems such as dynamic recurrent neural networks can be effectively represented by signal flow graphs (SFGs). By this method, complex systems are described as a general connection of many simple components, each of them implementing a simple one-input, one-output transformation, as in an electrical circuit. Even if graph representations are popular in the neural network community, they are often used for qualitative description rather than for rigorous representation and computational purposes. In this article, a method for both on-line and batch-backward gradient computation of a system output or cost function with respect to system parameters is derived by the SFG representation theory and its known properties. The system can be any causal, in general nonlinear and time-variant, dynamic system represented by an SFG, in particular any feedforward, time-delay, or recurrent neural network. In this work, we use discrete-time notation, but the same theory holds for the continuous-time case. The gradient is obtained in a straightforward way by the analysis of two SFGs, the original one and its adjoint (obtained from the first by simple transformations), without the complex chain rule expansions of derivatives usually employed. This method can be used for sensitivity analysis and for learning both off-line and on-line. On-line learning is particularly important since it is required by many real applications, such as digital signal processing, system identification and control, channel equalization, and predistortion.

Algorithms↗

PubMed2004

A graph grammar approach to artificial life.

We present the high-level language of relational growth grammars (RGGs) as a formalism designed for the specification of ALife models. RGGs can be seen as an extension of the well-known parametric Lindenmayer systems and contain rule-based, procedural, and object-oriented features. They are defined as rewriting systems operating on graphs with the edges coming from a set of user-defined relations, whereas the nodes can be associated with objects. We demonstrate their ability to represent genes, regulatory networks of metabolites, and morphologically structured organisms, as well as developmental aspects of these entities, in a common formal framework. Mutation, crossing over, selection, and the dynamics of a network of gene regulation can all be represented with simple graph rewriting rules. This is demonstrated in some detail on the classical example of Dawkins' biomorphs and the ABC model of flower morphogenesis: other applications are briefly sketched. An interactive program was implemented, enabling the execution of the formalism and the visualization of the results.

Algorithms↗

PubMed2006

Visualizing evolutionary dynamics of self-replicators: a graph-based approach.

We present a general approach for evaluating and visualizing evolutionary dynamics of self-replicators using a graph-based representation for genealogy. Through a transformation from the space of species and mutations to the space of nodes and links, evolutionary dynamics are understood as a flow in graph space. A formalism is introduced to quantify such genealogical flows in terms of the complete history of localized evolutionary events recorded at the finest level of detail. Represented in a multidimensional viewing space, collective dynamical properties of an evolving genealogy are characterized in the form of aggregate flows. We demonstrate the effectiveness of this approach by using it to compare the evolutionary exploration behavior of self-replicating loops under two different environmental settings.

Artificial Intelligence↗

PubMed2004

Clustering under the line graph transformation: application to reaction network.

BACKGROUND: Many real networks can be understood as two complementary networks with two kind of nodes. This is the case of metabolic networks where the first network has chemical compounds as nodes and the second one has nodes as reactions. In general, the second network may be related to the first one by a technique called line graph transformation (i.e., edges in an initial network are transformed into nodes). Recently, the main topological properties of the metabolic networks have been properly described by means of a hierarchical model. While the chemical compound network has been classified as hierarchical network, a detailed study of the chemical reaction network had not been carried out. RESULTS: We have applied the line graph transformation to a hierarchical network and the degree-dependent clustering coefficient C(k) is calculated for the transformed network. C(k) indicates the probability that two nearest neighbours of a vertex of degree k are connected to each other. While C(k) follows the scaling law C(k) approximately k(-1.1) for the initial hierarchical network, C(k) scales weakly as k0.08 for the transformed network. This theoretical prediction was compared with the experimental data of chemical reactions from the KEGG database finding a good agreement. CONCLUSIONS: The weak scaling found for the transformed network indicates that the reaction network can be identified as a degree-independent clustering network. By using this result, the hierarchical classification of the reaction network is discussed.

Algorithms↗

PubMed1995

Theoretical analyses of chiasmata using a novel chiasma graph method applied to Chinese hamsters, mice, and dog.

Some basic concepts of chiasma (including chiasma distribution, chiasma frequency, interstitial and terminal chiasmata, and chiasma interference) are reexamined theoretically in the light of gene shuffling, and a new method for chiasma analysis termed the chiasma graph is proposed. Chiasma graphs are developed for three mammals with greatly different chromosome numbers: Chinese hamster (with n = 11), mice (n = 20), and a dog (n = 39). The results demonstrate that interstitial chiasmata can contribute both to gene shuffling and to the binding of bivalents, but that so-called terminal chiasmata are in fact mostly achiasmatic terminal associations, the main function of which is to bind bivalents. For this reason, terminal chiasmata should be excluded when chiasma frequency is estimated. It is also demonstrated that interstitial chiasmata distribute on bivalents randomly and uniformly, except at the centromere and telomere. Interference distance fluctuates almost randomly above a minimum value equivalent to about 1.8% of total bivalent length at diakinesis. These results indicate that chiasma formation in mammals is principally a random event. The demonstrated minimum interference distance seems consistent with the polymerization model for chiasma formation. Some cytological aspects of crossing-over are discussed with reference to the minimum interaction theory for eukaryotic chromosome evolution.

Animals↗

PubMed1995

Musical versus visual graphs: cross-modal equivalence in perception of time series data.

By applying multidimensional scaling procedures and other quantitative analyses to perceptual dissimilarity judgments, we compared the perceptual structure of visual line graphs depicting simulated time series data with that of auditory displays (musical graphs) presenting the same data. Highly similar and meaningful perceptual structures were demonstrated for both auditory and visual modalities, showing that important data characteristics (function slope, shape, and level) were perceptually salient in either presentation mode. Auditory graphics may be a highly useful alternative to traditional visual graphics for a variety of data presentation applications.

Analysis of Variance↗

PubMed1999

Information structure and the relative efficacy of tables and graphs.

Users and system designers often prefer to display information with graphs rather than with tables. However, empirical studies that compared task performance with the two display types frequently revealed either an advantage of tables over graphs or no differences between the displays. This apparent contradiction may result from previous studies in which the importance of the structure that usually exists in displayed information is overlooked. We predict that graphic displays will have an advantage over tables when the displayed information has structure and when this structure is relevant for the task. These conditions generally exist in the actual use of information displays, but have seldom been assessed in experiments. In the present study participants in an experiment performed an information extraction task and a prediction task with unstructured or structured data and with different levels of prior information about the structure. The results showed that the information structure and prior knowledge about the existence of structure affected the advantage of graphic displays over tables when task performance depended on the use of structure. Existing approaches to the study of displays were analyzed in view of these findings. Actual or potential applications of this research include the development of better displays for process control and decision support and better operator training programs.

Analysis of Variance↗

PubMed1990

Community people's preference of hand drawn face graph as a health informing device.

Although the cartoon of a face is an effective device to visualize the image of numerical indices, its use is not popular among community health personnel. In the present study, we used the face graph as an aid for health informing and educating activities in the setting of a community health activity. For this purpose, we designed a special sheet to draw face by hand. By using this sheet, each person can draw his/her 'face' from one's laboratory data index under the guidance of additional lines. The acceptability of this hand drawn face was evaluated by 283 people aged 65 years and over at a health counseling session. For both men and women, a higher percentage preferred face (37% for men, 40% for women) over numeral (23% for men, 17% for women). The preference for the face graph was also observed at each of three age groups within each sex. The highest affinity to face (64%) was observed for the 14 women who reported as cataract patients.

Aged↗

PubMed2002

Using graph theory to describe and model chromosome aberrations.

A comprehensive description of chromosome aberrations is introduced that is suitable for all cytogenetic protocols (e.g. solid staining, banding, FISH, mFISH, SKY, bar coding) and for mathematical analyses. "Aberration multigraphs" systematically characterize and interrelate three basic aberration elements: (1) the initial configuration of chromosome breaks; (2) the exchange process, whose cycle structure helps to describe aberration complexity; and (3) the final configuration of rearranged chromosomes, which determines the observed pattern but may contain cryptic misrejoinings in addition. New aberration classification methods and a far-reaching generalization of mPAINT descriptors, applicable to any protocol, emerge. The difficult problem of trying to infer actual exchange processes from cytogenetically observed final patterns is analyzed using computer algorithms, adaptations of known theorems on cubic graphs, and some new graph-theoretical constructs. Results include the following: (1) For a painting protocol, unambiguously inferring the occurrence of a high-order cycle requires a corresponding number of different colors; (2) cycle structure can be computed by a simple trick directly from mPAINT descriptors if the initial configuration has no more than one break per homologue pair; and (3) higher-order cycles are more frequent than the obligate cycle structure specifies. Aberration multigraphs are a powerful new way to describe, classify and quantitatively analyze radiation-induced chromosome aberrations. They pinpoint (but do not eliminate) the problem that, with present cytogenetic techniques, one observed pattern corresponds to many possible initial configurations and exchange processes.

Algorithms↗

PubMed2006

Quantifying population substructure: extending the graph-theoretic approach.

Among the few universal themes in ecology is that resources, energy, and organisms themselves, are patchily distributed. This patchy distribution imposes a need for some level of dispersal or connectivity among spatially separate patches in order to allow organisms to acquire sufficient resources for survival. To date, general patterns of connectivity have not emerged. This is, in part, because different species respond to different scales of patchiness. I propose an extension of the graph-theoretic approach to control for such differences and reveal potential generalities about how natural populations are organized. Using statistical methods and simple applications of graph theory, continuum percolation, and metapopulation models, I demonstrate a pattern of hierarchical clustering among populations in both a plant-pathogen system at an extent of 1000 m and gene flow in a salamander species across a subcontinental range. Results suggest that some patches or populations have a disproportionately high importance to the maintenance of overall connectivity in the system within and across scales.

Animals↗

PubMed1988

Theft reduction in a grocery store through product identification and graphing of losses for employees.

Shoplifting and employee theft constitute a major problem for retailers. Previous research has described techniques for effectively reducing either type of theft but has not addressed the problem of thefts of unspecified origin. In a grocery store we evaluated the effect of identifying for employees frequently stolen products from three groups of items and graphing, twice weekly in the lunchroom, losses for the separate groups. After the products were identified and losses graphed, thefts from the three groups dropped from eight per day to two per day.

Journal Article↗

PubMed1993

Straight-line graphs for the prediction of growth of the upper extremities.

A simple graphic method was used for the prediction of growth and the determination of when a corrective procedure should be performed to equalize the lengths of the upper extremities. Straight-line graphs, similar to those described by Moseley for the lower extremities, were constructed for the radius, ulna, and humerus. The data for the current study were derived from a multidisciplinary, longitudinal study of growth in 244 healthy children (123 boys and 121 girls)--from infancy to skeletal maturity--and from previously constructed graphs depicting remaining growth. The use of this method can simplify the planning of an equalization procedure for an upper extremity.

Adolescent↗