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PubMed2004

Hydrogen-bonded polyrotaxane-like structure containing cyclic (H2O)4 in [Zn(OAc)2(mu-bpe)]2.H2O: X-ray and neutron diffraction studies.

The reaction of 4,4'-bipyridylethane (bpe) and 4,4'-dipyridyl disulfide (dpds) with Zn(OAc)2.2H2O has led to the formation of two coordination polymers, [Zn(OAc)2(mu-bpe)].2H2O (1) and [Zn(OAc)2(mu-dpds)] (2). Both the compounds have zigzag coordination polymeric structures as revealed by X-ray crystallography. However, the presence of two lattice water molecules in 1 results in an interesting difference between the crystal structures. In 1, the carboxylate carbonyl oxygen atoms of the Zn(OAc)2 groups from two different adjacent zigzag polymers and four lattice water molecules form 24-membered hydrogen-bonded rings (graph set notation, R6 (6)(24)). One of the two bpe ligands associated with each Zn(II) center passes through the center of this ring to form a two-dimensional hydrogen-bonded coordination polymeric structure. In the solid state, the adjacent 24-membered hydrogen-bonded rings further fuse together through O-H...O hydrogen bonds among four waters to form cyclic (H2O)4. This results in a one-dimensional hydrogen-bonded ribbon-like polymer comprising fused alternating 24- and eight-membered O-H...O hydrogen-bonded rings. One of the bpe ligands passes through the center of the larger ring to produce an unexpected single self-penetrating three-dimensional hydrogen-bonded network with polyrotaxane-like association. A neutron diffraction study provides a detailed description of the hydrogen bonds involved.

Journal Article↗
PubMed2005

Supervised nonlinear dimensionality reduction for visualization and classification.

When performing visualization and classification, people often confront the problem of dimensionality reduction. Isomap is one of the most promising nonlinear dimensionality reduction techniques. However, when Isomap is applied to real-world data, it shows some limitations, such as being sensitive to noise. In this paper, an improved version of Isomap, namely S-Isomap, is proposed. S-Isomap utilizes class information to guide the procedure of nonlinear dimensionality reduction. Such a kind of procedure is called supervised nonlinear dimensionality reduction. In S-Isomap, the neighborhood graph of the input data is constructed according to a certain kind of dissimilarity between data points, which is specially designed to integrate the class information. The dissimilarity has several good properties which help to discover the true neighborhood of the data and, thus, makes S-Isomap a robust technique for both visualization and classification, especially for real-world problems. In the visualization experiments, S-Isomap is compared with Isomap, LLE, and WeightedIso. The results show that S-Isomap performs the best. In the classification experiments, S-Isomap is used as a preprocess of classification and compared with Isomap, WeightedIso, as well as some other well-established classification methods, including the K-nearest neighbor classifier, BP neural network, J4.8 decision tree, and SVM. The results reveal that S-Isomap excels compared to Isomap and WeightedIso in classification, and it is highly competitive with those well-known classification methods.

Algorithms↗
PubMed2006

Probabilistic models of cognition: conceptual foundations.

Remarkable progress in the mathematics and computer science of probability has led to a revolution in the scope of probabilistic models. In particular, 'sophisticated' probabilistic methods apply to structured relational systems such as graphs and grammars, of immediate relevance to the cognitive sciences. This Special Issue outlines progress in this rapidly developing field, which provides a potentially unifying perspective across a wide range of domains and levels of explanation. Here, we introduce the historical and conceptual foundations of the approach, explore how the approach relates to studies of explicit probabilistic reasoning, and give a brief overview of the field as it stands today.

Algorithms↗
PubMed1991

A computer method for visual presentation and programmed evaluation of labor.

Manual graphing of the progress of labor is considered useful but is not often done. The early detection of some deviations requires special graphics aids. Our objective was to develop an easy-to-use computer program for the integrated visual presentation of information characterizing the progress of labor. Through the use of inexpensive personal computers equipped with graphics monitors, the program provides a combined graphics display of timed progressive cervical dilatation, fetal station, and stimulation of uterine activity (oxytocin infusion). For the early detection of abnormalities, phase-specific normal ranges (reference areas) are displayed. In addition, protraction/arrest as well as precipitate labor disorders are highlighted and computer messages are displayed. The program was evaluated through the assessment of 405 labors entered into a local area network of computers. On average, the program identified 1.5 abnormalities per recorded labor (2.0 for labors resulting in vaginal delivery). The graphic presentation of the labor curve, produced within 3 seconds, displayed 27% more information than the tabular format on the same screen area and provided a single-screen display of the labor curve even for patients with excessive data. The computer-generated display of labor curves facilitates visual presentation and interpretation of labor progress and can also help to translate quality assurance criteria into clinical practice.

Computer Graphics↗
PubMed2005

KEGG as a glycome informatics resource.

Bioinformatics approaches to carbohydrate research have recently begun using large amounts of protein and carbohydrate data. In this field called glycome informatics, the foremost necessity is a comprehensive resource for genome-scale bioinformatics analysis of glycan data. Although the accumulation of experimental data may be useful as a reference of biological and biochemical information on carbohydrates, this is insufficient for bioinformatics analysis. Thus, we have developed a glycome informatics resource (http://www.genome.jp/kegg/glycan/) in KEGG (Kyoto Encyclopedia of Genes and Genomes), an integrated knowledge base of protein networks, genomic information, and chemical information. This review describes three noteworthy features: (1) GLYCAN, a database of carbohydrate structures; (2) glycan-related pathways; and (3) Composite Structure Map (CSM), a map illustrating all possible variations of carbohydrate structures within organisms. GLYCAN includes two useful tools: an intuitive drawing tool called KegDraw, and an efficient glycan search and alignment tool called KEGG Carbohydrate Matcher (KCaM). KEGG's glycan biosynthesis and metabolism pathways, integrating carbohydrate structures, proteins, and reactions, are also a pivotal resource. CSM is constructed as a bridge between carbohydrate functions and structures. CSM is able to display, for example, expression data of glycosyltransferases in a compact manner. In all the KEGG resources, various objects including KEGG pathways, chemical compounds, as well as carbohydrate structures are commonly represented as graphs, which are widely studied and utilized in the computer science field.

Carbohydrates↗
PubMed1996

Health professional workstations and their integration in a hospital information system: the pragmatic approach MEDIAS.

Within the daily workload at a ward there is a considerable amount of information processing. It is the task of a systematic management of hospital information systems to provide health professionals with the right information in the right place at the right time. This paper deals with the consequences for the management of hospital information systems if health professional workstations are introduced as a means for this information logistic and with the experiences gained in the Heidelberg University Hospital. Health professional workstations are formally defined in the context of a three level graph-based model of hospital information systems. It is found that health professional workstations have communication needs not only on the physical level of computer systems in the hospital information system but also on the logical tool level, which is the level of application systems. On this level communication servers or brokers are of considerable importance. In Heidelberg there are about 200 health professional workstations (MEDIAS) in routine use.

Computer Communication Networks↗
PubMed1997

Selection biases invalidate current low birthweight weight-for-gestation standards. The Northern Neonatal Network.

OBJECTIVE: To obtain unbiased estimates of the variation of birthweight with gestation in infants born before 32 weeks of gestation. SETTING: The former Northern Regional Health Authority. DESIGN: Information on birthweight was collected during a collaborative study of every registered and unregistered birth at 22 to 31 weeks of gestation in the region in 1983 and 1990 to 1991. These birthweights were then related to computer-generated Tyneside norms for all registered births at 28 to 42 weeks of gestation between 1984 and 1991. Some local information was also collected on fetal weight after termination of pregnancy on social grounds at 16 to 21 weeks of gestation. RESULTS: Weight centiles constructed after excluding infants with a gross, externally visible, malformation and those dying before the onset of labour suggest that previously published European standards have overestimated birthweight in infants < 28 weeks of gestation, some low centiles being 30% in error. Female and first-born infants weighed 4% less than their male and later-born counterparts at all gestations studied. A single correction factor can therefore be used to correct for sex and parity, eliminating the need for separate centile graphs. Twin pregnancy was associated with a 10% reduction in mean birthweight in pregnancies lasting < 37 weeks, and this difference increased progressively in pregnancies lasting longer than this. CONCLUSION: The small number of low birthweight infants in previous datasets and the selective exclusion of all nonregistered births have made previous second trimester weight-for-gestation norms unreliable.

Birth Weight↗
PubMed1998

Workflow management for multimedia information in clinical laboratories.

Workflow management is a serious concern in any organisation and a clinical laboratory is a particularly good example of where the information system (LIS) needs to be well integrated with the physical system comprising the doctors, technicians and the machines necessary to analyse and report on samples. It is the points of synchronisation between events and decision making in the outside world and control flow inside the information system that constitute the problem domain of workflow management. We propose an extension to the workflow management solution described in the OpenLabs architecture specification in which the emphasis is moved away from an essentially message orientated workflow system to one where the system may reasonably expect to deal with data that includes many different types of information such as images, diagrams, graphs and sound. Our key point is extensibility; the proposed extension of the OpenLabs architecture is able to deal with new data types without significant modification of the workflow management software. Our approach has been based on using some of the desirable features of the Hypertext Markup Language (HTML) and Uniform Resource Locators (URLs) found in the World Wide Web (WWW) and the use of industry standard object technology based on the Object Management Group's (OMG) Common Object Request Broker Architecture (CORBA).

Clinical Laboratory Information Systems↗
PubMed2002

Enriching the structure of the UMLS semantic network.

The Unified Medical Language System's (UMLS's) Semantic Network (SN)---consisting of a network of semantic types---has a two-tree structure, where each semantic type has at most one parent semantic type. This arrangement is restrictive because some semantic types are, by their definition, specializations of several parents. As a proposed enhancement to the SN, its semantic types have previously been partitioned into groups, each of which contains semantic types of some specific area. However, some groups of this proposed partition contain forest (i.e., multiple-tree) structures or even isolated semantic types. Both situations imply a disconnected internal structure. Connectivity is actually one way to assess the proposed "semantic validity" principle for partitions. It is a desired, although not required, property. In this paper, we introduce a methodology for identifying "missing" IS-A links and adding them to the SN. This process transforms the SN into a Directed Acyclic Graph (DAG) structure, with semantic types permitted to have multiple parents. A result of our methodology is the transformation of the proposed SN partition into groups satisfying the connectivity property.

Semantics↗
PubMed1999

Variable selection and multivariate methods for the identification of microorganisms by flow cytometry.

BACKGROUND: When exploited fully, flow cytometry can be used to provide multiparametric data for each cell in the sample of interest. While this makes flow cytometry a powerful technique for discriminating between different cell types, the data can be difficult to interpret. Traditionally, dual-parameter plots are used to visualize flow cytometric data, and for a data set consisting of seven parameters, one should examine 21 of these plots. A more efficient method is to reduce the dimensionality of the data (e.g., using unsupervised methods such as principal components analysis) so that fewer graphs need to be examined, or to use supervised multivariate data analysis methods to give a prediction of the identity of the analyzed particles. MATERIALS AND METHODS: We collected multiparametric data sets for microbiological samples stained with six cocktails of fluorescent stains. Multivariate data analysis methods were explored as a means of microbial detection and identification. RESULTS: We show that while all cocktails and all methods gave good accuracy of predictions (>94%), careful selection of both the stains and the analysis method could improve this figure (to > 99% accuracy), even in a data set that was not used in the formation of the supervised multivariate calibration model. CONCLUSIONS: Flow cytometry provides a rapid method of obtaining multiparametric data for distinguishing between microorganisms. Multivariate data analysis methods have an important role to play in extracting the information from the data obtained. Artificial neural networks proved to be the most suitable method of data analysis.

Bacillus subtilis↗
PubMed2002

Curvature of co-links uncovers hidden thematic layers in the World Wide Web.

Beyond the information stored in pages of the World Wide Web, novel types of "meta-information" are created when pages connect to each other. Such meta-information is a collective effect of independent agents writing and linking pages, hidden from the casual user. Accessing it and understanding the interrelation between connectivity and content in the World Wide Web is a challenging problem [Botafogo, R. A. & Shneiderman, B. (1991) in Proceedings of Hypertext (Assoc. Comput. Mach., New York), pp. 63-77 and Albert, R. & Barabási, A.-L. (2002) Rev. Mod. Phys. 74, 47-97]. We demonstrate here how thematic relationships can be located precisely by looking only at the graph of hyperlinks, gleaning content and context from the Web without having to read what is in the pages. We begin by noting that reciprocal links (co-links) between pages signal a mutual recognition of authors and then focus on triangles containing such links, because triangles indicate a transitive relation. The importance of triangles is quantified by the clustering coefficient [Watts, D. J. & Strogatz, S. H. (1999) Nature (London) 393, 440-442], which we interpret as a curvature [Bridson, M. R. & Haefliger, A. (1999) Metric Spaces of Non-Positive Curvature (Springer, Berlin)]. This curvature defines a World Wide Web landscape whose connected regions of high curvature characterize a common topic. We show experimentally that reciprocity and curvature, when combined, accurately capture this meta-information for a wide variety of topics. As an example of future directions we analyze the neural network of Caenorhabditis elegans, using the same methods.

Animals↗
PubMed2005

Automatic detection of subsystem/pathway variants in genome analysis.

MOTIVATION: Proteins work together in pathways and networks, collectively comprising the cellular machinery. A subsystem (a generalization of pathway concept) is a group of related functional roles (such as enzymes) jointly involved in a specific aspect of the cellular machinery. Subsystems provide a natural framework for comparative genome analysis and functional annotation. A subsystem may be implemented in a number of different functional variants in individual species. In order to reliably project functional assignments across multiple genomes, we have to be able to identify the variants implemented in each genome. The analysis of such variants across diverse species is an interesting problem by itself and may provide new evolutionary insights. However, no computational techniques are presently available for an automated detection and analysis of subsystem variants. RESULTS: Here we formulate the subsystem variant detection problem as finding the minimum number of subgraphs of a subsystem, which is represented as a graph, and solve the optimization problem by integer programming approach. The performance of our method was tested on subsystems encoded in the SEED, a genomic integration platform developed by the Fellowship for Interpretation of Genomes as a component of a large-scale effort on comparative analysis and annotation of multiple diverse genomes. Here we illustrate the results obtained for two expert-encoded subsystems of the biosynthesis of Coenzyme A and FMN/FAD cofactors. Applications of variant detection, to support genomic annotations and to assess divergence of species, are briefly discussed in the context of these universally conserved and essential metabolic subsystems. SUPPLEMENTARY INFORMATION: The details of the variant detection results are available at http://ffas.burnham.org/svar/supp.html.

Animals↗
PubMed1995

Identification of human gene structure using linear discriminant functions and dynamic programming.

Development of advanced technique to identify gene structure is one of the main challenges of the Human Genome Project. Discriminant analysis was applied to the construction of recognition functions for various components of gene structure. Linear discriminant functions for splice sites, 5'-coding, internal exon, and 3'-coding region recognition have been developed. A gene structure prediction system FGENE has been developed based on the exon recognition functions. We compute a graph of mutual compatibility of different exons and present a gene structure models as paths of this directed acyclic graph. For an optimal model selection we apply a variant of dynamic programming algorithm to search for the path in the graph with the maximal value of the corresponding discriminant functions. Prediction by FGENE for 185 complete human gene sequences has 81% exact exon recognition accuracy and 91% accuracy at the level of individual exon nucleotides with the correlation coefficient (C) equals 0.90. Testing FGENE on 35 genes not used in the development of discriminant functions shows 71% accuracy of exact exon prediction and 89% at the nucleotide level (C = 0.86). FGENE compares very favorably with the other programs currently used to predict protein-coding regions. Analysis of uncharacterized human sequences based on our methods for splice site (HSPL, RNASPL), internal exons (HEXON), all type of exons (FEXH) and human (FGENEH) and bacterial (CDSB) gene structure prediction and recognition of human and bacterial sequences (HBR) (to test a library for E. coli contamination) is available through the University of Houston, Weizmann Institute of Science network server and a WWW page of the Human Genome Center at Baylor College of Medicine.

Algorithms↗
PubMed1999

Propagating distributions up directed acyclic graphs.

In a previous article, we considered game trees as graphical models. Adopting an evaluation function that returned a probability distribution over values likely to be taken at a given position, we described how to build a model of uncertainty and use it for utility-directed growth of the search tree and for deciding on a move after search was completed. In some games, such as chess and Othello, the same position can occur more than once, collapsing the game tree to a directed acyclic graph (DAG). This induces correlations among the distributions at sibling nodes. This article discusses some issues that arise in extending our algorithms to a DAG. We give a simply described algorithm for correctly propagating distributions up a game DAG, taking account of dependencies induced by the DAG structure. This algorithm is exponential time in the worst case. We prove that it is #P complete to propagate distributions up a game DAG correctly. We suggest how our exact propagation algorithm can yield a fast but inexact heuristic.

Algorithms↗
PubMed1999

Revealing hidden interval graph structure in STS-content data.

MOTIVATION: STS-content data for genomic mapping contain numerous errors and anomalies resulting in cross-links among distant regions of the genome. Identification of contigs within the data is an important and difficult problem. RESULTS: This paper introduces a graph algorithm which creates a simplified view of STS-content data. The shape of the resulting structure graph provides a quality check - coherent data produce a straight line, while anomalous data produce branches and loops. In the latter case, it is sometimes possible to disentangle the various paths into subsets of the data covering contiguous regions of the genome, i.e. contigs. These straight subgraphs can then be analyzed in standard ways to construct a physical map. A theoretical basis for the method is presented along with examples of its application to current STS data from human genome centers. AVAILABILITY: Freely available on request.

Algorithms↗
PubMed2006

Payoff-monotonic game dynamics and the maximum clique problem.

Evolutionary game-theoretic models and, in particular, the so-called replicator equations have recently proven to be remarkably effective at approximately solving the maximum clique and related problems. The approach is centered around a classic result from graph theory that formulates the maximum clique problem as a standard (continuous) quadratic program and exploits the dynamical properties of these models, which, under a certain symmetry assumption, possess a Lyapunov function. In this letter, we generalize previous work along these lines in several respects. We introduce a wide family of game-dynamic equations known as payoff-monotonic dynamics, of which replicator dynamics are a special instance, and show that they enjoy precisely the same dynamical properties as standard replicator equations. These properties make any member of this family a potential heuristic for solving standard quadratic programs and, in particular, the maximum clique problem. Extensive simulations, performed on random as well as DIMACS benchmark graphs, show that this class contains dynamics that are considerably faster than and at least as accurate as replicator equations. One problem associated with these models, however, relates to their inability to escape from poor local solutions. To overcome this drawback, we focus on a particular subclass of payoff-monotonic dynamics used to model the evolution of behavior via imitation processes and study the stability of their equilibria when a regularization parameter is allowed to take on negative values. A detailed analysis of these properties suggests a whole class of annealed imitation heuristics for the maximum clique problem, which are based on the idea of varying the parameter during the imitation optimization process in a principled way, so as to avoid unwanted inefficient solutions. Experiments show that the proposed annealing procedure does help to avoid poor local optima by initially driving the dynamics toward promising regions in state space. Furthermore, the models outperform state-of-the-art neural network algorithms for maximum clique, such as mean field annealing, and compare well with powerful continuous-based heuristics.

Journal Article↗
PubMed2003

Telemedicine system using a cellular telephone for continuous ambulatory peritoneal dialysis patients.

We developed a new telemedicine system to monitor the condition of continuous ambulatory peritoneal dialysis (CAPD) patients by using a cellular telephone and an Internet Web site. All data for the CAPD patients--blood pressure, heart rate, body weight, ultrafiltration volume, and urine volume--are collected and sent directly by cellular telephone to a data server that was constructed at the NTT DoCoMo Company data center. The system is directly connected to Internet by application service provider (ASP) technology. Anywhere, at any time, each patient can confirm changes in their data in graph form by using a cellular telephone or a computer connection to an Internet Web site. The average of each type of data is calculated and shown at the Web site. All data collected by cellular telephone are calculated and, in real time, sent directly to the treating physician's office over the Internet. Abnormal data are sent directly to the treating physician's office and shown in the host computer with an emergency signal (emergency alarm system). In addition, CAPD patients can easily contact the medical staff in the Kidney and Dialysis Center of Saitama Medical School (main hospital) using the same telemedicine system. We are using this telemedicine system for 46 CAPD patients being treated by Saitama Medical School. The cost of using the system is just US$3.00 or less per month for each patient. This newly developed system has great advantages for CAPD patients, especially elderly and handicapped patients. The system can be expanded into a network that serves all CAPD patients and all hospitals in Japan.

Humans↗
PubMed2006

Comments on "the 1993 DIMACS graph coloring challenge" and "energy function-based approaches to graph coloring".

Since all graphs in the 1993 DIMACS graph coloring challenge are undirected, each edge should be only counted once. However, in some files each edge is counted once, whereas in others each edge is counted twice; so a systematical check on the DIMACS challenge is made to eliminate the inconsistencies. Besides, the experimental results of a previous paper by Blas et al. counted each violated edges twice and neglected the inconsistencies in the DIMACS challenge. So the correct experimental results of a previous paper by Blas et al are also given.

Algorithms↗