A critical examination of node-similarity based graph matching algorithms

In this paper, we shall critically examine a special class of graph matching algorithms that follow the approach of node-similarity measurement. A high-level algorithm framework, namely node-similarity graph matching framework (NSGM framework), is proposed, from which, many existing graph matching algorithms can be subsumed, including the eigen-decomposition method of Umeyama, the polynomial-transformation method of Almohamad, the hubs and authorities method of Kleinberg, and the kronecker product successive projection methods of Wyk, etc. In addition, improved algorithms can be developed from the NSGM framework with respects to the corresponding results in graph theory. As the observation, it is pointed out that, in general, any algorithm which can be subsumed from NSGM framework fails to work well for graphs with non-trivial auto-isomorphism structure.

A robust approach to subsequence matching

In terms of a general time theory which addresses time-elements as typed point-based intervals, a formal characterization of time-series and state-sequences is introduced. Based on this framework, the subsequence matching problem is specially tackled by means of being transferred into bipartite graph matching problem. Then a hybrid similarity model with high tolerance of inversion, crossover and noise is proposed for matching the corresponding bipartite graphs involving both temporal and non-temporal measurements. Experimental results on reconstructed time-series data from UCI KDD Archive demonstrate that such an approach is more effective comparing with the traditional similarity model based algorithms, promising robust techniques for lager time-series databases and real-life applications such as Content-based Video Retrieval (CBVR), etc.

Ecological Investigations with the Continuous Plankton Recorder: The Phytoplankton in the Southern North Sea. 1932-37.

1. The changes in the composition and distribution of the plankton of the southern North Sea have been investigated month by month, from June 1932 to December 1937; the present report deals with the phytoplankton. The survey was carried out by the Continuous Plankton Recorder, towed at a standard depth of 10 metres, by ships on regular steamship lines across the North Sea from Hull towards the Skagerrak, to Bremen and to Rotterdam, and later between London and Esbjerg. 2. The material and methods are described, together with a discussion on the validity of this type of survey and some comparison of its results with those obtained by other methods (pp. 76-86). 3. Particular attention has been paid to Rhizosolenia styliformis (pp. 92- 107), Biddulphia sinensis (pp. 108-115), Phaeocystis (pp. 149-153), and the Dinoflagellates (pp. 134-149); of these the first three are known to be of particular importance in relation to the herring fisheries. More generalised data are available for the principal diatoms other than R. styliformis and B. sinensis (pp. 116-134). 4. The main part of the work is an ecological study of the phytoplankton changes in time and space over the 5½ years. Each year is marked by some distinct variations in the abundance and the times of increase, maximum numbers and decline as recorded in the different forms. These variations in the annual cycles are compared on the different lines by a series of graphs arranged against a time scale of months, a set for each year being placed side by side (Plates I-XXI). More detailed studies by more frequent records were made in the autumns of 1934, 1935, 1936 and 1937 (cf. Figs. 3 and 4). The changes in spatial distribution are shown by a series of monthly maps arranged in a similar manner for each year (Plates XXII-LXIV). These intensive studies of the changes in time and space are also intended to form the basis for correlations with other features in the general ecology of the area (e. g. the zooplankton, hydrology, meteorology and fisheries) to be made in later publications. 5. Whilst each form has shown its own peculiar features, a trend towards a general increase in the phytoplankton as a whole has been observed during the period, although the years 1934 and 1936 have in some respects shown deviations and regressive features, and not all organisms have revealed the same trend. The possible relation of this gradual trend to other events observed in recent years in these and neighbouring waters is discussed (pp. 162-167). 6. The application of these results to the study of patchiness (pp. 154-158), inter-relationships in the plankton (pp. 159-160) and to water movements (pp. 160-162) is briefly discussed.

Fecundity and reproductive strategies in deep-sea incirrate octopuses (Cephalopoda: Octopoda).

Coleoid cephalopods show flexibility in their reproductive strategies or mode of spawning, which can range from simultaneous terminal spawning over a short period at the end of the animal’s life to continuous spawning over a long period of the animal’s life. Although a simultaneous terminal spawning strategy is typical of shallow water temperate octopuses, it is not known whether deep-sea octopods would have the same reproductive strategy. The reproductive strategies and fecundity were investigated in nine species of deep-sea incirrate octopuses: Bathypolypus arcticus, Bathypolypus bairdii, Bathypolypus ergasticus, Bathypolypus sponsalis, Bathypolypus valdiviae, Benthoctopus levis, Benthoctopus normani, Benthoctopus sp., and Graneledone verrucosa (total n = 85). Egg-length frequency graphs and multivariate analysis (principal components analysis) suggest that B. sponsalis has a synchronous ovulation pattern and therefore a simultaneous terminal spawning strategy. Although a simultaneous terminal spawning strategy is most likely for B. levis and B. normani, the egg-length frequency graphs and multivariate analysis also suggest a greater variation in egglengths which could lead to spawning over an extended period.

Compact Toffoli gate using weighted graph states

We introduce three compact graph states that can be used to perform a measurement-based Toffoli gate. Given a weighted graph of six, seven, or eight qubits, we show that success probabilities of 1/4, 1/2, and 1, respectively, can be achieved. Our study puts a measurement-based version of this important quantum logic gate within the reach of current experiments. As the graphs are setup independent, they could be realized in a variety of systems, including linear optics and ion traps.

The chronic fatigue syndrome: A comparative pathway analysis

In this paper, we introduce a method to detect pathological pathways of a disease. We aim to identify biological processes rather than single genes affected by the chronic fatigue syndrome (CFS). So far, CFS has neither diagnostic clinical signals nor abnormalities that could be diagnosed by laboratory examinations. It is also unclear if the CFS represents one disease or can be subdivided in different categories. We use information from clinical trials, the gene ontology (GO) database as well as gene expression data to identify undirected dependency graphs (UDGs) representing biological processes according to the GO database. The structural comparison of UDGs of sick versus non-sick patients allows us to make predictions about the modification of pathways due to pathogenesis.

Rigorous conditions for food-web intervality in high-dimensional trophic niche spaces

Food webs represent trophic (feeding) interactions in ecosystems. Since the late 1970s, it has been recognized that food-webs have a surprisingly close relationship to interval graphs. One interpretation of food-web intervality is that trophic niche space is low-dimensional, meaning that the trophic character of a species can be expressed by a single or at most a few quantitative traits. In a companion paper we demonstrated, by simulating a minimal food-web model, that food webs are also expected to be interval when niche-space is high-dimensional. Here we characterize the fundamental mechanisms underlying this phenomenon by proving a set of rigorous conditions for food-web intervality in high-dimensional niche spaces. Our results apply to a large class of food-web models, including the special case previously studied numerically.

The structural information content of chemical networks

We present an information-theoretic method to measure the structural information content of networks and apply it to chemical graphs. As a result, we find that our entropy measure is more general than classical information indices known in mathematical and computational chemistry. Further, we demonstrate that our measure reflects the essence of molecular branching meaningfully by determining the structural information content of some chemical graphs numerically.

Structural information content of networks: Graph entropy based on local vertex functionals

In this paper we define the structural information content of graphs as their corresponding graph entropy. This definition is based on local vertex functionals obtained by calculating-spheres via the algorithm of Dijkstra. We prove that the graph entropy and, hence, the local vertex functionals can be computed with polynomial time complexity enabling the application of our measure for large graphs. In this paper we present numerical results for the graph entropy of chemical graphs and discuss resulting properties. (C) 2007 Elsevier Ltd. All rights reserved.

Algorithmic computation of knot polynomials of secondary structure elements of proteins

The classification of protein structures is an important and still outstanding problem. The purpose of this paper is threefold. First, we utilize a relation between the Tutte and homfly polynomial to show that the Alexander-Conway polynomial can be algorithmically computed for a given planar graph. Second, as special cases of planar graphs, we use polymer graphs of protein structures. More precisely, we use three building blocks of the three-dimensional protein structure-alpha-helix, antiparallel beta-sheet, and parallel beta-sheet-and calculate, for their corresponding polymer graphs, the Tutte polynomials analytically by providing recurrence equations for all three secondary structure elements. Third, we present numerical results comparing the results from our analytical calculations with the numerical results of our algorithm-not only to test consistency, but also to demonstrate that all assigned polynomials are unique labels of the secondary structure elements. This paves the way for an automatic classification of protein structures.

Workspace evaluation of manipulators through finite-partition of SE(3)

Workspace analysis and optimization are important in a manipulator design. As the complete workspace of a 6-DOF manipulator is embedded into a 6-imensional space, it is difficult to quantify and qualify it. Most literatures only considered the 3-D sub workspaces of the complete 6-D workspace. In this paper, a finite-partition approach of the Special Euclidean group SE(3) is proposed based on the topology properties of SE(3), which is the product of Special Orthogonal group SO(3) and R^3. It is known that the SO(3) is homeomorphic to a solid ball D^3 with antipodal points identified while the geometry of R^3 can be regarded as a cuboid. The complete 6-D workspace SE(3) is at the first time parametrically and proportionally partitioned into a number of elements with uniform convergence based on its geometry. As a result, a basis volume element of SE(3) is formed by the product of a basis volume element of R^3 and a basis volume element of SO(3), which is the product of a basis volume element of D^3 and its associated integration measure. By this way, the integration of the complete 6-D workspace volume becomes the simple summation of the basis volume elements of SE(3). Two new global performance indices, i.e., workspace volume ratio Wr and global condition index GCI, are defined over the complete 6-D workspace. A newly proposed 3 RPPS parallel manipulator is optimized based on this finite-partition approach. As a result, the optimal dimensions for maximal workspace are obtained, and the optimal performance points in the workspace are identified.

Signal and variability within a Holocene peat bog - Chronological uncertainties of pollen, macrofossil and fungal proxies

A single raised bog from the eastern Netherlands has been repeatedly analysed and ¹⁴C dated over the past few decades. Here we assess the within-site variability of fossil proxy data through comparing the regional
pollen, macrofossils and non-pollen palynomorphs of four of these profiles. High-resolution chronologies were obtained using ¹⁴C dating and Bayesian age-depth modelling. Where chronologies of profiles overlap, proxy curves are compared between the profiles using greyscale graphs that visualise chronological uncertainties. Even at this small spatial scale, there is considerable variability of the fossil proxy curves. Implications regarding signal (climate) and noise (internal dynamics) of the different types of fossil proxies are discussed. Single cores are of limited value for reconstructing centennial-scale climate change, and only by combining multiple cores and proxies can we obtain a reliable understanding of past environmental change and possible forcing factors (e.g., solar variability).

The Computational Complexity of Dominance and Consistency in CP-Nets

We investigate the computational complexity of testing dominance and consistency in CP-nets. Previously, the complexity of dominance has been determined for restricted classes in which the dependency graph of the CP-net is acyclic. However, there are preferences of interest that define cyclic dependency graphs; these are modeled with general CP-nets. In our main results, we show here that both dominance and consistency for general CP-nets are PSPACE-complete. We then consider the concept of strong dominance, dominance equivalence and dominance incomparability, and several notions of optimality, and identify the complexity of the corresponding decision problems. The reductions used in the proofs are from STRIPS planning, and thus reinforce the earlier established connections between both areas.

Developing Approaches for Solving a Telecommunications Feature Subscription Problem

Call control features (e.g., call-divert, voice-mail) are primitive options to which users can subscribe off-line to personalise their service. The configuration of a feature subscription involves choosing and sequencing features from a catalogue and is subject to constraints that prevent undesirable feature interactions at run-time. When the subscription requested by a user is inconsistent, one problem is to find an optimal relaxation, which is a generalisation of the feedback vertex set problem on directed graphs, and thus it is an NP-hard task. We present several constraint programming formulations of the problem. We also present formulations using partial weighted maximum Boolean satisfiability and mixed integer linear programming. We study all these formulations by experimentally comparing them on a variety of randomly generated instances of the feature subscription problem.

Veiled Aspects of Bach Reception in the Long Nineteenth Century Exposed through a Macro-examination of Printed Music: with Particular Focus on The Well-Tempered Clavier

It presents questions that have arisen as a result of more than 20 years of collecting the data for the Bach Bibliography. Taking editions of The Well-Tempered Clavier as an example and using figures and graphs extracted from the Bach Bibliography, Tomita explores the various facets of the work's reception including its market appeal, the ambitions that steered its editors and publishers, and trends in its interpretation.