Whitham Deformations of Seiberg-Witten Curves for Classical Gauge Groups

Gorsky et al. presented an explicit construction of Whitham deformations of the Seiberg-Witten curve for the $SU(N+1)$ \calN = 2 SUSY Yang-Mills theory. We extend their result to all classical gauge groups and some other cases such as the spectral curve of the $A^{(2)}_{2N}$ affine Toda Toda system. Our construction, too, uses fractional powers of the superpotential $W(x)$ that characterizes the curve. We also consider the $u$-plane integral of topologically twisted theories on four-dimensional manifolds $X$ with $b_2^{+}(X) = 1$ in the language of these explicitly constructed Whitham deformations and an integrable hierarchy of the KdV type hidden behind.Comment: latex, 39pp, no figure; some more comments and references on integrable systems are added, and many typos are correcte

SIMCOMP/SUBCOMP: chemical structure search servers for network analyses

One of the greatest challenges in bioinformatics is to shed light on the relationship between genomic and chemical significances of metabolic pathways. Here, we demonstrate two types of chemical structure search servers: SIMCOMP (http://www.genome.jp/tools/simcomp/) for the chemical similarity search and SUBCOMP (http://www.genome.jp/tools/subcomp/) for the chemical substructure search, where both servers provide links to the KEGG PATHWAY and BRITE databases. The SIMCOMP is a graph-based method for searching the maximal common subgraph isomorphism by finding the maximal cliques in the association graph. In contrast, the SUBCOMP is an extended method for solving the subgraph isomorphism problem. The obtained links to PATHWAY or BRITE databases can be used to interpret as the biological meanings of chemical structures from the viewpoint of the various biological functions including metabolic networks

Symmetries and tau function of higher dimensional dispersionless integrable hierarchies

A higher dimensional analogue of the dispersionless KP hierarchy is introduced. In addition to the two-dimensional ``phase space'' variables $(k,x)$ of the dispersionless KP hierarchy, this hierarchy has extra spatial dimensions compactified to a two (or any even) dimensional torus. Integrability of this hierarchy and the existence of an infinite dimensional of ``additional symmetries'' are ensured by an underlying twistor theoretical structure (or a nonlinear Riemann-Hilbert problem). An analogue of the tau function, whose logarithm gives the $F$ function (``free energy'' or ``prepotential'' in the contest of matrix models and topological conformal field theories), is constructed. The infinite dimensional symmetries can be extended to this tau (or $F$) function. The extended symmetries, just like those of the dispersionless KP hierarchy, obey an anomalous commutation relations.Comment: 50 pages, (Changes: a few references are added; numbering of formulas are slightly modified

Space-efficient Feature Maps for String Alignment Kernels

String kernels are attractive data analysis tools for analyzing string data. Among them, alignment kernels are known for their high prediction accuracies in string classifications when tested in combination with SVM in various applications. However, alignment kernels have a crucial drawback in that they scale poorly due to their quadratic computation complexity in the number of input strings, which limits large-scale applications in practice. We address this need by presenting the first approximation for string alignment kernels, which we call space-efficient feature maps for edit distance with moves (SFMEDM), by leveraging a metric embedding named edit sensitive parsing (ESP) and feature maps (FMs) of random Fourier features (RFFs) for large-scale string analyses. The original FMs for RFFs consume a huge amount of memory proportional to the dimension d of input vectors and the dimension D of output vectors, which prohibits its large-scale applications. We present novel space-efficient feature maps (SFMs) of RFFs for a space reduction from O(dD) of the original FMs to O(d) of SFMs with a theoretical guarantee with respect to concentration bounds. We experimentally test SFMEDM on its ability to learn SVM for large-scale string classifications with various massive string data, and we demonstrate the superior performance of SFMEDM with respect to prediction accuracy, scalability and computation efficiency.Comment: Full version for ICDM'19 pape

Non-degenerate solutions of universal Whitham hierarchy

The notion of non-degenerate solutions for the dispersionless Toda hierarchy is generalized to the universal Whitham hierarchy of genus zero with $M+1$ marked points. These solutions are characterized by a Riemann-Hilbert problem (generalized string equations) with respect to two-dimensional canonical transformations, and may be thought of as a kind of general solutions of the hierarchy. The Riemann-Hilbert problem contains $M$ arbitrary functions $H_a(z_0,z_a)$, $a = 1,...,M$, which play the role of generating functions of two-dimensional canonical transformations. The solution of the Riemann-Hilbert problem is described by period maps on the space of $(M+1)$-tuples $(z_\alpha(p) : \alpha = 0,1,...,M)$ of conformal maps from $M$ disks of the Riemann sphere and their complements to the Riemann sphere. The period maps are defined by an infinite number of contour integrals that generalize the notion of harmonic moments. The $F$-function (free energy) of these solutions is also shown to have a contour integral representation.Comment: latex2e, using amsmath, amssym and amsthm packages, 32 pages, no figur

MACiE: a database of enzyme reaction mechanisms.

SUMMARY: MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction. AVAILABILITY: http://www-mitchell.ch.cam.ac.uk/macie/.EPSRC (G.L.H. and J.B.O.M.), the BBSRC (G.J.B. and J.M.T.—CASE studentship in association with Roche Products Ltd; N.M.O.B. and J.B.O.M.—grant BB/C51320X/1), the Chilean Government’s Ministerio de Planificacio´n y Cooperacio´n and Cambridge Overseas Trust (D.E.A.) for funding and Unilever for supporting the Centre for Molecular Science Informatics.application note restricted to 2 printed pages web site: http://www-mitchell.ch.cam.ac.uk/macie

Flexible construction of hierarchical scale-free networks with general exponent

Extensive studies have been done to understand the principles behind architectures of real networks. Recently, evidences for hierarchical organization in many real networks have also been reported. Here, we present a new hierarchical model which reproduces the main experimental properties observed in real networks: scale-free of degree distribution $P(k)$ (frequency of the nodes that are connected to $k$ other nodes decays as a power-law $P(k)\sim k^{-\gamma}$) and power-law scaling of the clustering coefficient $C(k)\sim k^{-1}$. The major novelties of our model can be summarized as follows: {\it (a)} The model generates networks with scale-free distribution for the degree of nodes with general exponent $\gamma > 2$, and arbitrarily close to any specified value, being able to reproduce most of the observed hierarchical scale-free topologies. In contrast, previous models can not obtain values of $\gamma > 2.58$. {\it (b)} Our model has structural flexibility because {\it (i)} it can incorporate various types of basic building blocks (e.g., triangles, tetrahedrons and, in general, fully connected clusters of $n$ nodes) and {\it (ii)} it allows a large variety of configurations (i.e., the model can use more than $n-1$ copies of basic blocks of $n$ nodes). The structural features of our proposed model might lead to a better understanding of architectures of biological and non-biological networks.Comment: RevTeX, 5 pages, 4 figure

Software that goes with the flow in systems biology

A recent article in BMC Bioinformatics describes new advances in workflow systems for computational modeling in systems biology. Such systems can accelerate, and improve the consistency of, modeling through automation not only at the simulation and results-production stages, but also at the model-generation stage. Their work is a harbinger of the next generation of more powerful software for systems biologists

E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs

Motivation: The IUBMB's Enzyme Nomenclature system, commonly known as the Enzyme Commission (EC) numbers, plays key roles in classifying enzymatic reactions and in linking the enzyme genes or proteins to reactions in metabolic pathways. There are numerous reactions known to be present in various pathways but without any official EC numbers, most of which have no hope to be given ones because of the lack of the published articles on enzyme assays