4,314 research outputs found
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
Metabolite essentiality elucidates robustness of Escherichia coli metabolism
Complex biological systems are very robust to genetic and environmental
changes at all levels of organization. Many biological functions of Escherichia
coli metabolism can be sustained against single-gene or even multiple-gene
mutations by using redundant or alternative pathways. Thus, only a limited
number of genes have been identified to be lethal to the cell. In this regard,
the reaction-centric gene deletion study has a limitation in understanding the
metabolic robustness. Here, we report the use of flux-sum, which is the
summation of all incoming or outgoing fluxes around a particular metabolite
under pseudo-steady state conditions, as a good conserved property for
elucidating such robustness of E. coli from the metabolite point of view. The
functional behavior, as well as the structural and evolutionary properties of
metabolites essential to the cell survival, was investigated by means of a
constraints-based flux analysis under perturbed conditions. The essential
metabolites are capable of maintaining a steady flux-sum even against severe
perturbation by actively redistributing the relevant fluxes. Disrupting the
flux-sum maintenance was found to suppress cell growth. This approach of
analyzing metabolite essentiality provides insight into cellular robustness and
concomitant fragility, which can be used for several applications, including
the development of new drugs for treating pathogens.Comment: Supplements available at
http://stat.kaist.ac.kr/publication/2007/PJKim_pnas_supplement.pd
Characteristics of Japanese wrestlers with respect to function and structure of limbs
It is well known that hypertrophy and strength gain of the human skeletal muscle are induced by muscle training. It has also been shown that the training effect on size and strength of the skeletal muscle are altered the different athletic training protocols (1, 4). From these findings, it seems possible that wrestlers possess the hypertrophied muscle and stronger muscle strength by specific training.
In the present study, we assess the functional and structural characteristics of the skeletal muscle in Japanese wrestlers
Complex networks theory for analyzing metabolic networks
One of the main tasks of post-genomic informatics is to systematically
investigate all molecules and their interactions within a living cell so as to
understand how these molecules and the interactions between them relate to the
function of the organism, while networks are appropriate abstract description
of all kinds of interactions. In the past few years, great achievement has been
made in developing theory of complex networks for revealing the organizing
principles that govern the formation and evolution of various complex
biological, technological and social networks. This paper reviews the
accomplishments in constructing genome-based metabolic networks and describes
how the theory of complex networks is applied to analyze metabolic networks.Comment: 13 pages, 2 figure
-analogue of modified KP hierarchy and its quasi-classical limit
A -analogue of the tau function of the modified KP hierarchy is defined by
a change of independent variables. This tau function satisfies a system of
bilinear -difference equations. These bilinear equations are translated to
the language of wave functions, which turn out to satisfy a system of linear
-difference equations. These linear -difference equations are used to
formulate the Lax formalism and the description of quasi-classical limit. These
results can be generalized to a -analogue of the Toda hierarchy. The results
on the -analogue of the Toda hierarchy might have an application to the
random partition calculus in gauge theories and topological strings.Comment: latex2e, a4 paper 15 pages, no figure; (v2) a few references are
adde
Integrable Structure of Supersymmetric Yang-Mills and Melting Crystal
We study loop operators of SYM in background.
For the case of U(1) theory, the generating function of correlation functions
of the loop operators reproduces the partition function of melting crystal
model with external potential. We argue the common integrable structure of
SYM and melting crystal model.Comment: 12 pages, 1 figure, based on an invited talk presented at the
international workshop "Progress of String Theory and Quantum Field Theory"
(Osaka City University, December 7-10, 2007), to be published in the
proceeding
Functional cartography of complex metabolic networks
High-throughput techniques are leading to an explosive growth in the size of
biological databases and creating the opportunity to revolutionize our
understanding of life and disease. Interpretation of these data remains,
however, a major scientific challenge. Here, we propose a methodology that
enables us to extract and display information contained in complex networks.
Specifically, we demonstrate that one can (i) find functional modules in
complex networks, and (ii) classify nodes into universal roles according to
their pattern of intra- and inter-module connections. The method thus yields a
``cartographic representation'' of complex networks. Metabolic networks are
among the most challenging biological networks and, arguably, the ones with
more potential for immediate applicability. We use our method to analyze the
metabolic networks of twelve organisms from three different super-kingdoms. We
find that, typically, 80% of the nodes are only connected to other nodes within
their respective modules, and that nodes with different roles are affected by
different evolutionary constraints and pressures. Remarkably, we find that
low-degree metabolites that connect different modules are more conserved than
hubs whose links are mostly within a single module.Comment: 17 pages, 4 figures. Go to http://amaral.northwestern.edu for the PDF
file of the reprin
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