16,654 research outputs found
Prediction of protein-protein interactions using one-class classification methods and integrating diverse data
This research addresses the problem of prediction of protein-protein interactions (PPI)
when integrating diverse kinds of biological information. This task has been commonly
viewed as a binary classification problem (whether any two proteins do or do not interact)
and several different machine learning techniques have been employed to solve this
task. However the nature of the data creates two major problems which can affect results.
These are firstly imbalanced class problems due to the number of positive examples (pairs
of proteins which really interact) being much smaller than the number of negative ones.
Secondly the selection of negative examples can be based on some unreliable assumptions
which could introduce some bias in the classification results.
Here we propose the use of one-class classification (OCC) methods to deal with the task of
prediction of PPI. OCC methods utilise examples of just one class to generate a predictive
model which consequently is independent of the kind of negative examples selected; additionally
these approaches are known to cope with imbalanced class problems. We have
designed and carried out a performance evaluation study of several OCC methods for this
task, and have found that the Parzen density estimation approach outperforms the rest. We
also undertook a comparative performance evaluation between the Parzen OCC method
and several conventional learning techniques, considering different scenarios, for example
varying the number of negative examples used for training purposes. We found that the
Parzen OCC method in general performs competitively with traditional approaches and in
many situations outperforms them. Finally we evaluated the ability of the Parzen OCC
approach to predict new potential PPI targets, and validated these results by searching for
biological evidence in the literature
Thermodynamic quantum critical behavior of the Kondo necklace model
We obtain the phase diagram and thermodynamic behavior of the Kondo necklace
model for arbitrary dimensions using a representation for the localized and
conduction electrons in terms of local Kondo singlet and triplet operators. A
decoupling scheme on the double time Green's functions yields the dispersion
relation for the excitations of the system. We show that in there is
an antiferromagnetically ordered state at finite temperatures terminating at a
quantum critical point (QCP). In 2-d, long range magnetic order occurs only at
T=0. The line of Neel transitions for varies with the distance to the
quantum critical point QCP as, where the shift
exponent . In the paramagnetic side of the phase diagram, the
spin gap behaves as for consistent with
the value found for the dynamical critical exponent. We also find in this
region a power law temperature dependence in the specific heat for
and along the non-Fermi liquid trajectory. For , in the so-called Kondo spin liquid phase, the thermodynamic
behavior is dominated by an exponential temperature dependence.Comment: Submitted to PR
Combined Relativistic and static analysis for all Delta B=2 operators
We analyse matrix elements of Delta B=2 operators by combining QCD results
with the ones obtained in the static limit of HQET. The matching of all the QCD
operators to HQET is made at NLO order. To do that we have to include the
anomalous dimension matrix up to two loops, both in QCD and HQET, and the one
loop matching for all the Delta B=2 operators. The matrix elements of these
operators are relevant for the prediction of the B-\bar B mixing, B_s meson
width difference and supersymmetric effects in Delta B=2 transitions.Comment: 3 pages, 1 figure. Lattice2001(heavyquark
Automation on the generation of genome scale metabolic models
Background: Nowadays, the reconstruction of genome scale metabolic models is
a non-automatized and interactive process based on decision taking. This
lengthy process usually requires a full year of one person's work in order to
satisfactory collect, analyze and validate the list of all metabolic reactions
present in a specific organism. In order to write this list, one manually has
to go through a huge amount of genomic, metabolomic and physiological
information. Currently, there is no optimal algorithm that allows one to
automatically go through all this information and generate the models taking
into account probabilistic criteria of unicity and completeness that a
biologist would consider. Results: This work presents the automation of a
methodology for the reconstruction of genome scale metabolic models for any
organism. The methodology that follows is the automatized version of the steps
implemented manually for the reconstruction of the genome scale metabolic model
of a photosynthetic organism, {\it Synechocystis sp. PCC6803}. The steps for
the reconstruction are implemented in a computational platform (COPABI) that
generates the models from the probabilistic algorithms that have been
developed. Conclusions: For validation of the developed algorithm robustness,
the metabolic models of several organisms generated by the platform have been
studied together with published models that have been manually curated. Network
properties of the models like connectivity and average shortest mean path of
the different models have been compared and analyzed.Comment: 24 pages, 2 figures, 2 table
Renormalization Constants of Quark Operators for the Non-Perturbatively Improved Wilson Action
We present the results of an extensive lattice calculation of the
renormalization constants of bilinear and four-quark operators for the
non-perturbatively O(a)-improved Wilson action. The results are obtained in the
quenched approximation at four values of the lattice coupling by using the
non-perturbative RI/MOM renormalization method. Several sources of systematic
uncertainties, including discretization errors and final volume effects, are
examined. The contribution of the Goldstone pole, which in some cases may
affect the extrapolation of the renormalization constants to the chiral limit,
is non-perturbatively subtracted. The scale independent renormalization
constants of bilinear quark operators have been also computed by using the
lattice chiral Ward identities approach and compared with those obtained with
the RI-MOM method. For those renormalization constants the non-perturbative
estimates of which have been already presented in the literature we find an
agreement which is typically at the level of 1%.Comment: 36 pages, 13 figures. Minor changes in the text and in one figure.
Accepted for publication on JHE
B-parameters of the complete set of matrix elements of (Delta B = 2) operators from the lattice
We compute on the lattice the ``bag'' parameters of the five (Delta B = 2)
operators of the supersymmetric basis, by combining their values determined in
full QCD and in the static limit of HQET. The extrapolation of the QCD results
from the accessible heavy-light meson masses to the B-meson mass is constrained
by the static result. The matching of the corresponding results in HQET and in
QCD is for the first time made at NLO accuracy in the MSbar(NDR)
renormalization scheme. All results are obtained in the quenched approximation.Comment: 27 pages (5 figures
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