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 $d$ 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 $d\geq 3$ 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 $d>2$ varies with the distance to the quantum critical point QCP $|g|$ as, $T_N \propto |g|^{\psi}$ where the shift exponent $\psi=1/(d-1)$. In the paramagnetic side of the phase diagram, the spin gap behaves as $\Delta\approx \sqrt{|g|}$ for $d \ge 3$ consistent with the value $z=1$ found for the dynamical critical exponent. We also find in this region a power law temperature dependence in the specific heat for $k_BT\gg\Delta$ and along the non-Fermi liquid trajectory. For $k_BT \ll\Delta$, 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