Avoiding spurious feedback loops in the reconstruction of gene regulatory networks with dynamic bayesian networks

Feedback loops and recurrent structures are essential to the regulation and stable control of complex biological systems. The application of dynamic as opposed to static Bayesian networks is promising in that, in principle, these feedback loops can be learned. However, we show that the widely applied BGe score is susceptible to learning spurious feedback loops, which are a consequence of non-linear regulation and autocorrelation in the data. We propose a non-linear generalisation of the BGe model, based on a mixture model, and demonstrate that this approach successfully represses spurious feedback loops

Algorithms for Highly Symmetric Linear and Integer Programs

This paper deals with exploiting symmetry for solving linear and integer programming problems. Basic properties of linear representations of finite groups can be used to reduce symmetric linear programming to solving linear programs of lower dimension. Combining this approach with knowledge of the geometry of feasible integer solutions yields an algorithm for solving highly symmetric integer linear programs which only takes time which is linear in the number of constraints and quadratic in the dimension.Comment: 21 pages, 1 figure; some references and further comments added, title slightly change

Robust high-dimensional precision matrix estimation

The dependency structure of multivariate data can be analyzed using the covariance matrix $\Sigma$. In many fields the precision matrix $\Sigma^{-1}$ is even more informative. As the sample covariance estimator is singular in high-dimensions, it cannot be used to obtain a precision matrix estimator. A popular high-dimensional estimator is the graphical lasso, but it lacks robustness. We consider the high-dimensional independent contamination model. Here, even a small percentage of contaminated cells in the data matrix may lead to a high percentage of contaminated rows. Downweighting entire observations, which is done by traditional robust procedures, would then results in a loss of information. In this paper, we formally prove that replacing the sample covariance matrix in the graphical lasso with an elementwise robust covariance matrix leads to an elementwise robust, sparse precision matrix estimator computable in high-dimensions. Examples of such elementwise robust covariance estimators are given. The final precision matrix estimator is positive definite, has a high breakdown point under elementwise contamination and can be computed fast

Quantum Geons and Noncommutative Spacetimes

Physical considerations strongly indicate that spacetime at Planck scales is noncommutative. A popular model for such a spacetime is the Moyal plane. The Poincar\`e group algebra acts on it with a Drinfel'd-twisted coproduct. But the latter is not appropriate for more complicated spacetimes such as those containing the Friedman-Sorkin (topological) geons. They have rich diffeomorphism groups and in particular mapping class groups, so that the statistics groups for N identical geons is strikingly different from the permutation group $S_N$. We generalise the Drinfel'd twist to (essentially) generic groups including to finite and discrete ones and use it to modify the commutative spacetime algebras of geons as well to noncommutative algebras. The latter support twisted actions of diffeos of geon spacetimes and associated twisted statistics. The notion of covariant fields for geons is formulated and their twisted versions are constructed from their untwisted versions. Non-associative spacetime algebras arise naturally in our analysis. Physical consequences, such as the violation of Pauli principle, seem to be the outcomes of such nonassociativity. The richness of the statistics groups of identical geons comes from the nontrivial fundamental groups of their spatial slices. As discussed long ago, extended objects like rings and D-branes also have similar rich fundamental groups. This work is recalled and its relevance to the present quantum geon context is pointed out.Comment: 41 page

Neutron Stars and Nuclei in the Modified Relativistic Hartree Approximation

We have examined the properties of neutron-rich matter and finite nuclei in the modified relativistic Hartree approximation for several values of the renormalization scale, $\mu$, around the standard choice of $\mu$ equal to the nucleon mass $M$. Observed neutron star masses do not effectively constrain the value of $\mu$. However for finite nuclei the value $\mu/M=0.79$, suggested by nuclear matter data, provides a good account of the bulk properties with a sigma mass of about 600 MeV. This value of $\mu/M$ renders the effective three and four body scalar self-couplings to be zero at 60\% of equilibrium nuclear matter density, rather than in the vacuum. We have also found that the matter part of the exchange diagram has little impact on the bulk properties of neutron stars.Comment: 33 pages, Latex, 8 figures (available from authors by fax), Minnesota preprint NUC-MINN-93/7-

Three-body non-additive forces between spin-polarized alkali atoms

Three-body non-additive forces in systems of three spin-polarized alkali atoms (Li, Na, K, Rb and Cs) are investigated using high-level ab initio calculations. The non-additive forces are found to be large, especially near the equilateral equilibrium geometries. For Li, they increase the three-atom potential well depth by a factor of 4 and reduce the equilibrium interatomic distance by 0.9 A. The non-additive forces originate principally from chemical bonding arising from sp mixing effects.Comment: 4 pages, 3 figures (in 5 files

Vector Bundle Moduli and Small Instanton Transitions

We give the general presciption for calculating the moduli of irreducible, stable SU(n) holomorphic vector bundles with positive spectral covers over elliptically fibered Calabi-Yau threefolds. Explicit results are presented for Hirzebruch base surfaces B=F_r. The transition moduli that are produced by chirality changing small instanton phase transitions are defined and specifically enumerated. The origin of these moduli, as the deformations of the spectral cover restricted to the ``lift'' of the horizontal curve of the M5-brane, is discussed. We present an alternative description of the transition moduli as the sections of rank n holomorphic vector bundles over the M5-brane curve and give explicit examples. Vector bundle moduli appear as gauge singlet scalar fields in the effective low-energy actions of heterotic superstrings and heterotic M-theory.Comment: 52 pages, LATEX, corrected typo

Vector Bundle Moduli Superpotentials in Heterotic Superstrings and M-Theory

The non-perturbative superpotential generated by a heterotic superstring wrapped once around a genus-zero holomorphic curve is proportional to the Pfaffian involving the determinant of a Dirac operator on this curve. We show that the space of zero modes of this Dirac operator is the kernel of a linear mapping that is dependent on the associated vector bundle moduli. By explicitly computing the determinant of this map, one can deduce whether or not the dimension of the space of zero modes vanishes. It is shown that this information is sufficient to completely determine the Pfaffian and, hence, the non-perturbative superpotential as explicit holomorphic functions of the vector bundle moduli. This method is illustrated by a number of non-trivial examples.Comment: 81 pages, LaTeX, corrected typo

Gastric cancer and Helicobacter pylori: a combined analysis of 12 case control studies nested within prospective cohorts

BACKGROUND: The magnitude of the association between Helicobacter pylori and incidence of gastric cancer is unclear. H pylori infection and the circulating antibody response can be lost with development of cancer; thus retrospective studies are subject to bias resulting from classifi- cation of cases as H pylori negative when they were infected in the past. AIMS: To combine data from all case control studies nested within prospective cohorts to assess more reliably the relative risk of gastric cancer associated with H pylori infection.To investigate variation in relative risk by age, sex, cancer type and subsite, and interval between blood sampling and cancer diagnosis. METHODS: Studies were eligible if blood samples for H pylori serology were collected before diagnosis of gastric cancer in cases. Identified published studies and two unpublished studies were included. Individual subject data were obtained for each. Matched odds ratios (ORs) and 95% confidence intervals (95% CI) were calculated for the association between H pylori and gastric cancer. RESULTS: Twelve studies with 1228 gastric cancer cases were considered. The association with H pylori was restricted to noncardia cancers (OR 3.0; 95% CI 2.3–3.8) and was stronger when blood samples for H pylori serology were collected 10+ years before cancer diagnosis (5.9; 3.4–10.3). H pylori infection was not associated with an altered overall risk of cardia cancer (1.0; 0.7–1.4). CONCLUSIONS: These results suggest that 5.9 is the best estimate of the relative risk of non-cardia cancer associated with H pylori infection and that H pylori does not increase the risk of cardia cancer. They also support the idea that when H pylori status is assessed close to cancer diagnosis, the magnitude of the non-cardia association may be underestimated