Inferring meta-covariates in classification

This paper develops an alternative method for gene selection that combines model based clustering and binary classification. By averaging the covariates within the clusters obtained from model based clustering, we define “meta-covariates” and use them to build a probit regression model, thereby selecting clusters of similarly behaving genes, aiding interpretation. This simultaneous learning task is accomplished by an EM algorithm that optimises a single likelihood function which rewards good performance at both classification and clustering. We explore the performance of our methodology on a well known leukaemia dataset and use the Gene Ontology to interpret our results

Bayesian data integration and variable selection for pan‐cancer survival prediction using protein expression data

Accurate prognostic prediction using molecular information is a challenging area of research, which is essential to develop precision medicine. In this paper, we develop translational models to identify major actionable proteins that are associated with clinical outcomes, like the survival time of patients. There are considerable statistical and computational challenges due to the large dimension of the problems. Furthermore, data are available for different tumor types; hence data integration for various tumors is desirable. Having censored survival outcomes escalates one more level of complexity in the inferential procedure. We develop Bayesian hierarchical survival models, which accommodate all the challenges mentioned here. We use the hierarchical Bayesian accelerated failure time model for survival regression. Furthermore, we assume sparse horseshoe prior distribution for the regression coefficients to identify the major proteomic drivers. We borrow strength across tumor groups by introducing a correlation structure among the prior distributions. The proposed methods have been used to analyze data from the recently curated “The Cancer Proteome Atlas” (TCPA), which contains reverse‐phase protein arrays–based high‐quality protein expression data as well as detailed clinical annotation, including survival times. Our simulation and the TCPA data analysis illustrate the efficacy of the proposed integrative model, which links different tumors with the correlated prior structures.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154486/1/biom13132_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154486/2/biom13132.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154486/3/biom13132-sup-0003-supmat.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154486/4/biom13132-sup-0002-supplementary-v6-22Jul2019.pd

Shot Noise at High Temperatures

We consider the possibility of measuring non-equilibrium properties of the current correlation functions at high temperatures (and small bias). Through the example of the third cumulant of the current (${\cal{S}}_3$) we demonstrate that odd order correlation functions represent non-equilibrium physics even at small external bias and high temperatures. We calculate ${\cal{S}}_3=y(eV/T) e^2 I$ for a quasi-one-dimensional diffusive constriction. We calculate the scaling function $y$ in two regimes: when the scattering processes are purely elastic and when the inelastic electron-electron scattering is strong. In both cases we find that $y$ interpolates between two constants. In the low (high) temperature limit $y$ is strongly (weakly) enhanced (suppressed) by the electron-electron scattering.Comment: 11 pages 4 fig. submitted to Phys. Rev.

Full Counting Statistics of Multiple Andreev Reflections in incoherent diffusive superconducting junctions

We present a theory for the full distribution of current fluctuations in incoherent diffusive superconducting junctions, subjected to a voltage bias. This theory of full counting statistics of incoherent multiple Andreev reflections is valid for arbitrary applied voltage. We present a detailed discussion of the properties of the first four cumulants as well as the low and high voltage regimes of the full counting statistics. The work is an extension of the results of Pilgram and the author, Phys. Rev. Lett. 94, 086806 (2005).Comment: Included in special issue Spin Physics of Superconducting heterostructures of Applied Physics A: Materials Science & Processin

Integrable open supersymmetric U model with boundary impurity

An integrable version of the supersymmetric U model with open boundary conditions and an impurity situated at one end of the chain is introduced. The model is solved through the algebraic Bethe ansatz method and the Bethe ansatz equations are obtained.Comment: RevTeX, 8 pages, no figures, final version to appear in Phys. Lett.

Multifractal Analysis on the Return Series of Stock Markets Using MF-DFA Method

Part 3: Finance and Service ScienceInternational audienceAnalyzing the daily returns of NASDAQ Composite Index by using MF-DFA method has led to findings that the return series does not fit the normal distribution and its leptokurtic indicates that a single-scale index is insufficient to describe the stock price fluctuation. Furthermore, it is found that the long-term memory characteristics are a main source of multifractality in time series. Based on the main reason causing multifractality, a contrast of the original return series and the reordered return series is made to demonstrate the stock price index fluctuation, suggesting that the both return series have multifractality. In addition, the empirical results verify the validity of the measures which illustrates that the stock market fails to reach the weak form efficiency

Quantum Characterization of a Werner-like Mixture

We introduce a Werner-like mixture [R. F. Werner, Phys. Rev. A {\bf 40}, 4277 (1989)] by considering two correlated but different degrees of freedom, one with discrete variables and the other with continuous variables. We evaluate the mixedness of this state, and its degree of entanglement establishing its usefulness for quantum information processing like quantum teleportation. Then, we provide its tomographic characterization. Finally, we show how such a mixture can be generated and measured in a trapped system like one electron in a Penning trap.Comment: 8 pages ReVTeX, 8 eps figure

Break-Junction Tunneling on MgB_2

Tunneling data on magnesium diboride, MgB_2, are reviewed with a particular focus on superconductor-insulator-superconductor (SIS) junctions formed by a break-junction method. The collective tunneling literature reveals two distinct energy scales, a large gap, Delta_L~7.2 meV, close to the expected BCS value, and a small gap, Delta_S~2.4 meV. The SIS break junctions show clearly that the small gap closes near the bulk critical temperature, T_c=39 K. The SIS spectra allow proximity effects to be ruled out as the cause for the small gap and therefore make a strong case that MgB_2 is a coupled, two-band superconductor. While the break junctions sometimes reveal parallel contributions to the conductance from both bands, it is more often found that Delta_S dominates the spectra. In these cases, a subtle feature is observed near Delta_S+Delta_L that is reminiscent of strong-coupling effects. This feature is consistent with quasiparticle scattering contributions to the interband coupling which provides an important insight into the nature of two-band superconductivity in MgB_2.Comment: 9 pages, 10 pictures, accepted for publication in a special issue of Physica C on MgB2, minor change

Books

New BMJ ABC seriesABC of Spinal Cord Injury. 2nd ed. By D. Grundy and A Swain. Pp. 61. Illustrated. £11 London: BMJ 1993.ABC of Diabetes. 3rd ed. By Peter J. Watkins Pp. 56. Illustrated. London: BM]. 1993. Obtainable from IJbriger Book Distributors, Bloemfontein.ABC of Transfusion. 2nd ed. Ed by Marcela A. Contreras. Pp. 66. £14,50. London: BM]. 1993.ABC of Vascular Diseases. Ed by John H. N. Wolfe. Pp. 79. London: BM]. 1993.Female sterilisation Female Sterilization: A Guide to Provision of Services. Pp. x + 197. illustrated. Sfr. 41. Geneva: WHO. 1992.Cervical cancer Cervical Cancer Screening Programmes: Managerial Guidelines. By A. B. Miller. Pp. viii + 50. SFr.12. Geneva: WHO. 1992.Alcohol in southern Africa Liquor and Labor in Southern Africa. Ed by Jonathan Crush and Charles Ambler. Pp. 432. R99. Pietermaritzburg: Universiry of Tatal Press. 1992.Primary care in AIDS Primary AIDS Care. By Clive Evian. Pp. 267. Illustrated. R59,95. Joha=esburg: Jacana. 1993.Kliniese etiek Kliniese Etiek: 'n Christelike Benadering. 2de uitg. Deur Uys en Smit. Pp. 166. Kenwyn: Juta. 1992.Ovarian carcinoma Cancer of the Ovary. Ed by Maurice Markman and William J. Hoskins. Pp. xv + 442. Illustrated. $156,50. New York: Raven Press. 1992.Complications of cirrhosis Bailliere's Clinical Gastroenterology. International Practice and Research: Portal Hypertension. Ed by R. Shields. Pp. 208. Illustrated. £27,50. Kent: Harcourt Brace Jovanovich. 1992.Treating diarrhoea Readings on Diarrhoea. Pp. vi + 147. Illustrated. Sfr. 20. Geneva: WHO. 1992.Manual of arthroscopy Techniques in Therapeutic Arthroscopy. Ed by J. Serge Parisien. Pp. 385. Illustrated.$157,50. New York: Raven Press. 1993.Chemicals and birth defects Chemically Induced Birth Defects. 2nd ed. By James L. Schardein. Pp. xiv + 902. $250. New York: Marcel Dekker 1993.Virology Progress in Medical Virology. Vol. 40. Ed by J. L. Melnick. Pp. viii + 221. Illustrated. Sfr. 265. Basel: S. Karger. 1993.Perfused liver Perfused Liver: Clinical and Basic Applications. Ed by F. Ballet and R. G. Thurrnan. Pp. 398. Illustrated. £46. London: John Libbey. 1991

HiggsBounds: Confronting Arbitrary Higgs Sectors with Exclusion Bounds from LEP and the Tevatron

HiggsBounds is a computer code that tests theoretical predictions of models with arbitrary Higgs sectors against the exclusion bounds obtained from the Higgs searches at LEP and the Tevatron. The included experimental information comprises exclusion bounds at 95% C.L. on topological cross sections. In order to determine which search topology has the highest exclusion power, the program also includes, for each topology, information from the experiments on the expected exclusion bound, which would have been observed in case of a pure background distribution. Using the predictions of the desired model provided by the user as input, HiggsBounds determines the most sensitive channel and tests whether the considered parameter point is excluded at the 95% C.L. HiggsBounds is available as a Fortran 77 and Fortran 90 code. The code can be invoked as a command line version, a subroutine version and an online version. Examples of exclusion bounds obtained with HiggsBounds are discussed for the Standard Model, for a model with a fourth generation of quarks and leptons and for the Minimal Supersymmetric Standard Model with and without CP-violation. The experimental information on the exclusion bounds currently implemented in HiggsBounds will be updated as new results from the Higgs searches become available.Comment: 64 pages, 15 tables, 8 figures; three typos which made it to the published version corrected; the code (currently version 3.0.0beta including LHC Higgs search results) is available via: http://projects.hepforge.org/higgsbounds