Information dynamics: Temporal behavior of uncertainty measures

We carry out a systematic study of uncertainty measures that are generic to dynamical processes of varied origins, provided they induce suitable continuous probability distributions. The major technical tool are the information theory methods and inequalities satisfied by Fisher and Shannon information measures. We focus on a compatibility of these inequalities with the prescribed (deterministic, random or quantum) temporal behavior of pertinent probability densities.Comment: Incorporates cond-mat/0604538, title, abstract changed, text modified, to appear in Cent. Eur. J. Phy

The Value of Information for Populations in Varying Environments

The notion of information pervades informal descriptions of biological systems, but formal treatments face the problem of defining a quantitative measure of information rooted in a concept of fitness, which is itself an elusive notion. Here, we present a model of population dynamics where this problem is amenable to a mathematical analysis. In the limit where any information about future environmental variations is common to the members of the population, our model is equivalent to known models of financial investment. In this case, the population can be interpreted as a portfolio of financial assets and previous analyses have shown that a key quantity of Shannon's communication theory, the mutual information, sets a fundamental limit on the value of information. We show that this bound can be violated when accounting for features that are irrelevant in finance but inherent to biological systems, such as the stochasticity present at the individual level. This leads us to generalize the measures of uncertainty and information usually encountered in information theory

Statistical physics of low density parity check error correcting codes

We study the performance of Low Density Parity Check (LDPC) error-correcting codes using the methods of statistical physics. LDPC codes are based on the generation of codewords using Boolean sums of the original message bits by employing two randomly-constructed sparse matrices. These codes can be mapped onto Ising spin models and studied using common methods of statistical physics. We examine various regular constructions and obtain insight into their theoretical and practical limitations. We also briefly report on results obtained for irregular code constructions, for codes with non-binary alphabet, and on how a finite system size effects the error probability

Confocal microscopy of colloidal particles: towards reliable, optimum coordinates

Over the last decade, the light microscope has become increasingly useful as a quantitative tool for studying colloidal systems. The ability to obtain particle coordinates in bulk samples from micrographs is particularly appealing. In this paper we review and extend methods for optimal image formation of colloidal samples, which is vital for particle coordinates of the highest accuracy, and for extracting the most reliable coordinates from these images. We discuss in depth the accuracy of the coordinates, which is sensitive to the details of the colloidal system and the imaging system. Moreover, this accuracy can vary between particles, particularly in dense systems. We introduce a previously unreported error estimate and use it to develop an iterative method for finding particle coordinates. This individual-particle accuracy assessment also allows comparison between particle locations obtained from different experiments. Though aimed primarily at confocal microscopy studies of colloidal systems, the methods outlined here should transfer readily to many other feature extraction problems, especially where features may overlap one another.Comment: Accepted by Advances in Colloid and Interface Scienc

Supermassive Black Hole Binaries: The Search Continues

Gravitationally bound supermassive black hole binaries (SBHBs) are thought to be a natural product of galactic mergers and growth of the large scale structure in the universe. They however remain observationally elusive, thus raising a question about characteristic observational signatures associated with these systems. In this conference proceeding I discuss current theoretical understanding and latest advances and prospects in observational searches for SBHBs.Comment: 17 pages, 4 figures. To appear in the Proceedings of 2014 Sant Cugat Forum on Astrophysics. Astrophysics and Space Science Proceedings, ed. C.Sopuerta (Berlin: Springer-Verlag

Structural and dielectric properties of Sr2_{2}TiO4_{4} from first principles

We have investigated the structural and dielectric properties of Sr$_{2}$TiO$_{4}$,the first member of the Sr$_{n+1}$Ti$_{n}$O$_{3n+1}$ Ruddlesden-Popper series, within density functional theory. Motivated by recent work in which thin films of Sr$_{2}$TiO$_{4}$ were grown by molecular beam epitaxy (MBE) on SrTiO$_{3}$ substrates, the in-plane lattice parameter was fixed to the theoretically optimized lattice constant of cubic SrTiO$_{3}$ (n=$\infty$), while the out-of-plane lattice parameter and the internal structural parameters were relaxed. The fully relaxed structure was also investigated. Density functional perturbation theory was used to calculate the zone-center phonon frequencies, Born effective charges, and the electronic dielectric permittivity tensor. A detailed study of the contribution of individual infrared-active modes to the static dielectric permittivity tensor was performed. The calculated Raman and infrared phonon frequencies were found to be in agreement with experiment where available. Comparisons of the calculated static dielectric permittivity with experiments on both ceramic powders and epitaxial thin films are discussed.Comment: 11 pages, 1 figure, 8 tables, submitted to Phys. Rev.

Tomographic Representation of Minisuperspace Quantum Cosmology and Noether Symmetries

The probability representation, in which cosmological quantum states are described by a standard positive probability distribution, is constructed for minisuperspace models selected by Noether symmetries. In such a case, the tomographic probability distribution provides the classical evolution for the models and can be considered an approach to select "observable" universes. Some specific examples, derived from Extended Theories of Gravity, are worked out. We discuss also how to connect tomograms, symmetries and cosmological parameters.Comment: 15 page

Reply to: New Meta- and Mega-analyses of Magnetic Resonance Imaging Findings in Schizophrenia: Do They Really Increase Our Knowledge About the Nature of the Disease Process?

This work was supported by National Institute of Biomedical Imaging and Bioengineering Grant No. U54EB020403 (to the ENIGMA consortium)

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types