Stability of graph communities across time scales

The complexity of biological, social and engineering networks makes it desirable to find natural partitions into communities that can act as simplified descriptions and provide insight into the structure and function of the overall system. Although community detection methods abound, there is a lack of consensus on how to quantify and rank the quality of partitions. We show here that the quality of a partition can be measured in terms of its stability, defined in terms of the clustered autocovariance of a Markov process taking place on the graph. Because the stability has an intrinsic dependence on time scales of the graph, it allows us to compare and rank partitions at each time and also to establish the time spans over which partitions are optimal. Hence the Markov time acts effectively as an intrinsic resolution parameter that establishes a hierarchy of increasingly coarser clusterings. Within our framework we can then provide a unifying view of several standard partitioning measures: modularity and normalized cut size can be interpreted as one-step time measures, whereas Fiedler's spectral clustering emerges at long times. We apply our method to characterize the relevance and persistence of partitions over time for constructive and real networks, including hierarchical graphs and social networks. We also obtain reduced descriptions for atomic level protein structures over different time scales.Comment: submitted; updated bibliography from v

How Massless Neutrinos Affect the Cosmic Microwave Background Damping Tail

We explore the physical origin and robustness of constraints on the energy density in relativistic species prior to and during recombination, often expressed as constraints on an effective number of neutrino species, Neff. Constraints from current data combination of Wilkinson Microwave Anisotropy Probe (WMAP) and South Pole Telescope (SPT) are almost entirely due to the impact of the neutrinos on the expansion rate, and how those changes to the expansion rate alter the ratio of the photon diffusion scale to the sound horizon scale at recombination. We demonstrate that very little of the constraining power comes from the early Integrated Sachs-Wolfe (ISW) effect, and also provide a first determination of the amplitude of the early ISW effect. Varying the fraction of baryonic mass in Helium, Yp, also changes the ratio of damping to sound-horizon scales. We discuss the physical effects that prevent the resulting near-degeneracy between Neff and Yp from being a complete one. Examining light element abundance measurements, we see no significant evidence for evolution of Neff and the baryon-to-photon ratio from the epoch of big bang nucleosynthesis to decoupling. Finally, we consider measurements of the distance-redshift relation at low to intermediate redshifts and their implications for the value of Neff.Comment: 11 pages. Replaced version extends our discussion of origin of constraints and updates for current data, submitted to PR

Generalised state spaces and non-locality in fault tolerant quantum computing schemes

We develop connections between generalised notions of entanglement and quantum computational devices where the measurements available are restricted, either because they are noisy and/or because by design they are only along Pauli directions. By considering restricted measurements one can (by considering the dual positive operators) construct single particle state spaces that are different to the usual quantum state space. This leads to a modified notion of entanglement that can be very different to the quantum version (for example, Bell states can become separable). We use this approach to develop alternative methods of classical simulation that have strong connections to the study of non-local correlations: we construct noisy quantum computers that admit operations outside the Clifford set and can generate some forms of multiparty quantum entanglement, but are otherwise classical in that they can be efficiently simulated classically and cannot generate non-local statistics. Although the approach provides new regimes of noisy quantum evolution that can be efficiently simulated classically, it does not appear to lead to significant reductions of existing upper bounds to fault tolerance thresholds for common noise models.Comment: V2: 18 sides, 7 figures. Corrected two erroneous claims and one erroneous argumen

A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments

The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into account the non-trivial electrostatic screening coming from the solvent and the electrolytes. As a consequence the electrostatic potential has to be found by solving the generalized Poisson and the Poisson-Boltzmann equation for neutral and ionic solutions, respectively. In the present work solvers for both problems have been developed. A preconditioned conjugate gradient method has been implemented to the generalized Poisson equation and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations of a ordinary Poisson equation solver. In addition, a self-consistent procedure enables us to solve the non-linear Poisson-Boltzmann problem. Both solvers exhibit very high accuracy and parallel efficiency, and allow for the treatment of different boundary conditions, as for example surface systems. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and will be released as an independent program, suitable for integration in other codes

Human genetics and genomics research in Ecuador: historical survey, current state, and future directions

Background: In South America, the history of human genetics is extensive and its beginnings go back to the onset of the twentieth century. In Ecuador, the historical record of human genetics and genomics research is limited. In this context, our work analyzes the current status and historical panorama of these fields, based on bibliographic searches in Scopus, Google Scholar, PubMed, and Web of Science. Results: Our results determined that the oldest paper in human genetics coauthored by an Ecuadorian institution originates from the Central University of Ecuador in 1978. From a historical standpoint, the number of articles has increased since the 1990s. This growth has intensified and it is reflected in 137 manuscripts recorded from 2010 to 2019. Areas such as human population genetics, phylogeography, and forensic sciences are the core of genetics and genomics-associated research in Ecuador. Important advances have been made in the understanding of the bases of cancer, some genetic diseases, and congenital disorders. Fields such as pharmacogenetics and pharmacogenomics have begun to be explored during the last years. Conclusions: This work paints a comprehensive picture and provides additional insights into the future panorama of human genetic and genomic research in Ecuador as an example of an emerging, resource-limited country with interesting phylogeographic characteristics and public health implications

Extracting the hierarchical organization of complex systems

Extracting understanding from the growing ``sea'' of biological and socio-economic data is one of the most pressing scientific challenges facing us. Here, we introduce and validate an unsupervised method that is able to accurately extract the hierarchical organization of complex biological, social, and technological networks. We define an ensemble of hierarchically nested random graphs, which we use to validate the method. We then apply our method to real-world networks, including the air-transportation network, an electronic circuit, an email exchange network, and metabolic networks. We find that our method enables us to obtain an accurate multi-scale descriptions of a complex system.Comment: Figures in screen resolution. Version with full resolution figures available at http://amaral.chem-eng.northwestern.edu/Publications/Papers/sales-pardo-2007.pd

Statistical Mechanics of Semi-Supervised Clustering in Sparse Graphs

We theoretically study semi-supervised clustering in sparse graphs in the presence of pairwise constraints on the cluster assignments of nodes. We focus on bi-cluster graphs, and study the impact of semi-supervision for varying constraint density and overlap between the clusters. Recent results for unsupervised clustering in sparse graphs indicate that there is a critical ratio of within-cluster and between-cluster connectivities below which clusters cannot be recovered with better than random accuracy. The goal of this paper is to examine the impact of pairwise constraints on the clustering accuracy. Our results suggests that the addition of constraints does not provide automatic improvement over the unsupervised case. When the density of the constraints is sufficiently small, their only impact is to shift the detection threshold while preserving the criticality. Conversely, if the density of (hard) constraints is above the percolation threshold, the criticality is suppressed and the detection threshold disappears.Comment: 8 pages, 4 figure

Magnetic fields and Sunyaev-Zel'dovich effect in galaxy clusters

In this work we study the contribution of magnetic fields to the Sunyaev Zeldovich (SZ) effect in the intracluster medium. In particular we calculate the SZ angular power spectrum and the central temperature decrement. The effect of magnetic fields is included in the hydrostatic equilibrium equation by splitting the Lorentz force into two terms one being the force due to magnetic pressure which acts outwards and the other being magnetic tension which acts inwards. A perturbative approach is adopted to solve for the gas density profile for weak magnetic fields (< 4 micro G}). This leads to an enhancement of the gas density in the central regions for nearly radial magnetic field configurations. Previous works had considered the force due to magnetic pressure alone which is the case only for a special set of field configurations. However, we see that there exists possible sets of configurations of ICM magnetic fields where the force due to magnetic tension will dominate. Subsequently, this effect is extrapolated for typical field strengths (~ 10 micro G) and scaling arguments are used to estimate the angular power due to secondary anisotropies at cluster scales. In particular we find that it is possible to explain the excess power reported by CMB experiments like CBI, BIMA, ACBAR at l > 2000 with sigma_8 ~ 0.8 (WMAP 5 year data) for typical cluster magnetic fields. In addition we also see that the magnetic field effect on the SZ temperature decrement is more pronounced for low mass clusters ( ~ 2 keV). Future SZ detections of low mass clusters at few arc second resolution will be able to probe this effect more precisely. Thus, it will be instructive to explore the implications of this model in greater detail in future works.Comment: 20 pages, 8 figure

Repression of DNA-binding dependent glucocorticoid receptor-mediated gene expression

The glucocorticoid receptor (GR) affects the transcription of genes involved in diverse processes, including energy metabolism and the immune response, through DNA-binding dependent and independent mechanisms. The DNA-binding dependent mechanism occurs by direct binding of GR to glucocorticoid response elements (GREs) at regulatory regions of target genes. The DNA-binding independent mechanism involves binding of GR to transcription factors and coactivators that, in turn, contact DNA. A small molecule that competes with GR for binding to GREs could be expected to affect the DNA-dependent pathway selectively by interfering with the protein-DNA interface. We show that a DNA-binding polyamide that targets the consensus GRE sequence binds the glucocorticoid-induced zipper (GILZ) GRE, inhibits expression of GILZ and several other known GR target genes, and reduces GR occupancy at the GILZ promoter. Genome-wide expression analysis of the effects of this polyamide on a set of glucocorticoid-induced and -repressed genes could help to elucidate the mechanism of GR regulation for these genes