A neural network with modular hierarchical learning

This invention provides a new hierarchical approach for supervised neural learning of time dependent trajectories. The modular hierarchical methodology leads to architectures which are more structured than fully interconnected networks. The networks utilize a general feedforward flow of information and sparse recurrent connections to achieve dynamic effects. The advantages include the sparsity of units and connections, the modular organization. A further advantage is that the learning is much more circumscribed learning than in fully interconnected systems. The present invention is embodied by a neural network including a plurality of neural modules each having a pre-established performance capability wherein each neural module has an output outputting present results of the performance capability and an input for changing the present results of the performance capabilitiy. For pattern recognition applications, the performance capability may be an oscillation capability producing a repeating wave pattern as the present results. In the preferred embodiment, each of the plurality of neural modules includes a pre-established capability portion and a performance adjustment portion connected to control the pre-established capability portion

Large scale study of multiple-molecule queries

<p>Abstract</p> <p>Background</p> <p>In ligand-based screening, as well as in other chemoinformatics applications, one seeks to effectively search large repositories of molecules in order to retrieve molecules that are similar typically to a single molecule lead. However, in some case, multiple molecules from the same family are available to seed the query and search for other members of the same family.</p> <p>Multiple-molecule query methods have been less studied than single-molecule query methods. Furthermore, the previous studies have relied on proprietary data and sometimes have not used proper cross-validation methods to assess the results. In contrast, here we develop and compare multiple-molecule query methods using several large publicly available data sets and background. We also create a framework based on a strict cross-validation protocol to allow unbiased benchmarking for direct comparison in future studies across several performance metrics.</p> <p>Results</p> <p>Fourteen different multiple-molecule query methods were defined and benchmarked using: (1) 41 publicly available data sets of related molecules with similar biological activity; and (2) publicly available background data sets consisting of up to 175,000 molecules randomly extracted from the ChemDB database and other sources. Eight of the fourteen methods were parameter free, and six of them fit one or two free parameters to the data using a careful cross-validation protocol. All the methods were assessed and compared for their ability to retrieve members of the same family against the background data set by using several performance metrics including the Area Under the Accumulation Curve (AUAC), Area Under the Curve (AUC), F1-measure, and BEDROC metrics.</p> <p>Consistent with the previous literature, the best parameter-free methods are the MAX-SIM and MIN-RANK methods, which score a molecule to a family by the maximum similarity, or minimum ranking, obtained across the family. One new parameterized method introduced in this study and two previously defined methods, the Exponential Tanimoto Discriminant (ETD), the Tanimoto Power Discriminant (TPD), and the Binary Kernel Discriminant (<b>BKD</b>), outperform most other methods but are more complex, requiring one or two parameters to be fit to the data.</p> <p>Conclusion</p> <p>Fourteen methods for multiple-molecule querying of chemical databases, including novel methods, (ETD) and (TPD), are validated using publicly available data sets, standard cross-validation protocols, and established metrics. The best results are obtained with ETD, TPD, BKD, MAX-SIM, and MIN-RANK. These results can be replicated and compared with the results of future studies using data freely downloadable from <url>http://cdb.ics.uci.edu/</url>.</p

The HELLAS2XMM survey: XI. Unveiling the nature of X-ray Bright Optically Normal Galaxies

X-ray Bright Optically Normal Galaxies (XBONGs) constitute a small but not negligible fraction of hard X-ray selected sources in recent Chandra and XMM-Newton surveys. Even though several possibilities were proposed to explain why a relatively luminous hard X-ray source does not leave any significant signature of its presence in terms of optical emission lines, the nature of XBONGs is still subject of debate. We aim to a better understanding of their nature by means of a multiwavelength and morphological analysis of a small sample of these sources. Good-quality photometric near-infrared data (ISAAC/VLT) of four low-redshift (z=0.1-0.3) XBONGs, selected from the HELLAS2XMM survey, have been used to search for the presence of the putative nucleus, applying the surface-brightness decomposition technique through the least-squares fitting program GALFIT. The surface brightness decomposition allows us to reveal a nuclear point-like source, likely to be responsible of the X-ray emission, in two out of the four sources. The results indicate that moderate amounts of gas and dust, covering a large solid angle (possibly 4pi) at the nuclear source, combined with the low nuclear activity, may explain the lack of optical emission lines. The third XBONG is associated with an X-ray extended source and no nuclear excess is detected in the near infrared at the limits of our observations. The last source is associated to a close (d< 1 arcsec) double system and the fitting procedure cannot achieve a firm conclusion.Comment: 20 pages, 12 figures, A&A in pres

The XMM Large Scale Structure Survey: Properties and Two-Point Angular Correlations of Point-like Sources

We analyze X-ray sources detected over 4.2 pseudo-contiguous sq. deg. in the 0.5-2 keV and 2-10 keV bands down to fluxes of 2x10^{-15} and 8x10^{-15} erg/s/cm^2 respectively, as part of the XMM Large Scale Structure Survey. The logN-logS in both bands shows a steep slope at bright fluxes, but agrees well with other determinations below ~2x10^{-14} erg/s/cm^2. The detected sources resolve close to 30 per cent of the X-ray background in the 2-10 keV band. We study the two-point angular clustering of point sources using nearest neighbours and correlation function statistics and find a weak, positive signal for ~1130 sources in the 0.5-2 keV band, but no correlation for ~400 sources in the 2-10 keV band below scales of 100 arcsec. A sub-sample of ~200 faint sources with hard X-ray count ratios, that is likely to be dominated by obscured AGN, does show a positive signal with the data allowing for a large scaling of the angular correlation length, but only at the ~2 (3) sigma level, based on re-sampling (Poisson) statistics. We discuss possible implications and emphasize the importance of wider, complete surveys in order to fully understand the large scale structure of the X-ray sky.Comment: A&A in press; High resolution version at http://www-xray.ast.cam.ac.uk/~pg/publications.htm

XMM-Newton observations of Extremely Red Objects and the link with luminous, X-ray obscured Quasars

We present the results of a deep (about 80 ks) XMM-Newton survey of the largest sample of near-infrared selected Extremely Red Objects (R-K>5) available to date to K_S< 19.2. At the relatively bright X-ray fluxes (F_{2-10 keV}> 4x10^{-15} cgs) and near-infrared magnitude probed by the present observations, the fraction of AGN (i.e., X-ray detected) among the ERO population is small (~3.5%); conversely, the fraction of EROs among hard X-ray selected sources is much higher (~20%). The X-ray properties of EROs detected in our XMM-Newton observation indicate absorption in excess of 10^{22} cm^{-2} in a large fraction of them. We have also considered additional samples of X-ray detected EROs available in the literature. X-ray spectral analysis of the highest S/N sources unambiguously indicates that large columns of cold gas (even >10^{23} cm^{-2}) are the rule rather than the exception. The X-ray, optical, and near-infrared properties of those X-ray selected EROs with a spectroscopic or photometric redshift nicely match those expected for quasars 2, the high-luminosity, high-redshift obscured AGNs predicted in baseline XRB synthesis models. A close correlation is detected between X- and K-band fluxes. For the AGN EROs this is consistent, under reasonable assumptions, with the relation established locally between the host galaxies and their central black holes. This suggest that the majority of EROs are powered by massive black holes accreting, on average, at about 0.03-0.1 of the Eddington limit.Comment: 33 pages, 10 figures, to appear in A&

High precision X-ray logN-logS distributions: implications for the obscured AGN population

We have constrained the extragalactic source count distributions over a broad range of X-ray fluxes and in various energy bands to test whether the predictions from X-ray background synthesis models agree with the observational constraints provided by our measurements. We have used 1129 XMM-Newton observations at |b|>20 deg covering a sky area of 132.3 deg^2 to compile the largest complete samples of X-ray objects to date in the 0.5-1 keV, 1-2 keV, 2-4.5 keV, 4.5-10 keV, 0.5-2 keV and 2-10 keV energy bands. Our survey includes in excess of 30,000 sources down to ~10^-15 erg/cm^2/s below 2 keV and down to ~10^{-14} erg/cm^2/s above 2 keV. A break in the source count distributions was detected in all energy bands except the 4.5-10 keV band. An analytical model comprising 2 power-law components cannot adequately describe the curvature seen in the source count distributions. The shape of the logN(>S)-logS is strongly dependent on the energy band with a general steepening apparent as we move to higher energies. This is due to non-AGN populations, comprised mainly of stars and clusters of galaxies, contribute up to 30% of the source population at energies 10^{-13} erg/cm^2/s, and these populations of objects have significantly flatter source count distributions than AGN. We find a substantial increase in the relative fraction of hard X-ray sources at higher energies, from >55% below 2 keV to >77% above 2 keV. However the majority of sources detected above 4.5 keV still have significant flux below 2 keV. Comparison with predictions from the synthesis models suggest that the models might be overpredicting the number of faint absorbed AGN, which would call for fine adjustment of some model parameters such as the obscured to unobscured AGN ratio and/or the distribution of column densities at intermediate obscuration.Comment: Accepted for publication in Astronomy and Astrophysics. Abridged Abstract. 23 pages, 47 figures, 8 table

AGRICOH: A Consortium of Agricultural Cohorts

AGRICOH is a recently formed consortium of agricultural cohort studies involving 22 cohorts from nine countries in five continents: South Africa (1), Canada (3), Costa Rica (2), USA (6), Republic of Korea (1), New Zealand (2), Denmark (1), France (3) and Norway (3). The aim of AGRICOH, initiated by the US National Cancer Institute (NCI) and coordinated by the International Agency for Research on Cancer (IARC), is to promote and sustain collaboration and pooling of data to investigate the association between a wide range of agricultural exposures and a wide range of health outcomes, with a particular focus on associations that cannot easily be addressed in individual studies because of rare exposures (e.g., use of infrequently applied chemicals) or relatively rare outcomes (e.g., certain types of cancer, neurologic and auto-immune diseases). To facilitate future projects the need for data harmonization of selected variables is required and is underway. Altogether, AGRICOH provides excellent opportunities for studying cancer, respiratory, neurologic, and auto-immune diseases as well as reproductive and allergic disorders, injuries and overall mortality in association with a wide array of exposures, prominent among these the application of pesticides

The HELLAS2XMM survey. V. Near-Infrared observations of X-ray sources with extreme X/O ratios

We present the results of deep near-infrared observations of 11 hard X-ray selected sources in the Hellas2XMM survey, with faint optical magnitude (R>24) and high X-ray-to-optical flux ratio. All but one of the sources have been detected in the Ks band, with bright counterparts (Ks<19) and red colors (R-K>5), and therefore belong to the ERO population. A detailed analysis of the surface brightness profiles allows us to classify all of the NIR counterparts. There are 2 point-like objects, 7 elliptical galaxies and one source with a disky profile. None of the extended sources shows any evidence for the presence of a central unresolved object tracing the putative X-ray emitting AGN. Using both the R-K colors and the morphological information, we have estimated for all the sources a ``minimum photometric redshift'', ranging between 0.8 and 2.4; the elliptical hosts have zmin=0.9-1.4. We computed the X-ray properties using these redshifts: most of the sources have NH>10^{22}, with unabsorbed X-ray luminosities up to 10^{45}erg s^{-1}. These objects therefore belong to the population of obscured (Type II) quasars and, from a statistical point of view, they turn out to be a non-negligible fraction (~10%) of the most luminous AGN. Selecting the high X/O sources for a follow-up study in the NIR is therefore a powerful technique aimed at studying at high redshift the hosts of Type II AGN. Overall, our results seem to indicate that the hosts are mostly elliptical galaxies at z~1, and that these near-IR bright objects would be among the most massive spheroids at these epochs.Comment: 15 pages, 8 figures. Accepted for publication in A&A. V2: minor typos correcte