Portable compiler optimisation across embedded programs and microarchitectures using machine learning

Building an optimising compiler is a difficult and time consuming task which must be repeated for each generation of a microprocessor. As the underlying microarchitecture changes from one generation to the next, the compiler must be retuned to optimise specifically for that new system. It may take several releases of the compiler to effectively exploit a processor’s performance potential, by which time a new generation has appeared and the process starts again. We address this challenge by developing a portable optimising compiler. Our approach employs machine learning to automatically learn the best optimisations to apply for any new program on a new microarchitectural configuration. It achieves this by learning a model off-line which maps a microarchitecture description plus the hardware counters from a single run of the program to the best compiler optimisation passes. Our compiler gains 67 % of the maximum speedup obtainable by an iterative compiler search using 1000 evaluations. We obtain, on average, a 1.16x speedup over the highest default optimisation level across an entire microarchitecture configuration space, achieving a 4.3x speedup in the best case. We demonstrate the robustness of this technique by applying it to an extended microarchitectural space where we achieve comparable performance

Hydrogen Phases on the Surface of a Strongly Magnetized Neutron Star

The outermost layers of some neutron stars are likely to be dominated by hydrogen, as a result of fast gravitational settling of heavier elements. These layers directly mediate thermal radiation from the stars, and determine the characteristics of X-ray/EUV spectra. For a neutron star with surface temperature T\lo 10^6 K and magnetic field B\go 10^{12} G, various forms of hydrogen can be present in the envelope, including atom, poly-molecules, and condensed metal. We study the physical properties of different hydrogen phases on the surface of a strongly magnetized neutron star for a wide range of field strength $B$ and surface temperature $T$. Depending on the values of $B$ and $T$, the outer envelope can be either in a nondegenerate gaseous phase or in a degenerate metallic phase. For T\go 10^5 K and moderately strong magnetic field, B\lo 10^{13} G, the envelope is nondegenerate and the surface material gradually transforms into a degenerate Coulomb plasma as density increases. For higher field strength, $B>> 10^{13}$ G, there exists a first-order phase transition from the nondegenerate gaseous phase to the condensed metallic phase. The column density of saturated vapor above the metallic hydrogen decreases rapidly as the magnetic field increases or/and temperature decreases. Thus the thermal radiation can directly emerge from the degenerate metallic hydrogen surface. The characteristics of surface X-ray/EUV emission for different phases are discussed. A separate study concerning the possibility of magnetic field induced nuclear fusion of hydrogen on the neutron star surface is also presented.Comment: TeX, 35 pages including 6 postscript figures. To be published in Ap

Unravelling the immune signature of Plasmodium falciparum transmission-reducing immunity

Infection with Plasmodium can elicit antibodies that inhibit parasite survival in the mosquito, when they are ingested in an infectious blood meal. Here, we determine the transmission-reducing activity (TRA) of naturally acquired antibodies from 648 malaria-exposed individuals using lab-based mosquito-feeding assays. Transmission inhibition is significantly associated with antibody responses to Pfs48/45, Pfs230, and to 43 novel gametocyte proteins assessed by protein microarray. In field-based mosquito-feeding assays the likelihood and rate of mosquito infection are significantly lower for individuals reactive to Pfs48/45, Pfs230 or to combinations of the novel TRA-associated proteins. We also show that naturally acquired purified antibodies against key transmission-blocking epitopes of Pfs48/45 and Pfs230 are mechanistically involved in TRA, whereas sera depleted of these antibodies retain high-level, complement-independent TRA. Our analysis demonstrates that host antibody responses to gametocyte proteins are associated with reduced malaria transmission efficiency from humans to mosquitoes

Cultural differences in postnatal quality of life among German-speaking women - a prospective survey in two countries.

Assessment of quality of life after childbirth is an important health-outcome measurement for new mothers and is of special interest in midwifery. The Mother-Generated Index (MGI) is a validated instrument to assess postnatal quality of life. The tool has not been applied for making a cross-cultural comparison before. This study investigated (a) responses to the MGI in German-speaking women in Germany and Switzerland; and (b) associations between MGI scores on the one hand and maternity and midwifery care on the other

Caribbean Corals in Crisis: Record Thermal Stress, Bleaching, and Mortality in 2005

BACKGROUND The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. METHODOLOGY/PRINCIPAL FINDINGS Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. CONCLUSIONS/SIGNIFICANCE Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.This work was partially supported by salaries from the NOAA Coral Reef Conservation Program to the NOAA Coral Reef Conservation Program authors. NOAA provided funding to Caribbean ReefCheck investigators to undertake surveys of bleaching and mortality. Otherwise, no funding from outside authors' institutions was necessary for the undertaking of this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Cepred: Predicting the Co-Expression Patterns of the Human Intronic microRNAs with Their Host Genes

Identifying the tissues in which a microRNA is expressed could enhance the understanding of the functions, the biological processes, and the diseases associated with that microRNA. However, the mechanisms of microRNA biogenesis and expression remain largely unclear and the identification of the tissues in which a microRNA is expressed is limited. Here, we present a machine learning based approach to predict whether an intronic microRNA show high co-expression with its host gene, by doing so, we could infer the tissues in which a microRNA is high expressed through the expression profile of its host gene. Our approach is able to achieve an accuracy of 79% in the leave-one-out cross validation and 95% on an independent testing dataset. We further estimated our method through comparing the predicted tissue specific microRNAs and the tissue specific microRNAs identified by biological experiments. This study presented a valuable tool to predict the co-expression patterns between human intronic microRNAs and their host genes, which would also help to understand the microRNA expression and regulation mechanisms. Finally, this framework can be easily extended to other species

Hydrogen Molecules In Superstrong Magnetic Field: II. Excitation Levels

We study the energy levels of H$_2$ molecules in a superstrong magnetic field (B\go 10^{12} G), typically found on the surfaces of neutron stars. The interatomic interaction potentials are calculated by a Hartree-Fock method with multi-configurations assuming electrons are in the ground Landau state. Both the aligned configurations and arbitrary orientations of the molecular axis with respect to the magnetic field axis are considered. Different types of molecular excitations are then studied: electronic excitations, aligned (along the magnetic axis) vibrational excitations, transverse vibrational excitations (a constrained rotation of the molecular axis around the magnetic field line). Similar results for the molecular ion H$_2^+$ are also obtained and compared with previous variational calculations. Both numerical results and analytical fitting formulae are given for a wide range of field strengths. In contrast to the zero-field case, it is found that the transverse vibrational excitation energies can be larger than the aligned vibration excitation, and they both can be comparable or larger than the electronic excitations. For B\go B_{crit}=4.23\times 10^{13} G, the Landau energy of proton is appreciable and there is some controversy regarding the dissociation energy of H$_2$. We show that H$_2$ is bound even for $B>>B_{crit}$ and that neither proton has a Landau excitation in the ground molecular state.Comment: Revtex (45 pages), 3 postscript figures; Phys. Rev. A in pres