International Summer School, ‘ From Genome to Life’

This report from the International Summer School ‘From Genome to Life’, held at the Institute d'Etudes Scientifiques de Cargèse in Corsica in July 2002, covers the talks of the invited speakers. The topics of the talks can be broadly grouped into the areas of genome annotation, comparative and evolutionary genomics, functional genomics, proteomics, structural genomics, pharmacogenomics, and organelle genomes, epigenetics and RNA

BDS GNSS for Earth Observation

For millennia, human communities have wondered about the possibility of observing phenomena in their surroundings, and in particular those affecting the Earth on which they live. More generally, it can be conceptually defined as Earth observation (EO) and is the collection of information about the biological, chemical and physical systems of planet Earth. It can be undertaken through sensors in direct contact with the ground or airborne platforms (such as weather balloons and stations) or remote-sensing technologies. However, the definition of EO has only become significant in the last 50 years, since it has been possible to send artificial satellites out of Earth’s orbit. Referring strictly to civil applications, satellites of this type were initially designed to provide satellite images; later, their purpose expanded to include the study of information on land characteristics, growing vegetation, crops, and environmental pollution. The data collected are used for several purposes, including the identification of natural resources and the production of accurate cartography. Satellite observations can cover the land, the atmosphere, and the oceans. Remote-sensing satellites may be equipped with passive instrumentation such as infrared or cameras for imaging the visible or active instrumentation such as radar. Generally, such satellites are non-geostationary satellites, i.e., they move at a certain speed along orbits inclined with respect to the Earth’s equatorial plane, often in polar orbit, at low or medium altitude, Low Earth Orbit (LEO) and Medium Earth Orbit (MEO), thus covering the entire Earth’s surface in a certain scan time (properly called ’temporal resolution’), i.e., in a certain number of orbits around the Earth. The first remote-sensing satellites were the American NASA/USGS Landsat Program; subsequently, the European: ENVISAT (ENVironmental SATellite), ERS (European Remote-Sensing satellite), RapidEye, the French SPOT (Satellite Pour l’Observation de laTerre), and the Canadian RADARSAT satellites were launched. The IKONOS, QuickBird, and GeoEye-1 satellites were dedicated to cartography. The WorldView-1 and WorldView-2 satellites and the COSMO-SkyMed system are more recent. The latest generation are the low payloads called Small Satellites, e.g., the Chinese BuFeng-1 and Fengyun-3 series. Also, Global Navigation Satellite Systems (GNSSs) have captured the attention of researchers worldwide for a multitude of Earth monitoring and exploration applications. On the other hand, over the past 40 years, GNSSs have become an essential part of many human activities. As is widely noted, there are currently four fully operational GNSSs; two of these were developed for military purposes (American NAVstar GPS and Russian GLONASS), whilst two others were developed for civil purposes such as the Chinese BeiDou satellite navigation system (BDS) and the European Galileo. In addition, many other regional GNSSs, such as the South Korean Regional Positioning System (KPS), the Japanese quasi-zenital satellite system (QZSS), and the Indian Regional Navigation Satellite System (IRNSS/NavIC), will become available in the next few years, which will have enormous potential for scientific applications and geomatics professionals. In addition to their traditional role of providing global positioning, navigation, and timing (PNT) information, GNSS navigation signals are now being used in new and innovative ways. Across the globe, new fields of scientific study are opening up to examine how signals can provide information about the characteristics of the atmosphere and even the surfaces from which they are reflected before being collected by a receiver. EO researchers monitor global environmental systems using in situ and remote monitoring tools. Their findings provide tools to support decision makers in various areas of interest, from security to the natural environment. GNSS signals are considered an important new source of information because they are a free, real-time, and globally available resource for the EO community

Data-driven action-value functions for evaluating players in professional team sports

As more and larger event stream datasets for professional sports become available, there is growing interest in modeling the complex play dynamics to evaluate player performance. Among these models, a common player evaluation method is assigning values to player actions. Traditional action-values metrics, however, consider very limited game context and player information. Furthermore, they provide directly related to goals (e.g., shots), not all actions. Recent work has shown that reinforcement learning provided powerful methods for addressing quantifying the value of player actions in sports. This dissertation develops deep reinforcement learning (DRL) methods for estimating action values in sports. We make several contributions to DRL for sports. First, we develop neural network architectures that learn an action-value Q-function from sports events logs to estimate each team\u27s expected success given the current match context. Specifically, our architecture models the game history with a recurrent network and predicts the probability that a team scores the next goal. From the learned Q-values, we derive a Goal Impact Metric (GIM) for evaluating a player\u27s performance over a game season. We show that the resulting player rankings are consistent with standard player metrics and temporally consistent within and across seasons. Second, we address the interpretability of the learned Q-values. While neural networks provided accurate estimates, the black-box structure prohibits understanding the influence of different game features on the action values. To interpret the Q-function and understand the influence of game features on action values, we design an interpretable mimic learning framework for the DRL. The framework is based on a Linear Model U-Tree (LMUT) as a transparent mimic model, which facilitates extracting the function rules and computing the feature importance for action values. Third, we incorporate information about specific players into the action values, by introducing a deep player representation framework. In this framework, each player is assigned a latent feature vector called an embedding, with the property that statistically similar players are mapped to nearby embeddings. To compute embeddings that summarize the statistical information about players, we implement a Variational Recurrent Ladder Agent Encoder (VaRLAE) to learn a contextualized representation for when and how players are likely to act. We learn and evaluate deep Q-functions from event data for both ice hockey and soccer. These are challenging continuous-flow games where game context and medium-term consequences are crucial for properly assessing the impact of a player\u27s actions

Cross-Correlator Implementations Enabling Aperture Synthesis for Geostationary-Based Remote Sensing

An ever-increasing demand for weather prediction and high climate modelling accuracy drives the need for better atmospheric data collection. These demands include better spatial and temporal coverage of mainly humidity and temperature distributions in the atmosphere. A new type of remote sensing satellite technology is emerging, originating in the field of radio astronomy where telescope aperture upscaling could not keep up with the increasing demand for higher resolution. Aperture synthesis imaging takes an array of receivers and emulates apertures extending way beyond what is possible with any single antenna. In the field of Earth remote sensing, the same idea could be used to construct satellites observing in the microwave region at a high resolution with foldable antenna arrays. If placed in a geostationary orbit, these could produce images with high temporal resolution, however, such altitudes make the resolution requirement and, hence, signal processing very demanding. The relentless development in miniaturization of integrated circuits has in recent years made the concept of high resolution aperture synthesis imaging aboard a satellite platform viable.The work presented in this thesis addresses the challenge of performing the vital signal processing required aboard an aperture synthesis imager; namely the cross-correlation. A number of factors make the application challenging; the very restrictive power budgets of satellites, the immense amount of signal processing required for larger arrays, and the environmental aspects of in-space operation. The design, fabrication and evaluation of two cross-correlator application-specific integrated circuits (ASICs), one analog-to-digital converter (ADC) ASIC and one complete cross-correlator back-end is presented. Design concepts such as clocking schemes, data routing and reconfigurable accuracy for the cross-correlators and offset compensation and interfacing of the ADCs are explained. The underlying reasons for design choices as well as ASIC design and testing methodologies are described. The ASICs are put into their proper context as part of an interferometer system, and some different cross-correlator back-end architectures are explored.The result from this work is a very power-efficient, high-performance way of constructing cross-correlators which clearly demonstrates the viability of space-borne microwave imaging interferometer back-ends

Overview of the JET results in support to ITER

The 2014–2016 JET results are reviewed in the light of their significance for optimising the ITER research plan for the active and non-active operation. More than 60 h of plasma operation with ITER first wall materials successfully took place since its installation in 2011. New multi-machine scaling of the type I-ELM divertor energy flux density to ITER is supported by first principle modelling. ITER relevant disruption experiments and first principle modelling are reported with a set of three disruption mitigation valves mimicking the ITER setup. Insights of the L–H power threshold in Deuterium and Hydrogen are given, stressing the importance of the magnetic configurations and the recent measurements of fine-scale structures in the edge radial electric. Dimensionless scans of the core and pedestal confinement provide new information to elucidate the importance of the first wall material on the fusion performance. H-mode plasmas at ITER triangularity (H = 1 at βN ~ 1.8 and n/nGW ~ 0.6) have been sustained at 2 MA during 5 s. The ITER neutronics codes have been validated on high performance experiments. Prospects for the coming D–T campaign and 14 MeV neutron calibration strategy are reviewed.European Commission (EUROfusion 633053

Roadmap on Electronic Structure Codes in the Exascale Era

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing.Comment: Submitted as a roadmap article to Modelling and Simulation in Materials Science and Engineering; Address any correspondence to Vikram Gavini ([email protected]) and Danny Perez ([email protected]

Roadmap on Electronic Structure Codes in the Exascale Era

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing

Report on TID algorithms

This deliverable presents the TID detection algorithms as improved in response to design principles stated in T2.1 and their testing in the lab environment, verification against measurements taken during quiet and disturbed periods of time, benchmarking for their transition to operations, and final validation to the user requirements of accuracy, timeliness, and coverage.TechTIDE project, funded by the European Commission Horizon 2020 research and innovation program [AD-1], will establish a pre-operational system to demonstrate reliability of a set of TID (Travelling Ionospheric Disturbances) detection methodologies to issue warnings of the occurrence of TIDs over the region extending from Europe to South Africa. TechTIDE warning system will estimate the parameters that specify the TID characteristics and the inferred perturbation, with all additional geophysical information to the users to help them assess the risks and to develop mitigation techniques, tailored to their application. This document is TechTIDE D2.2 “Report on the TID algorithms” and it is an output of TechTIDE Task 2.2 (Development of the TID identification algorithms and products) of the WP2 (TID identification methodologies) which has the final goal to release the basic algorithms for the TID identification and to test a first version of the value-added products for implementation in the TechTIDE warning system. The document highlights four aspects of the TID algorithm release process, (1) Developmentbased on the concept, techniques, and algorithms as stated in TechTIDE D2.1, (2) Verification, an internal testing process that ensures algorithm correctness, (3) Benchmarkingneeded to prepare algorithms to transition to operations, and (4) Validation, an external process of ensuring that developed algorithms are compliant with the stated end user expectations.Postprint (published version

Roadmap on Electronic Structure Codes in the Exascale Era

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing

Overview of the JET results in support to ITER

The 2014–2016 JET results are reviewed in the light of their significance for optimising the ITER research plan for the active and non-active operation. More than 60 h of plasma operation with ITER first wall materials successfully took place since its installation in 2011. New multi-machine scaling of the type I-ELM divertor energy flux density to ITER is supported by first principle modelling. ITER relevant disruption experiments and first principle modelling are reported with a set of three disruption mitigation valves mimicking the ITER setup. Insights of the L–H power threshold in Deuterium and Hydrogen are given, stressing the importance of the magnetic configurations and the recent measurements of fine-scale structures in the edge radial electric. Dimensionless scans of the core and pedestal confinement provide new information to elucidate the importance of the first wall material on the fusion performance. H-mode plasmas at ITER triangularity (H  =  1 at β N ~ 1.8 and n/n GW ~ 0.6) have been sustained at 2 MA during 5 s. The ITER neutronics codes have been validated on high performance experiments. Prospects for the coming D–T campaign and 14 MeV neutron calibration strategy are reviewed