Learning from networked examples

Many machine learning algorithms are based on the assumption that training examples are drawn independently. However, this assumption does not hold anymore when learning from a networked sample because two or more training examples may share some common objects, and hence share the features of these shared objects. We show that the classic approach of ignoring this problem potentially can have a harmful effect on the accuracy of statistics, and then consider alternatives. One of these is to only use independent examples, discarding other information. However, this is clearly suboptimal. We analyze sample error bounds in this networked setting, providing significantly improved results. An important component of our approach is formed by efficient sample weighting schemes, which leads to novel concentration inequalities

The archive solution for distributed workflow management agents of the CMS experiment at LHC

The CMS experiment at the CERN LHC developed the Workflow Management Archive system to persistently store unstructured framework job report documents produced by distributed workflow management agents. In this paper we present its architecture, implementation, deployment, and integration with the CMS and CERN computing infrastructures, such as central HDFS and Hadoop Spark cluster. The system leverages modern technologies such as a document oriented database and the Hadoop eco-system to provide the necessary flexibility to reliably process, store, and aggregate $\mathcal{O}$(1M) documents on a daily basis. We describe the data transformation, the short and long term storage layers, the query language, along with the aggregation pipeline developed to visualize various performance metrics to assist CMS data operators in assessing the performance of the CMS computing system.Comment: This is a pre-print of an article published in Computing and Software for Big Science. The final authenticated version is available online at: https://doi.org/10.1007/s41781-018-0005-

The CMS DBS Query Language

The CMS experiment has implemented a flexible and powerful system enabling users to find data within the CMS physics data catalog. The Dataset Bookkeeping Service (DBS) comprises a database and the services used to store and access metadata related to CMS physics data. To this, we have added a generalized query system in addition to the existing web and programmatic interfaces to the DBS. This query system is based on a query language that hides the complexity of the underlying database structure by discovering the join conditions between database tables. This provides a way of querying the system that is simple and straightforward for CMS data managers and physicists to use without requiring knowledge of the database tables or keys. The DBS Query Language uses the ANTLR tool to build the input query parser and tokenizer, followed by a query builder that uses a graph representation of the DBS schema to construct the SQL query sent to underlying database. We will describe the design of the query system, provide details of the language components and overview of how this component fits into the overall data discovery system architecture

Which horticultural activities are more effective for children’s recovery from stress and mental fatigue? A quasi-experimental study

IntroductionStudies have established the benefits of horticultural therapy and activities for human health and well-being. Nonetheless, limited research has been conducted on the potential restorative advantages and distinctions between different types of horticultural activities in terms of stress reduction.MethodsThis study employed a quantitative research method to investigate the stress recovery benefits of five horticultural activities (flower arrangement, sowing and transplanting seeds, kokedama crafting, pressed flower card making, and decorative bottle painting with dried flowers) and one reference activity (short composition writing) for children. The experiment was conducted in a children’s activity center’s multi-purpose classroom with 48 elementary students aged 9–12 years. The subjects first took a stress test to induce stress and then engaged in horticultural activities for 20 min. Physiological stress was assessed using electrocardiograms and electroencephalograms as feedback indicators. Psychological and emotional changes were determined using the Positive and Negative Affect Schedule for Children and Self-Assessment Manikin scales.ResultsThe results demonstrated that horticultural activities greatly reduced physiological fatigue, and their recovery benefits were significantly greater than those of the reference activity. The recovery effects from different horticultural activities were similar across physiological indicators, although flower arrangement and sowing and transplanting seeds exhibited relatively robust recovery benefits. The heart rate and α-EEG-based generalized estimating equation revealed that horticultural activities offered significantly better relative recovery at each time phase of operation than the reference activity, with girls showing a 3.68% higher relative recovery value than boys. Flower arrangement and kokedama crafting offered better physiological recovery for students with prior horticultural experience, and these two activities received the highest scores in terms of positive effects and the “pleasure” dimension. Students believed that participating in horticultural activities resulted in a noteworthy increase in personal confidence and a greater sense of achievement.ConclusionThe study suggests that horticultural activities that involve real and vibrant plants or natural materials and are more attractive have more stress-relieving benefits. We conclude that horticultural activities are beneficial leisure activities that aid in stress relief for children and that it is important to consider the attributes of activities when developing horticultural programs for elementary students

The CMS dataset bookkeeping service

The CMS Dataset Bookkeeping Service (DBS) has been developed to catalog all CMS event data from Monte Carlo and Detector sources. It provides the ability to identify MC or trigger source, track data provenance, construct datasets for analysis, and discover interesting data. CMS requires processing and analysis activities at various service levels and the DBS system provides support for localized processing or private analysis, as well as global access for CMS users at large. Catalog entries can be moved among the various service levels with a simple set of migration tools, thus forming a loose federation of databases. DBS is available to CMS users via a Python API, Command Line, and a Discovery web page interfaces. The system is built as a multi-tier web application with Java servlets running under Tomcat, with connections via JDBC to Oracle or MySQL database backends. Clients connect to the service through HTTP or HTTPS with authentication provided by GRID certificates and authorization through VOMS. DBS is an integral part of the overall CMS Data Management and Workflow Management systems

Antibiotics and antibiotic resistance genes in global lakes:A review and meta-analysis

Lakes are an important source of freshwater, containing nearly 90% of the liquid surface fresh water worldwide. Long retention times in lakes mean pollutants from discharges slowly circulate around the lakes and may lead to high ecological risk for ecosystem and human health. In recent decades, antibiotics and antibiotic resistance genes (ARGs) have been regarded as emerging pollutants. The occurrence and distribution of antibiotics and ARGs in global freshwater lakes are summarized to show the pollution level of antibiotics and ARGs and to identify some of the potential risks to ecosystem and human health. Fifty-seven antibiotics were reported at least once in the studied lakes. Our meta-analysis shows that sulfamethoxazole, sulfamerazine, sulfameter, tetracycline, oxytetracycline, erythromycin, and roxithromycin were found at high concentrations in both lake water and lake sediment. There is no significant difference in the concentration of sulfonamides in lake water from China and that from other countries worldwide; however, there was a significant difference in quinolones. Erythromycin had the lowest predicted hazardous concentration for 5% of the species (HC5) and the highest ecological risk in lakes. There was no significant difference in the concentration of sulfonamide resistance genes (sul1 and sul2) in lake water and river water. There is surprisingly limited research on the role of aquatic biota in propagation of ARGs in freshwater lakes. As an environment that is susceptible to cumulative build-up of pollutants, lakes provide an important environment to study the fate of antibiotics and transport of ARGs with a broad range of niches including bacterial community, aquatic plants and animals

Classical Simulation of Relativistic Quantum Mechanics in Periodic Optical Structures

Spatial and/or temporal propagation of light waves in periodic optical structures offers a rather unique possibility to realize in a purely classical setting the optical analogues of a wide variety of quantum phenomena rooted in relativistic wave equations. In this work a brief overview of a few optical analogues of relativistic quantum phenomena, based on either spatial light transport in engineered photonic lattices or on temporal pulse propagation in Bragg grating structures, is presented. Examples include spatial and temporal photonic analogues of the Zitterbewegung of a relativistic electron, Klein tunneling, vacuum decay and pair-production, the Dirac oscillator, the relativistic Kronig-Penney model, and optical realizations of non-Hermitian extensions of relativistic wave equations.Comment: review article (invited), 14 pages, 7 figures, 105 reference

Real-time Monitoring for the Next Core-Collapse Supernova in JUNO

Core-collapse supernova (CCSN) is one of the most energetic astrophysical events in the Universe. The early and prompt detection of neutrinos before (pre-SN) and during the SN burst is a unique opportunity to realize the multi-messenger observation of the CCSN events. In this work, we describe the monitoring concept and present the sensitivity of the system to the pre-SN and SN neutrinos at the Jiangmen Underground Neutrino Observatory (JUNO), which is a 20 kton liquid scintillator detector under construction in South China. The real-time monitoring system is designed with both the prompt monitors on the electronic board and online monitors at the data acquisition stage, in order to ensure both the alert speed and alert coverage of progenitor stars. By assuming a false alert rate of 1 per year, this monitoring system can be sensitive to the pre-SN neutrinos up to the distance of about 1.6 (0.9) kpc and SN neutrinos up to about 370 (360) kpc for a progenitor mass of 30$M_{\odot}$ for the case of normal (inverted) mass ordering. The pointing ability of the CCSN is evaluated by using the accumulated event anisotropy of the inverse beta decay interactions from pre-SN or SN neutrinos, which, along with the early alert, can play important roles for the followup multi-messenger observations of the next Galactic or nearby extragalactic CCSN.Comment: 24 pages, 9 figure

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe