Asynchronous Training of Word Embeddings for Large Text Corpora

Word embeddings are a powerful approach for analyzing language and have been widely popular in numerous tasks in information retrieval and text mining. Training embeddings over huge corpora is computationally expensive because the input is typically sequentially processed and parameters are synchronously updated. Distributed architectures for asynchronous training that have been proposed either focus on scaling vocabulary sizes and dimensionality or suffer from expensive synchronization latencies. In this paper, we propose a scalable approach to train word embeddings by partitioning the input space instead in order to scale to massive text corpora while not sacrificing the performance of the embeddings. Our training procedure does not involve any parameter synchronization except a final sub-model merge phase that typically executes in a few minutes. Our distributed training scales seamlessly to large corpus sizes and we get comparable and sometimes even up to 45% performance improvement in a variety of NLP benchmarks using models trained by our distributed procedure which requires $1/10$ of the time taken by the baseline approach. Finally we also show that we are robust to missing words in sub-models and are able to effectively reconstruct word representations.Comment: This paper contains 9 pages and has been accepted in the WSDM201

The Effects of a High Fat Meal on Blood Flow Regulation during Arm Exercise

A diet high in saturated fats results in endothelial dysfunction and can lead to atherosclerosis, a precursor to cardiovascular disease. Exercise training is a potent stimulus though to mitigate the negative effects of a high saturated fat diet; however, it is unclear how high-saturated fat meal (HSFM) consumption impacts blood flow regulation during a single exercise session. PURPOSE: This study sought to examine the impact of a single HSFM on peripheral vascular function during an acute upper limb exercise bout. METHODS: Ten young healthy individuals completed two sessions of progressive handgrip exercise. Subjects either consumed a HSFM (0.84 g of fat/kg of body weight) 4 hours prior or remained fasted before the exercise bout. Progressive rhythmic handgrip exercise (6kg, 12kg, 18kg) was performed for 3 minutes per stage at rate of 1 Hz. The brachial artery (BA) diameter and blood velocity was obtained using Doppler Ultrasound (GE Logiq e) and BA blood flow was calculated with these values. RESULTS: BA blood flow and flow mediated dilation (normalized for shear rate) during the handgrip exercise significant increased from baseline in all workloads, but no differences were revealed in response to the HSFM consumption. CONCLUSION: Progressive handgrip exercise augmented BA blood flow and flow mediated dilation in both testing days; however, there was no significant differences following the HSFM consumption. This suggests that upper limb blood flow regulation during exercise is unaltered by a high fat meal in young healthy individuals.https://scholarscompass.vcu.edu/gradposters/1060/thumbnail.jp

Integrated ground-based and remotely sensed data to support global studies of environmental change

Data centers routinely archive and distribute large databases of high quality and with rigorous documentation but, to meet the needs of global studies effectively and efficiently, data centers must go beyond these traditional roles. Global studies of environmental change require integrated databases of multiple data types that are accurately coordinated in terms of spatial, temporal and thematic properties. Such datasets must be designed and developed jointly by scientific researchers, computer specialists, and policy analysts. The presentation focuses on our approach for organizing data from ground-based research programs so that the data can be linked with remotely sensed data and other map data into integrated databases with spatial, temporal, and thematic characteristics relevant to global studies. The development of an integrated database for Net Primary Productivity is described to illustrate the process

Quadriceps exercise intolerance in patients with chronic obstructive pulmonary disease: the potential role of altered skeletal muscle mitochondrial respiration

This study sought to determine if qualitative alterations in skeletal muscle mitochondrial respiration, associated with decreased mitochondrial efficiency, contribute to exercise intolerance in patients with chronic obstructive pulmonary disease (COPD). Using permeabilized muscle fibers from the vastus lateralis of 13 patients with COPD and 12 healthy controls, complex I (CI) and complex II (CII)-driven State 3 mitochondrial respiration were measured separately (State 3:CI and State 3:CII) and in combination (State 3:CI+CII). State 2 respiration was also measured. Exercise tolerance was assessed by knee extensor exercise (KE) time to fatigue. Per milligram of muscle, State 3:CI+CII and State 3:CI were reduced in COPD (P \u3c 0.05), while State 3:CII and State 2 were not different between groups. To determine if this altered pattern of respiration represented qualitative changes in mitochondrial function, respiration states were examined as percentages of peak respiration (State 3:CI+CII), which revealed altered contributions from State 3:CI (Con 83.7 ± 3.4, COPD 72.1 ± 2.4%Peak, P \u3c 0.05) and State 3:CII (Con 64.9 ± 3.2, COPD 79.5 ± 3.0%Peak, P \u3c 0.05) respiration, but not State 2 respiration in COPD. Importantly, a diminished contribution of CI-driven respiration relative to the metabolically less-efficient CII-driven respiration (CI/CII) was also observed in COPD (Con 1.28 ± 0.09, COPD 0.81 ± 0.05, P \u3c 0.05), which was related to exercise tolerance of the patients (r = 0.64, P \u3c 0.05). Overall, this study indicates that COPD is associated with qualitative alterations in skeletal muscle mitochondria that affect the contribution of CI and CII-driven respiration, which potentially contributes to the exercise intolerance associated with this disease

Electron correlation effects in electron-hole recombination in organic light-emitting diodes

We develop a general theory of electron--hole recombination in organic light emitting diodes that leads to formation of emissive singlet excitons and nonemissive triplet excitons. We briefly review other existing theories and show how our approach is substantively different from these theories. Using an exact time-dependent approach to the interchain/intermolecular charge-transfer within a long-range interacting model we find that, (i) the relative yield of the singlet exciton in polymers is considerably larger than the 25% predicted from statistical considerations, (ii) the singlet exciton yield increases with chain length in oligomers, and, (iii) in small molecules containing nitrogen heteroatoms, the relative yield of the singlet exciton is considerably smaller and may be even close to 25%. The above results are independent of whether or not the bond-charge repulsion, X_perp, is included in the interchain part of the Hamiltonian for the two-chain system. The larger (smaller) yield of the singlet (triplet) exciton in carbon-based long-chain polymers is a consequence of both its ionic (covalent) nature and smaller (larger) binding energy. In nitrogen containing monomers, wavefunctions are closer to the noninteracting limit, and this decreases (increases) the relative yield of the singlet (triplet) exciton. Our results are in qualitative agreement with electroluminescence experiments involving both molecular and polymeric light emitters. The time-dependent approach developed here for describing intermolecular charge-transfer processes is completely general and may be applied to many other such processes.Comment: 19 pages, 11 figure

Altered gene expression profiles impair the nervous system development in individuals with 15q13.3 microdeletion

The 15q13.3 microdeletion has pleiotropic effects ranging from apparently healthy to severely affected individuals. The underlying basis of the variable phenotype remains elusive. We analyzed gene expression using blood from three individuals with 15q13.3 microdeletion and brain cortex tissue from ten mice Df[h15q13]/+. We assessed differentially expressed genes (DEGs), protein–protein interaction (PPI) functional modules, and gene expression in brain developmental stages. The deleted genes’ haploinsufficiency was not transcriptionally compensated, suggesting a dosage effect may contribute to the pathomechanism. DEGs shared between tested individuals and a corresponding mouse model show a significant overlap including genes involved in monogenic neurodevelopmental disorders. Yet, network-wide dysregulatory effects suggest the phenotype is not caused by a single critical gene. A significant proportion of blood DEGs, silenced in adult brain, have maximum expression during the prenatal brain development. Based on DEGs and their PPI partners we identified altered functional modules related to developmental processes, including nervous system development. We show that the 15q13.3 microdeletion has a ubiquitous impact on the transcriptome pattern, especially dysregulation of genes involved in brain development. The high phenotypic variability seen in 15q13.3 microdeletion could stem from an increased vulnerability during brain development, instead of a specific pathomechanism

Sequence-based prediction for vaccine strain selection and identification of antigenic variability in foot-and-mouth disease virus

Identifying when past exposure to an infectious disease will protect against newly emerging strains is central to understanding the spread and the severity of epidemics, but the prediction of viral cross-protection remains an important unsolved problem. For foot-and-mouth disease virus (FMDV) research in particular, improved methods for predicting this cross-protection are critical for predicting the severity of outbreaks within endemic settings where multiple serotypes and subtypes commonly co-circulate, as well as for deciding whether appropriate vaccine(s) exist and how much they could mitigate the effects of any outbreak. To identify antigenic relationships and their predictors, we used linear mixed effects models to account for variation in pairwise cross-neutralization titres using only viral sequences and structural data. We identified those substitutions in surface-exposed structural proteins that are correlates of loss of cross-reactivity. These allowed prediction of both the best vaccine match for any single virus and the breadth of coverage of new vaccine candidates from their capsid sequences as effectively as or better than serology. Sub-sequences chosen by the model-building process all contained sites that are known epitopes on other serotypes. Furthermore, for the SAT1 serotype, for which epitopes have never previously been identified, we provide strong evidence - by controlling for phylogenetic structure - for the presence of three epitopes across a panel of viruses and quantify the relative significance of some individual residues in determining cross-neutralization. Identifying and quantifying the importance of sites that predict viral strain cross-reactivity not just for single viruses but across entire serotypes can help in the design of vaccines with better targeting and broader coverage. These techniques can be generalized to any infectious agents where cross-reactivity assays have been carried out. As the parameterization uses pre-existing datasets, this approach quickly and cheaply increases both our understanding of antigenic relationships and our power to control disease

Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text

<p>Abstract</p> <p>Background</p> <p>Pharmacogenomics studies the relationship between genetic variation and the variation in drug response phenotypes. The field is rapidly gaining importance: it promises drugs targeted to particular subpopulations based on genetic background. The pharmacogenomics literature has expanded rapidly, but is dispersed in many journals. It is challenging, therefore, to identify important associations between drugs and molecular entities – particularly genes and gene variants, and thus these critical connections are often lost. Text mining techniques can allow us to convert the free-style text to a computable, searchable format in which pharmacogenomic concepts (such as genes, drugs, polymorphisms, and diseases) are identified, and important links between these concepts are recorded. Availability of full text articles as input into text mining engines is key, as literature abstracts often do not contain sufficient information to identify these pharmacogenomic associations.</p> <p>Results</p> <p>Thus, building on a tool called Textpresso, we have created the Pharmspresso tool to assist in identifying important pharmacogenomic facts in full text articles. Pharmspresso parses text to find references to human genes, polymorphisms, drugs and diseases and their relationships. It presents these as a series of marked-up text fragments, in which key concepts are visually highlighted. To evaluate Pharmspresso, we used a gold standard of 45 human-curated articles. Pharmspresso identified 78%, 61%, and 74% of target gene, polymorphism, and drug concepts, respectively.</p> <p>Conclusion</p> <p>Pharmspresso is a text analysis tool that extracts pharmacogenomic concepts from the literature automatically and thus captures our current understanding of gene-drug interactions in a computable form. We have made Pharmspresso available at <url>http://pharmspresso.stanford.edu</url>.</p

V-I characteristics in the vicinity of order-disorder transition in vortex matter

The shape of the V-I characteristics leading to a peak in the differential resistance r_d=dV/dI in the vicinity of the order-disorder transition in NbSe2 is investigated. r_d is large when measured by dc current. However, for a small Iac on a dc bias r_d decreases rapidly with frequency, even at a few Hz, and displays a large out-of-phase signal. In contrast, the ac response increases with frequency in the absence of dc bias. These surprisingly opposite phenomena and the peak in r_d are shown to result from a dynamic coexistence of two vortex matter phases rather than from the commonly assumed plastic depinning.Comment: 12 pages 4 figures. Accepted for publication in PRB rapi

Indium contamination from the indium-tin-oxide electrode in polymer light-emitting diodes

We have found that polymer light-emitting diodes (LEDs) contain high concentrations of metal impurities prior to operation. Narrow peaks in the electroluminescence spectrum unambiguously demonstrate the presence of atomic indium and aluminum. Rutherford backscattering spectroscopy (RBS) and x-ray photoelectron spectroscopy (XPS) depth profiling data corroborate this result. An average indium concentration of 5 x 10(19)atoms/cm(3) originating from the indium-tin-oxide (ITO) electrode has been found in the polymer layer. (C) 1996 American Institute of Physics