Showing papers by "National Research University – Higher School of Economics published in 2019"

SciPy 1.0--Fundamental Algorithms for Scientific Computing in Python

Abstract: SciPy is an open source scientific computing library for the Python programming language. SciPy 1.0 was released in late 2017, about 16 years after the original version 0.1 release. SciPy has become a de facto standard for leveraging scientific algorithms in the Python programming language, with more than 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories, and millions of downloads per year. This includes usage of SciPy in almost half of all machine learning projects on GitHub, and usage by high profile projects including LIGO gravitational wave analysis and creation of the first-ever image of a black hole (M87). The library includes functionality spanning clustering, Fourier transforms, integration, interpolation, file I/O, linear algebra, image processing, orthogonal distance regression, minimization algorithms, signal processing, sparse matrix handling, computational geometry, and statistics. In this work, we provide an overview of the capabilities and development practices of the SciPy library and highlight some recent technical developments.

Global, regional, and national burden of traumatic brain injury and spinal cord injury, 1990-2016: a systematic analysis for the Global Burden of disease Study 2016

Abstract: Summary Background Traumatic brain injury (TBI) and spinal cord injury (SCI) are increasingly recognised as global health priorities in view of the preventability of most injuries and the complex and expensive medical care they necessitate. We aimed to measure the incidence, prevalence, and years of life lived with disability (YLDs) for TBI and SCI from all causes of injury in every country, to describe how these measures have changed between 1990 and 2016, and to estimate the proportion of TBI and SCI cases caused by different types of injury. Methods We used results from the Global Burden of Diseases, Injuries, and Risk Factors (GBD) Study 2016 to measure the global, regional, and national burden of TBI and SCI by age and sex. We measured the incidence and prevalence of all causes of injury requiring medical care in inpatient and outpatient records, literature studies, and survey data. By use of clinical record data, we estimated the proportion of each cause of injury that required medical care that would result in TBI or SCI being considered as the nature of injury. We used literature studies to establish standardised mortality ratios and applied differential equations to convert incidence to prevalence of long-term disability. Finally, we applied GBD disability weights to calculate YLDs. We used a Bayesian meta-regression tool for epidemiological modelling, used cause-specific mortality rates for non-fatal estimation, and adjusted our results for disability experienced with comorbid conditions. We also analysed results on the basis of the Socio-demographic Index, a compound measure of income per capita, education, and fertility. Findings In 2016, there were 27·08 million (95% uncertainty interval [UI] 24·30–30·30 million) new cases of TBI and 0·93 million (0·78–1·16 million) new cases of SCI, with age-standardised incidence rates of 369 (331–412) per 100 000 population for TBI and 13 (11–16) per 100 000 for SCI. In 2016, the number of prevalent cases of TBI was 55·50 million (53·40–57·62 million) and of SCI was 27·04 million (24·98–30·15 million). From 1990 to 2016, the age-standardised prevalence of TBI increased by 8·4% (95% UI 7·7 to 9·2), whereas that of SCI did not change significantly (−0·2% [–2·1 to 2·7]). Age-standardised incidence rates increased by 3·6% (1·8 to 5·5) for TBI, but did not change significantly for SCI (−3·6% [–7·4 to 4·0]). TBI caused 8·1 million (95% UI 6·0–10·4 million) YLDs and SCI caused 9·5 million (6·7–12·4 million) YLDs in 2016, corresponding to age-standardised rates of 111 (82–141) per 100 000 for TBI and 130 (90–170) per 100 000 for SCI. Falls and road injuries were the leading causes of new cases of TBI and SCI in most regions. Interpretation TBI and SCI constitute a considerable portion of the global injury burden and are caused primarily by falls and road injuries. The increase in incidence of TBI over time might continue in view of increases in population density, population ageing, and increasing use of motor vehicles, motorcycles, and bicycles. The number of individuals living with SCI is expected to increase in view of population growth, which is concerning because of the specialised care that people with SCI can require. Our study was limited by data sparsity in some regions, and it will be important to invest greater resources in collection of data for TBI and SCI to improve the accuracy of future assessments. Funding Bill & Melinda Gates Foundation.

A Simple Baseline for Bayesian Uncertainty in Deep Learning

Abstract: We propose SWA-Gaussian (SWAG), a simple, scalable, and general purpose approach for uncertainty representation and calibration in deep learning. Stochastic Weight Averaging (SWA), which computes the first moment of stochastic gradient descent (SGD) iterates with a modified learning rate schedule, has recently been shown to improve generalization in deep learning. With SWAG, we fit a Gaussian using the SWA solution as the first moment and a low rank plus diagonal covariance also derived from the SGD iterates, forming an approximate posterior distribution over neural network weights; we then sample from this Gaussian distribution to perform Bayesian model averaging. We empirically find that SWAG approximates the shape of the true posterior, in accordance with results describing the stationary distribution of SGD iterates. Moreover, we demonstrate that SWAG performs well on a wide variety of tasks, including out of sample detection, calibration, and transfer learning, in comparison to many popular alternatives including variational inference, MC dropout, KFAC Laplace, and temperature scaling.

Global, regional, and national burden of suicide mortality 1990 to 2016: systematic analysis for the Global Burden of Disease Study 2016

Abstract: Objectives To use the estimates from the Global Burden of Disease Study 2016 to describe patterns of suicide mortality globally, regionally, and for 195 countries and territories by age, sex, and Socio-demographic index, and to describe temporal trends between 1990 and 2016. Design Systematic analysis. Main outcome measures Crude and age standardised rates from suicide mortality and years of life lost were compared across regions and countries, and by age, sex, and Socio-demographic index (a composite measure of fertility, income, and education). Results The total number of deaths from suicide increased by 6.7% (95% uncertainty interval 0.4% to 15.6%) globally over the 27 year study period to 817 000 (762 000 to 884 000) deaths in 2016. However, the age standardised mortality rate for suicide decreased by 32.7% (27.2% to 36.6%) worldwide between 1990 and 2016, similar to the decline in the global age standardised mortality rate of 30.6%. Suicide was the leading cause of age standardised years of life lost in the Global Burden of Disease region of high income Asia Pacific and was among the top 10 leading causes in eastern Europe, central Europe, western Europe, central Asia, Australasia, southern Latin America, and high income North America. Rates for men were higher than for women across regions, countries, and age groups, except for the 15 to 19 age group. There was variation in the female to male ratio, with higher ratios at lower levels of Socio-demographic index. Women experienced greater decreases in mortality rates (49.0%, 95% uncertainty interval 42.6% to 54.6%) than men (23.8%, 15.6% to 32.7%). Conclusions Age standardised mortality rates for suicide have greatly reduced since 1990, but suicide remains an important contributor to mortality worldwide. Suicide mortality was variable across locations, between sexes, and between age groups. Suicide prevention strategies can be targeted towards vulnerable populations if they are informed by variations in mortality rates.

Search for Lepton-Universality Violation in B + →K + ℓ+ ℓ- Decays

Abstract: A measurement of the ratio of branching fractions of the decays B + → K + μ + μ − and B + → K + e + e − is presented. The proton-proton collision data used correspond to an integrated luminosity of 5.0 fb − 1 recorded with the LHCb experiment at center-of-mass energies of 7, 8, and 13 TeV. For the dilepton mass-squared range 1.1 < q 2 < 6.0 GeV 2 / c 4 the ratio of branching fractions is measured to be R K = 0.84 6 + 0.060 − 0.054 + 0.016 − 0.014 , where the first uncertainty is statistical and the second systematic. This is the most precise measurement of R K to date and is compatible with the standard model at the level of 2.5 standard deviations.

Gene expression across mammalian organ development

Abstract: The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early organogenesis to adulthood for human, rhesus macaque, mouse, rat, rabbit, opossum and chicken. Comparisons of gene expression patterns identified correspondences of developmental stages across species, and differences in the timing of key events during the development of the gonads. We found that the breadth of gene expression and the extent of purifying selection gradually decrease during development, whereas the amount of positive selection and expression of new genes increase. We identified differences in the temporal trajectories of expression of individual genes across species, with brain tissues showing the smallest percentage of trajectory changes, and the liver and testis showing the largest. Our work provides a resource of developmental transcriptomes of seven organs across seven species, and comparative analyses that characterize the development and evolution of mammalian organs.

Observation of a Narrow Pentaquark State, Pc (4312)+, and of the Two-Peak Structure of the Pc (4450)+

Abstract: A narrow pentaquark state, P_{c}(4312)^{+}, decaying to J/ψp, is discovered with a statistical significance of 7.3σ in a data sample of Λ_{b}^{0}→J/ψpK^{-} decays, which is an order of magnitude larger than that previously analyzed by the LHCb Collaboration. The P_{c}(4450)^{+} pentaquark structure formerly reported by LHCb is confirmed and observed to consist of two narrow overlapping peaks, P_{c}(4440)^{+} and P_{c}(4457)^{+}, where the statistical significance of this two-peak interpretation is 5.4σ. The proximity of the Σ_{c}^{+}D[over ¯]^{0} and Σ_{c}^{+}D[over ¯]^{*0} thresholds to the observed narrow peaks suggests that they play an important role in the dynamics of these states.

Reductive Amination in the Synthesis of Pharmaceuticals.

Abstract: Reductive amination plays a paramount role in pharmaceutical and medicinal chemistry owing to its synthetic merits and the ubiquitous presence of amines among biologically active compounds. It is one of the key approaches to C-N bond construction due to its operational easiness and a wide toolbox of protocols. Recent studies show that at least a quarter of C-N bond-forming reactions in the pharmaceutical industry are performed via reductive amination. This Review concisely compiles information on 71 medical substances that are synthesized by reductive amination. Compounds are grouped according to the principle of action, which includes drugs affecting the central nervous system, drugs affecting the cardiovascular system, anticancer drugs, antibiotics, antiviral and antifungal medicines, drugs affecting the urinary system, drugs affecting the respiratory system, antidiabetic medications, drugs affecting the gastrointestinal tract, and drugs regulating metabolic processes. A general synthetic scheme is provided for each compound, and the description is focused on reductive amination steps. The green chemistry metric of reaction mass efficiency was calculated for all reactions.

Nuclear lamina integrity is required for proper spatial organization of chromatin in Drosophila

Abstract: How the nuclear lamina (NL) impacts on global chromatin architecture is poorly understood. Here, we show that NL disruption in Drosophila S2 cells leads to chromatin compaction and repositioning from the nuclear envelope. This increases the chromatin density in a fraction of topologically-associating domains (TADs) enriched in active chromatin and enhances interactions between active and inactive chromatin. Importantly, upon NL disruption the NL-associated TADs become more acetylated at histone H3 and less compact, while background transcription is derepressed. Two-colour FISH confirms that a TAD becomes less compact following its release from the NL. Finally, polymer simulations show that chromatin binding to the NL can per se compact attached TADs. Collectively, our findings demonstrate a dual function of the NL in shaping the 3D genome. Attachment of TADs to the NL makes them more condensed but decreases the overall chromatin density in the nucleus by stretching interphase chromosomes. The role of the nuclear lamina (NL) in chromatin architecture is still poorly understood. Here, the authors provide evidence that disruption of the NL in Drosophila cells leads to overall chromatin compaction and repositioning from the nuclear envelope, whereas lamina-associated regions become less compacted and transcription within them is increased.

Transcriptome of Extracellular Vesicles: State-of-the-Art

Abstract: Exosomes and microvesicles are two major categories of extracellular vesicles (EVs) released by almost all cell types and are highly abundant in biological fluids. Both the molecular composition of EVs and their release are thought to be strictly regulated by external stimuli. Multiple studies have consistently demonstrated that EVs transfer proteins, lipids and RNA between various cell types, thus mediating intercellular communication, and signaling. Importantly, small non-coding RNAs within EVs are thought to be major contributors to the molecular events occurring in the recipient cell. Furthermore, RNA cargo in exosomes and microvesicles could hold tremendous potential as non-invasive biomarkers for multiple disorders, including pathologies of the immune system. This mini-review is aimed to provide the state-of-the-art in the EVs-associated RNA transcriptome field, as well as the comprehensive analysis of previous studies characterizing RNA content within EVs released by various cells using next-generation sequencing. Finally, we highlight the technical challenges associated with obtaining pure EVs and deep sequencing of the EV-associated RNAs.

On Post-Minkowskian Hamiltonians in General Relativity

Abstract: We describe the computation of post-Minkowskian Hamiltonians in General Relativity from scattering amplitudes. Using a relativistic Lippmann-Schwinger equation, we relate perturbative amplitudes of massive scalars coupled to gravity to the post-Minkowskian Hamiltonians of classical General Relativity to any order in Newton's constant. We illustrate this by deriving an Hamiltonian for binary black holes without spin up to 2nd order in the post-Minkowskian expansion and demonstrate explicitly the equivalence with the recently proposed method based on an effective field theory matching.

Mapping 123 million neonatal, infant and child deaths between 2000 and 2017

Abstract: Since 2000, many countries have achieved considerable success in improving child survival, but localized progress remains unclear. To inform efforts towards United Nations Sustainable Development Goal 3.2—to end preventable child deaths by 2030—we need consistently estimated data at the subnational level regarding child mortality rates and trends. Here we quantified, for the period 2000–2017, the subnational variation in mortality rates and number of deaths of neonates, infants and children under 5 years of age within 99 low- and middle-income countries using a geostatistical survival model. We estimated that 32% of children under 5 in these countries lived in districts that had attained rates of 25 or fewer child deaths per 1,000 live births by 2017, and that 58% of child deaths between 2000 and 2017 in these countries could have been averted in the absence of geographical inequality. This study enables the identification of high-mortality clusters, patterns of progress and geographical inequalities to inform appropriate investments and implementations that will help to improve the health of all populations.

Engineering Graphene Flakes for Wearable Textile Sensors via Highly Scalable and Ultrafast Yarn Dyeing Technique.

Abstract: Multifunctional wearable e-textiles have been a focus of much attention due to their great potential for healthcare, sportswear, fitness, space, and military applications. Among them, electroconductive textile yarn shows great promise for use as next-generation flexible sensors without compromising the properties and comfort of usual textiles. However, the current manufacturing process of metal-based electroconductive textile yarn is expensive, unscalable, and environmentally unfriendly. Here we report a highly scalable and ultrafast production of graphene-based flexible, washable, and bendable wearable textile sensors. We engineer graphene flakes and their dispersions in order to select the best formulation for wearable textile application. We then use a high-speed yarn dyeing technique to dye (coat) textile yarn with graphene-based inks. Such graphene-based yarns are then integrated into a knitted structure as a flexible sensor and could send data wirelessly to a device via a self-powered RFID or a low-...

Observation of CP Violation in Charm Decays

Abstract: A search for charge-parity (CP) violation in D^{0}→K^{-}K^{+} and D^{0}→π^{-}π^{+} decays is reported, using pp collision data corresponding to an integrated luminosity of 5.9 fb^{-1} collected at a center-of-mass energy of 13 TeV with the LHCb detector. The flavor of the charm meson is inferred from the charge of the pion in D^{*}(2010)^{+}→D^{0}π^{+} decays or from the charge of the muon in B[over ¯]→D^{0}μ^{-}ν[over ¯]_{μ}X decays. The difference between the CP asymmetries in D^{0}→K^{-}K^{+} and D^{0}→π^{-}π^{+} decays is measured to be ΔA_{CP}=[-18.2±3.2(stat)±0.9(syst)]×10^{-4} for π-tagged and ΔA_{CP}=[-9±8(stat)±5(syst)]×10^{-4} for μ-tagged D^{0} mesons. Combining these with previous LHCb results leads to ΔA_{CP}=(-15.4±2.9)×10^{-4}, where the uncertainty includes both statistical and systematic contributions. The measured value differs from zero by more than 5 standard deviations. This is the first observation of CP violation in the decay of charm hadrons.

Clarifying the Concept of Well-Being: Psychological Need Satisfaction as the Common Core Connecting Eudaimonic and Subjective Well-Being:

Abstract: Interest in the experience of well-being, as both a research topic and as a policy goal, has significantly increased in recent decades. Although subjective well-being (SWB)—composed of positive aff...

Politicizing Europe in times of crisis

Abstract: This paper starts from the premise that the politicization of Europe is indicative of a new structuring conflict that involves a set of processes which put the national political community under st...

Beta Oscillations in Working Memory, Executive Control of Movement and Thought, and Sensorimotor Function

Abstract: Beta oscillations (∼13 to 30 Hz) have been observed during many perceptual, cognitive, and motor processes in a plethora of brain recording studies. Although the function of beta oscillations (hereafter "beta" for short) is unlikely to be explained by any single monolithic description, we here discuss several convergent findings. In prefrontal cortex (PFC), increased beta appears at the end of a trial when working memory information needs to be erased. A similar "clear-out" function might apply during the stopping of action and the stopping of long-term memory retrieval (stopping thoughts), where increased prefrontal beta is also observed. A different apparent role for beta in PFC occurs during the delay period of working memory tasks: it might serve to maintain the current contents and/or to prevent interference from distraction. We confront the challenge of relating these observations to the large literature on beta recorded from sensorimotor cortex. Potentially, the clear-out of working memory in PFC has its counterpart in the postmovement clear-out of the motor plan in sensorimotor cortex. However, recent studies support alternative interpretations. In addition, we flag emerging research on different frequencies of beta and the relationship between beta and single-neuron spiking. We also discuss where beta might be generated: basal ganglia, cortex, or both. We end by considering the clinical implications for adaptive deep-brain stimulation.

Coulomb branches of $3d$ $\mathcal{N}=4$ quiver gauge theories and slices in the affine Grassmannian

Abstract: This is a companion paper of arXiv:1601.03586. We study Coulomb branches of unframed and framed quiver gauge theories of type $ADE$. In the unframed case they are isomorphic to the moduli space of based rational maps from ${\\mathbb C}P^1$ to the flag variety. In the framed case they are slices in the affine Grassmannian and their generalization. In the appendix, written jointly with Joel Kamnitzer, Ryosuke Kodera, Ben Webster, and Alex Weekes, we identify the quantized Coulomb branch with the truncated shifted Yangian.

Neural Oblivious Decision Ensembles for Deep Learning on Tabular Data

Abstract: Nowadays, deep neural networks (DNNs) have become the main instrument for machine learning tasks within a wide range of domains, including vision, NLP, and speech. Meanwhile, in an important case of heterogenous tabular data, the advantage of DNNs over shallow counterparts remains questionable. In particular, there is no sufficient evidence that deep learning machinery allows constructing methods that outperform gradient boosting decision trees (GBDT), which are often the top choice for tabular problems. In this paper, we introduce Neural Oblivious Decision Ensembles (NODE), a new deep learning architecture, designed to work with any tabular data. In a nutshell, the proposed NODE architecture generalizes ensembles of oblivious decision trees, but benefits from both end-to-end gradient-based optimization and the power of multi-layer hierarchical representation learning. With an extensive experimental comparison to the leading GBDT packages on a large number of tabular datasets, we demonstrate the advantage of the proposed NODE architecture, which outperforms the competitors on most of the tasks. We open-source the PyTorch implementation of NODE and believe that it will become a universal framework for machine learning on tabular data.

Multiple mechanisms link prestimulus neural oscillations to sensory responses.

Abstract: Spontaneous fluctuations of neural activity may explain why sensory responses vary across repeated presentations of the same physical stimulus. To test this hypothesis, we recorded electroencephalography in humans during stimulation with identical visual stimuli and analyzed how prestimulus neural oscillations modulate different stages of sensory processing reflected by distinct components of the event-related potential (ERP). We found that strong prestimulus alpha- and beta-band power resulted in a suppression of early ERP components (C1 and N150) and in an amplification of late components (after 0.4 s), even after controlling for fluctuations in 1/f aperiodic signal and sleepiness. Whereas functional inhibition of sensory processing underlies the reduction of early ERP responses, we found that the modulation of non-zero-mean oscillations (baseline shift) accounted for the amplification of late responses. Distinguishing between these two mechanisms is crucial for understanding how internal brain states modulate the processing of incoming sensory information.

Empowering Women: The Role of Emancipative Forces in Board Gender Diversity

Abstract: This study investigates the effect of country-level emancipative forces on corporate gender diversity around the world. Based on Welzel’s (Freedom rising: human empowerment and the quest for emancipation. Cambridge University Press, New York, 2013) theory of emancipation, we develop an emancipatory framework of board gender diversity that explains how action resources, emancipative values and civic entitlements enable, motivate and encourage women to take leadership roles on corporate boards. Using a sample of 6390 firms operating in 30 countries around the world, our results show positive single and combined effects of the framework components on board gender diversity. Our research adds to the existing literature in a twofold manner. First, our integrated framework offers a more encompassing, complete and theoretically richer picture of the key drivers of board gender diversity. Second, by testing the framework empirically, we extend the evidence on national drivers of board gender diversity.

Entrepreneurship and Economic Growth: The Experience of Developed and Developing Countries

Abstract: This chapter elaborates on entrepreneurship in developed and developing countries and focuses on the optimization of entrepreneurial activities. Various scenarios are considered: independent functioning of the market, integration in the form of reorganization (mergers and acquisitions), integration in the form of clustering, and integration in the form of innovational networks and technological parks. The optimal structure of the integration processes and best-case scenarios for its implementation to accelerate the rate and increase the quality of economic growth are substantiated. The potential for uptake of integration processes in stimulating economic growth through entrepreneurship is determined by the level of institutionalization in an economy. In developed countries, all forms of company integration are characterized by the high level of institutionalization, which allows for their effective use for economic growth. Independent companies, mergers, and acquisitions restrain economic growth and reduce its quality, while clusters, technological parks, and innovational networks accelerate the rate of economic growth and increase its quality. In developing countries, integration processes in entrepreneurship have a different influence on economic growth and require further institutionalization.

Statistics of eigenstates near the localization transition on random regular graphs

Abstract: Anderson localization on random regular graphs (RRG) attracts much attention in view of its relation to many-body localization. Here, the authors study the statistics of eigenfunctions and energy levels on RRG, focussing on the delocalized (ergodic) phase and the critical regime. Results of exact diagonalization are in outstanding agreement with analytical theory based on the saddle-point analysis of the effective supersymmetric action supplemented by numerical solution of the corresponding self-consistency equation.

Fair Division in the Internet Age

Abstract: Fair division, a key concern in the design of many social institutions, has for 70 years been the subject of interdisciplinary research at the interface of mathematics, economics, and game theory. ...

Brain ventricular volume changes induced by long-duration spaceflight

Abstract: Long-duration spaceflight induces detrimental changes in human physiology. Its residual effects and mechanisms remain unclear. We prospectively investigated the changes in cerebrospinal fluid (CSF) volume of the brain ventricular regions in space crew by means of a region of interest analysis on structural brain scans. Cosmonaut MRI data were investigated preflight (n = 11), postflight (n = 11), and at long-term follow-up 7 mo after landing (n = 7). Post hoc analyses revealed a significant difference between preflight and postflight values for all supratentorial ventricular structures, i.e., lateral ventricle (mean % change ± SE = 13.3 ± 1.9), third ventricle (mean % change ± SE = 10.4 ± 1.1), and the total ventricular volume (mean % change ± SE = 11.6 ± 1.5) (all P < 0.0001), with higher volumes at postflight. At follow-up, these structures did not quite reach baseline levels, with still residual increases in volume for the lateral ventricle (mean % change ± SE = 7.7 ± 1.6; P = 0.0009), the third ventricle (mean % change ± SE = 4.7 ± 1.3; P = 0.0063), and the total ventricular volume (mean % change ± SE = 6.4 ± 1.3; P = 0.0008). This spatiotemporal pattern of CSF compartment enlargement and recovery points to a reduced CSF resorption in microgravity as the underlying cause. Our results warrant more detailed and longer longitudinal follow-up. The clinical impact of our findings on the long-term cosmonauts' health and their relation to ocular changes reported in space travelers requires further prospective studies.