nils-herrmann/clean_scirepeval huggingface dataset:
Variable-Order de Bruijn Graphs

The de Bruijn graph GK of a set of strings Sis a key data structure in genome assembly that represents overlaps between all the K-length substrings of S. Construction and navigation of the graph is a space and time bottleneck in practice and the main hurdle for assembling large genomes. This problem is compounded because state-of-the-art assemblers do not build the de Bruijn graph for a single order (value of K) but for multiple values of K: they builddde Bruijn graphs, each with a specific order, i.e., GK1, GK2, GKd. Al-though, this paradigm increases the quality of the assembly produce but it greatly increases runtime, because of the need to construct graphs instead of one. In this paper, we show how to augment a succinct de Bruijn graph representation by Bowe et al. ( 2012) to support new operations that let us change order on the fly, effectively representing all de Bruijn graphs of order up to some maximum Kin a single data structure. Our experiments show our variable-order de Bruijn graph only modestly increases space usage, construction time, and navigation time compared to a single order graph.
Forced desorption of semiflexible polymers, adsorbed and driven by molecular motors.

We formulate and characterize a model to describe the dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the filament. The stochastic binding-unbinding of the motor proteins and their ability to move along the polymer generate active forces. As the pulling force reaches a threshold value, the polymer eventually desorbs from the substrate. Performing underdamped Langevin dynamics simulation of the polymer, and with stochastic motor activity, we obtain desorption phase diagrams. The correlation time for fluctuations in the desorbed fraction increases as one approaches complete desorption, captured quantitatively by a power law spectral density. We present theoretical analysis of the phase diagram using mean field approximations in the weakly bending limit of the polymer and performing linear stability analysis. This predicts an increase in the desorption force with the polymer bending rigidity, active velocity and processivity of the motor proteins to capture the main features of the simulation results.
Exploiting Parallelism for Hard Problems in Abstract Argumentation

Abstract argumentation framework (AF) is a unifying framework able to encompass a variety of nonmonotonic reasoning approaches, logic programming and computational argumentation. Yet, efficient approaches for most of the decision and enumeration problems associated to AFs are missing, thus limiting the efficacy of argumentation-based approaches in real domains. In this paper, we present an algorithm for enumerating the preferred extensions of abstract argumentation frameworks which exploits parallel computation. To this purpose, the SCC-recursive semantics definition schema is adopted, where extensions are defined at the level of specific sub-frameworks. The algorithm shows significant performance improvements in large frameworks, in terms of number of solutions found and speedup.
Logical Limitations to Machine Ethics with Consequences to Lethal Autonomous Weapons

Lethal Autonomous Weapons promise to revolutionize warfare -- and raise a multitude of ethical and legal questions. It has thus been suggested to program values and principles of conduct (such as the Geneva Conventions) into the machines' control, thereby rendering them both physically and morally superior to human combatants. 
We employ mathematical logic and theoretical computer science to explore fundamental limitations to the moral behaviour of intelligent machines in a series of "Gedankenexperiments": Refining and sharpening variants of the Trolley Problem leads us to construct an (admittedly artificial but) fully deterministic situation where a robot is presented with two choices: one morally clearly preferable over the other -- yet, based on the undecidability of the Halting problem, it provably cannot decide algorithmically which one. Our considerations have surprising implications to the question of responsibility and liability for an autonomous system's actions and lead to specific technical recommendations.
User Session Identification Based on Strong Regularities in Inter-activity Time

Session identification is a common strategy used to develop metrics for web analytics and perform behavioral analyses of user-facing systems. Past work has argued that session identification strategies based on an inactivity threshold is inherently arbitrary or has advocated that thresholds be set at about 30 minutes. In this work, we demonstrate a strong regularity in the temporal rhythms of user initiated events across several different domains of online activity (incl. video gaming, search, page views and volunteer contributions). We describe a methodology for identifying clusters of user activity and argue that the regularity with which these activity clusters appear implies a good rule-of-thumb inactivity threshold of about 1 hour. We conclude with implications that these temporal rhythms may have for system design based on our observations and theories of goal-directed human activity.
Observation of three-mode parametric instability

Three-mode parametric interactions occur in triply resonant optomechanical systems: Photons from an optical pump mode are coherently scattered to a high-order mode by mechanical motion of the cavity mirrors, and these modes resonantly interact via radiation pressure force when some conditions are met. They can either pump energy into acoustic modes, leading to parametric instability, or extract mechanical energy, leading to optomechanical cooling. Such effects are predicted to occur in long baseline advanced gravitational-wave detectors, possibly jeopardizing their stable operation. We have demonstrated both three-mode cooling and amplification in two different three-mode optomechanical systems. We report an observation of the three-mode parametric instability in a free-space Fabry-Perot cavity, with ring-up amplitude saturation.
Gravitational waves and scalar perturbations from spectator fields

The most conventional mechanism for gravitational waves (gw) production during inflation is the amplification of vacuum metric fluctuations. In this case the gw production can be uniquely related to the inflationary expansion rate H. For example, a gw detection close to the present experimental limit (tensor-to-scalar ratio r ∼ 0.1) would indicate an inflationary expansion rate close to 1014 GeV. This conclusion, however, would be invalid if the observed gw originated from a different source. We construct and study one of the possible covariant formulations of the mechanism suggested in , where a spectator field σ with a sound speed cs ≪ 1 acts as a source for gw during inflation. In our formulation σ is described by a so-called P(X) Lagrangian and a non-minimal coupling to gravity. This field interacts only gravitationally with the inflaton, which has a standard action. We compute the amount of scalar and tensor density fluctuations produced by σ and find that, in our realization, r is not enhanced with respect to the standard result but it is strongly sensitive to cs, thus breaking the direct r ↔ H connection.
Neutron stars and supernova explosions in the framework of Landau's theory

A general formula of the symmetry energy for many-body interaction is proposed and the commonly used two-body interaction symmetry energy is recovered. Within Landau's theory (Lt), we generalize two equations of state (EoS) CCS$\delta$3 and CCS$\delta$5 to asymmetric nuclear matter. We assume that the density and density difference between protons and neutrons divided by their sum are order parameters. We use different EoS to study neutron stars by solving the TOV equations. We demonstrate that different EoS give different mass and radius relation for neutron stars even when they have exactly the same ground state (gs) properties ($E/A$, $\rho_0$, $K$, $S$, $L$ and $K_{sym}$). Furthermore, for one EoS we change $K_{sym}$ and fix all the other gs parameters. We find that for some $K_{sym}$ the EoS becomes unstable at high density even for neutron matter. This suggests that a neutron star (NS) can exist below and above the instability region but in different states: a quark gluon plasma (QGP) at high density and baryonic matter at low density. If the star's central density is in the instability region, then we associate these conditions to the occurrence of Supernovae (SN).
Bose–Einstein condensation of 162Dy and 160Dy

We report Bose–Einstein condensation of two isotopes of the highly magnetic element dysprosium: 162Dy and 160 ?> Dy. For 162Dy, condensates with 105 atoms form below T = 50 nK. We find the evaporation efficiency for the isotope 160Dy to be poor; however, by utilizing a low-field Fano–Feshbach resonance to carefully change the scattering properties, it is possible to produce a Bose–Einstein condensate of 160Dy with 103 atoms. The 162Dy BEC reported is an order of magnitude larger in atom number than that of the previously reported 164Dy BEC, and it may be produced within 18 s.
Compact binary systems in scalar-tensor gravity. III. Scalar waves and energy flux

We derive the scalar waveform generated by a binary of nonspinning compact objects (black holes or neutron stars) in a general class of scalar-tensor theories of gravity. The waveform is accurate to 1.5 post-Newtonian order [$O((v/c)^3)$] beyond the leading-order tensor gravitational waves (the "Newtonian quadrupole"). To solve the scalar-tensor field equations, we adapt the direct integration of the relaxed Einstein equations formalism developed by Will, Wiseman, and Pati. The internal gravity of the compact objects is treated with an approach developed by Eardley. We find that the scalar waves are described by the same small set of parameters which describes the equations of motion and tensor waves. For black hole--black hole binaries, the scalar waveform vanishes, as expected from previous results which show that these systems in scalar-tensor theory are indistinguishable from their general relativistic counterparts. For black hole--neutron star binaries, the scalar waveform simplifies considerably from the generic case, essentially depending on only a single parameter up to first post-Newtonian order. With both the tensor and scalar waveforms in hand, we calculate the total energy flux carried by the outgoing waves. This quantity is computed to first post-Newtonian order relative to the "quadrupole formula" and agrees with previous, lower order calculations.
Long Term Risk: A Martingale Approach

This paper extends the long‐term factorization of the stochastic discount factor introduced and studied by Alvarez and Jermann (2005) in discrete‐time ergodic environments and by Hansen and Scheinkman (2009) and Hansen (2012) in Markovian environments to general semimartingale environments. The transitory component discounts at the stochastic rate of return on the long bond and is factorized into discounting at the long‐term yield and a positive semimartingale that extends the principal eigenfunction of Hansen and Scheinkman (2009) to the semimartingale setting. The permanent component is a martingale that accomplishes a change of probabilities to the long forward measure, the limit of T‐forward measures. The change of probabilities from the data‐generating to the long forward measure absorbs the long‐term risk‐return trade‐off and interprets the latter as the long‐term risk‐neutral measure.
Social Media Fingerprints of Unemployment

Recent widespread adoption of electronic and pervasive technologies has enabled the study of human behavior at an unprecedented level, uncovering universal patterns underlying human activity, mobility, and interpersonal communication. In the present work, we investigate whether deviations from these universal patterns may reveal information about the socio-economical status of geographical regions. We quantify the extent to which deviations in diurnal rhythm, mobility patterns, and communication styles across regions relate to their unemployment incidence. For this we examine a country-scale publicly articulated social media dataset, where we quantify individual behavioral features from over 19 million geo-located messages distributed among more than 340 different Spanish economic regions, inferred by computing communities of cohesive mobility fluxes. We find that regions exhibiting more diverse mobility fluxes, earlier diurnal rhythms, and more correct grammatical styles display lower unemployment rates. As a result, we provide a simple model able to produce accurate, easily interpretable reconstruction of regional unemployment incidence from their social-media digital fingerprints alone. Our results show that cost-effective economical indicators can be built based on publicly-available social media datasets.
A geometrically motivated parametric model in manifold estimation

The general aim of manifold estimation is reconstructing, by statistical methods, an m-dimensional compact manifold S on d (with m≤d) or estimating some relevant quantities related to the geometric properties of S. Focussing on the cases d=2 and d=3, with m=d or m=d−1, we will assume that the data are given by the distances to S from points randomly chosen on a band surrounding S. The aim of this paper is to show that, if S belongs to a wide class of compact sets (which we call sets with polynomial volume), the proposed statistical model leads to a relatively simple parametric formulation. In this setup, standard methodologies (method of moments, maximum likelihood) can be used to estimate some interesting geometric parameters, including curvatures and Euler characteristic. We will particularly focus on the estimation of the (d−1)-dimensional boundary measure (in Minkowski's sense) of S. It turns out, however, that the estimation problem is not straightforward since the standard estimators show a remarkably pathological behaviour: while they are consistent and asymptotically normal, their expectations are infinite. The theoretical and practical consequences of this fact are discussed in some detail.
On Coarse Graining of Information and Its Application to Pattern Recognition

We propose a method based on finite mixture models for classifying a set of observations into number of different categories. In order to demonstrate the method, we show how the component densities for the mixture model can be derived by using the maximum entropy method in conjunction with conservation of Pythagorean means. Several examples of distributions belonging to the Pythagorean family are derived. A discussion on estimation of model parameters and the number of categories is also given.
Deciding what to display: maximizing the information value of social media

In information-rich environments, the competition for users' attention leads to a flood of content from which people often find hard to sort out the most relevant and useful pieces. Using Twitter as a case study, we applied an attention economy solution to generate the most informative tweets for its users. By considering the novelty and popularity of tweets as objective measures of their relevance and utility, we used the Huberman-Wu algorithm to automatically select the ones that will receive the most attention in the next time interval. Their predicted popularity was confirmed by using Twitter data collected for a period of 2 months.
Connecting local active forces to macroscopic stress in elastic media.

In contrast with ordinary materials, living matter drives its own motion by generating active, out-of-equilibrium internal stresses. These stresses typically originate from localized active elements embedded in an elastic medium, such as molecular motors inside the cell or contractile cells in a tissue. While many large-scale phenomenological theories of such active media have been developed, a systematic understanding of the emergence of stress from the local force-generating elements is lacking. In this paper, we present a rigorous theoretical framework to study this relationship. We show that the medium's macroscopic active stress tensor is equal to the active elements' force dipole tensor per unit volume in both continuum and discrete linear homogeneous media of arbitrary geometries. This relationship is conserved on average in the presence of disorder, but can be violated in nonlinear elastic media. Such effects can lead to either a reinforcement or an attenuation of the active stresses, giving us a glimpse of the ways in which nature might harness microscopic forces to create active materials.
Statistically Significant Detection of Linguistic Change

We propose a new computational approach for tracking and detecting statistically significant linguistic shifts in the meaning and usage of words. Such linguistic shifts are especially prevalent on the Internet, where the rapid exchange of ideas can quickly change a word's meaning. Our meta-analysis approach constructs property time series of word usage, and then uses statistically sound change point detection algorithms to identify significant linguistic shifts. We consider and analyze three approaches of increasing complexity to generate such linguistic property time series, the culmination of which uses distributional characteristics inferred from word co-occurrences. Using recently proposed deep neural language models, we first train vector representations of words for each time period. Second, we warp the vector spaces into one unified coordinate system. Finally, we construct a distance-based distributional time series for each word to track its linguistic displacement over time. We demonstrate that our approach is scalable by tracking linguistic change across years of micro-blogging using Twitter, a decade of product reviews using a corpus of movie reviews from Amazon, and a century of written books using the Google Book Ngrams. Our analysis reveals interesting patterns of language usage change commensurate with each medium.
Cosmology on a cosmic ring

We derive the modified Friedmann equations for a generalization of the Dvali-Gabadadze-Porrati (DGP) model in which the brane has one additional compact dimension. The main new feature is the emission of gravitational waves into the bulk. We study two classes of solutions: first, if the compact dimension is stabilized, the waves vanish and one exactly recovers DGP cosmology. However, a stabilization by means of physical matter is not possible for a tension-dominated brane, thus implying a late time modification of 4D cosmology different from DGP. Second, for a freely expanding compact direction, we find exact attractor solutions with zero 4D Hubble parameter despite the presence of a 4D cosmological constant. The model hence constitutes an explicit example of dynamical degravitation at the full nonlinear level. Without stabilization, however, there is no 4D regime and the model is ruled out observationally, as we demonstrate explicitly by comparing to supernova data.
Spin-orbit-free topological insulators

We review a class of translational-invariant insulators without spin–orbit coupling, as may be realized in intrinsically spinless systems, e.g., photonic crystals and ultra-cold atoms. Some of these insulators have no time-reversal symmetry as well, i.e., the relevant symmetries are purely crystalline. Nevertheless, topological phases exist which are distinguished by their robust surface modes. To describe these phases, we introduce the notions of (a) a halved-mirror chirality: an integer invariant which characterizes half-mirror planes in the 3D Brillouin zone, and (b) a bent Chern number: the traditional Thouless–Kohmoto–Nightingale–Nijs invariant generalized to bent 2D manifolds. Like other well-known topological phases, their band topology is unveiled by the crystalline analog of Berry phases, i.e., parallel transport across certain non-contractible loops in the Brillouin zone. We also identify certain topological phases without any robust surface modes—they are uniquely distinguished by parallel transport along bent loops, whose shapes are determined by the symmetry group. Finally, we describe the Weyl semimetallic phase that intermediates two distinct, gapped phases.
Photothermal transfer function of dielectric mirrors for precision measurements

The photothermal transfer function from absorbed power incident on a dielectric mirror to the effective mirror position is calculated using the coating design as input. The effect is found to change in amplitude and sign for frequencies corresponding to diffusion length comparable to the coating thickness. Transfer functions are calculated for the $Ti$-doped ${\mathrm{Ta}}_{2}{\mathrm{O}}_{5}:{\mathrm{SiO}}_{2}$ coating used in Advanced LIGO and for a crystalline ${\mathrm{Al}}_{\mathrm{x}}{\mathrm{Ga}}_{1\ensuremath{-}\mathrm{x}}\mathrm{As}$ coating. The shape of the transfer function at high frequencies is shown to be a sensitive indicator of the effective absorption depth, providing a potentially powerful tool to distinguish coating-internal absorption from surface contamination related absorption. The sign change of the photothermal effect could also be useful to stabilize radiation pressure-based optomechanical systems. High frequency corrections to the previously published thermo-optic noise estimates are also provided. Finally, estimating the quality of the thermo-optic noise cancellation occurring in fine-tuned ${\mathrm{Al}}_{\mathrm{x}}{\mathrm{Ga}}_{1\ensuremath{-}\mathrm{x}}\mathrm{As}$ coatings requires the detailed heat flow analysis done in this paper.
Lattice QCD evidence that the Λ(1405) resonance is an antikaon-nucleon molecule.

For almost 50 years the structure of the Λ(1405) resonance has been a mystery. Even though it contains a heavy strange quark and has odd parity, its mass is lower than any other excited spin-1/2 baryon. Dalitz and co-workers speculated that it might be a molecular state of an antikaon bound to a nucleon. However, a standard quark-model structure is also admissible. Although the intervening years have seen considerable effort, there has been no convincing resolution. Here we present a new lattice QCD simulation showing that the strange magnetic form factor of the Λ(1405) vanishes, signaling the formation of an antikaon-nucleon molecule. Together with a Hamiltonian effective-field-theory model analysis of the lattice QCD energy levels, this strongly suggests that the structure is dominated by a bound antikaon-nucleon component. This result clarifies that not all states occurring in nature can be described within a simple quark model framework and points to the existence of exotic molecular meson-nucleon bound states.
Person Re-identification Based on Color Histogram and Spatial Configuration of Dominant Color Regions

There is a requirement to determine whether a given person of interest has already been observed over a network of cameras in video surveillance systems. A human appearance obtained in one camera is usually different from the ones obtained in another camera due to difference in illumination, pose and viewpoint, camera parameters. Being related to appearance-based approaches for person re-identification, we propose a novel method based on the dominant color histogram and spatial configuration of dominant color regions on human body parts. Dominant color histogram and spatial configuration of the dominant color regions based on dominant color descriptor(DCD) can be considered to be robust to illumination and pose, viewpoint changes. The proposed method is evaluated using benchmark video datasets. Experimental results using the cumulative matching characteristic(CMC) curve demonstrate the effectiveness of our approach for person re-identification.