nils-herrmann/clean_scirepeval huggingface dataset:
Dirichlet Process Parsimonious Mixtures for clustering

The parsimonious Gaussian mixture models, which exploit an eigenvalue decomposition of the group covariance matrices of the Gaussian mixture, have shown their success in particular in cluster analysis. Their estimation is in general performed by maximum likelihood estimation and has also been considered from a parametric Bayesian prospective. We propose new Dirichlet Process Parsimonious mixtures (DPPM) which represent a Bayesian nonparametric formulation of these parsimonious Gaussian mixture models. The proposed DPPM models are Bayesian nonparametric parsimonious mixture models that allow to simultaneously infer the model parameters, the optimal number of mixture components and the optimal parsimonious mixture structure from the data. We develop a Gibbs sampling technique for maximum a posteriori (MAP) estimation of the developed DPMM models and provide a Bayesian model selection framework by using Bayes factors. We apply them to cluster simulated data and real data sets, and compare them to the standard parsimonious mixture models. The obtained results highlight the effectiveness of the proposed nonparametric parsimonious mixture models as a good nonparametric alternative for the parametric parsimonious models.
Gravitational waves from periodic three-body systems.

Three bodies moving in a periodic orbit under the influence of Newtonian gravity ought to emit gravitational waves. We have calculated the gravitational radiation quadrupolar waveforms and the corresponding luminosities for the 13+11 recently discovered three-body periodic orbits in Newtonian gravity. These waves clearly allow one to distinguish between their sources: all 13+11 orbits have different waveforms and their luminosities (evaluated at the same orbit energy and body mass) vary by up to 13 orders of magnitude in the mean, and up to 20 orders of magnitude for the peak values.
Calculating tumor trajectory and dose-of-the-day using cone-beam CT projections.

Cone-beam CT (CBCT) projection images provide anatomical data in real-time over several respiratory cycles, forming a comprehensive picture of tumor movement. The authors developed and validated a method which uses these projections to determine the trajectory of and dose to highly mobile tumors during each fraction of treatment.



CBCT images of a respiration phantom were acquired, the trajectory of which mimicked a lung tumor with high amplitude (up to 2.5 cm) and hysteresis. A template-matching algorithm was used to identify the location of a steel BB in each CBCT projection, and a Gaussian probability density function for the absolute BB position was calculated which best fit the observed trajectory of the BB in the imager geometry. Two modifications of the trajectory reconstruction were investigated: first, using respiratory phase information to refine the trajectory estimation (Phase), and second, using the Monte Carlo (MC) method to sample the estimated Gaussian tumor position distribution. The accuracies of the proposed methods were evaluated by comparing the known and calculated BB trajectories in phantom-simulated clinical scenarios using abdominal tumor volumes.



With all methods, the mean position of the BB was determined with accuracy better than 0.1 mm, and root-mean-square trajectory errors averaged 3.8% ± 1.1% of the marker amplitude. Dosimetric calculations using Phase methods were more accurate, with mean absolute error less than 0.5%, and with error less than 1% in the highest-noise trajectory. MC-based trajectories prevent the overestimation of dose, but when viewed in an absolute sense, add a small amount of dosimetric error (<0.1%).



Marker trajectory and target dose-of-the-day were accurately calculated using CBCT projections. This technique provides a method to evaluate highly mobile tumors using ordinary CBCT data, and could facilitate better strategies to mitigate or compensate for motion during stereotactic body radiotherapy.
Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans

Large-scale neural recordings in freely moving animals are important for understanding how patterns of activity across a population of neurons generates animal behavior. Previously, recordings have been limited to either small brain regions or to immobilized or anesthetized animals exhibiting limited behavior. This work records from neurons with cellular resolution throughout the entire brain of the nematode Caenorhabditis elegans during free locomotion. Neurons are found whose activity correlates with behaviors including forward and backward locomotion and turning. A growing body of evidence suggests that animal behavior is sometimes generated by the collective activity of many neurons. It is hoped that methods like this will provide quantitative datasets that yield insights into how brain-wide neural dynamics encode animal action and perception. The ability to acquire large-scale recordings of neuronal activity in awake and unrestrained animals is needed to provide new insights into how populations of neurons generate animal behavior. We present an instrument capable of recording intracellular calcium transients from the majority of neurons in the head of a freely behaving Caenorhabditis elegans with cellular resolution while simultaneously recording the animal’s position, posture, and locomotion. This instrument provides whole-brain imaging with cellular resolution in an unrestrained and behaving animal. We use spinning-disk confocal microscopy to capture 3D volumetric fluorescent images of neurons expressing the calcium indicator GCaMP6s at 6 head-volumes/s. A suite of three cameras monitor neuronal fluorescence and the animal’s position and orientation. Custom software tracks the 3D position of the animal’s head in real time and two feedback loops adjust a motorized stage and objective to keep the animal’s head within the field of view as the animal roams freely. We observe calcium transients from up to 77 neurons for over 4 min and correlate this activity with the animal’s behavior. We characterize noise in the system due to animal motion and show that, across worms, multiple neurons show significant correlations with modes of behavior corresponding to forward, backward, and turning locomotion.
A Superintroduction to Google Matrices for Undergraduates

In this paper we consider so-called Google matrices and show that all eigenvalues ($\lambda$) of them have a fundamental property $|\lambda|\leq 1$. The stochastic eigenvector corresponding to $\lambda=1$ called the PageRank vector plays a central role in the Google's software. We study it in detail and present some important problems. 
The purpose of the paper is to make {\bf the heart of Google} clearer for undergraduates.
Correction: Computational Fact Checking from Knowledge Networks

There is an error in the last sentence of the “Validation on factual statements” section of the Results. The sentence should read: With this method we estimate that, in the four subject areas, true statements are assigned higher truth values than false ones with probability 95%, 98%, 100%, and 95%, respectively. 
 
Fig 4 is incorrect. Please view the corrected figure below. 
 
 
 
Fig 4 
 
Receiver Operating Characteristic for the multiple questions task. 
 
 
 
For each confusion matrix depicted in Fig 3 we compute ROC curves where true statements correspond to the diagonal and false statements to off-diagonal elements. The red dashed line represents the performance of a random classifier.
Thermodynamic aspects of dark energy fluids

In this paper we have investigated the limits imposed by thermodynamics on a dark energy fluid. We have obtained the heat capacities and the compressibilities for a dark energy fluid. The thermal and mechanical stabilities require these quantities to be positive. We have shown that dark energy fluids must satisfy the stability conditions and that such requirement put difficulties in the cosmic fluid models with negative constant EoS parameters. We have also shown that the observational constraints imposed by SN Ia, BAO and $H(z)$ data on a general dark energy fluid with a time-dependent EoS parameter are in conflict with the constraints imposed by thermodynamics. This result indicates that dark energy fluid models are unphysical.
Direct Dark Matter Search with XENON100

The XENON100 experiment is the second phase of the XENON program for the direct detection of the dark matter in the universe. The XENON100 detector is a two-phase Time Projection Chamber filled with 161 kg of ultra pure liquid xenon. The results from 224.6 live days of dark matter search with XENON100 are presented. No evidence for dark matter in the form of WIMPs is found, excluding spin-independent WIMP-nucleon scattering cross sections above 2 $\times$ 10$^{-45}$ cm$^2$ for a 55 GeV/c$^2$ WIMP at 90% confidence level (C.L.). The most stringent limit is established on the spin-dependent WIMP-neutron interaction for WIMP masses above 6 GeV/c$^2$, with a minimum cross section of 3.5 $\times$ 10$^{-40}$ cm$^2$ (90% C.L.) for a 45 GeV/c$^2$ WIMP. The same dataset is used to search for axions and axion-like-particles. The best limits to date are set on the axion-electron coupling constant for solar axions, $g_{Ae}$ < 7.7 $\times$ 10$^{-12}$ (90% C.L.), and for axion-like-particles, $g_{Ae}$ < 1 $\times$ 10$^{-12}$ (90% C.L.) for masses between 5 and 10 keV/c$^2$.
Dispersionless spin waves in Gadolinium Gallium Garnet

We report the results of neutron scattering on a powder sample of Gd3Ga5O12 at high magnetic fields. We find that in high fields (B & 1.8 T) the system is not fully polarized, but has a small canting of the moments induced by the dipolar interaction. We show that the degree of canting is accurately predicted by the standard Hamiltonian which includes the dipolar interaction. The inelastic scattering is dominated at large momentum transfers by a band of almost dispersionless excitations. We show that these correspond to the spin waves localized on ten site rings, expected for a system described by a nearest neighbor interaction, and that the spectrum at high fields B & 1.8 T is well-described by a spin wave theory. The phase for fields . 1.8 T is characterized by an antiferromagnetic Bragg peak at (210) and an incommensurate peak.
3.55 keV line from exciting dark matter without a hidden sector

In this study, models in which dark matter particles can scatter into a slightly heavier state which promptly decays to the lighter state and a photon (known as eXciting Dark Matter, or XDM) have been shown to be capable of generating the 3.55 keV line observed from galaxy clusters, while suppressing the flux of such a line from smaller halos, including dwarf galaxies. In most of the XDM models discussed in the literature, this up-scattering is mediated by a new light particle, and dark matter annihilations proceed into pairs of this same light state. In these models, the dark matter and the mediator effectively reside within a hidden sector, without sizable couplings to the Standard Model. In this paper, we explore a model of XDM that does not include a hidden sector. Instead, the dark matter both up-scatters and annihilates through the near resonant exchange of an O(102) GeV pseudoscalar with large Yukawa couplings to the dark matter and smaller, but non-neglibile, couplings to Standard Model fermions. The dark matter and the mediator are each mixtures of Standard Model singlets and SU(2)W doublets. We identify parameter space in which this model can simultaneously generate the 3.55 keV line and the gamma-ray excessmore » observed from the Galactic center, without conflicting with constraints from colliders, direct detection experiments, or observations of dwarf galaxies.« less
A Bayesian method for pulsar template generation

Extracting Times of Arrival from pulsar radio signals depends on the knowledge of the pulsars pulse profile and how this template is generated. We examine pulsar template generation with Bayesian methods. We will contrast the classical generation mechanism of averaging intensity profiles with a new approach based on Bayesian inference. We introduce the Bayesian measurement model imposed and derive the algorithm to reconstruct a "statistical template" out of noisy data. The properties of these "statistical templates" are analysed with simulated and real measurement data from PSR B1133+16. We explain how to put this new form of template to use in analysing secondary parameters of interest and give various examples: We implement a nonlinear filter for determining ToAs of pulsars. Applying this method to data from PSR J1713+0747 we derive ToAs self consistently, meaning all epochs were timed and we used the same epochs for template generation. While the average template contains fluctuations and noise as unavoidable artifacts, we find that the "statistical template" derived by Bayesian inference quantifies fluctuations and remaining uncertainty. This is why the algorithm suggested turns out to reconstruct templates of statistical significance from ten to fifty single pulses. A moving data window of fifty pulses, taking out one single pulse at the beginning and adding one at the end of the window unravels the characteristics of the methods to be compared. It shows that the change induced in the classical reconstruction is dominated by random fluctuations for the average template, while statistically significant changes drive the dynamics of the proposed method's reconstruction. The analysis of phase shifts with simulated data reveals that the proposed nonlinear algorithm is able to reconstruct correct phase information along with an acceptable estimation of the remaining uncertainty.
Probing Precise Location of Radio Core in TeV Blazar Mrk 501 with VERA at 43 GHz

We investigate the position of the radio core in a blazar by multi-epoch astrometric observations at 43 GHz. Using the VLBI Exploration of Radio Astrometry (VERA), we have conducted four adjacent observations in February 2011 and another four in October 2011, and succeeded in measuring the position of the radio core in the TeV blazar Mrk 501 relative to a distant compact quasar NRAO 512. During our observations, we find that (1) there is no positional change within ~0.2 mas or ~2.0 pc de-projected with $\pm1\sigma$ error for the weighted-mean phase-referenced positions of Mrk 501 core relative to NRAO 512 over four adjacent days, and (2) there is an indication of position change for 3C 345 core relative to NRAO 512. By applying our results to the standard internal shock model for blazars, we constrain the bulk Lorenz factors of the ejecta.
Phonon-assisted gain in a semiconductor double quantum dot maser.

We develop a microscopic model for the recently demonstrated double-quantum-dot maser. In characterizing the gain of this device we find that, in addition to the direct stimulated emission of photons, there is a large contribution from the simultaneous emission of a photon and a phonon, i.e., the phonon sideband. We show that this phonon-assisted gain typically dominates the overall gain, which leads to masing. Recent experimental data are well fit with our model.
Universal properties of many-body delocalization transitions

We study the dynamical melting of "hot" one-dimensional many-body localized systems. As disorder is weakened below a critical value these non-thermal quantum glasses melt via a continuous dynamical phase transition into classical thermal liquids. By accounting for collective resonant tunneling processes, we derive and numerically solve an effective model for such quantum-to-classical transitions and compute their universal critical properties. Notably, the classical thermal liquid exhibits a broad regime of anomalously slow sub-diffusive equilibration dynamics and energy transport. The subdiffusive regime is characterized by a continuously evolving dynamical critical exponent that diverges with a universal power at the transition. Our approach elucidates the universal long-distance, low-energy scaling structure of many-body delocalization transitions in one dimension, in a way that is transparently connected to the underlying microscopic physics.
Galactic center excess in γ rays from annihilation of self-interacting dark matter.

Observations by the Fermi Large-Area Telescope have uncovered a significant γ-ray excess directed toward the Milky Way Galactic Center. There has been no detection of a similar signal in the stacked population of Milky Way dwarf spheroidal galaxies. Additionally, astronomical observations indicate that dwarf galaxies and other faint galaxies are less dense than predicted by the simplest cold dark matter models. We show that a self-interacting dark matter model with a particle mass of roughly 50 GeV annihilating to the mediator responsible for the strong self-interaction can simultaneously explain all three observations. The mediator is necessarily unstable, and its mass must be below about 100 MeV in order to decrease the dark matter density of faint galaxies. If the mediator decays to electron-positron pairs with a cross section on the order of the thermal relic value, then we find that these pairs can up-scatter the interstellar radiation field in the Galactic center and produce the observed γ-ray excess.
Two-dimensional Valence Bond Solid (AKLT) states from t2g electrons

Si· ~ Sj) n , making these states seemingly unrealistic on bipartite lattices, where one expects a simple antiferromagnetic order. We show that those interactions can be generated by orbital physics in multiorbital Mott insulators. We focus on t2g electrons on the honeycomb lattice and propose a physical realization of the spin-3/2 AKLT state. We find a phase transition from the AKLT to the Neel state on increasing Hund’s rule coupling, which is confirmed by density matrix renormalization group (DMRG) simulations. An experimental signature of the AKLT state consists of protected, free spins-1/2 on lattice vacancies, which may be detected in the spin susceptibility.
Phases of d-orbital bosons in optical lattices

We explore the properties of bosonic atoms loaded into the d bands of an isotropic square optical lattice. Following the recent experimental success reported in Zhai et al (2013 ), in which populating d bands with a 99 % ?> fidelity was demonstrated, we present a theoretical study of the possible phases that can appear in this system. Using the Gutzwiller ansatz for the three d band orbitals we map the boundaries of the Mott insulating phases. For not too large occupation, two of the orbitals are predominantly occupied, while the third, of a slightly higher energy, remains almost unpopulated. In this regime, in the superfluid phase we find the formation of a vortex lattice, where the vortices come in vortex/anti-vortex pairs with two pairs locked to every site. Due to the orientation of the vortices time-reversal symmetry is spontaneously broken. This state also breaks a discrete Z 2 ?> -symmetry. We further derive an effective spin-1/2 model that describe the relevant physics of the lowest Mott-phase with unit filling. We argue that the corresponding two dimensional phase diagram should be rich with several different phases. We also explain how to generate anti-symmetric spin interactions that can give rise to novel effects like spin canting.
High energy physics signatures from inflation and conformal symmetry of de Sitter

During inflation, the geometry of spacetime is described by a (quasi‐)de Sitter phase. Inflationary observables are determined by the underlying (softly broken) de Sitter isometry group SO(1,4) which acts like a conformal group on R3 : when the fluctuations are on super‐Hubble scales, the correlators of the scalar fields are constrained by conformal invariance. Heavy fields with mass m larger than the Hubble rate H correspond to operators with imaginary dimensions in the dual Euclidean three‐dimensional conformal field theory. By making use of the dS/CFT correspondence we show that, besides the Boltzmann suppression expected from the thermal properties of de Sitter space, the generic effect of heavy fields in the inflationary correlators of the light fields is to introduce power‐law suppressed corrections of the form O(H2/m2) . This can be seen, for instance, at the level of the four‐point correlator for which we provide the correction due to a massive scalar field exchange.
Bell on Bell's theorem: The changing face of nonlocality

Between 1964 and 1990, the notion of nonlocality in Bell's papers underwent a profound change as his nonlocality theorem gradually became detached from quantum mechanics, and referred to wider probabilistic theories involving correlations between separated beables. The proposition that standard quantum mechanics is itself nonlocal (more precisely, that it violates `local causality') became divorced from the Bell theorem per se from 1976 on, although this important point is widely overlooked in the literature. In 1990, the year of his death, Bell would express serious misgivings about the mathematical form of the local causality condition, and leave ill-defined the issue of the consistency between special relativity and violation of the Bell-type inequality. In our view, the significance of the Bell theorem, both in its deterministic and stochastic forms, can only be fully understood by taking into account the fact that a fully Lorentz-covariant version of quantum theory, free of action-at-a-distance, can be articulated in the Everett interpretation.
The Roberts–(A)dS spacetime

Global structure of the (anti-)de Sitter ((A)dS) generalization of the Roberts solution in general relativity with a massless scalar field and its topological generalization are clarified. In the case with a negative cosmological constant, the spacetime is asymptotically locally AdS and it contains a black-hole event horizon depending on the parameters. The spacetime may be attached to the exact AdS spacetime in a regular manner on a null hypersurface and the resulting spacetime represents gravitational collapse from a regular initial datum. The higher-dimensional counterpart of this Roberts–(A)dS solution with a flat base manifold is also given.
Pattern formation in a minimal model of continuum dislocation plasticity

The spontaneous emergence of heterogeneous dislocation patterns is a conspicuous feature of plastic deformation and strain hardening of crystalline solids. Despite long-standing efforts in the materials science and physics of defect communities, there is no general consensus regarding the physical mechanism which leads to the formation of dislocation patterns. In order to establish the fundamental mechanism, we formulate an extremely simplified, minimal model to investigate the formation of patterns based on the continuum theory of fluxes of curved dislocations. We demonstrate that strain hardening as embodied in a Taylor-type dislocation density dependence of the flow stress, in conjunction with the structure of the kinematic equations that govern dislocation motion under the action of external stresses, is already sufficient for the formation of dislocation patterns that are consistent with the principle of similitude.
Power-efficient production of photon pairs in a tapered chalcogenide microwire

Using tapered fibers of As2Se3 chalcogenide glass, we produce photon pairs at telecommunication wavelengths with low pump powers. We found maximum coincidences-to-accidentals ratios of $2.13\pm0.07$ for degenerate pumping with 3.2 {\mu}W average power, and $1.33\pm0.03$ for non-degenerate pumping with 1.0 {\mu}W and 1.5 {\mu}W average power of the two pumps. Our results show that the ultrahigh nonlinearity in these microwires could allow single-photon pumping to produce photon pairs, enabling the production of large entangled states, heralding of single photons after lossy transmission, and photonic quantum information processing with nonlinear optics.