nils-herrmann/clean_scirepeval huggingface dataset:
Panphasia: a user guide

We make a very large realisation of a Gaussian white noise field, called PANPHASIA, public by releasing software that computes this field. Panphasia is designed specifically for setting up Gaussian initial conditions for cosmological simulations and resimulations of structure formation. We make available both software to compute the field itself and codes to illustrate applications including a modified version of a public serial initial conditions generator. We document the software and present the results of a few basic tests of the field. The properties and method of construction of Panphasia are described in full in a companion paper Jenkins 2013.
A State-Space Approach for Optimal Traffic Monitoring via Network Flow Sampling

The robustness and integrity of IP networks require efficient tools for traffic monitoring and analysis, which scale well with traffic volume and network size. We address the problem of optimal large-scale flow monitoring of computer networks under resource constraints. We propose a stochastic optimization framework where traffic measurements are done by exploiting the spatial (across network links) and temporal relationship of traffic flows. Specifically, given the network topology, the state-space characterization of network flows and sampling constraints at each monitoring station, we seek an optimal packet sampling strategy that yields the best traffic volume estimation for all flows of the network. The optimal sampling design is the result of a concave minimization problem; then, Kalman filtering is employed to yield a sequence of traffic estimates for each network flow. We evaluate our algorithm using real-world Internet2 data.
Algorithm independent bounds on community detection problems and associated transitions in stochastic block model graphs

We derive rigorous bounds for well-defined community structure in complex networks for a stochastic block model (SBM) benchmark. In particular, we analyze the effect of inter-community "noise" (inter-community edges) on any "community detection" algorithm's ability to correctly group nodes assigned to a planted partition, a problem which has been proven to be NP complete in a standard rendition. Our result does not rely on the use of any one particular algorithm nor on the analysis of the limitations of inference. Rather, we turn the problem on its head and work backwards to examine when, in the first place, well defined structure may exist in SBMs.The method that we introduce here could potentially be applied to other computational problems. The objective of community detection algorithms is to partition a given network into optimally disjoint subgraphs (or communities). Similar to k-SAT and other combinatorial optimization problems, "community detection" exhibits different phases. Networks that lie in the "unsolvable phase" lack well-defined structure and thus have no partition that is meaningful. Solvable systems splinter into two disparate phases: those in the "hard" phase and those in the "easy" phase. As befits its name, within the easy phase, a partition is easy to achieve by known algorithms. When a network lies in the hard phase, it still has an underlying structure yet finding a meaningful partition which can be checked in polynomial time requires an exhaustive computational effort that rapidly increases with the size of the graph. When taken together, (i) the rigorous results that we report here on when graphs have an underlying structure and (ii) recent results concerning the limits of rather general algorithms, suggest bounds on the hard phase.
Extended QCD

Two milestones on the path to the theory of QCD were the invention of the quark model [1, 2], and the discovery that pions arise as Goldstone bosons due to a chiral symmetry breaking condensate of fermions in the vacuum . The latter phenomenon has been verified in lattice QCD (where the vacuum exhibits a quark condensate, rather than the nucleon condensate originally envisaged), but the quark model remains just a heuristic picture – albeit a successful one – with no direct connection to QCD beyond sharing fermion degrees of freedom and some of the same symmetries. In fact, the quark model, with its massive, weakly interacting quarks, has no realization of chiral symmetry, and no way to explain a massless pion in the chiral limit. An attempt to reconcile the quark model with spontaneously broken chiral symmetry was made in the chiral quark model of Georgi and Manohar  where quarks and gluons coexist with pions at low energy. The model assumes a weak gluon coupling below the chiral symmetry breaking scale in order to explain why constituent quarks appear to be weakly interacting, but results in an unrealistically low confinement scale and light glueballs. The model also does not quantitatively explain what happens to the quark-antiquark bound state with the quantum numbers of the pion, and similarly has not been derived from QCD. Recently the energy range over which this model should apply was extended by invoking the large-Nc expansion , but the basic question of how weakly interacting (yet confined) massive quarks can arise from QCD remains unresolved.
Prehistoric sanctuaries in Daunia

Daunia is a region in northern Apulia with many interesting archaeological sites, particularly of the Neolithic and Bronze Age. Beginning from the fifth millennium BC, the farmers living in the wide plain of Daunia dug hypogea and holes in sites that could be considered prehistoric sanctuaries. The characteristics of the rows of holes indicate a ritual use, and the archaeologists tend to exclude other applications, such as post holes and cultivations. The rows have possibly an astronomical orientation, and in the sanctuary discovered near Ordona, some stars of the Centaurus-Crux group (may be alpha Centauri itself) could have been used as targets. In past centuries, astronomers and scholars have remarked this spectacular region of the sky, and its possible relevance for the ancient civilizations was pointed out for example by G.V. Schiaparelli in 1903. In his work on the astronomy in the Old Testament, he mentioned in particular the observations of the astronomer W.S. Jacob and of other scholars. It would be probably worth to make simulations in order to reproduce the 'Jacob effect', that is the diffused light (a sort of faint twilight) produced by such very rich stellar region of the sky.
Recoil properties of fragments formed in 4.4 GeV deuteron-induced reactions on a gold target

The recoil properties of fragments produced by the interaction of 4.4 GeV deuterons with a ${}^{197}$Au target have been studied. New experimental data on recoil properties for 90 nuclei, varying from ${}^{24}$Na to ${}^{198}$Au, were obtained. The technique applied was the thick-target thick-catcher and induced activity method. The deuteron beam was obtained from the Nuclotron of the Laboratory of High Energies (LHE), Joint Institute for Nuclear Research (JINR), Dubna. The experimental data were analyzed on the basis of the standard two-step vector model formalism. From the analysis of the reaction investigated here, we could find evidence that the cooling process of excited nuclei can be due to the coexistence of different decay modes such as evaporation, fission, and (multi)fragmentation. Fission and multifragmentation can contribute appreciably to the formation of products in the intermediate mass range. The kinematic characteristics of residual nuclei formed in the present deuteron-induced reaction have been compared to those from proton-induced reactions with gold target.
A computational approach to politeness with application to social factors

We propose a computational framework for identifying linguistic aspects of politeness. Our starting point is a new corpus of requests annotated for politeness, which we use to evaluate aspects of politeness theory and to uncover new interactions between politeness markers and context. These findings guide our construction of a classifier with domain-independent lexical and syntactic features operationalizing key components of politeness theory, such as indirection, deference, impersonalization and modality. Our classifier achieves close to human performance and is effective across domains. We use our framework to study the relationship between politeness and social power, showing that polite Wikipedia editors are more likely to achieve high status through elections, but, once elevated, they become less polite. We see a similar negative correlation between politeness and power on Stack Exchange, where users at the top of the reputation scale are less polite than those at the bottom. Finally, we apply our classifier to a preliminary analysis of politeness variation by gender and community.
Proposal for a Cosmic Axion Spin Precession Experiment (CASPEr)

We propose an experiment to search for QCD axion and axionlike-particle dark matter. Nuclei that are interacting with the background axion dark matter acquire time-varying C P -odd nuclear moments such as an electric dipole moment. In analogy with nuclear magnetic resonance, these moments cause precession of nuclear spins in a material sample in the presence of an electric field. Precision magnetometry can be used to search for such precession. An initial phase of this experiment could cover many orders of magnitude in axionlike-particle parameter space beyond the current astrophysical and laboratory limits. And with established techniques, the proposed experimental scheme has sensitivity to QCD axion masses m a ≲ 1 0 - 9 eV , corresponding to theoretically well-motivated axion decay constants f a ≳ 1 0 16 GeV . With further improvements, this experiment could ultimately cover the entire range of masses m a ≲ μ eV , complementary to cavity searches.
Understanding the Predictive Power of Computational Mechanics and Echo State Networks in Social Media

There is a large amount of interest in understanding users of social media in order to predict their behavior in this space. Despite this interest, user predictability in social media is not well-understood. To examine this question, we consider a network of fifteen thousand users on Twitter over a seven week period. We apply two contrasting modeling paradigms: computational mechanics and echo state networks. Both methods attempt to model the behavior of users on the basis of their past behavior. We demonstrate that the behavior of users on Twitter can be well-modeled as processes with self-feedback. We find that the two modeling approaches perform very similarly for most users, but that they differ in performance on a small subset of the users. By exploring the properties of these performance-differentiated users, we highlight the challenges faced in applying predictive models to dynamic social data.
The complex hybrid origins of the root knot nematodes revealed through comparative genomics

Root knot nematodes (RKN) can infect most of the world’s agricultural crop species and are among the most important of all plant pathogens. As yet however we have little understanding of their origins or the genomic basis of their extreme polyphagy. The most damaging pathogens reproduce by obligatory mitotic parthenogenesis and it has been suggested that these species originated from interspecific hybridizations between unknown parental taxa. We have sequenced the genome of the diploid meiotic parthenogen Meloidogyne floridensis, and use a comparative genomic approach to test the hypothesis that this species was involved in the hybrid origin of the tropical mitotic parthenogen Meloidogyne incognita. Phylogenomic analysis of gene families from M. floridensis, M. incognita and an outgroup species Meloidogyne hapla was carried out to trace the evolutionary history of these species’ genomes, and we demonstrate that M. floridensis was one of the parental species in the hybrid origins of M. incognita. Analysis of the M. floridensis genome itself revealed many gene loci present in divergent copies, as they are in M. incognita, indicating that it too had a hybrid origin. The triploid M. incognita is shown to be a complex double-hybrid between M. floridensis and a third, unidentified, parent. The agriculturally important RKN have very complex origins involving the mixing of several parental genomes by hybridization and their extreme polyphagy and success in agricultural environments may be related to this hybridization, producing transgressive variation on which natural selection can act. It is now clear that studying RKN variation via individual marker loci may fail due to the species’ convoluted origins, and multi-species population genomics is essential to understand the hybrid diversity and adaptive variation of this important species complex. This comparative genomic analysis provides a compelling example of the importance and complexity of hybridization in generating animal species diversity more generally.
Two-neutrino double-β decay Fermi transition and two-nucleon interaction

An exactly solvable model for a description of the two-neutrino double beta decay transition of the Fermi type is considered. By using perturbation theory an explicit dependence of the two-neutrino double beta decay matrix element on the like-nucleon pairing, particle-particle and particle-hole proton-neutron interactions by assuming a weak violation of isospin symmetry of Hamiltonian expressed with generators of the SO(5) group. It is found that there is a dominance of double beta decay transition through a single state of the intermediate nucleus. Then, an energy weighted sum rule connecting Delta Z=2 nuclei is presented and discussed. It is suggested that this sum rule can be exploited to study the residual interactions of the nuclear Hamiltonian.
Scaling Up Robust MDPs by Reinforcement Learning

We consider large-scale Markov decision processes (MDPs) with parameter uncertainty, under the robust MDP paradigm. Previous studies showed that robust MDPs, based on a minimax approach to handle uncertainty, can be solved using dynamic programming for small to medium sized problems. However, due to the "curse of dimensionality", MDPs that model real-life problems are typically prohibitively large for such approaches. In this work we employ a reinforcement learning approach to tackle this planning problem: we develop a robust approximate dynamic programming method based on a projected fixed point equation to approximately solve large scale robust MDPs. We show that the proposed method provably succeeds under certain technical conditions, and demonstrate its effectiveness through simulation of an option pricing problem. To the best of our knowledge, this is the first attempt to scale up the robust MDPs paradigm.
A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data

Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this complex information. We present a Bayesian method for inferring the phylogenetic relationship among related organisms found within metagenomic samples. Our approach exploits variation in the frequency of taxa among samples to simultaneously infer each lineage haplotype, the phylogenetic tree connecting them, and their frequency within each sample. Applications of the algorithm to simulated data show that our method can recover a substantial fraction of the phylogenetic structure even in the presence of high rates of migration among sample sites. We provide examples of the method applied to data from green sulfur bacteria recovered from an Antarctic lake, plastids from mixed Plasmodium falciparum infections, and virulent Neisseria meningitidis samples.
Data reliability in complex directed networks

The availability of data from many different sources and fields of science has made it possible to map out an increasing number of networks of contacts and interactions. However, quantifying how reliable these data are remains an open problem. From Biology to Sociology and Economics, the identification of false and missing positives has become a problem that calls for a solution. In this work we extend one of the newest, best performing models—due to Guimerá and Sales-Pardo in 2009—to directed networks. The new methodology is able to identify missing and spurious directed interactions with more precision than previous approaches, which renders it particularly useful for analyzing data reliability in systems like trophic webs, gene regulatory networks, communication patterns and several social systems. We also show, using real-world networks, how the method can be employed to help search for new interactions in an efficient way.
THE INTERNATIONAL LINEAR COLLIDER

In this paper, we describe the key features of the recently completed technical design for the International Linear Collider (ILC), a 200–500 GeV linear electron–positron collider (expandable to 1 TeV) that is based on 1.3 GHz superconducting radio-frequency (SCRF) technology. The machine parameters and detector characteristics have been chosen to complement the Large Hadron Collider physics, including the discovery of the Higgs boson, and to further exploit this new particle physics energy frontier with a precision instrument. The linear collider design is the result of nearly 20 years of R&D, resulting in a mature conceptual design for the ILC project that reflects an international consensus. We summarize the physics goals and capability of the ILC, the enabling R&D and resulting accelerator design, as well as the concepts for two complementary detectors. The ILC is technically ready to be proposed and built as a next generation lepton collider, perhaps to be built in stages beginning as a Higgs factory.
An on-shell approach to factorization

Factorization is possible due to the universal behavior of Yang-Mills theories in soft and collinear limits. Here, we take a small step towards a more transparent understanding of these limits by proving a form of perturbative factorization at tree level using on-shell spinor helicity methods. We present a concrete and self-contained expression of factorization in which matrix elements in QCD are related to products of other matrix elements in QCD up to leading order in a power-counting parameter determined by the momenta of certain physical on-shell states. Our approach uses only the scaling of momenta in soft and collinear limits, avoiding any assignment of scaling behavior to unphysical (and gauge-dependent) fields. The proof of factorization exploits many advantages of helicity spinors, such as the freedom to choose different reference vectors for polarizations in different collinear sectors. An advantage of this approach is that once factorization is shown to hold in QCD, the transition to soft-collinear effective theory is effortless.
Internal bremsstrahlung signatures in light of direct dark matter searches

Although proposed long ago, the search for internal bremsstrahlung signatures has only recently been made possible by the excellent energy resolution of ground-based and satellite-borne gamma-ray instruments. Here, we investigate thoroughly the current status of internal bremsstrahlung searches in light of the results of direct dark matter searches and in the framework of a minimal mass-degenerate scenario consisting of a Majorana dark matter particle that couples to a fermion and a scalar via a Yukawa coupling. The upper limits on the annihilation cross section set by Fermi-LAT and H.E.S.S. extend uninterrupted from tens of GeV up to tens of TeV and are rather insensitive to the mass degeneracy in the particle physics model. In contrast, direct searches are best in the moderate to low mass splitting regime, where XENON100 limits overshadow Fermi-LAT and H.E.S.S. up to TeV masses if dark matter couples to one of the light quarks. In our minimal scenario we examine carefully the prospects for GAMMA-400, CTA and XENON1T, all planned to come online in the near future, and find that: (a) CTA and XENON1T are fully complementary, with CTA most sensitive to multi-TeV masses and mass splittings around 10%, and XENON1T probing best small mass splittingsmore » up to TeV masses; and (b) current constraints from XENON100 already preclude the observation of any spectral feature with GAMMA-400 in spite of its impressive energy resolution, unless dark matter does not couple predominantly to light quarks. Finally, we point out that, unlike for direct searches, the possibility of detecting thermal relics in upcoming internal bremsstrahlung searches requires, depending on the concrete scenario, boost factors larger than 5–10.« less
Social ranking techniques for the web

The proliferation of social media has the potential for changing the structure and organization of the web. In the past, scientists have looked at the web as a large connected component to understand how the topology of hyperlinks correlates with the quality of information contained in the page and they proposed techniques to rank information contained in web pages. We argue that information from web pages and network data on social relationships can be combined to create a personalized and socially connected web. In this paper, we look at the web as a composition of two networks, one consisting of information in web pages and the other of personal data shared on social media web sites. Together, they allow us to analyze how social media tunnels the flow of information from person to person and how to use the structure of the social network to rank, deliver, and organize information specifically for each individual user. We validate our social ranking concepts through a ranking experiment conducted on web pages that users shared on Google Buzz and Twitter.
Metaheuristics in Flood Disaster Management and Risk Assessment

A conceptual area is divided into units or barangays, each was allowed to evolve under a physical constraint. A risk assessment method is then used to identify the flood risk in each community using the following risk factors: the area's urbanized area ratio, literacy rate, mortality rate, poverty incidence, radio/TV penetration, and state of structural and non-structural measures. Vulnerability is defined as a weighted-sum of these components. A „penalty‟ was imposed for reduced vulnerability. Optimization comparison was done with MatLab‟s Genetic Algorithms and Simulated Annealing; Results showed „extreme‟ solutions and realistic designs, for simulated annealing and genetic algorithm, respectively.
The hard hexagon partition function for complex fugacity

We study the analyticity of the partition function of the hard hexagon model in the complex fugacity plane by computing zeros and transfer matrix eigenvalues for large finite size systems. We find that the partition function per site computed by Baxter in the thermodynamic limit for positive real values of the fugacity is not sufficient to describe the analyticity in the full complex fugacity plane. We also obtain a new algebraic equation for the low density partition function per site.