nils-herrmann/clean_scirepeval huggingface dataset:
A Supervised Neural Autoregressive Topic Model for Simultaneous Image Classification and Annotation

Topic modeling based on latent Dirichlet allocation (LDA) has been a framework of choice to perform scene recognition and annotation. Recently, a new type of topic model called the Document Neural Autoregressive Distribution Estimator (DocNADE) was proposed and demonstrated state-of-the-art performance for document modeling. In this work, we show how to successfully apply and extend this model to the context of visual scene modeling. Specifically, we propose SupDocNADE, a supervised extension of DocNADE, that increases the discriminative power of the hidden topic features by incorporating label information into the training objective of the model. We also describe how to leverage information about the spatial position of the visual words and how to embed additional image annotations, so as to simultaneously perform image classification and annotation. We test our model on the Scene15, LabelMe and UIUC-Sports datasets and show that it compares favorably to other topic models such as the supervised variant of LDA.
Minimal fine tuning in supersymmetric Higgs inflation

We investigate characteristic features of a realistic parameter choice for primordial inflation with the supersymmetric Higgs inflaton as an example of a particle physics inflation model. We discuss constraints from observational results and analyze the degree of fine tuning needed to induce slow-roll inflation for a wide range of soft supersymmetry-breaking scales. The observed amplitude of density fluctuations implies that the minimal fine tuning for the combined electroweak scale and inflaton flatness predicts a spectral index of n(s) = 0.950 - 0.965, which includes the central value from observational data.
Quantum simulations of the early universe

A procedure is described whereby a linearly coupled spinor Bose condensate can be used as a physically accessible quantum simulator of the early universe. In particular, an experiment to generate an analog of an unstable vacuum in a relativistic scalar field theory is proposed. This is related to quantum theories of the inflationary phase of the early universe. There is an unstable vacuum sector whose dynamics correspond to the quantum sine‐Gordon equations in one, two or three space dimensions. Numerical simulations of the expected behavior are reported using a truncated Wigner phase‐space method, giving evidence for the dynamical formation of complex spatial clusters. Preliminary results showing the dependence on coupling strength, condensate size and dimensionality are obtained.
Narrowing the gap on heritability of common disease by direct estimation in case-control GWAS

One of the major developments in recent years in the search for missing heritability of human phenotypes is the adoption of linear mixed-effects models (LMMs) to estimate heritability due to genetic variants which are not significantly associated with the phenotype. A variant of the LMM approach has been adapted to case-control studies and applied to many major diseases by Lee et al. (2011), successfully accounting for a considerable portion of the missing heritability. For example, for Crohn's disease their estimated heritability was 22% compared to 50-60% from family studies. In this letter we propose to estimate heritability of disease directly by regression of phenotype similarities on genotype correlations, corrected to account for ascertainment. We refer to this method as genetic correlation regression (GCR). Using GCR we estimate the heritability of Crohn's disease at 34% using the same data. We demonstrate through extensive simulation that our method yields unbiased heritability estimates, which are consistently higher than LMM estimates. Moreover, we develop a heuristic correction to LMM estimates, which can be applied to published LMM results. Applying our heuristic correction increases the estimated heritability of multiple sclerosis from 30% to 52.6%.
Band structure in the polymer quantization of the harmonic oscillator

We discuss the detailed structure of the spectrum of the Hamiltonian for the polymerized harmonic oscillator and compare it with the spectrum in the standard quantization. As we will see the non-separability of the Hilbert space implies that the point spectrum consists of bands similar to the ones appearing in the treatment of periodic potentials. This feature of the spectrum of the polymeric harmonic oscillator may be relevant for the discussion of the polymer quantization of the scalar field and may have interesting consequences for the statistical mechanics of these models.
Toward a model-independent constraint of the high-density dependence of the symmetry energy

Neutron-proton elliptic flow difference and ratio have been shown to be promising observables in the attempt to constrain the density dependence of the symmetry energy above the saturation point from heavy-ion collision data. Their dependence on model parameters such as microscopic nucleon-nucleon cross sections, compressibility of nuclear matter, optical potential, and symmetry energy parametrization is thoroughly studied. By using a parametrization of the symmetry energy derived from the momentum-dependent Gogny force in conjunction with the T\"ubingen quantum molecular dynamics (QMD) model and comparing the results with the experimental FOPI-LAND data for ${}^{197}$Au +${}^{197}$Au collisions at 400 MeV/nucleon, a moderately stiff (${L}_{\mathrm{sym}}=122\ifmmode\pm\else\textpm\fi{}57$ MeV and ${K}_{\mathrm{sym}}=229\ifmmode\pm\else\textpm\fi{}363$ MeV) symmetry energy is extracted, a result that agrees with that of a similar study that employed the UrQMD transport model and a power-law parametrization of the symmetry energy. This contrasts with diverging results extracted from the FOPI ${\ensuremath{\pi}}^{\ensuremath{-}}/{\ensuremath{\pi}}^{+}$ ratio available in the literature.
Dilepton Measurements at STAR

In the study of hot and dense nuclear matter, created in relativistic heavy-ion collisions, dilepton measurements play an essential role. Leptons, when compared to hadrons, have only little interaction with the strongly interacting system. Thus, dileptons provide ideal penetrating probes that allow the study of such a system throughout its space-time evolution. In the low mass range (Mll < 1.1 GeV/c2), the dominant source of dileptons originates from the decay of vector mesons which may see effects from chiral symmetry restoration. In the intermediate mass range (1.1 < Mll < 3.0 GeV/c2), the main contributions to the mass spectrum are expected to originate from the thermal radiation of a quark-gluon plasma as well as the decays of charm mesons. In the high mass range (Mll > 3.0 GeV/c2), dilepton measurements are expected to see contributions from primordial processes involving heavy quarks, and Drell-Yan production. With the introduction of the Time-of-Flight detector, the STAR detector has been able to perform large acceptance, high purity electron identification. In this contribution, we will present STAR's recent dielectron measurements in the low and intermediate mass range for RHIC beam energies ranging between 19.6 and 200 GeV. Compared to electrons, muon measurements have the advantage of reduced bremsstrahlung radiation in the surrounding detector materials. With the upcoming detector upgrades, specifically the muon detector (MTD), STAR will be able to include such measurements in its (di-)lepton studies. We will discuss the future dilepton program at STAR and the physics cases for these upgrades.
On the Importance of Conceptual Thinking Outside the Simulation Box

Any ambitious construction project requires architects for its design and engineers who apply the design to the real world. As scientific research shifts towards large groups which focus on the engineering aspects of linking data to existing models, architectural skills are becoming rare among young theorists. Senior researchers should mentor qualified students and postdocs to think creatively about the big picture without unwarranted loyalty to ancient blueprints from past generations of architects.
Ursa Major II – reproducing the observed properties through tidal disruption

Recent deep photometry of the dwarf spheroidal Ursa Major II's morphology, and spectroscopy of individual stars, have provided a number of new constraints on its properties. With a velocity dispersion $\sim$6 km s$^{-1}$, and under the assumption that the galaxy is virialised, the mass-to-light ratio is found to be approaching $\sim$2000 - apparently heavily dark matter dominated. Using N-Body simulations, we demonstrate that the observed luminosity, ellipticity, irregular morphology, velocity gradient, and the velocity dispersion can be well reproduced through processes associated with tidal mass loss, and in the absence of dark matter. These results highlight the considerable uncertainty that exists in measurements of the dark matter content of Ursa Major II. The dynamics of the inner tidal tails, and tidal stream, causes the observed velocity dispersion of stars to be boosted to values of $>$5 km s$^{-1}$ ($>$20 km s$^{-1}$ at times). This effect is responsible for raising the velocity dispersion of our model to the observed values in UMaII. We test an iterative rejection technique for removing unbound stars from samples of UMaII stars whose positions on the sky, and line-of-sight velocities, are provided. We find this technique is very effective at providing an accurate bound mass from this information, and only fails when the galaxy has a bound mass less than 10$%$ of its initial mass. However when $ $3 orders of magnitude are seen. Additionally we find that mass measurements are sensitive to measurement uncertainty in line-of-sight velocities. Measurement uncertainties of 1-4 km s$^{-1}$ result in mass overestimates by a factor of $\sim$1.3-5.7.
Neutrino mass hierarchy determination with IceCube-PINGU

We discuss the neutrino mass hierarchy determination with atmospheric neutrinos in PINGU (\Precision IceCube Next Generation Upgrade"), based on a simulation with the GLoBES software including the full three avor framework and parameter degeneracy, and we compare it to long-baseline experiment options. We demonstrate that the atmospheric mass hierarchy sensitivity depends on the achievable experiment properties and we identify the main targets for optimization, whereas the impact of a large number of tested systematical errors turns out to be small. Depending on the values of 23, , and the true hierarchy, a 90%CL to 3 discovery after three years of operation seems conceivable. We also emphasize the synergy with existing beam and reactor experiments, driven by NO A, such as the complementary coverage of the parameter space. Finally, we point out that a low intensity neutrino beam with a relatively short decay pipe could be used to determine the mass hierarchy with a sensitivity comparable to the LBNE experiment irrespective of the directional resolution of the detector.
All the shapes of spaces: a census of small 3-manifolds

In this work we present a complete (no misses, no duplicates) census for closed, connected, orientable and prime 3-manifolds induced by plane graphs with a bipartition of its edge set (blinks) up to $k=9$ edges. Blinks form a universal encoding for such manifolds. In fact, each such a manifold is a subtle class of blinks, \cite{lins2013B}. Blinks are in 1-1 correpondence with {\em blackboard framed links}, \cite {kauffman1991knots, kauffman1994tlr} We hope that this census becomes as useful for the study of concrete examples of 3-manifolds as the tables of knots are in the study of knots and links.
Diurnal astronomy: using sticks and threads to find our latitude on Earth

It is well known that the length and orientation of a shadow cast by a vertical gnomon depends on the time of the day and on the season of the year. But it also depends on the latitude of the site of observation. During the equinoxes, the temporal sequence of the shadows cast by each of the points that form any object follows a straight line from west to east. A simple construction using sticks and threads can be used to materialize the plane of celestial equator's local projection, giving us a way to calculate our astronomical latitude during daytime with high precision.
Computing the hadronic vacuum polarization function by analytic continuation

We propose a method to compute the hadronic vacuum polarization function on the lattice at continuous values of photon momenta bridging between the spacelike and timelike regions. We provide two independent demonstrations to show that this method leads to the desired hadronic vacuum polarization function in Minkowski spacetime. We present with the example of the leading-order QCD correction to the muon anomalous magnetic moment that this approach can provide a valuable alternative method for calculations of physical quantities where the hadronic vacuum polarization function enters.
Model-Free CPPI

We consider Constant Proportion Portfolio Insurance (CPPI) and its dynamic extension, which may be called Dynamic Proportion Portfolio Insurance (DPPI). It is shown that these investment strategies work within the setting of Follmer's pathwise Ito calculus, which makes no probabilistic assumptions whatsoever. This shows, on one hand, that CPPI and DPPI are completely independent of any choice of a particular model for the dynamics of asset prices. They even make sense beyond the class of semimartingale sample paths and can be successfully defined for models admitting arbitrage, including some models based on fractional Brownian motion. On the other hand, the result can be seen as a case study for the general issue of robustness in the face of model uncertainty in finance.
Fluctuation analysis of the three agent groups herding model

We derive a system of stochastic differential equations simulating the dynamics of the three agent groups with herding interaction. Proposed approach can be valuable in the modeling of the complex socio-economic systems with similar composition of the agents. We demonstrate how the sophisticated statistical features of the absolute return in the financial markets can be reproduced by extending the herding interaction of the agents and introducing the third agent state. As well we consider possible extension of proposed herding model introducing additional exogenous noise. Such consistent microscopic and macroscopic model precisely reproduces empirical power law statistics of the return in the financial markets.
A Robust Version of Convex Integral Functionals

We study the pointwise supremum of convex integral functionals $\mathcal{I}_{f,\gamma}(\xi)= \sup_{Q} \left( \int_\Omega f(\omega,\xi(\omega))Q(d\omega)-\gamma(Q)\right)$ on $L^\infty(\Omega,\mathcal{F},\mathbb{P})$ where $f:\Omega\times\mathbb{R}\rightarrow\overline{\mathbb{R}}$ is a proper normal convex integrand, $\gamma$ is a proper convex function on the set of probability measures absolutely continuous w.r.t. $\mathbb{P}$, and the supremum is taken over all such measures. We give a pair of upper and lower bounds for the conjugate of $\mathcal{I}_{f,\gamma}$ as direct sums of a common regular part and respective singular parts; they coincide when $\mathrm{dom}(\gamma)=\{\mathbb{P}\}$ as Rockafellar's result, while both inequalities can generally be strict. We then investigate when the conjugate eliminates the singular measures, which a fortiori yields the equality in bounds, and its relation to other finer regularity properties of the original functional and of the conjugate.
Semi-bounded Rationality: A model for decision making

In this paper the theory of semi-bounded rationality is proposed as an extension of the theory of bounded rationality. In particular, it is proposed that a decision making process involves two components and these are the correlation machine, which estimates missing values, and the causal machine, which relates the cause to the effect. Rational decision making involves using information which is almost always imperfect and incomplete as well as some intelligent machine which if it is a human being is inconsistent to make decisions. In the theory of bounded rationality this decision is made irrespective of the fact that the information to be used is incomplete and imperfect and the human brain is inconsistent and thus this decision that is to be made is taken within the bounds of these limitations. In the theory of semi-bounded rationality, signal processing is used to filter noise and outliers in the information and the correlation machine is applied to complete the missing information and artificial intelligence is used to make more consistent decisions.
Augmenting transcriptome assembly combinatorially

RNA-seq allows detection and precise quantification of transcripts, provides comprehensive understanding of exon/intron boundaries, aids discovery of alternatively spliced isoforms and fusion transcripts along with measurement of allele-specific expression. Researchers interested in studying and constructing transcriptomes, especially for non-model species, often face the conundrum of choosing from a number of available de novo and genome-guided assemblers. A comprehensive comparative study is required to assess and evaluate their efficiency and sensitivity for transcript assembly, reconstruction and recovery. None of the popular assembly tools in use today achieves requisite sensitivity, specificity or recovery of full-length transcripts on its own. Hence, it is imperative that methods be developed in order to augment assemblies generated from multiple tools, with minimal compounding of error. Here, we present an approach to combinatorially augment transciptome assembly based on a rigorous comparative study of popular de novo and genome-guided transcriptome assembly tools.
AdS/CFT for accelerator physics

The crucial property of particle colliders is their ability to convert (e.g. electrical) energy into the mass of heavy particles. We have become used to the extremely low efficiency of this conversion and the severe limitations on the mass scale of heavy particles which can be reached. In view of this situation, it appears reasonable to ask whether a perfect conversion machine of this type (a perfect `collider') exists even in principle and whether there is a highest mass scale which can be reached by such a machine. It turns out that, with a number of assumptions, such a machine is conceivable in a world with a strongly-coupled, approximately scale invariant 4d field theory with 5d gravity dual. This machine can be realized as a 5d tower built on the IR brane (in Randall-Sundrum model language). Transporting mass to the tip of this tower is, under certain conditions, equivalent to producing heavy point-like 4d particles. Hence, this can be thought of as a perfect `collider'. In the simple, `pure Randall-Sundrum setting' that we analyse, this machine can only reach a certain maximal energy scale, which falls as the gravity-dual of the 4d QFT approaches the strong coupling domain. On these grounds, one might expect that a no-go theorem (in the spirit of that of Carnot for the conversion of heat into work) exists for weakly-coupled QFTs. We end with some speculations about collider efficiencies at weak coupling, involving possibly the concept of entanglement entropy.
Quark (Anti) Nugget Dark Matter

Prepared for Snowmass 2013  We review a testable dark matter model outside of the standard WIMP paradigm in which the observed ratio Omega_{dark} ~ 5 Omega_{visible} for visible and dark matter densities finds its natural explanation as a result of their common QCD origin. Special emphasis is placed on the observational consequences of this model and on the detection prospects for present or planned experiments. In particular, we argue that the relative intensities for a number of observed excesses of emission (covering more than 11 orders of magnitude) can be explained by this model without any new fundamental parameters as all relative intensities for these emissions are determined by standard and well established physics.
Multi-core Computation of Transfer Matrices for Strip Lattices in the Potts Model

The transfer-matrix technique is a convenient way for studying strip lattices in the Potts model since the computational costs depend just on the periodic part of the lattice and not on the whole. However, even when the cost is reduced, the transfer-matrix technique is still an NP-hard problem since the time T (|V |, |E|) needed to compute the matrix grows exponentially as a function of the graph width. In this work, we present a parallel transfer-matrix implementation that scales performance under multi-core architectures. The construction of the matrix is based on several repetitions of the deletion-contraction technique, allowing parallelism suitable to multi-core machines. Our experimental results show that the multi-core implementation achieves speedups of 3.7X with p = 4 processors and 5.7X with p = 8. The efficiency of the implementation lies between 60% and 95%, achieving the best balance of speedup and efficiency at p = 4 processors for actual multi-core architectures. The algorithm also takes advantage of the lattice symmetry, making the transfer matrix computation to run up to 2X faster than its non-symmetric counterpart and use up to a quarter of the original space.
How well do we need to measure the Higgs boson mass and self-coupling?

Much of the discussion regarding future measurements of the Higgs boson mass and self-coupling is focussed on how well various collider options can do. In this article we ask a physics-based question of how well do we need colliders to measure these quantities to have an impact on discovery of new physics or an impact in how we understand the role of the Higgs boson in nature. We address the question within the framework of the Standard Model and various beyond the Standard Model scenarios, including supersymmetry and theories of composite Higgs bosons. We conclude that the LHC’s stated ability to measure the Higgs boson to better than 150 MeV will be as good as we will ever need to know the Higgs boson mass in the foreseeable future. On the other hand, we estimate that the self-coupling will likely need to be measured to better than 20% to see a deviation from the Standard Model expectation. This is a challenging target for future collider and upgrade scenarios.
Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs

The identification of the H3K4 trimethylase, PRDM9, as the gene responsible for recombination hotspot localization has provided considerable insight into the mechanisms by which recombination is initiated in mammals. However, uniquely amongst mammals, canids appear to lack a functional version of PRDM9 and may therefore provide a model for understanding recombination that occurs in the absence of PRDM9, and thus how PRDM9 functions to shape the recombination landscape. We have constructed a fine-scale genetic map from patterns of linkage disequilibrium assessed using high-throughput sequence data from 51 free-ranging dogs, Canis lupus familiaris. While broad-scale properties of recombination appear similar to other mammalian species, our fine-scale estimates indicate that canine highly elevated recombination rates are observed in the vicinity of CpG rich regions including gene promoter regions, but show little association with H3K4 trimethylation marks identified in spermatocytes. By comparison to genomic data from the Andean fox, Lycalopex culpaeus, we show that biased gene conversion is a plausible mechanism by which the high CpG content of the dog genome could have occurred.