nils-herrmann/clean_scirepeval huggingface dataset:
Path Integrals and Reality

We define the idea of {\it real path quantum theory}, a realist generalisation of quantum theory in which it is postulated that the configuration space path actually followed by a closed quantum system is probabilistically chosen. This is done a postulate defining probabilities for paths, which we propose are determined by an expression involving path amplitudes and a distance function that quantifies path separation. We suggest a possible form for a path probability postulate and explore possible choices of distance function, including choices suitable for Lorentz or generally covariant versions of real path quantum theory. We set out toy models of quantum interferometry and show that in these models the probability postulate and specific distance functions do indeed give a physically sensible path ontology. These functions can be chosen so as to predict quantum interference for interference of microscopic quantum systems and the failure of interference for macroscopic quantum systems. More generally, they predict interference when the beams are close, and its failure when they are far apart, as determined by the distance function. If taken seriously in its present relatively unconstrained form, real path quantum theory thus motivates experimental tests of quantum interference in all unexplored regimes defined by potentially physically interesting parameters, including the mass of the beam object, the beam separation distance, the beam separation time, and many others. We discuss open questions raised by these ideas.
CAN WE REPRODUCE THE X-RAY BACKGROUND SPECTRAL SHAPE USING LOCAL ACTIVE GALACTIC NUCLEI?

The X-ray background (XRB) is due to the aggregate of active galactic nuclei (AGNs), which peak in activity at z ∼ 1 and is often modeled as the sum of different proportions of unabsorbed, moderately, and heavily absorbed AGN. We present the summed spectrum of a complete sample of local AGN (the Northern Galactic Cap of the 58 month Swift/BAT catalog, z < 0.2) using 0.4–200 keV data and directly determine the different proportions of unabsorbed, moderately and heavily absorbed AGN that make up the summed spectrum. This stacked low redshift AGN spectrum is remarkably similar in shape to the XRB spectrum (when shifted to z ∼ 1), but the observed proportions of different absorption populations differ from most XRB synthesis models. AGN with Compton-thick absorption account for only ∼12% of the sample, but produce a significant contribution to the overall spectrum. We confirm that Compton reflection is more prominent in moderately absorbed AGN and that the photon index differs intrinsically between unabsorbed and absorbed AGN. The AGN in our sample account for only ∼1% of the XRB intensity. The reproduction of the XRB spectral shape suggests that strong evolution in individual AGN properties is not required between z ∼ 0 and 1.
Classifying quantum phases with the Kirby torus trick

Classifying phases of local quantum systems is a general problem that includes special cases such as free fermions, commuting projectors, and others. An important distinction in this classification should be made between classifying periodic and aperiodic systems. A related distinction is that between homotopy invariants (invariants which remain constant so long as certain general properties such as locality, gap, and others hold) and locally computable invariants (properties of the system that cannot change from one region to another without producing a gapless edge between them). We attack this problem using a technique inspired by Kirby's "torus trick" in topology. We use this trick to reproduce results for free fermions (in particular, using the trick to reduce the aperiodic classification to the simpler problem of periodic classification). We also show that a similar trick works for interacting phases which are nontrivial but lack anyons; these results include symmetry protected phases. A key part of this work is an attempt to classify quantum cellular automata (QCA).
Can MOND type hypotheses be tested in a free fall laboratory environment

The extremely small accelerations of objects required for the the onset of modified Newtonian dynamics, or MOND, makes testing the hypothesis in conventional terrestrial laboratories virtually impossible. This is due to the large background acceleration of Earth, which is transmitted to the acceleration of test objects within an apparatus. We show however, that it may be possible to test MOND-type hypotheses with experiments using a conventional apparatus capable of tracking very small accelerations of its components, but performed in locally inertial frames such as artificial satellites and other freely falling laboratories. For example, experiments involving an optical interferometer or a torsion balance in these laboratories would show nonlinear dynamics, and displacement amplitudes larger than expected. These experiments may also be able to test potential violations of the strong equivalence principle by MOND and to distinguish between its two possible interpretations (modified inertia and modified gravity). The asymptotic flatness of galaxy rotation curves in spiral galaxies and the related apparent mass discrepancy according to Newtonian dynamics led to the proposal of dark matter . Dark matter has also been inferred from observations of apparent magnitudes of Type Ia supernovae at large redshifts within the standard FreedmanRobertson-Walker cosmological paradigm and could account for as much as about 28% of the mass-energy density of the observable Universe . Although several dark matter candidates have been proposed, including weakly interacting massive particles, axions etc., none has been directly observed so far. Another proposal known as modified Newtonian dynamics (MOND) postulates the modification of the law of gravity to a µ(a/a0) = GM r 2 , (1)
Active Sensing as Bayes-Optimal Sequential Decision Making

Sensory inference under conditions of uncertainty is a major problem in both machine learning and computational neuroscience. An important but poorly understood aspect of sensory processing is the role of active sensing. Here, we present a Bayes-optimal inference and control framework for active sensing, C-DAC (Context-Dependent Active Controller). Unlike previously proposed algorithms that optimize abstract statistical objectives such as information maximization (Infomax) [Butko & Movellan, 2010] or one-step look-ahead accuracy [Najemnik & Geisler, 2005], our active sensing model directly minimizes a combination of behavioral costs, such as temporal delay, response error, and effort. We simulate these algorithms on a simple visual search task to illustrate scenarios in which context-sensitivity is particularly beneficial and optimization with respect to generic statistical objectives particularly inadequate. Motivated by the geometric properties of the C-DAC policy, we present both parametric and non-parametric approximations, which retain context-sensitivity while significantly reducing computational complexity. These approximations enable us to investigate the more complex problem involving peripheral vision, and we notice that the difference between C-DAC and statistical policies becomes even more evident in this scenario.
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs of next- generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge.



Here, we present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse. Using as our benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy and faster execution.



Source code and user manual are available at http://sourceforge.net/projects/soapdenovotrans/.
Hedging without sweat: a genetic programming approach

Hedging in the presence of transaction costs leads to complex optimization problems. These problems typically lack closed-form solutions, and their implementation relies on numerical methods that provide hedging strategies for specific parameter values. In this paper, we use a genetic programming algorithm to derive explicit formulas for near-optimal hedging strategies under nonlinear transaction costs. The strategies are valid over a large range of parameter values and require no information about the structure of the optimal hedging strategy.
Ovopub: Modular data publication with minimal provenance

With the growth of the Semantic Web as a medium for creating, consuming, mashing up and republishing data, our ability to trace any statement(s) back to their origin is becoming ever more important. Several approaches have now been proposed to associate statements with provenance, with multiple applications in data publication, attribution and argumentation. Here, we describe the ovopub, a modular model for data publication that enables encapsulation, aggregation, integrity checking, and selective-source query answering. We describe the ovopub RDF specification, key design patterns and their application in the publication and referral to data in the life sciences.
The Riemann hypothesis proved

The Riemann hypothesis is proved by quantum-extending the zeta Riemann function to a quantum mapping between quantum $1$-spheres with quantum algebra $A=\mathbb{C}$, in the sense of A. Pr\'astaro \cite{PRAS01, PRAS02}. Algebraic topologic properties of quantum-complex manifolds and suitable bordism groups of morphisms in the category $\mathfrak{Q}_{\mathbb{C}}$ of quantum-complex manifolds are utilized.
Complementarity and Searches for Dark Matter in the pMSSM

The search for and identification of neutralino dark matter in supersymmetry requires a multi-pronged approach with important roles played by collider, direct and indirect dark matter detection experiments. In this report, we summarize the sensitivity of such searches at the 7, 8 (and eventually 14) TeV LHC, combined with those by Fermi, CTA, IceCube/DeepCore, COUPP and XENON1T, to such particles within the context of the 19-parameter p(henomenological)MSSM. This report provides an outline of the current status of our results and our expectations for future analyses.
Observations of feedback from radio-quiet quasars – II. Kinematics of ionized gas nebulae

The prevalence and energetics of quasar feedback is a major unresolved problem in galaxy formation theory. In this paper, we present Gemini Integral Field Unit observations of ionized gas around eleven luminous, obscured, radio-quiet quasars at z~0.5 out to ~15 kpc from the quasar; specifically, we measure the kinematics and morphology of [O III]5007 emission. The round morphologies of the nebulae and the large line-of-sight velocity widths (with velocities containing 80% of the emission as high as 1000 km/s combined with relatively small velocity difference across them (from 90 to 520 km/s) point toward wide-angle quasi-spherical outflows. We use the observed velocity widths to estimate a median outflow velocity of 760 km/s, similar to or above the escape velocities from the host galaxies. The line-of-sight velocity dispersion declines slightly toward outer parts of the nebulae (by 3% per kpc on average). The majority of nebulae show blueshifted excesses in their line profiles across most of their extents, signifying gas outflows. For the median outflow velocity, we find a kinetic energy flow between 4x10^{44} and 3x10^{45} erg/s and mass outflow rate between 2000 and 20000 Msun/yr. These values are large enough for the observed quasar winds to have a significant impact on their host galaxies. The median rate of converting bolometric luminosity to kinetic energy of ionized gas clouds is ~2%. We report four new candidates for "super-bubbles" -- outflows that may have broken out of the denser regions of the host galaxy.
Theory of post-Newtonian radiation and reaction

We address issues with extant formulations of dissipative effects in the effective field theory (EFT) which describes the post-Newtonian (PN) inspiral of two gravitating bodies by (re)formulating several parts of the theory. Novel ingredients include gauge invariant spherical fields in the radiation zone; a system zone which preserves time reversal such that its violation arises not from local odd propagation but rather from interaction with the radiation sector in a way which resembles the balayage method; 2-way multipoles to perform zone matching within the EFT action; and a double-field radiation-reaction action which is the non-quantum version of the Closed Time Path formalism and generalizes to any theory with directed propagators including theories which are defined by equations of motion rather than an action. This formulation unifies the treatment of outgoing radiation and its reaction force. We demonstrate the theory in the scalar, electromagnetic and gravitational cases by economizing the following: the expression for the radiation source multipoles; the derivation of the leading outgoing radiation and associated reaction force such that it is maximally reduced to mere multiplication; and the derivation of the gravitational next to leading PN order. In fact we present a novel expression for the +1PN correction to all mass multipoles. We introduce useful definitions for multi-index summation, for the normalization of Bessel functions and for the normalization of the gravito-magnetic vector potential.
Quantum Objects

In this paper, we suggest an alternative interpretation for the quantum state vector, which, by considering temporal parts for physical objects, aims to give an intelligible account of measurement problem in quantum mechanics. We examine the capacity of this interpretation as for explaining three measurement problems: the problem of outcome, the problem of statistics and the problem of effect. We argue that, this interpretation of the state vector, while providing a satisfactory account, as rationally plausible as its rivals, for the measurement problem, shows yet another limitation of our perceptual experience, i.e. our inability to perceive unsharp reality.
Implications of the Higgs discovery for gravity and cosmology

The discovery of the Higgs boson is one of the greatest discoveries in this century. The standard model is finally complete. Apart from its significance in particle physics, this discovery has profound implications for gravity and cosmology in particular. Many perturbative quantum gravity interactions involving scalars are not suppressed by powers of Planck mass. Since gravity couples anything with mass to anything with mass, then Higgs must be strongly coupled to any other fundamental scalar in nature, even if the gauge couplings are absent in the original Lagrangian. Since the Large Hadron Collider data indicate that the Higgs is very much standard model-like, there is very little room for nonstandard model processes, e.g. invisible decays. This severely complicates any model that involves light enough scalar that the Higgs can kinematically decay to. Most notably, these are the quintessence models, models including light axions, and light scalar dark matter models.
Fluid Mechanics of Strings

We consider conserved currents in an interacting network of one-dimensional objects (or strings). Singular currents localized on a single string are considered in general, and a formal procedure for coarse-graining over many strings is developed. This procedure is applied to strings described by the Nambu-Goto action such as cosmic strings. In addition to conserved currents corresponding to the energy-momentum tensor, we obtain conserved currents corresponding to an antisymmetric tensor hF µ� i = hx ′µ u x � − u x µ x ′� i, where u x µ and x ′µ are the velocity and tangent vectors of strings. Under the assumption of local equilibrium we derive a complete set of hydrodynamic equations for strings.
Time and dark matter from the conformal symmetries of Euclidean space

Starting with the conformal symmetries of Euclidean space, we construct a manifold where time manifests as a part of the geometry. Though there is no matter present in the geometry studied here, geometric terms analogous to dark energy and dark matter appear when we write down the Einstein tensor. Specifically, the quotient of the conformal group of Euclidean four-space by its Weyl subgroup results in a geometry possessing many of the properties of relativistic phase space, including both a natural symplectic form and non-degenerate Killing metric. We show that the general solution posesses orthogonal Lagrangian submanifolds, with the induced metric and the spin connection on the submanifolds necessarily Lorentzian, despite the Euclidean starting point. Using an orthonormal frame adapted to the phase space properties, we also find two new tensor fields not present in Riemannian geometry. The first is a combination of the Weyl vector with the scale factor on the metric, and determines the timelike directions on the submanifolds. The second comes from the components of the spin connection, symmetric with respect to the new metric. Though this field comes from the spin connection, it transforms homogeneously. Finally, we show that in the absence of Cartan curvature and sources, the configuration space has geometric terms equivalent to a perfect fluid and a cosmological constant.
Graph cluster randomization: network exposure to multiple universes

A/B testing is a standard approach for evaluating the effect of online experiments; the goal is to estimate the `average treatment effect' of a new feature or condition by exposing a sample of the overall population to it. A drawback with A/B testing is that it is poorly suited for experiments involving social interference, when the treatment of individuals spills over to neighboring individuals along an underlying social network. In this work, we propose a novel methodology using graph clustering to analyze average treatment effects under social interference. To begin, we characterize graph-theoretic conditions under which individuals can be considered to be `network exposed' to an experiment. We then show how graph cluster randomization admits an efficient exact algorithm to compute the probabilities for each vertex being network exposed under several of these exposure conditions. Using these probabilities as inverse weights, a Horvitz-Thompson estimator can then provide an effect estimate that is unbiased, provided that the exposure model has been properly specified. Given an estimator that is unbiased, we focus on minimizing the variance. First, we develop simple sufficient conditions for the variance of the estimator to be asymptotically small in n, the size of the graph. However, for general randomization schemes, this variance can be lower bounded by an exponential function of the degrees of a graph. In contrast, we show that if a graph satisfies a restricted-growth condition on the growth rate of neighborhoods, then there exists a natural clustering algorithm, based on vertex neighborhoods, for which the variance of the estimator can be upper bounded by a linear function of the degrees. Thus we show that proper cluster randomization can lead to exponentially lower estimator variance when experimentally measuring average treatment effects under interference.
Subgraph pattern matching over uncertain graphs with identity linkage uncertainty

There is a growing need for methods that can represent and query uncertain graphs. These uncertain graphs are often the result of an information extraction and integration system that attempts to extract an entity graph or a knowledge graph from multiple unstructured sources , . Such an integration typically leads to identity uncertainty, as different data sources may use different references to the same underlying real-world entities. Integration usually also introduces additional uncertainty on node attributes and edge existence. In this paper, we propose the notion of a probabilistic entity graph (PEG), a formal model that uniformly and systematically addresses these three types of uncertainty. A PEG is a probabilistic graph model that defines a distribution over possible graphs at the entity level. We introduce a general framework for constructing a PEG given uncertain data at the reference level and develop efficient algorithms to answer subgraph pattern matching queries in this setting. Our algorithms are based on two novel ideas: context-aware path indexing and reduction by join-candidates, which drastically reduce the query search space. A comprehensive experimental evaluation shows that our approach outperforms baseline implementations by orders of magnitude.
Observing light-by-light scattering at the Large Hadron Collider.

Elastic light-by-light scattering (γγ→γγ) is open to study at the Large Hadron Collider thanks to the large quasireal photon fluxes available in electromagnetic interactions of protons (p) and lead (Pb) ions. The γγ→γγ cross sections for diphoton masses m(γγ)>5 GeV amount to 12 fb, 26 pb, and 35 nb in p-p, p-Pb, and Pb-Pb collisions at nucleon-nucleon center-of-mass energies √(s(NN))=14, 8.8, and 5.5 TeV, respectively. Such a measurement has no substantial background in Pb-Pb collisions where one expects about 20 signal events per run, after typical detector acceptance and reconstruction efficiency selections.
Lensless imaging by compressive sensing

In this paper, we propose a lensless compressive imaging architecture. The architecture consists of two components, an aperture assembly and a sensor. No lens is used. The aperture assembly consists of a two dimensional array of aperture elements. The transmittance of each aperture element is independently controllable. The sensor is a single detection element. A compressive sensing matrix is implemented by adjusting the transmittance of the individual aperture elements according to the values of the sensing matrix. The proposed architecture is simple and reliable because no lens is used. The architecture can be used for capturing images of visible and other spectra such as infrared, or millimeter waves, in surveillance applications for detecting anomalies or extracting features such as speed of moving objects. Multiple sensors may be used with a single aperture assembly to capture multiview images simultaneously. A prototype was built by using a LCD panel and a photoelectric sensor for capturing images of visible spectrum.