nils-herrmann/clean_scirepeval huggingface dataset:
Fast construction of FM-index for long sequence reads

We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the reverse (complement) lexicographical order without a separate sorting step. The implementation is among the fastest for indexing short reads and the only one that practically works for reads of averaged kilobases in length.



https://github.com/lh3/ropebwt2 CONTACT: hengli@broadinstitute.org.
Search for bosonic superweakly interacting massive dark matter particles with the XMASS-I detector.

Bosonic superweakly interacting massive particles (super-WIMPs) are a candidate for warm dark matter. With the absorption of such a boson by a xenon atom, these dark matter candidates would deposit an energy equivalent to their rest mass in the detector. This is the first direct detection experiment exploring the vector super-WIMPs in the mass range between 40 and 120 keV. With the use of 165.9 day of data, no significant excess above background was observed in the fiducial mass of 41 kg. The present limit for the vector super-WIMPs excludes the possibility that such particles constitute all of dark matter. The absence of a signal also provides the most stringent direct constraint on the coupling constant of pseudoscalar super-WIMPs to electrons. The unprecedented sensitivity was achieved exploiting the low background at a level 10(-4)  kg-1 keVee-1 day-1 in the detector.
High-energy neutrinos from radio galaxies

The IceCube experiment has recently reported the first observation of high-energy cosmic neutrinos. Their origin is still unknown. In this paper, we investigate the possibility that they originate in active galaxies. We show that hadronic interactions (pp) in the generally less powerful, more frequent, FR-I radio galaxies are one of the candidate source classes being able to accommodate the observation while the more powerful, less frequent, class of FR-II radio galaxies has too low of a column depths to explain the signal.
Graphene for Terahertz Applications

The optoelectronic properties of graphene are being explored for possible use in plasmonics and metamaterials at terahertz frequencies. Graphene is a one-atom-thick sheet of carbon atoms arranged in a honeycomb lattice. First obtained by exfoliation of graphite in 2004 (1), graphene has since evolved into a thriving research topic because of its attractive mechanical, thermal, and electrical properties (2–4), particularly the exceptionally high electron mobility. Such properties promise to revolutionize many applications (2–4), ranging from solar cells and light-emitting devices to touch screens, photodetectors (4), microwave transistors (5), and ultrafast lasers (6). We discuss here a number of special qualities of graphene that also make it desirable for devices manipulating terahertz waves.
Effects of deception in social networks

Honesty plays a crucial role in any situation where organisms exchange information or resources. Dishonesty can thus be expected to have damaging effects on social coherence if agents cannot trust the information or goods they receive. However, a distinction is often drawn between prosocial lies (‘white’ lies) and antisocial lying (i.e. deception for personal gain), with the former being considered much less destructive than the latter. We use an agent-based model to show that antisocial lying causes social networks to become increasingly fragmented. Antisocial dishonesty thus places strong constraints on the size and cohesion of social communities, providing a major hurdle that organisms have to overcome (e.g. by evolving counter-deception strategies) in order to evolve large, socially cohesive communities. In contrast, white lies can prove to be beneficial in smoothing the flow of interactions and facilitating a larger, more integrated network. Our results demonstrate that these group-level effects can arise as emergent properties of interactions at the dyadic level. The balance between prosocial and antisocial lies may set constraints on the structure of social networks, and hence the shape of society as a whole.
Two planets around Kapteyn's star: a cold and a temperate super-Earth orbiting the nearest halo red dwarf

Exoplanets of a few Earth masses can be now detected around nearby low-mass stars using Doppler spectroscopy. In this paper, we investigate the radial velocity variations of Kapteyn's star, which is both a sub-dwarf M-star and the nearest halo object to the Sun. The observations comprise archival and new HARPS, HIRES and PFS Doppler measurements. Two Doppler signals are detected at periods of 48 and 120 days using likelihood periodograms and a Bayesian analysis of the data. Using the same techniques, the activity indicies and archival ASAS-3 photometry show evidence for low-level activity periodicities of the order of several hundred days. However, there are no significant correlations with the radial velocity variations on the same time-scales. The inclusion of planetary Keplerian signals in the model results in levels of correlated and excess white noise that are remarkably low compared to younger G, K and M dwarfs. We conclude that Kapteyn's star is most probably orbited by two super-Earth mass planets, one of which is orbiting in its circumstellar habitable zone, becoming the oldest potentially habitable planet known to date. The presence and long-term survival of a planetary system seems a remarkable feat given the peculiar origin and kinematic history of Kapteyn's star. The detection of super-Earth mass planets around halo stars provides important insights into planet-formation processes in the early days of the Milky Way.
Supervised classification-based stock prediction and portfolio optimization

As the number of publicly traded companies as well as the amount of their financial data grows rapidly, it is highly desired to have tracking, analysis, and eventually stock selections automated. There have been few works focusing on estimating the stock prices of individual companies. However, many of those have worked with very small number of financial parameters. In this work, we apply machine learning techniques to address automated stock picking, while using a larger number of financial parameters for individual companies than the previous studies. Our approaches are based on the supervision of prediction parameters using company fundamentals, time-series properties, and correlation information between different stocks. We examine a variety of supervised learning techniques and found that using stock fundamentals is a useful approach for the classification problem, when combined with the high dimensional data handling capabilities of support vector machine. The portfolio our system suggests by predicting the behavior of stocks results in a 3% larger growth on average than the overall market within a 3-month time period, as the out-of-sample test suggests.
Black holes in the presence of dark energy

The new, rapidly developing field of theoretical research—studies of dark energy interacting with black holes (and, in particular, accreting onto black holes)—is reviewed. The term ‘dark energy’ is meant to cover a wide range of field theory models, as well as perfect fluids with various equations of state, including cosmological dark energy. Various accretion models are analyzed in terms of the simplest test field approximation or by allowing back reaction on the black-hole metric. The behavior of various types of dark energy in the vicinity of Schwarzschild and electrically charged black holes is examined. Nontrivial effects due to the presence of dark energy in the black hole vicinity are discussed. In particular, a physical explanation is given of why the black hole mass decreases when phantom energy is being accreted, a process in which the basic energy conditions of the famous theorem of nondecreasing horizon area in classical black holes are violated. The theoretical possibility of a signal escaping from beneath the black hole event horizon is discussed for a number of dark energy models. Finally, the violation of the laws of thermodynamics by black holes in the presence of noncanonical fields is considered.
Binaries in the field: fossils of the star formation process?

Recent observations of binary stars in the Galactic field show that the binary fraction and the mean orbital separation both decrease as a function of decreasing primary mass. We present N-body simulations of the effects of dynamical evolution in star-forming regions on primordial binary stars to determine whether these observed trends can be explained by the dynamical processing of a common binary population. We find that dynamical processing of a binary population with an initial binary fraction of unity and an initial excess of intermediate/wide separation (100–104 au) binaries does not reproduce the observed properties in the field, even in initially dense (∼103 M⊙ pc−3) star-forming regions. If instead we adopt a field-like population as the initial conditions, most brown dwarf and M-dwarf binaries are dynamically hard and their overall fractions and separation distributions are unaffected by dynamical evolution. G-dwarf and A-star binaries in the field are dynamically intermediate in our simulated dense regions and dynamical processing does destroy some systems with separations >100 au. However, the formation of wide binaries through the dissolution of supervirial regions is a strong function of primary mass, and the wide G-dwarf and A-star binaries that are destroyed by dynamical evolution in subvirial regions are replenished by the formation of binaries in supervirial regions. We therefore suggest that the binary population in the field is indicative of the primordial binary population in star-forming regions, at least for systems with primary masses in the range 0.02–3.0 M⊙.
Effect of Spatial Heterogeneity on Near-Limit Propagation of a Stable Detonation

The effect of introducing a spatial heterogeneity into an explosive medium is studied computationally by examining the detonation velocity near the limit to propagation in a thin explosive layer. The explosive system studied is an ideal gas with a single exothermic reaction governed by a pressure-dependent reaction rate ($p^n$) with a pressure exponent of $n = 3$. A pressure-dependent reaction rate, rather than the exponential dependence of reaction on temperature of Arrhenius kinetics, is used so that the detonation wave is stable in the homogeneous case and can be modelled with simple, analytical techniques, and thus the effect of introducing heterogeneity can be clearly identified. The two-dimensional slab of explosive is bounded by a layer of inert gas with the same thermodynamic properties as the explosive. The heterogeneity is introduced into the explosive via a large-amplitude, two-dimensional sinusoidal ripple in density in the initialization of the simulation, while maintaining a constant pressure. The computational simulations are initialized with a ZND solution for the ideal CJ detonation, and the detonation is allowed to propagate into the explosive layer. The simulations show that the detonation in the heterogeneous media exhibits a cellular-like structure of complex shock interactions. The detonation is able to propagate into a significantly thinner layer of explosive and can exhibit a greater velocity than the corresponding homogeneous case. A parametric study of varying the wavelength of the sinusoid shows the existence of an optimal size of heterogeneity at which the favorable effect is the greatest corresponding to a wavelength that is approximately 10 to 50 times the half reaction zone length of the ideal CJ detonation. As the wavelength is decreased to the size of the reaction zone length, the behavior reverts back to the homogeneous case.
Comment on "Strong constraints on magnetized white dwarfs surpassing the Chandrasekhar mass limit"

We show that the upper bound for the central magnetic field of a super-Chandrasekhar white dwarf calculated by Nityananda and Konar [ (2014)] is completely erroneous. This in turn strengthens the argument in favor of the stability of the recently proposed magnetized super-Chandrasekhar white dwarfs. We also point out several other numerical errors in their work. Overall we conclude, based on our calculations, that the arguments put forth by Nityananda and Konar are fallacious and misleading.
A new soft X-ray magnetic circular dichroism facility at the BSRF beamline 4B7B

X-ray magnetic circular dichroism (XMCD) has become an important and powerful tool because it allows the study of material properties in combination with elemental specificity, chemical state specificity, and magnetic specificity. A new soft X-ray magnetic circular dichroism apparatus has been developed at the Beijing Synchrotron Radiation Facility (BSRF). The apparatus combines three experimental conditions: an ultra-high-vacuum environment, moderate magnetic fields and in-situ sample preparation to measure the absorption signal. We designed a C-type dipole electromagnet that provides magnetic fields up to 0.5 T in parallel (or anti-parallel) direction relative to the incoming X-ray beam. The performances of the electromagnet are measured and the results show good agreement with the simulation ones. Following film grown in situ by evaporation methods, XMCD measurements are performed. Combined polarization corrections, the magnetic moments of the Fe and Co films determined by sum rules are consistent with other theoretical predictions and experimental measurements.
Kerr-Newman black holes with stationary charged scalar clouds

It is shown that Kerr-Newman black holes can support linear charged scalar fields in their exterior regions. To that end, we solve analytically the Klein-Gordon wave equation for a stationary charged massive scalar field in the background of a near-extremal Kerr-Newman black hole. In particular, we derive a simple analytical formula which describes the physical properties of these stationary bound-state resonances of the charged massive scalar fields in the Kerr-Newman blackhole spacetime.
Unbiased sampling of network ensembles

Sampling random graphs with given properties is a key step in the analysis of networks, as random ensembles represent basic null models required to identify patterns such as communities and motifs. An important requirement is that the sampling process is unbiased and efficient. The main approaches are microcanonical, i.e. they sample graphs that match the enforced constraints exactly. Unfortunately, when applied to strongly heterogeneous networks (like most real-world examples), the majority of these approaches become biased and/or time-consuming. Moreover, the algorithms defined in the simplest cases, such as binary graphs with given degrees, are not easily generalizable to more complicated ensembles. Here we propose a solution to the problem via the introduction of a ‘Maximize and Sample’ (‘Max & Sam’ for short) method to correctly sample ensembles of networks where the constraints are ‘soft’, i.e. realized as ensemble averages. Our method is based on exact maximum-entropy distributions and is therefore unbiased by construction, even for strongly heterogeneous networks. It is also more computationally efficient than most microcanonical alternatives. Finally, it works for both binary and weighted networks with a variety of constraints, including combined degree-strength sequences and full reciprocity structure, for which no alternative method exists. Our canonical approach can in principle be turned into an unbiased microcanonical one, via a restriction to the relevant subset. Importantly, the analysis of the fluctuations of the constraints suggests that the microcanonical and canonical versions of all the ensembles considered here are not equivalent. We show various real-world applications and provide a code implementing all our algorithms.
Discovering Structure in High-Dimensional Data Through Correlation Explanation

We introduce a method to learn a hierarchy of successively more abstract representations of complex data based on optimizing an information-theoretic objective. Intuitively, the optimization searches for a set of latent factors that best explain the correlations in the data as measured by multivariate mutual information. The method is unsupervised, requires no model assumptions, and scales linearly with the number of variables which makes it an attractive approach for very high dimensional systems. We demonstrate that Correlation Explanation (CorEx) automatically discovers meaningful structure for data from diverse sources including personality tests, DNA, and human language.
Notes on Alpha Stream Optimization

In these notes we discuss investment allocation to multiple alpha streams traded on the same execution platform, including when trades are crossed internally resulting in turnover reduction. We discuss approaches to alpha weight optimization where one maximizes P&L subject to bounds on volatility (or Sharpe ratio). The presence of negative alpha weights, which are allowed when alpha streams are traded on the same execution platform, complicates the optimization problem. By using factor model approach to alpha covariance matrix, the original optimization problem can be viewed as a 1-dimensional root searching problem plus an optimization problem that requires a finite number of iterations. We discuss this approach without costs and with linear costs, and also with nonlinear costs in a certain approximation, which makes the allocation problem tractable without forgoing nonlinear portfolio capacity bound effects.
An accurate single-electron pump based on a highly tunable silicon quantum dot.

Nanoscale single-electron pumps can be used to generate accurate currents, and can potentially serve to realize a new standard of electrical current based on elementary charge. Here, we use a silicon-based quantum dot with tunable tunnel barriers as an accurate source of quantized current. The charge transfer accuracy of our pump can be dramatically enhanced by controlling the electrostatic confinement of the dot using purposely engineered gate electrodes. Improvements in the operational robustness, as well as suppression of nonadiabatic transitions that reduce pumping accuracy, are achieved via small adjustments of the gate voltages. We can produce an output current in excess of 80 pA with experimentally determined relative uncertainty below 50 parts per million.
On The Communication Complexity of Finding an (Approximate) Stable Marriage

In this paper, we consider the communication complexity of protocols that compute stable matchings. We work within the context of Gale and Shapley's original stable marriage problem\cite{GS62}: $n$ men and $n$ women each privately hold a total and strict ordering on all of the members of the opposite gender. They wish to collaborate in order to find a stable matching---a pairing of the men and women such that no unmatched pair mutually prefer each other to their assigned partners in the matching. We show that any communication protocol (deterministic, nondeterministic, or randomized) that correctly ouputs a stable matching requires $\Omega(n^2)$ bits of communication. Thus, the original algorithm of Gale and Shapley is communication-optimal up to a logarithmic factor. We then introduce a "divorce metric" on the set of all matchings, which allows us to consider approximately stable matchings. We describe an efficient algorithm to compute the "distance to stability" of a given matching. We then show that even under the relaxed requirement that a protocol only yield an approximate stable matching, the $\Omega(n^2)$ communication lower bound still holds.
On codes over 𝓡k, m and constructions for new binary self-dual codes

In this work, we study codes over the ring 𝓡k, m = 𝔽2[u, v]/ 〈uk, vm, uv − vu〉, which is a family of Frobenius, characteristic 2 extensions of the binary field. We introduce a distance and duality preserving Gray map from 𝓡k, m to F2km$\mathbb{F}_2^{km}$ together with a Lee weight. After proving the MacWilliams identities for codes over 𝓡k, m for all the relevant weight enumerators, we construct many binary self-dual codes as the Gray images of self-dual codes over 𝓡k, m. In addition to many extremal binary self-dual codes obtained in this way, including a new construction for the extended binary Golay code, we find 175 new Type I binary self-dual codes of parameters [72, 36, 12] and 105 new Type II binary self-dual codes of parameter [72, 36, 12].
Equation and test of possible delay time of Newton force

Recently, a simple heuristic modification of the Newton potential with a non- zero delay-time τG has been proposed. Our modification is largely suppressed for purely gravitational interactions, it becomes relevant under non-gravitational accelerations of the sources. We illustrate how the choice τG ∼ 1 ms may already influence the 5 th digit of G determined by Cavendish experiments. Re-evaluation of old Cavendish experiments and implementing slightly modified new ones may confirm the proposal or, at least, put a stronger upper limit on τG.
The standard model and the constituents of leptons and quarks

A complete set of postulates of the standard model of the electroweak interaction and mass generation is formulated and confirmed deriving the Lagrangian for the standard model. A massive fermion is formed by a right-handed and a left-handed elementary massless fermion, exchanging a scalar doublet. The elementary massless fermions forming leptons belong to an approximate SU(3) octet. The charges are quantised due to this symmetry. Pacs 12.10 Dm Standard model; Higgs mechanism; electroweak interaction The standard model of the electroweak interaction and mass generation, the model of Glashow, Weinberg and Salam , very successfully describes all experimental observations in particle physics made so far. The recent discovery of the Higgs particle at CERN by ATLAS and CMS is the final proof of the validity of the standard model. After the discoveries of neutrino oscillations and of the Higgs particle, the standard model deserves a detailed and consistent formulation. Describing the minimal standard model in an unconventional language, in this note it is assumed that leptons and quarks are formed by particles, which are more elementary. From their properties a set of postulates of the minimal standard model is worked out. As a proof of the postulates, the well established Lagrangian of the standard model is derived.
Subgraph covers - An information theoretic approach to motif analysis in networks

Many real world networks contain a statistically surprising number of certain subgraphs, called network motifs. In the prevalent approach to motif analysis, network motifs are detected by comparing subgraph frequencies in the original network with a statistical null model. In this paper we propose an alternative approach to motif analysis where network motifs are defined to be connectivity patterns that occur in a subgraph cover that represents the network using minimal total information. A subgraph cover is defined to be a set of subgraphs such that every edge of the graph is contained in at least one of the subgraphs in the cover. Some recently introduced random graph models that can incorporate significant densities of motifs have natural formulations in terms of subgraph covers and the presented approach can be used to match networks with such models. To prove the practical value of our approach we also present a heuristic for the resulting NP-hard optimization problem and give results for several real world networks.