nils-herrmann/clean_scirepeval huggingface dataset:
Nanopore Sequencing of the phi X 174 genome

Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost, and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and DNA control to interpret the procession of ion current levels observed during the translocation of DNA through the pore MspA. As approximately four nucleotides affect the ion current of each level, we measured the ion current corresponding to all 256 four-nucleotide combinations (quadromers). This quadromer map is highly predictive of ion current levels of previously unmeasured sequences derived from the bacteriophage phi X 174 genome. Furthermore, we show nanopore sequencing reads of phi X 174 up to 4,500 bases in length that can be unambiguously aligned to the phi X 174 reference genome, and demonstrate proof-of-concept utility with respect to hybrid genome assembly and polymorphism detection. All methods and data are made fully available.
Distributed Stochastic Optimization of the Regularized Risk

Many machine learning algorithms minimize a regularized risk, and stochastic optimization is widely used for this task. When working with massive data, it is desirable to perform stochastic optimization in parallel. Unfortunately, many existing stochastic optimization algorithms cannot be parallelized efficiently. In this paper we show that one can rewrite the regularized risk minimization problem as an equivalent saddle-point problem, and propose an efficient distributed stochastic optimization (DSO) algorithm. We prove the algorithm's rate of convergence; remarkably, our analysis shows that the algorithm scales almost linearly with the number of processors. We also verify with empirical evaluations that the proposed algorithm is competitive with other parallel, general purpose stochastic and batch optimization algorithms for regularized risk minimization.
BEETL-fastq: a searchable compressed archive for DNA reads

FASTQ is a standard file format for DNA sequencing data, which stores both nucleotides and quality scores. A typical sequencing study can easily generate hundreds of gigabytes of FASTQ files, while public archives such as ENA and NCBI and large international collaborations such as the Cancer Genome Atlas can accumulate many terabytes of data in this format. Compression tools such as gzip are often used to reduce the storage burden but have the disadvantage that the data must be decompressed before they can be used. Here, we present BEETL-fastq, a tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. Importantly, the full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input.



We show that 6.6 terabytes of human reads in FASTQ format can be transformed into 1.7 terabytes of indexed files, from where we can search for 1, 10, 100, 1000 and a million of 30-mers in 3, 8, 14, 45 and 567 s, respectively, plus 20 ms per output read. Useful applications of the search capability are highlighted, including the genotyping of structural variant breakpoints and 'in silico pull-down' experiments in which only the reads that cover a region of interest are selectively extracted for the purposes of variant calling or visualization.



BEETL-fastq is part of the BEETL library, available as a github repository at github.com/BEETL/BEETL.
Compton thick active galactic nuclei in Chandra surveys

We present the results from an X-ray spectral analysis of active galactic nuclei (AGN) in the Chandra Deep Field-South, AEGIS-XD and Chandra-COSMOS surveys, fo- cussing on the identication and characterisation of the most heavily obscured, Comp- nd evidence that the covering factor of the obscuring material decreases with LX for all redshifts, consistent with the receding torus model, and that this factor increases with redshift, consistent with an increase in the obscured fraction towards higher redshifts. The strong relationship between the parameters of obscuration and LX points towards an origin intrinsic to the AGN, however the increase of the covering factor with redshift may point towards contributions to the obscuration by the host galaxy. We make NH, (with uncertainties), observed X-ray uxes and intrinsic 2-10 keV luminosities for all sources analysed in this work publicly available in an online catalogue.
ULTRA-SHORT PERIOD BINARIES FROM THE CATALINA SURVEYS

We investigate the properties of 367 ultra-short period binary candidates selected from 31,000 sources recently identified from Catalina Surveys data. Based on light curve morphology, along with WISE, Sloan Digital Sky Survey, and GALEX multi-color photometry, we identify two distinct groups of binaries with periods below the 0.22 day contact binary minimum. In contrast to most recent work, we spectroscopically confirm the existence of M dwarf+M dwarf contact binary systems. By measuring the radial velocity variations for five of the shortest-period systems, we find examples of rare cool white dwarf (WD)+M dwarf binaries. Only a few such systems are currently known. Unlike warmer WD systems, their UV flux and optical colors and spectra are dominated by the M-dwarf companion. We contrast our discoveries with previous photometrically selected ultra-short period contact binary candidates and highlight the ongoing need for confirmation using spectra and associated radial velocity measurements. Overall, our analysis increases the number of ultra-short period contact binary candidates by more than an order of magnitude.
Mapping the nano-Hertz gravitational wave sky

We describe a new method for extracting gravitational wave signals from pulsar timing data. We show that any gravitational wave signal can be decomposed into an orthogonal set of sky maps, with the number of maps equal to the number of pulsars in the timing array. These maps may be used as a basis to construct gravitational wave templates for any type of source, including collections of point sources. A variant of the standard Hellings-Downs correlation analysis is recovered for statistically isotropic signals. The template based approach allows us to probe potential anisotropies in the signal and produce maps of the gravitational wave sky.
Probing the ν =2/3 fractional quantum Hall edge by momentum-resolved tunneling

The nature of the fractional quantum Hall state with filling factor $\nu=2/3$ and its edge modes continues to remain an open problem in low-dimensional condensed matter physics. Here, we suggest an experimental setting to probe the $\nu=2/3$ edge by tunnel-coupling it to a $\nu=1$ integer quantum Hall edge in another layer of a two-dimensional electron gas (2DEG). In this double-layer geometry, the momentum of tunneling electrons may be boosted by an auxiliary magnetic field parallel to the two planes of 2DEGs. We evaluate the current as a function of bias voltage and the boosting magnetic field. Its threshold behavior yields information about the spectral function of the $\nu=2/3$ edge, in particular about the nature of the chiral edge modes. Our theory accounts also for the effects of Coulomb interaction and disorder.
Renormalization for Philosophers

We have two aims. The main one is to expound the idea of renormalization in quantum field theory, with no technical prerequisites (Sections 2 and 3). Our motivation is that renormalization is undoubtedly one of the great ideas—and great successes--of twentieth-century physics. Also it has strongly influenced in diverse ways, how physicists conceive of physical theories. So it is of considerable philosophical interest. Second, we will briefly relate renormalization to Ernest Nagel's account of inter-theoretic relations, especially reduction (Section 4). 
 
One theme will be a contrast between two approaches to renormalization. The old approach, which prevailed from ca. 1945 to 1970, treated renormalizability as a necessary condition for being an acceptable quantum field theory. On this approach, it is a piece of great good fortune that high energy physicists can formulate renormalizable quantum field theories that are so empirically successful. But the new approach to renormalization (from 1970 onwards) explains why the phenomena we see, at the energies we can access in our particle accelerators, are described by a renormalizable quantum field theory. For whatever non-renormalizable interactions may occur at yet higher energies, they are insignificant at accessible energies. Thus the new approach explains why our best fundamental theories have a feature, viz. renormalizability, which the old approach treated as a selection principle for theories. 
 
That is worth saying since philosophers tend to think of scientific explanation as only explaining an individual event, or perhaps a single law, or at most deducing one theory as a special case of another. Here we see a framework in which there is a space of theories. And this framework is powerful enough to deduce that what seemed “manna from heaven” (that some renormalizable theories are empirically successful) is to be expected: the good fortune is generic. 
 
We also maintain that universality, a concept stressed in renormalization theory, is essentially the familiar philosophical idea of multiple realizability; and that it causes no problems for reductions of a Nagelian kind.
Uncovering Randomness and Success in Society

An understanding of how individuals shape and impact the evolution of society is vastly limited due to the unavailability of large-scale reliable datasets that can simultaneously capture information regarding individual movements and social interactions. We believe that the popular Indian film industry, “Bollywood”, can provide a social network apt for such a study. Bollywood provides massive amounts of real, unbiased data that spans more than 100 years, and hence this network has been used as a model for the present paper. The nodes which maintain a moderate degree or widely cooperate with the other nodes of the network tend to be more fit (measured as the success of the node in the industry) in comparison to the other nodes. The analysis carried forth in the current work, using a conjoined framework of complex network theory and random matrix theory, aims to quantify the elements that determine the fitness of an individual node and the factors that contribute to the robustness of a network. The authors of this paper believe that the method of study used in the current paper can be extended to study various other industries and organizations.
An Entropy Search Portfolio for Bayesian Optimization

Bayesian optimization is a sample-efficient method for black-box global optimization. How- ever, the performance of a Bayesian optimization method very much depends on its exploration strategy, i.e. the choice of acquisition function, and it is not clear a priori which choice will result in superior performance. While portfolio methods provide an effective, principled way of combining a collection of acquisition functions, they are often based on measures of past performance which can be misleading. To address this issue, we introduce the Entropy Search Portfolio (ESP): a novel approach to portfolio construction which is motivated by information theoretic considerations. We show that ESP outperforms existing portfolio methods on several real and synthetic problems, including geostatistical datasets and simulated control tasks. We not only show that ESP is able to offer performance as good as the best, but unknown, acquisition function, but surprisingly it often gives better performance. Finally, over a wide range of conditions we find that ESP is robust to the inclusion of poor acquisition functions.
Photonic crystal optics in cold atomic gases

We describe propagation of light in a gas with periodic density modulation, demonstrating photonic-crystal-like refraction with negative refraction angles. We address the role of poorly defined boundaries and damping, and derive an optical analog of the quantum adiabatic theorem. For Cs atoms in an optical lattice, we show that relying on semi-adiabatic propagation one can excite and spatially split positively and negatively refracting modes at experimentally available gas densities.
Mapping gravitational-wave backgrounds using methods from CMB analysis: Application to pulsar timing arrays

We describe an alternative approach to the analysis of gravitational-wave backgrounds, based on the formalism used to characterize the polarization of the cosmic microwave background. In contrast to standard analyses, this approach makes no assumptions about the nature of the background and so has the potential to reveal much more about the physical processes that generated it. An arbitrary background can be decomposed into modes whose angular dependence on the sky is given by gradients and curls of spherical harmonics. We derive the pulsar timing overlap reduction functions for the individual modes, which are given by simple combinations of spherical harmonics evaluated at the pulsar locations. We show how these can be used to recover the components of an arbitrary background, giving explicit results for both isotropic and anisotropic uncorrelated backgrounds. We also find that the response of a pulsar timing array to curl modes is identically zero, so half of the gravitational-wave sky will never be observed using pulsar timing, no matter how many pulsars are included in the array. An isotropic, unpolarized and uncorrelated background can be accurately represented using only three modes, and so a search of this type will be only slightly more complicated than the standard cross-correlation search using the Hellings and Downs overlap reduction function. However, by measuring the components of individual modes of the background and checking for consistency with isotropy, this approach has the potential to reveal much more information. Each individual mode on its own describes a background that is correlated between different points on the sky. A measurement of the components that indicates the presence of correlations in the background on large angular scales would suggest startling new physics.
Damping of glacial‐interglacial cycles from anthropogenic forcing

Climate variability over the past million years shows a strong glacial‐interglacial cycle of ∼100,000 years as a combined result of Milankovitch orbital forcing and climatic resonance. It has been suggested that anthropogenic contributions to radiative forcing may extend the length of the present interglacial, but the effects of anthropogenic forcing on the periodicity of glacial‐interglacial cycles has received little attention. Here I demonstrate that moderate anthropogenic forcing can act to damp this 100,000 year cycle and reduce climate variability from orbital forcing. Future changes in solar insolation alone will continue to drive a 100,000 year climate cycle over the next million years, but the presence of anthropogenic warming can force the climate into an ice‐free state that only weakly responds to orbital forcing. Sufficiently strong anthropogenic forcing that eliminates the glacial‐interglacial cycle may serve as an indication of an epoch transition from the Pleistocene to the Anthropocene.
Analytical computation of the epidemic threshold on temporal networks

The time variation of contacts in a networked system may fundamentally alter the properties of spreading processes and affect the condition for large-scale propagation, as encoded in the epidemic threshold. Despite the great interest in the problem for the physics, applied mathematics, computer science and epidemiology communities, a full theoretical understanding is still missing and currently limited to the cases where the time-scale separation holds between spreading and network dynamics or to specific temporal network models. We consider a Markov chain description of the Susceptible-Infectious-Susceptible process on an arbitrary temporal network. By adopting a multilayer perspective, we develop a general analytical derivation of the epidemic threshold in terms of the spectral radius of a matrix that encodes both network structure and disease dynamics. The accuracy of the approach is confirmed on a set of temporal models and empirical networks and against numerical results. In addition, we explore how the threshold changes when varying the overall time of observation of the temporal network, so as to provide insights on the optimal time window for data collection of empirical temporal networked systems. Our framework is both of fundamental and practical interest, as it offers novel understanding of the interplay between temporal networks and spreading dynamics.
3D Printing of Scintillating Materials

Scintillating materials are commonly used in charged particle detectors as detector elements due to their ease of manufacture, relatively low cost, and good timing resolution. The most common type of scintillator is the plastic scintillator, in which wavelength shifting dopants are embedded in a polystyrene matrix. A charged particle, traversing the polystyrene base excited some of the polymer molecules, causing them to emit UV light upon recombination. Typically, 2,5-diphenyloxazole (PPO) is used as a first step to down-convert the UV light to longer wavelength, peaking at 350nm. Due to the short absorption length of the polymer base in the UV range, a second wavelength shifting dopant, typically 1,4-di-(5-phenyl-2-oxazolyl)-benzene (POPOP), with an emission wavelength peak at 410 nm is used to further shift the emitted light to the visible range, while keeping the wavelength short enough to be effectively detected by the detection element (usually a photocathode). Scintillators are nowadays typically made by either casting of a resin+hardener combination, or by extrusion of a molten scintillator. These cast or extruded scintillator bar are t hen machined to the required geometry using standard machining techniques (note that the low melting/softening point of scintillators and to the requirements of a clean surface for ligh t collection places severe constraints on the requirements f rom the machine shop, i.e., low temperature machining and extreme cleanliness with the additional need to polish the sci ntillator parts after machining). We note that while cast sci ntillators are more versatile in their possible designs, they su ffer from long production times (up to 2 weeks for polymerization) and are also not amenable to complex geometries due to the requirement of producing a complicated mold. We approach the problem of scintillator manufacturing differently. Rather than taking a top-down approach (i.e. machining a solid block into a preferred shape subtractive manufacturing), we take a bottom-up approach, using newly developed 3D printing techniques to directly print the requir ed
What is India speaking: The "Hinglish" invasion

While language competition models of diachronic language shift are increasingly sophisticated, drawing on sociolinguistic components like variable language prestige, distance from language centers and intermediate bilingual transitionary populations, in one significant way they fall short. They fail to consider contact-based outcomes resulting in mixed language practices, e.g. outcome scenarios such as creoles or unmarked code switching as an emergent communicative norm. On these lines something very interesting is uncovered in India, where traditionally there have been monolingual Hindi speakers and Hindi/English bilinguals, but virtually no monolingual English speakers. While the Indian census data reports a sharp increase in the proportion of Hindi/English bilinguals, we argue that the number of Hindi/English bilinguals in India is inaccurate, given a new class of urban individuals speaking a mixed lect of Hindi and English, popularly known as "Hinglish". Based on predator-prey, sociolinguistic theories, salient local ecological factors and the rural-urban divide in India, we propose a new mathematical model of interacting monolingual Hindi speakers, Hindi/English bilinguals and Hinglish speakers. The model yields globally asymptotic stable states of coexistence, as well as bilingual extinction. To validate our model, sociolinguistic data from different Indian classes are contrasted with census reports: We see that purported urban Hindi/English bilinguals are unable to maintain fluent Hindi speech and instead produce Hinglish, whereas rural speakers evidence monolingual Hindi. Thus we present evidence for the first time where an unrecognized mixed lect involving English but not "English", has possibly taken over a sizeable faction of a large global population.
Tidal invariants for compact binaries on quasicircular orbits

we dene and calculate at O( ) (conservative) shifts in the eigenvalues of the electric- and magnetic-type tidal tensors, and a (dissipative) shift in a scalar product between their eigenbases. This approach yields four gauge-invariant functions, from which one may construct other tidal quantities such as the curvature scalars and the speciality index. First, we analyze the general case of a geodesic in a regular perturbed vacuum spacetime admitting a helical Killing vector and a reection symmetry. Next, we specialize to focus on circular orbits in the equatorial plane of Kerr spacetime at O( ). We present accurate numerical results for the Schwarzschild case for orbital radii up to the light-ring, calculated via independent implementations in Lorenz and Regge-Wheeler gauges. We show that our results are consistent with leading-order post-Newtonian expansions, and demonstrate the existence of additional structure in the strong-eld regime. We anticipate that our strong-eld results will inform (e.g.) eective
MSSM dark matter and a light slepton sector: The incredible bulk

Recent experimental results from the LHC have placed strong constraints on the masses of colored superpartners. The MSSM parameter space is also constrained by the measurement of the Higgs boson mass, and the requirement that the relic density of lightest neutralinos be consistent with observations. Although large regions of the MSSM parameter space can be excluded by these combined bounds, leptophilic versions of the MSSM can survive these constraints. In this paper we consider a scenario in which the requirements of minimal flavor violation, vanishing $CP$-violation, and mass universality are relaxed, specifically focusing on scenarios with light sleptons. We find a large region of parameter space, analogous to the original bulk region, for which the lightest neutralino is a thermal relic with an abundance consistent with that of dark matter. We find that these leptophilic models are constrained by measurements of the magnetic and electric dipole moments of the electron and muon, and that these models have interesting signatures at a variety of indirect detection experiments.
Variational Gaussian Process State-Space Models

State-space models have been successfully used for more than fifty years in different areas of science and engineering. We present a procedure for efficient variational Bayesian learning of nonlinear state-space models based on sparse Gaussian processes. The result of learning is a tractable posterior over nonlinear dynamical systems. In comparison to conventional parametric models, we offer the possibility to straightforwardly trade off model capacity and computational cost whilst avoiding overfitting. Our main algorithm uses a hybrid inference approach combining variational Bayes and sequential Monte Carlo. We also present stochastic variational inference and online learning approaches for fast learning with long time series.