nils-herrmann/clean_scirepeval huggingface dataset:
Phase transitions in semisupervised clustering of sparse networks

Predicting labels of nodes in a network, such as community memberships or demographic variables, is an important problem with applications in social and biological networks. A recently discovered phase transition puts fundamental limits on the accuracy of these predictions if we have access only to the network topology. However, if we know the correct labels of some fraction α of the nodes, we can do better. We study the phase diagram of this semisupervised learning problem for networks generated by the stochastic block model. We use the cavity method and the associated belief propagation algorithm to study what accuracy can be achieved as a function of α. For k=2 groups, we find that the detectability transition disappears for any α>0, in agreement with previous work. For larger k where a hard but detectable regime exists, we find that the easy/hard transition (the point at which efficient algorithms can do better than chance) becomes a line of transitions where the accuracy jumps discontinuously at a critical value of α. This line ends in a critical point with a second-order transition, beyond which the accuracy is a continuous function of α. We demonstrate qualitatively similar transitions in two real-world networks.
Belief Revision and Trust

Belief revision is the process in which an agent incorporates a new piece of information together with a pre-existing set of beliefs. When the new information comes in the form of a report from another agent, then it is clear that we must first determine whether or not that agent should be trusted. In this paper, we provide a formal approach to modeling trust as a pre-processing step before belief revision. We emphasize that trust is not simply a relation between agents; the trust that one agent has in another is often restricted to a particular domain of expertise. We demonstrate that this form of trust can be captured by associating a state-partition with each agent, then relativizing all reports to this state partition before performing belief revision. In this manner, we incorporate only the part of a report that falls under the perceived domain of expertise of the reporting agent. Unfortunately, state partitions based on expertise do not allow us to compare the relative strength of trust held with respect to different agents. To address this problem, we introduce pseudometrics over states to represent differing degrees of trust. This allows us to incorporate simultaneous reports from multiple agents in a way that ensures the most trusted reports will be believed.
Regularization by Early Stopping for Online Learning Algorithms

SILVIA VILLAAbstract. We study the learning algorithm corresponding to the incremental gradient descent deﬁned by theempirical risk over an inﬁnite dimensional hypotheses space. We consider a statistical learning setting and showthat, provided with a universal step-size and a suitable early stopping rule, the learning algorithm thus obtained isuniversally consistent and derive ﬁnite sample bounds. Our results provide a theoretical foundation for consideringearly stopping in online learning algorithms and shed light on the effect of allowing for multiple passes over the data.Key words. Online learning, incremental gradient descent, consistency
The quantum laws of physics: a new description of dynamics and causality

It is possible to completely explain all aspects of quantum mechanics by expressing the relations between physical properties in terms of complex conditional probabilities ( A 89, 042115(2014)). These fully deterministic probabilities replace the classical notions of phase space geometries and continuous trajectories with a more accurate description that takes into account the role of dynamics in the emergence of reality. We can then understand why so many previous attempts to find a detailed explanation of quantum phenomena have failed: the assumption of a static reality breaks down when the interaction needed to obtain a real effect exceeds Planck`s constant. Beyond that limit, complex conditional probabilities are the only valid expression of the fundamental laws of physics.
LTLf and LDLf Monitoring: A Technical Report

Runtime monitoring is one of the central tasks to provide operational decision support to running business processes, and check on-the-fly whether they comply with constraints and rules. We study runtime monitoring of properties expressed in LTL on finite traces (LTLf) and in its extension LDLf. LDLf is a powerful logic that captures all monadic second order logic on finite traces, which is obtained by combining regular expressions and LTLf, adopting the syntax of propositional dynamic logic (PDL). Interestingly, in spite of its greater expressivity, LDLf has exactly the same computational complexity of LTLf. We show that LDLf is able to capture, in the logic itself, not only the constraints to be monitored, but also the de-facto standard RV-LTL monitors. This makes it possible to declaratively capture monitoring metaconstraints, and check them by relying on usual logical services instead of ad-hoc algorithms. This, in turn, enables to flexibly monitor constraints depending on the monitoring state of other constraints, e.g., "compensation" constraints that are only checked when others are detected to be violated. In addition, we devise a direct translation of LDLf formulas into nondeterministic automata, avoiding to detour to Buechi automata or alternating automata, and we use it to implement a monitoring plug-in for the PROM suite.
Electron-doped phosphorene: A potential monolayer superconductor

We predict by first-principles calculations that the electron-doped phosphorene is a potential BCS-like superconductor. The stretching modes at the Brillouin-zone center are remarkably softened by the electron-doping, which results in the strong electron-phonon coupling. The superconductivity can be introduced by a doped electron density above , and may exist over the liquid-helium temperature when 2.6 \times10^{14}\ \text{cm}^{-2}$ ?> . The superconductivity can be significantly tuned and enhanced by applying tensile strain. The maximum critical temperature of electron-doped phosphorene is predicted to be higher than 10 K. The superconductivity of phosphorene will significantly broaden the applications of this novel material.
Fast MLE Computation for the Dirichlet Multinomial

Given a collection of categorical data, we want to find the parameters of a Dirichlet distribution which maximizes the likelihood of that data. Newton's method is typically used for this purpose but current implementations require reading through the entire dataset on each iteration. In this paper, we propose a modification which requires only a single pass through the dataset and substantially decreases running time. Furthermore we analyze both theoretically and empirically the performance of the proposed algorithm, and provide an open source implementation.
Hierarchical clustering of DNA k-mer counts in RNA-seq fastq files reveals batch effects

Batch effects are artificial sources of variation due to experimental design. Batch effect is a widespread phenomenon in high througput data which can be minimized but not always be avoided. Therefore mechanisms for detection of batch effects are needed which requires comparison of multiple samples. Due to large data volumes 1e12 Bytes this can be technical challenging. 
We describe the application of hierarchical clustering (HC) on DNA k-mer profiles of multiple fastq files which creates tree structures based on similarity of sequence content. Ideally, HC tree adjacency reflects experimental treatment groups but the algorithm may also agglomerate according to sample preparation groups which then indicates the presence of batch effects. This introduces a new perspective in quality control. 
In order to perform fast analysis on large data sets we implemented a new algorithm. The algorithm and user interface are implemented a new R-package (seqTools). The result is now available on R-Forge for Linux and Windows. 
Using this implementation, we compared the transcriptome sequence content of 61 human tissue samples on 8 different flowcells. We pairwise compared flowcells where at least 4 samples from the same tissue type (fibroblasts or jurkat cells) were present and 30) does not remove the identified batch effects.
Is Consciousness Computable? Quantifying Integrated Information Using Algorithmic Information Theory

In this article we review Tononi's (2008) theory of consciousness as integrated information. We argue that previous formalizations of integrated information (e.g. Griffith, 2014) depend on information loss. Since lossy integration would necessitate continuous damage to existing memories, we propose it is more natural to frame consciousness as a lossless integrative process and provide a formalization of this idea using algorithmic information theory. We prove that complete lossless integration requires noncomputable functions. This result implies that if unitary consciousness exists, it cannot be modelled computationally.
Cosmological bounces in spatially flat FRW spacetimes in metric f(R) gravity

The present work analyzes the various conditions in which there can be a bouncing universe solution in f(R) gravity. In the article an interesting method, to analyze the bouncing FRW solutions in a spatially flat universe using f(R) gravity models using an effective Einstein frame description of the process, is presented. The analysis shows that a cosmological bounce in the f(R) theory need not be described by an equivalent bounce in the Einstein frame description of the process where actually there may be no bounce at all. Nevertheless the Einstein frame description of the bouncing phenomena turns out to be immensely important as the dynamics of the bounce becomes amenable to logic based on general relativistic intuition. The theory of scalar cosmological perturbations in the bouncing universe models in f(R) theories has also been worked out in the Einstein frame.
Generalized full-vector multi-mode matching analysis of whispering gallery microcavities.

We outline a full-vectorial three-dimensional multi-mode matching technique in a cylindrical coordinate system that addresses the mutual coupling among multiple modes co-propagating in a perturbed whispering gallery mode microcavity. In addition to its superior accuracy in respect to our previously implemented single-mode matching technique, this current technique is suitable for modelling waveguide-to-cavity coupling where the influence of multi-mode coupling is non-negligible. Using this methodology, a robust scheme for hybrid integration of a microcavity onto a silicon-on-insulator platform is proposed.
UV surface brightness of galaxies from the local universe to z ~ 5

The Tolman test for surface brightness (SB) dimming was originally proposed as a test for the expansion of the universe. The test, which is independent of the details of the assumed cosmology, is based on comparisons of the SB of identical objects at different cosmological distances. Claims have been made that the Tolman test provides compelling evidence against a static model for the universe. In this paper we reconsider this subject by adopting a static Euclidean universe (SEU) with a linear Hubble relation at all z (which is not the standard Einstein–de Sitter model), resulting in a relation between flux and luminosity that is virtually indistinguishable from the one used for ΛCDM models. Based on the analysis of the UV SB of luminous disk galaxies from HUDF and GALEX datasets, reaching from the local universe to z ~ 5, we show that the SB remains constant as expected in a static universe. A re-analysis of previously published data used for the Tolman test at lower redshift, when treated within the same framework, confirms the results of the present analysis by extending our claim to elliptical galaxies. We conclude that available observations of galactic SB are consistent with a SEU model. We do not claim that the consistency of the adopted model with SB data is sufficient by itself to confirm what would be a radical transformation in our understanding of the cosmos. However, we believe this result is more than sufficient reason to examine this combination of hypotheses further.
A CANDIDATE MASSIVE BLACK HOLE IN THE LOW-METALLICITY DWARF GALAXY PAIR MRK 709

The incidence and properties of present-day dwarf galaxies hosting massive black holes (BHs) can provide important constraints on the origin of high-redshift BH seeds. Here we present high-resolution X-ray and radio observations of the low-metallicity, star-forming, dwarf-galaxy system Mrk 709 with the Chandra X-ray Observatory and the Karl G. Jansky Very Large Array. These data reveal spatially coincident hard X-ray and radio point sources with luminosities suggesting the presence of an accreting massive BH (MBH  ∼  105–7 M☉). Based on imaging from the Sloan Digital Sky Survey (SDSS), we find that Mrk 709 consists of a pair of compact dwarf galaxies that appear to be interacting with one another. The position of the candidate massive BH is consistent with the optical center of the southern galaxy (Mrk 709 S), while no evidence for an active BH is seen in the northern galaxy (Mrk 709 N). We derive stellar masses of M⋆  ∼  2.5  ×  109M☉ and M⋆  ∼  1.1  ×  109 M☉ for Mrk 709 S and Mrk 709 N, respectively, and present an analysis of the SDSS spectrum of the BH host Mrk 709 S. At a metallicity of just ∼10% solar, Mrk 709 is among the most metal-poor galaxies with evidence for an active galactic nucleus. Moreover, this discovery adds to the growing body of evidence that massive BHs can form in dwarf galaxies and that deep, high-resolution X-ray and radio observations are ideally suited to reveal accreting massive BHs hidden at optical wavelengths.
Parton distribution amplitudes of light vector mesons

A rainbow-ladder truncation of QCD's Dyson-Schwinger equations is used to calculate rho- and phi-meson valence-quark (twist-two parton) distribution amplitudes (PDAs) via a light-front projection of their Bethe-Salpeter wave functions, which possess S- and D-wave components of comparable size in the meson rest frame. All computed PDAs are broad concave functions, whose dilation with respect to the asymptotic distribution is an expression of dynamical chiral symmetry breaking. The PDAs can be used to define an ordering of valence-quark light-front spatial-extent within mesons: this size is smallest within the pion and increases through the perp-polarisation to the parallel-polarisation of the vector mesons; effects associated with the breaking of SU(3)-flavour symmetry are significantly smaller than those associated with altering the polarisation of vector mesons. Notably, the predicted pointwise behaviour of the rho-meson PDAs is in quantitative agreement with that inferred recently via an analysis of diffractive vector-meson photoproduction experiments.
Carbon monoxide intensity mapping at moderate redshifts

We present a study of the feasibility of an intensity-mapping survey targeting the 115 GHz CO(1-0) rotational transition at $z\sim3$. We consider four possible models and estimate the spatial and angular power spectra of CO fluctuations predicted by each of them. The frequency bandwidths of most proposed CO intensity mapping spectrographs are too small to use the Limber approximation to calculate the angular power spectrum, so we present an alternative method for calculating the angular power spectrum. The models we consider span two orders of magnitude in signal amplitude, so there is a significant amount of uncertainty in the theoretical predictions of this signal. We then consider a parameterized set of hypothetical spectrographs designed to measure this power spectrum and predict the signal-to-noise ratios expected under these models. With the spectrographs we consider we find that three of the four models give an SNR greater than 10 within one year of observation. We also study the effects on SNR of varying the parameters of the survey in order to demonstrate the importance of carefully considering survey parameters when planning such an experiment.
RESOLVED STAR FORMATION ON SUB-GALACTIC SCALES IN A MERGER AT z = 1.7

We present a detailed analysis of Hubble Space Telescope (HST) Wide Field Camera 3 (WFC3) G141 grism spectroscopy for seven star-forming regions of the highly magnified lensed starburst galaxy RCSGA 032727-132609 at z = 1.704. We measure the spatial variations of the extinction in RCS0327 through the observed Hγ/Hβ emission line ratios, finding a constant average extinction of E(B − V)gas = 0.40 ± 0.07. We infer that the star formation is enhanced as a result of an ongoing interaction, with measured star formation rates derived from demagnified, extinction-corrected Hβ line fluxes for the individual star-forming clumps falling >1–2 dex above the star formation sequence. When combining the HST/WFC3 [O iii] λ5007/Hβ emission line ratio measurements with [N ii]/Hα line ratios from Wuyts et al., we find that the majority of the individual star-forming regions fall along the local “normal” abundance sequence. With the first detections of the He i λ5876 and He ii λ4686 recombination lines in a distant galaxy, we probe the massive-star content of the star-forming regions in RCS0327. The majority of the star-forming regions have a He i λ5876 to Hβ ratio consistent with the saturated maximum value, which is only possible if they still contain hot O-stars. Two regions have lower ratios, implying that their last burst of new star formation ended ∼5 Myr ago. Together, the He i λ5876 and He ii λ4686 to Hβ line ratios provide indirect evidence for the order in which star formation is stopping in individual star-forming knots of this high-redshift merger. We place the spatial variations of the extinction, star formation rate and ionization conditions in the context of the star formation history of RCS0327.
Exchangeable Variable Models

A sequence of random variables is exchangeable if its joint distribution is invariant under variable permutations. We introduce exchangeable variable models (EVMs) as a novel class of probabilistic models whose basic building blocks are partially exchangeable sequences, a generalization of exchangeable sequences. We prove that a family of tractable EVMs is optimal under zeroone loss for a large class of functions, including parity and threshold functions, and strictly subsumes existing tractable independence-based model families. Extensive experiments show that EVMs outperform state of the art classifiers such as SVMs and probabilistic models which are solely based on independence assumptions.
Probing the elastic limit of DNA bending

Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured the opening rates of small dsDNA loops with contour lengths ranging between 40 and 200 bp using single-molecule Fluorescence Resonance Energy Transfer. The relationship of loop lifetime to loop size revealed a critical transition in bending stress. Above the critical loop size, the loop lifetime changed with loop size in a manner consistent with elastic bending stress, but below it, became less sensitive to loop size, indicative of softened dsDNA. The critical loop size increased from ∼60 bp to ∼100 bp with the addition of 5 mM magnesium. We show that our result is in quantitative agreement with the kinkable worm-like chain model, and furthermore, can reproduce previously reported looping probabilities of dsDNA over the range between 50 and 200 bp. Our findings shed new light on the energetics of sharply bent dsDNA.
Spectral line broadening in magnetized black holes

We consider weakly magnetized non-rotating black holes. In the presence of a regular magnetic field the motion of charged particles in the vicinity of a black hole is modified. As a result, the position of the innermost stable circular orbit (ISCO) becomes closer to the horizon. When the Lorentz force is repulsive (directed from the black hole) the ISCO radius can reach the gravitational radius. In the process of accretion charged particles (ions) of the accreting matter can be accumulated near their ISCO, while neutral particles fall down to the black hole after they reach 6M radius. The sharp spectral line Fe α, emitted by iron ions at such orbits, is broadened when the emission is registered by a distant observer. In this paper we study this broadening effect and discuss how one can extract information concerning the strength of the magnetic field from the observed spectrum.
KVA: Capital Valuation Adjustment

Credit (CVA), Debit (DVA) and Funding Valuation Adjustments (FVA) are now familiar valuation adjustments made to the value of a portfolio of derivatives to account for credit risks and funding costs. However, recent changes in the regulatory regime and the increases in regulatory capital requirements has led many banks to include the cost of capital in derivative pricing. This paper formalises the addition of cost of capital by extending the Burgard-Kjaer (2013) semi-replication approach to CVA and FVA to include an addition capital term, Capital Valuation Adjustment (KVA, i.e. Kapital Valuation Adjustment to distinguish from CVA.) The utilization of the capital for funding purposes is also considered. The use of the semi-replication approach means that the flexibility around the treatment of self-default is carried over into this analysis. The paper further considers the practical calculation of KVA with reference to the Basel II (BCBS-128) and Basel III (BCBS-189) capital regimes and their implementation via CRD IV. The paper also assesses how KVA may be hedged, given that any hedging transactions themselves lead to regulatory capital requirements and hence capital costs. Finally a number of numerical examples are presented to gauge the cost impact of KVA on vanilla derivative products.
On The Longest Chain Rule and Programmed Self-Destruction of Crypto Currencies

In this paper we revisit some major orthodoxies which lie at the heart of the bitcoin crypto currency and its numerous clones. In particular we look at The Longest Chain Rule, the monetary supply policies and the exact mechanisms which implement them. We claim that these built-in properties are not as brilliant as they are sometimes claimed. A closer examination reveals that they are closer to being... engineering mistakes which other crypto currencies have copied rather blindly. More precisely we show that the capacity of current crypto currencies to resist double spending attacks is poor and most current crypto currencies are highly vulnerable. Satoshi did not implement a timestamp for bitcoin transactions and the bitcoin software does not attempt to monitor double spending events. As a result major attacks involving hundreds of millions of dollars can occur and would not even be recorded. Hundreds of millions have been invested to pay for ASIC hashing infrastructure yet insufficient attention was paid to network neutrality and to insure that the protection layer it promises is effective and cannot be abused. In this paper we develop a theory of Programmed Self-Destruction of crypto currencies. We observe that most crypto currencies have mandated abrupt and sudden transitions. These affect their hash rate and therefore their protection against double spending attacks which we do not limit the to the notion of 51% attacks which is highly misleading. In addition we show that smaller bitcoin competitors are substantially more vulnerable. In addition to small hash rate, many bitcoin competitors mandate incredibly important adjustments in miner reward. We exhibit examples of 'alt-coins' which validate our theory and for which the process of programmed decline and rapid self-destruction has clearly already started.