nils-herrmann/clean_scirepeval huggingface dataset:
Building Water Models: A Different Approach

Simplified classical water models are currently an indispensable component in practical atomistic simulations. Yet, despite several decades of intense research, these models are still far from perfect. Presented here is an alternative approach to constructing widely used point charge water models. In contrast to the conventional approach, we do not impose any geometry constraints on the model other than the symmetry. Instead, we optimize the distribution of point charges to best describe the “electrostatics” of the water molecule. The resulting “optimal” 3-charge, 4-point rigid water model (OPC) reproduces a comprehensive set of bulk properties significantly more accurately than commonly used rigid models: average error relative to experiment is 0.76%. Close agreement with experiment holds over a wide range of temperatures. The improvements in the proposed model extend beyond bulk properties: compared to common rigid models, predicted hydration free energies of small molecules using OPC are uniformly closer to experiment, with root-mean-square error <1 kcal/mol.
The Digital Public Library of America Ingestion Ecosystem: Lessons Learned After One Year of Large-Scale Collaborative Metadata Aggregation

The Digital Public Library of America (DPLA) aggregates metadata for cultural heritage materials from 20 direct partners, or Hubs, across the United States. While the initial build-out of the DPLA's infrastructure used a lightweight ingestion system that was ultimately pushed into production, a year's experience has allowed DPLA and its partners to identify limitations to that system, the quality and scalability of metadata remediation and enhancement possible, and areas for collaboration and leadership across the partnership. Although improved infrastructure is needed to support aggregation at this scale and complexity, ultimately DPLA needs to balance responsibilities across the partnership and establish a strong community that shares ownership of the aggregation process.
Matrix Completion on Graphs

The problem of finding the missing values of a matrix given a few of its entries, called matrix completion, has gathered a lot of attention in the recent years. Although the problem under the standard low rank assumption is NP-hard, Cand\`es and Recht showed that it can be exactly relaxed if the number of observed entries is sufficiently large. In this work, we introduce a novel matrix completion model that makes use of proximity information about rows and columns by assuming they form communities. This assumption makes sense in several real-world problems like in recommender systems, where there are communities of people sharing preferences, while products form clusters that receive similar ratings. Our main goal is thus to find a low-rank solution that is structured by the proximities of rows and columns encoded by graphs. We borrow ideas from manifold learning to constrain our solution to be smooth on these graphs, in order to implicitly force row and column proximities. Our matrix recovery model is formulated as a convex non-smooth optimization problem, for which a well-posed iterative scheme is provided. We study and evaluate the proposed matrix completion on synthetic and real data, showing that the proposed structured low-rank recovery model outperforms the standard matrix completion model in many situations.
Dynamics in two networks based on stocks of the US stock market

We follow the main stocks belonging to the New York Stock Exchange and to Nasdaq from 2003 to 2012, through years of normality and of crisis, and study the dynamics of networks built on two measures expressing relations between those stocks: correlation, which is symmetric and measures how similar two stocks behave, and Transfer Entropy, which is non-symmetric and measures the influence of the time series of one stock onto another in terms of the information that the time series of one stock transmits to the time series of another stock. The two measures are used in the creation of two networks that evolve in time, revealing how the relations between stocks and industrial sectors changed in times of crisis. The two networks are also used in conjunction with a dynamic model of the spreading of volatility in order to detect which are the stocks that are most likely to spread crises, according to the model. This information may be used in the building of policies aiming to reduce the effect of financial crises.
Microtask Crowdsourcing for Disease Mention Annotation in PubMed Abstracts

Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language processing (BioNLP) projects attempt to address this challenge, but the state of the art still leaves much room for improvement. Progress in BioNLP research depends on large, annotated corpora for evaluating information extraction systems and training machine learning models. Traditionally, such corpora are created by small numbers of expert annotators often working over extended periods of time. Recent studies have shown that workers on microtask crowdsourcing platforms such as Amazon's Mechanical Turk (AMT) can, in aggregate, generate high-quality annotations of biomedical text. Here, we investigated the use of the AMT in capturing disease mentions in PubMed abstracts. We used the NCBI Disease corpus as a gold standard for refining and benchmarking our crowdsourcing protocol. After several iterations, we arrived at a protocol that reproduced the annotations of the 593 documents in the 'training set' of this gold standard with an overall F measure of 0.872 (precision 0.862, recall 0.883). The output can also be tuned to optimize for precision (max = 0.984 when recall = 0.269) or recall (max = 0.980 when precision = 0.436). Each document was completed by 15 workers, and their annotations were merged based on a simple voting method. In total 145 workers combined to complete all 593 documents in the span of 9 days at a cost of $.066 per abstract per worker. The quality of the annotations, as judged with the F measure, increases with the number of workers assigned to each task; however minimal performance gains were observed beyond 8 workers per task. These results add further evidence that microtask crowdsourcing can be a valuable tool for generating well-annotated corpora in BioNLP. Data produced for this analysis are available at http://figshare.com/articles/Disease_Mention_Annotation_with_Mechanical_Turk/1126402.
Quantum critical benchmark for density functional theory

Two electrons at the threshold of ionization represent a severe test case for electronic structure theory. A pseudospectral method yields a very accurate density of the two-electron ion with nuclear charge close to the critical value. Highly accurate energy components and potentials of Kohn-Sham density functional theory are given, as well as a useful parametrization of the critical density. The challenges for density functional approximations and the strength of correlation are also discussed.
Sensitivity analysis for finite Markov chains in discrete time

When the initial and transition probabilities of a finite Markov chain in discrete time are not well known, we should perform a sensitivity analysis. This is done by considering as basic uncertainty models the so-called credal sets that these probabilities are known or believed to belong to, and by allowing the probabilities to vary over such sets. This leads to the definition of an imprecise Markov chain. We show that the time evolution of such a system can be studied very efficiently using so-called lower and upper expectations. We also study how the inferred credal set about the state at time n evolves as n → ∞: under quite unrestrictive conditions, it converges to a uniquely invariant credal set, regardless of the credal set given for the initial state. This leads to a non-trivial generalisation of the classical Perron-Frobenius Theorem to imprecise Markov chains.
Quantum Annealing for Variational Bayes Inference

This paper presents studies on a deterministic annealing algorithm based on quantum annealing for variational Bayes (QAVB) inference, which can be seen as an extension of the simulated annealing for variational Bayes (SAVB) inference. QAVB is as easy as SAVB to implement. Experiments revealed QAVB finds a better local optimum than SAVB in terms of the variational free energy in latent Dirichlet allocation (LDA).
Gaussian Process Structural Equation Models with Latent Variables

In a variety of disciplines such as social sciences, psychology, medicine and economics, the recorded data are considered to be noisy measurements of latent variables connected by some causal structure. This corresponds to a family of graphical models known as the structural equation model with latent variables. While linear non-Gaussian variants have been well-studied, inference in nonparametric structural equation models is still underdeveloped. We introduce a sparse Gaussian process parameterization that defines a non-linear structure connecting latent variables, unlike common formulations of Gaussian process latent variable models. The sparse parameterization is given a full Bayesian treatment without compromising Markov chain Monte Carlo efficiency. We compare the stability of the sampling procedure and the predictive ability of the model against the current practice.
Guess Who Rated This Movie: Identifying Users Through Subspace Clustering

It is often the case that, within an online recommender system, multiple users share a common account. Can such shared accounts be identified solely on the basis of the userprovided ratings? Once a shared account is identified, can the different users sharing it be identified as well? Whenever such user identification is feasible, it opens the way to possible improvements in personalized recommendations, but also raises privacy concerns. We develop a model for composite accounts based on unions of linear subspaces, and use subspace clustering for carrying out the identification task. We show that a significant fraction of such accounts is identifiable in a reliable manner, and illustrate potential uses for personalized recommendation.
Probabilistic inverse reinforcement learning in unknown environments

We consider the problem of learning by demonstration from agents acting in unknown stochastic Markov environments or games. Our aim is to estimate agent preferences in order to construct improved policies for the same task that the agents are trying to solve. To do so, we extend previous probabilistic approaches for inverse reinforcement learning in known MDPs to the case of unknown dynamics or opponents. We do this by deriving two simplified probabilistic models of the demonstrator's policy and utility. For tractability, we use maximum a posteriori estimation rather than full Bayesian inference. Under a flat prior, this results in a convex optimisation problem. We find that the resulting algorithms are highly competitive against a variety of other methods for inverse reinforcement learning that do have knowledge of the dynamics.
The physics of hearing: fluid mechanics and the active process of the inner ear

Most sounds of interest consist of complex, time-dependent admixtures of tones of diverse frequencies and variable amplitudes. To detect and process these signals, the ear employs a highly nonlinear, adaptive, real-time spectral analyzer: the cochlea. Sound excites vibration of the eardrum and the three miniscule bones of the middle ear, the last of which acts as a piston to initiate oscillatory pressure changes within the liquid-filled chambers of the cochlea. The basilar membrane, an elastic band spiraling along the cochlea between two of these chambers, responds to these pressures by conducting a largely independent traveling wave for each frequency component of the input. Because the basilar membrane is graded in mass and stiffness along its length, however, each traveling wave grows in magnitude and decreases in wavelength until it peaks at a specific, frequency-dependent position: low frequencies propagate to the cochlear apex, whereas high frequencies culminate at the base. The oscillations of the basilar membrane deflect hair bundles, the mechanically sensitive organelles of the ear's sensory receptors, the hair cells. As mechanically sensitive ion channels open and close, each hair cell responds with an electrical signal that is chemically transmitted to an afferent nerve fiber and thence into the brain. In addition to transducing mechanical inputs, hair cells amplify them by two means. Channel gating endows a hair bundle with negative stiffness, an instability that interacts with the motor protein myosin-1c to produce a mechanical amplifier and oscillator. Acting through the piezoelectric membrane protein prestin, electrical responses also cause outer hair cells to elongate and shorten, thus pumping energy into the basilar membrane's movements. The two forms of motility constitute an active process that amplifies mechanical inputs, sharpens frequency discrimination, and confers a compressive nonlinearity on responsiveness. These features arise because the active process operates near a Hopf bifurcation, the generic properties of which explain several key features of hearing. Moreover, when the gain of the active process rises sufficiently in ultraquiet circumstances, the system traverses the bifurcation and even a normal ear actually emits sound. The remarkable properties of hearing thus stem from the propagation of traveling waves on a nonlinear and excitable medium.
Statistical guarantees for the EM algorithm: From population to sample-based analysis

We develop a general framework for proving rigorous guarantees on the performance of the EM algorithm and a variant known as gradient EM. Our analysis is divided into two parts: a treatment of these algorithms at the population level (in the limit of infinite data), followed by results that apply to updates based on a finite set of samples. First, we characterize the domain of attraction of any global maximizer of the population likelihood. This characterization is based on a novel view of the EM updates as a perturbed form of likelihood ascent, or in parallel, of the gradient EM updates as a perturbed form of standard gradient ascent. Leveraging this characterization, we then provide non-asymptotic guarantees on the EM and gradient EM algorithms when applied to a finite set of samples. We develop consequences of our general theory for three canonical examples of incomplete-data problems: mixture of Gaussians, mixture of regressions, and linear regression with covariates missing completely at random. In each case, our theory guarantees that with a suitable initialization, a relatively small number of EM (or gradient EM) steps will yield (with high probability) an estimate that is within statistical error of the MLE. We provide simulations to confirm this theoretically predicted behavior.
Mean-reversion and optimization

The purpose of these notes is to provide a systematic quantitative framework – in what is intended to be a ‘pedagogical’ fashion – for discussing mean-reversion and optimization. We start with pair trading and add complexity by following the sequence ‘mean-reversion via demeaning → regression → weighted regression → (constrained) optimization → factor models’. We discuss in detail how to do mean-reversion based on this approach, including common pitfalls encountered in practical applications, such as the difference between maximizing the Sharpe ratio and minimizing an objective function when trading costs are included. We also discuss explicit algorithms for optimization with linear costs, constraints and bounds. We also illustrate our discussion on an explicit intraday mean-reversion alpha.
Neutrinoless double beta decay experiments

Neutrinoles double beta decay is the only process known so far able to test the neutrino intrinsic nature: its experimental observation would imply that the lepton number is violated by two units and prove that neutrinos have a Majorana mass components, being their own anti-particle. While several experiments searching for such a rare decay have been performed in the past, a new generation of experiments using different isotopes and techniques have recently released their results or are raking data and will provide new limits, should no signal be observed, in the next few years to come. The present contribution reviews the latest public results on double beta decay searches and gives an overview on the expected sensitivities of the experiments in construction which will be able to set stronger limits in the near future.
Educational trajectories of graduate students in physics education research

Physics education research (PER) is a rapidly growing area of PhD specialization. In this article we examine the trajectories that led respondents into a PER graduate program as well as their expected future trajectories. Data were collected in the form of an online survey sent to graduate students in PER. Our findings show a lack of visibility of PER as a field of study, a dominance of work at the undergraduate level, and a mismatch of future desires and expectations. We suggest that greater exposure is needed so PER is known as a field of inquiry for graduates, that more emphasis should be placed on research beyond the undergraduate level, and that there needs to be stronger communication to graduate students about potential careers.
Co-Localization of Audio Sources in Images Using Binaural Features and Locally-Linear Regression

This paper addresses the problem of localizing audio sources using binaural measurements. We propose a supervised formulation that simultaneously localizes multiple sources at different locations. The approach is intrinsically efficient because, contrary to prior work, it relies neither on source separation, nor on monaural segregation. The method starts with a training stage that establishes a locally linear Gaussian regression model between the directional coordinates of all the sources and the auditory features extracted from binaural measurements. While fixed-length wide-spectrum sounds (white noise) are used for training to reliably estimate the model parameters, we show that the testing (localization) can be extended to variable-length sparse-spectrum sounds (such as speech), thus enabling a wide range of realistic applications. Indeed, we demonstrate that the method can be used for audio-visual fusion, namely to map speech signals onto images and hence to spatially align the audio and visual modalities, thus enabling to discriminate between speaking and non-speaking faces. We release a novel corpus of real-room recordings that allow quantitative evaluation of the co-localization method in the presence of one or two sound sources. Experiments demonstrate increased accuracy and speed relative to several state-of-the-art methods.
Epidemic processes in complex networks

In recent years the research community has accumulated overwhelming evidence for the emergence of complex and heterogeneous connectivity patterns in a wide range of biological and sociotechnical systems. The complex properties of real-world networks have a profound impact on the behavior of equilibrium and nonequilibrium phenomena occurring in various systems, and the study of epidemic spreading is central to our understanding of the unfolding of dynamical processes in complex networks. The theoretical analysis of epidemic spreading in heterogeneous networks requires the development of novel analytical frameworks, and it has produced results of conceptual and practical relevance. A coherent and comprehensive review of the vast research activity concerning epidemic processes is presented, detailing the successful theoretical approaches as well as making their limits and assumptions clear. Physicists, mathematicians, epidemiologists, computer, and social scientists share a common interest in studying epidemic spreading and rely on similar models for the description of the diffusion of pathogens, knowledge, and innovation. For this reason, while focusing on the main results and the paradigmatic models in infectious disease modeling, the major results concerning generalized social contagion processes are also presented. Finally, the research activity at the forefront in the study of epidemic spreading in coevolving, coupled, and time-varying networks is reported.
Sector-Based Factor Models for Asset Returns

Factor analysis is a statistical technique employed to evaluate how observed variables correlate through common factors and unique variables. While it is often used to analyze price movement in the unstable stock market, it does not always yield easily interpretable results. In this study, we develop improved factor models by explicitly incorporating sector information on our studied stocks. We add eleven sectors of stocks as defined by the IBES, represented by respective sector-specific factors, to non-specific market factors to revise the factor model. We then develop an expectation maximization (EM) algorithm to compute our revised model with 15 years' worth of S&P 500 stocks' daily close prices. Our results in most sectors show that nearly all of these factor components have the same sign, consistent with the intuitive idea that stocks in the same sector tend to rise and fall in coordination over time. Results obtained by the classic factor model, in contrast, had a homogeneous blend of positive and negative components. We conclude that results produced by our sector-based factor model are more interpretable than those produced by the classic non-sector-based model for at least some stock sectors.
Elasticity of 3D networks with rigid filaments and compliant crosslinks.

Disordered filamentous networks with compliant crosslinks exhibit a low linear elastic shear modulus at small strains, but stiffen dramatically at high strains. Experiments have shown that the elastic modulus can increase by up to three orders of magnitude while the networks withstand relatively large stresses without rupturing. Here, we perform an analytical and numerical study on model networks in three dimensions. Our model consists of a collection of randomly oriented rigid filaments connected by flexible crosslinks that are modeled as wormlike chains. Due to zero probability of filament intersection in three dimensions, our model networks are by construction prestressed in terms of initial tension in the crosslinks. We demonstrate how the linear elastic modulus can be related to the prestress in these networks. Under the assumption of affine deformations in the limit of infinite crosslink density, we show analytically that the nonlinear elastic regime in 1- and 2-dimensional networks is characterized by power-law scaling of the elastic modulus with the stress. In contrast, 3-dimensional networks show an exponential dependence of the modulus on stress. Independent of dimensionality, if the crosslink density is finite, we show that the only persistent scaling exponent is that of the single wormlike chain. We further show that there is no qualitative change in the stiffening behavior of filamentous networks even if the filaments are bending-compliant. Consequently, unlike suggested in prior work, the model system studied here cannot provide an explanation for the experimentally observed linear scaling of the modulus with the stress in filamentous networks.