nils-herrmann/clean_scirepeval huggingface dataset:
Will solid-state drives accelerate your bioinformatics? In-depth profiling, performance analysis and beyond

A wide variety of large-scale data have been produced in bioinformatics. In response, the need for efficient handling of biomedical big data has been partly met by parallel computing. However, the time demand of many bioinformatics programs still remains high for large-scale practical uses because of factors that hinder acceleration by parallelization. Recently, new generations of storage devices have emerged, such as NAND flash-based solid-state drives (SSDs), and with the renewed interest in near-data processing, they are increasingly becoming acceleration methods that can accompany parallel processing. In certain cases, a simple drop-in replacement of hard disk drives by SSDs results in dramatic speedup. Despite the various advantages and continuous cost reduction of SSDs, there has been little review of SSD-based profiling and performance exploration of important but time-consuming bioinformatics programs. For an informative review, we perform in-depth profiling and analysis of 23 key bioinformatics programs using multiple types of devices. Based on the insight we obtain from this research, we further discuss issues related to design and optimize bioinformatics algorithms and pipelines to fully exploit SSDs. The programs we profile cover traditional and emerging areas of importance, such as alignment, assembly, mapping, expression analysis, variant calling and metagenomics. We explain how acceleration by parallelization can be combined with SSDs for improved performance and also how using SSDs can expedite important bioinformatics pipelines, such as variant calling by the Genome Analysis Toolkit and transcriptome analysis using RNA sequencing. We hope that this review can provide useful directions and tips to accompany future bioinformatics algorithm design procedures that properly consider new generations of powerful storage devices.
From Pixels to Torques: Policy Learning with Deep Dynamical Models

Data-efficient learning in continuous state-action spaces using very high-dimensional observations remains a key challenge in developing fully autonomous systems. In this paper, we consider one instance of this challenge, the pixels-totorques problem, where an agent must learn a closed-loop control policy from pixel information only. We introduce a data-efficient, model-based reinforcement learning algorithm that learns such a closed-loop policy directly from pixel information. The key ingredient is a deep dynamical model that uses deep autoencoders to learn a low-dimensional embedding of images jointly with a prediction model in this low-dimensional feature space. This joint learning ensures that not only static properties of the data are accounted for, but also dynamic properties. This is crucial for long-term predictions, which lie at the core of the adaptive model predictive control strategy that we use for closedloop control. Compared to state-of-the-art reinforcement learning methods, our approach learns quickly, scales to high-dimensional state spaces and facilitates fully autonomous learning from pixels to torques.
Contextual Markov Decision Processes

We consider a planning problem where the dynamics and rewards of the environment depend on a hidden static parameter referred to as the context. The objective is to learn a strategy that maximizes the accumulated reward across all contexts. The new model, called Contextual Markov Decision Process (CMDP), can model a customer's behavior when interacting with a website (the learner). The customer's behavior depends on gender, age, location, device, etc. Based on that behavior, the website objective is to determine customer characteristics, and to optimize the interaction between them. Our work focuses on one basic scenario--finite horizon with a small known number of possible contexts. We suggest a family of algorithms with provable guarantees that learn the underlying models and the latent contexts, and optimize the CMDPs. Bounds are obtained for specific naive implementations, and extensions of the framework are discussed, laying the ground for future research.
Asymptotic Investment Behaviors under a Jump-Diffusion Risk Process

We study an optimal investment control problem for an insurance company. The surplus process follows the Cramer-Lundberg process with perturbation of a Brownian motion. The company can invest its surplus into a risk-free asset and a Black-Scholes risky asset. The optimization objective is to minimize the probability of ruin. We show by new operators that the minimal ruin probability function is a classical solution to the corresponding HJB equation. Asymptotic behaviors of the optimal investment control policy and the minimal ruin probability function are studied for low surplus levels with a general claim size distribution. Some new asymptotic results for large surplus levels in the case with exponential claim distributions are obtained. We consider two cases of investment control: unconstrained investment and investment with a limited amount.
Tensor Canonical Correlation Analysis for Multi-View Dimension Reduction

Canonical correlation analysis (CCA) has proven an effective tool for two-view dimension reduction due to its profound theoretical foundation and success in practical applications. In respect of multi-view learning, however, it is limited by its capability of only handling data represented by two-view features, while in many real-world applications, the number of views is frequently many more. Although the ad hoc way of simultaneously exploring all possible pairs of features can numerically deal with multi-view data, it ignores the high order statistics (correlation information) which can only be discovered by simultaneously exploring all features. Therefore, in this work, we develop tensor CCA (TCCA) which straightforwardly yet naturally generalizes CCA to handle the data of an arbitrary number of views by analyzing the covariance tensor of the different views. TCCA aims to directly maximize the canonical correlation of multiple (more than two) views. Crucially, we prove that the main problem of multi-view canonical correlation maximization is equivalent to finding the best rank-1 approximation of the data covariance tensor, which can be solved efficiently using the well-known alternating least squares (ALS) algorithm. As a consequence, the high order correlation information contained in the different views is explored and thus a more reliable common subspace shared by all features can be obtained. In addition, a non-linear extension of TCCA is presented. Experiments on various challenge tasks, including large scale biometric structure prediction, internet advertisement classification, and web image annotation, demonstrate the effectiveness of the proposed method.
Local and Global Inference for High Dimensional Nonparanormal Graphical Models

This paper proposes a unified framework to quantify local and global inferential uncertainty for high dimensional nonparanormal graphical models. In particular, we consider the problems of testing the presence of a single edge and constructing a uniform confidence subgraph. Due to the presence of unknown marginal transformations, we propose a pseudo likelihood based inferential approach. In sharp contrast to the existing high dimensional score test method, our method is free of tuning parameters given an initial estimator, and extends the scope of the existing likelihood based inferential framework. Furthermore, we propose a U-statistic multiplier bootstrap method to construct the confidence subgraph. We show that the constructed subgraph is contained in the true graph with probability greater than a given nominal level. Compared with existing methods for constructing confidence subgraphs, our method does not rely on Gaussian or sub-Gaussian assumptions. The theoretical properties of the proposed inferential methods are verified by thorough numerical experiments and real data analysis.
High dimensional errors-in-variables models with dependent measurements

Suppose that we observe $y \in \mathbb{R}^f$ and $X \in \mathbb{R}^{f \times m}$ in the following errors-in-variables model: \begin{eqnarray*} y & = & X_0 \beta^* + \epsilon \\ X & = & X_0 + W \end{eqnarray*} where $X_0$ is a $f \times m$ design matrix with independent subgaussian row vectors, $\epsilon \in \mathbb{R}^f$ is a noise vector and $W$ is a mean zero $f \times m$ random noise matrix with independent subgaussian column vectors, independent of $X_0$ and $\epsilon$. This model is significantly different from those analyzed in the literature in the sense that we allow the measurement error for each covariate to be a dependent vector across its $f$ observations. Such error structures appear in the science literature when modeling the trial-to-trial fluctuations in response strength shared across a set of neurons. 
Under sparsity and restrictive eigenvalue type of conditions, we show that one is able to recover a sparse vector $\beta^* \in \mathbb{R}^m$ from the model given a single observation matrix $X$ and the response vector $y$. We establish consistency in estimating $\beta^*$ and obtain the rates of convergence in the $\ell_q$ norm, where $q = 1, 2$ for the Lasso-type estimator, and for $q \in [1, 2]$ for a Dantzig-type conic programming estimator. We show error bounds which approach that of the regular Lasso and the Dantzig selector in case the errors in $W$ are tending to 0.
Counterfactual Risk Minimization: Learning from Logged Bandit Feedback

We develop a learning principle and an efficient algorithm for batch learning from logged bandit feedback. This learning setting is ubiquitous in online systems (e.g., ad placement, web search, recommendation), where an algorithm makes a prediction (e.g., ad ranking) for a given input (e.g., query) and observes bandit feedback (e.g., user clicks on presented ads). We first address the counterfactual nature of the learning problem through propensity scoring. Next, we prove generalization error bounds that account for the variance of the propensity-weighted empirical risk estimator. These constructive bounds give rise to the Counterfactual Risk Minimization (CRM) principle. We show how CRM can be used to derive a new learning method - called Policy Optimizer for Exponential Models (POEM) - for learning stochastic linear rules for structured output prediction. We present a decomposition of the POEM objective that enables efficient stochastic gradient optimization. POEM is evaluated on several multi-label classification problems showing substantially improved robustness and generalization performance compared to the state-of-the-art.
Gated Feedback Recurrent Neural Networks

In this work, we propose a novel recurrent neural network (RNN) architecture. The proposed RNN, gated-feedback RNN (GF-RNN), extends the existing approach of stacking multiple recurrent layers by allowing and controlling signals flowing from upper recurrent layers to lower layers using a global gating unit for each pair of layers. The recurrent signals exchanged between layers are gated adaptively based on the previous hidden states and the current input. We evaluated the proposed GF-RNN with different types of recurrent units, such as tanh, long short-term memory and gated recurrent units, on the tasks of character-level language modeling and Python program evaluation. Our empirical evaluation of different RNN units, revealed that in both tasks, the GF-RNN outperforms the conventional approaches to build deep stacked RNNs. We suggest that the improvement arises because the GFRNN can adaptively assign different layers to different timescales and layer-to-layer interactions (including the top-down ones which are not usually present in a stacked RNN) by learning to gate these interactions.
Towards a Learning Theory of Cause-Effect Inference

We pose causal inference as the problem of learning to classify probability distributions. In particular, we assume access to a collection $\{(S_i,l_i)\}_{i=1}^n$, where each $S_i$ is a sample drawn from the probability distribution of $X_i \times Y_i$, and $l_i$ is a binary label indicating whether "$X_i \to Y_i$" or "$X_i \leftarrow Y_i$". Given these data, we build a causal inference rule in two steps. First, we featurize each $S_i$ using the kernel mean embedding associated with some characteristic kernel. Second, we train a binary classifier on such embeddings to distinguish between causal directions. We present generalization bounds showing the statistical consistency and learning rates of the proposed approach, and provide a simple implementation that achieves state-of-the-art cause-effect inference. Furthermore, we extend our ideas to infer causal relationships between more than two variables.
Predicting Alzheimer's Disease - A Neuroimaging Study with 3D Convolutional Neural Networks

Pattern recognition methods using neuroimaging data for the diagnosis of Alzheimer's disease have been the subject of extensive research in recent years. In this paper, we use deep learning methods, and in particular sparse autoencoders and 3D convolutional neural networks, to build an algorithm that can predict the disease status of a patient, based on an MRI scan of the brain. We report on experiments using the ADNI data set involving 2,265 historical scans. We demonstrate that 3D convolutional neural networks outperform several other classifiers reported in the literature and produce state-of-art results.
Magnetic adatoms as memory bits: A quantum master equation analysis

Due to underlying symmetries the ground states of magnetic adatoms may be highly stable, which opens perspectives for application as single-atom memory. A specific example is a single holmium atom (with $J=8$) on a platinum (111) surface for which exceptionally long lifetimes were observed in recent scanning tunneling microscopy studies. For control and read-out the atom must be coupled to electronic contacts. Hence the spin dynamics of the system is governed by a quantum master equation. Our analysis shows that in general it cannot be reduced to a classical master equation in the basis of the unperturbed crystal-field Hamiltonian. Rather, depending on parameters and control fields, "environment induced superselection" principles choose the appropriate set of basis states, which in turn determines the specific relaxation channels and lifetimes. Our simulations suggest that in ideal situations the lifetimes should be even longer than observed in the experiment. We, therefore, investigate the influence of various perturbations. We also study the initialization process of the state of the Ho atom by applied voltage pulses and conclude that fast, high fidelity preparation, on a $100\,\text{ns}$ timescale, should be possible.
Deep Learning with Limited Numerical Precision

Training of large-scale deep neural networks is often constrained by the available computational resources. We study the effect of limited precision data representation and computation on neural network training. Within the context of low-precision fixed-point computations, we observe the rounding scheme to play a crucial role in determining the network's behavior during training. Our results show that deep networks can be trained using only 16-bit wide fixed-point number representation when using stochastic rounding, and incur little to no degradation in the classification accuracy. We also demonstrate an energy-efficient hardware accelerator that implements low-precision fixed-point arithmetic with stochastic rounding.
The Power of Randomization: Distributed Submodular Maximization on Massive Datasets

A wide variety of problems in machine learning, including exemplar clustering, document summarization, and sensor placement, can be cast as constrained submodular maximization problems. Unfortunately, the resulting submodular optimization problems are often too large to be solved on a single machine. We consider a distributed, greedy algorithm that combines previous approaches with randomization. The result is an algorithm that is embarrassingly parallel and achieves provable, constant factor, worstcase approximation guarantees. In our experiments, we demonstrate its efficiency in large problems with different kinds of constraints with objective values always close to what is achievable in the centralized setting.
Random Coordinate Descent Methods for Minimizing Decomposable Submodular Functions

Submodular function minimization is a fundamental optimization problem that arises in several applications in machine learning and computer vision. The problem is known to be solvable in polynomial time, but general purpose algorithms have high running times and are unsuitable for large-scale problems. Recent work have used convex optimization techniques to obtain very practical algorithms for minimizing functions that are sums of "simple" functions. In this paper, we use random coordinate descent methods to obtain algorithms with faster linear convergence rates and cheaper iteration costs. Compared to alternating projection methods, our algorithms do not rely on full-dimensional vector operations and they converge in significantly fewer iterations.
Sound emission from the gas of molecular superrotors.

We use an optical centrifuge to deposit a controllable amount of rotational energy into dense molecular ensembles. Subsequent rotation-translation energy transfer, mediated by thermal collisions, results in the localized heating of the gas and generates strong sound wave, clearly audible to the unaided ear. For the first time, the amplitude of the sound signal is analyzed as a function of the experimentally measured rotational energy and linear proportionality between the two observables is established.
An investigation into language complexity of World-of-Warcraft game-external texts

We present a language complexity analysis of World of Warcraft (WoW) community texts, which we compare to texts from a general corpus of web English. Results from several complexity types are presented, including lexical diversity, density, readability and syntactic complexity. The language of WoW texts is found to be comparable to the general corpus on some complexity measures, yet more specialized on other measures. Our findings can be used by educators willing to include game-related activities into school curricula.
Efficiency of energy funneling in the photosystem II supercomplex of higher plants† †Electronic supplementary information (ESI) available: The ESI contains the parameters for the used spectral densities and details the convergence of HEOM. See DOI: 10.1039/c5sc04296h

Energy transfer in the C2S2M2 supercomplex is sensitive to structural modulations induced e.g. by the reorganization process, and is limited by the uphill transfer from CP47 to the RC core.
Scalable Multilabel Prediction via Randomized Methods

Modeling the dependence between outputs is a fundamental challenge in multilabel classification. In this work we show that a generic regularized nonlinearity mapping independent predictions to joint predictions is sufficient to achieve state-of-the-art performance on a variety of benchmark problems. Crucially, we compute the joint predictions without ever obtaining any independent predictions, while incorporating low-rank and smoothness regularization. We achieve this by leveraging randomized algorithms for matrix decomposition and kernel approximation. Furthermore, our techniques are applicable to the multiclass setting. We apply our method to a variety of multiclass and multilabel data sets, obtaining state-of-the-art results.
The Hot QCD White Paper: Exploring the Phases of QCD at RHIC and the LHC

The past decade has seen huge advances in experimental measurements made in heavy ion collisions at the Relativistic Heavy Ion Collider (RHIC) and more recently at the Large Hadron Collider (LHC). These new data, in combination with theoretical advances from calculations made in a variety of frameworks, have led to a broad and deep knowledge of the properties of thermal QCD matter. Increasingly quantitative descriptions of the quark-gluon plasma (QGP) created in these collisions have established that the QGP is a strongly coupled liquid with the lowest value of specific viscosity ever measured. However, much remains to be learned about the precise nature of the initial state from which this liquid forms, how its properties vary across its phase diagram and how, at a microscopic level, the collective properties of this liquid emerge from the interactions among the individual quarks and gluons that must be visible if the liquid is probed with sufficiently high resolution. This white paper, prepared by the Hot QCD Writing Group as part of the U.S. Long Range Plan for Nuclear Physics, reviews the recent progress in the field of hot QCD and outlines the scientific opportunities in the next decade for resolving the outstanding issues in the field.
Generative Moment Matching Networks

We consider the problem of learning deep generative models from data. We formulate a method that generates an independent sample via a single feedforward pass through a multilayer perceptron, as in the recently proposed generative adversarial networks (Goodfellow et al., 2014). Training a generative adversarial network, however, requires careful optimization of a difficult minimax program. Instead, we utilize a technique from statistical hypothesis testing known as maximum mean discrepancy (MMD), which leads to a simple objective that can be interpreted as matching all orders of statistics between a dataset and samples from the model, and can be trained by backpropagation. We further boost the performance of this approach by combining our generative network with an auto-encoder network, using MMD to learn to generate codes that can then be decoded to produce samples. We show that the combination of these techniques yields excellent generative models compared to baseline approaches as measured on MNIST and the Toronto Face Database.
Cascading Bandits: Learning to Rank in the Cascade Model

A search engine usually outputs a list of K web pages. The user examines this list, from the first web page to the last, and chooses the first attractive page. This model of user behavior is known as the cascade model. In this paper, we propose cascading bandits, a learning variant of the cascade model where the objective is to identify K most attractive items. We formulate our problem as a stochastic combinatorial partial monitoring problem. We propose two algorithms for solving it, CascadeUCB1 and Cascade KL-UCB. We also prove gap-dependent upper bounds on the regret of these algorithms and derive a lower bound on the regret in cascading bandits. The lower bound matches the upper bound of Cascade KL-UCB up to a logarithmic factor. We experiment with our algorithms on several problems. The algorithms perform surprisingly well even when our modeling assumptions are violated.
Fluorescence Imaging In Vivo at Wavelengths beyond 1500 nm.

Compared to imaging in the visible and near-infrared regions below 900 nm, imaging in the second near-infrared window (NIR-II, 1000-1700 nm) is a promising method for deep-tissue high-resolution optical imaging in vivo mainly owing to the reduced scattering of photons traversing through biological tissues. Herein, semiconducting single-walled carbon nanotubes with large diameters were used for in vivo fluorescence imaging in the long-wavelength NIR region (1500-1700 nm, NIR-IIb). With this imaging agent, 3-4 μm wide capillary blood vessels at a depth of about 3 mm could be resolved. Meanwhile, the blood-flow speeds in multiple individual vessels could be mapped simultaneously. Furthermore, NIR-IIb tumor imaging of a live mouse was explored. NIR-IIb imaging can be generalized to a wide range of fluorophores emitting at up to 1700 nm for high-performance in vivo optical imaging.