nils-herrmann/clean_scirepeval huggingface dataset:
LDA-based document models for ad-hoc retrieval

Search algorithms incorporating some form of topic model have a long history in information retrieval. For example, cluster-based retrieval has been studied since the 60s and has recently produced good results in the language model framework. An approach to building topic models based on a formal generative model of documents, Latent Dirichlet Allocation (LDA), is heavily cited in the machine learning literature, but its feasibility and effectiveness in information retrieval is mostly unknown. In this paper, we study how to efficiently use LDA to improve ad-hoc retrieval. We propose an LDA-based document model within the language modeling framework, and evaluate it on several TREC collections. Gibbs sampling is employed to conduct approximate inference in LDA and the computational complexity is analyzed. We show that improvements over retrieval using cluster-based models can be obtained with reasonable efficiency.
Preserving Multi-party Machine Learning with Homomorphic Encryption

Privacy preserving multi-party machine learning approaches enable multiple parties to train a machine learning model from aggregate data while ensuring the privacy of their individual datasets is preserved. In this paper, we propose a privacy preserving multi-party machine learning approach based on homomorphic encryption where the machine learning algorithm of choice is deep neural networks. We develop theoretical foundation for implementing deep neural networks over encrypted data and utilize it in developing efficient and practical algorithms in encrypted domain.
A Case of Acquired Idiopathic Pterygium Inversum Unguis

Pterygium inversum unguis (PIU) is a rare nail abnormality in which the distal nail bed adheres to the ventral surface of the nail plate, with obliteration of the distal groove. Because of the rarity of this condition, its exact origin is unknown. This disorder can be either congenital or acquired, with or without a family history. The acquired forms may be idiopathic or secondary to systemic connective tissue diseases or other causes such as stroke, neurofibromatosis, leprosy, or the use of nail fortifiers. We present an unusual case of acquired idiopathic PIU of the 10 fingernails in a 22-year-old man.
Recommendations for using regenerative endodontic procedures in permanent immature traumatized teeth.

The regeneration of immature permanent teeth following trauma could be beneficial to reduce the risk of fracture and loss of millions of teeth each year. Regenerative endodontic procedures include revascularization, partial pulpotomy, and apexogenesis. Several case reports give these procedures a good prognosis as an alternative to apexification. Care is needed to deliver regenerative endodontic procedures that maintain or restore the vitality of teeth, but which also disinfect and remove necrotic tissues. Regeneration can be accomplished through the activity of the cells from the pulp, periodontium, vascular, and immune system. Most therapies use the host's own pulp or vascular cells for regeneration, but other types of dental stem cell therapies are under development. There are no standardized treatment protocols for endodontic regeneration. The purpose of this article is to review the recent literature and suggest guidelines for using regenerative endodontic procedures for the treatment of permanent immature traumatized teeth. Recommendations for the selection of regenerative and conventional procedures based on the type of tooth injury, fracture type, presence of necrosis or infection, periodontal status, presence of periapical lesions, stage of tooth development, vitality status, patient age, and patient health status will be reviewed. Because of the lack of long-term evidence to support the use of regenerative endodontic procedures in traumatized teeth with open apices, revascularization regeneration procedures should only be attempted if the tooth is not suitable for root canal obturation, and after apexogenesis, apexification, or partial pulpotomy treatments have already been attempted and have a poor prognosis.
Action recognition in the premotor cortex.

We recorded electrical activity from 532 neurons in the rostral part of inferior area 6 (area F5) of two macaque monkeys. Previous data had shown that neurons of this area discharge during goal-directed hand and mouth movements. We describe here the properties of a newly discovered set of F5 neurons ("mirror neurons', n = 92) all of which became active both when the monkey performed a given action and when it observed a similar action performed by the experimenter. Mirror neurons, in order to be visually triggered, required an interaction between the agent of the action and the object of it. The sight of the agent alone or of the object alone (three-dimensional objects, food) were ineffective. Hand and the mouth were by far the most effective agents. The actions most represented among those activating mirror neurons were grasping, manipulating and placing. In most mirror neurons (92%) there was a clear relation between the visual action they responded to and the motor response they coded. In approximately 30% of mirror neurons the congruence was very strict and the effective observed and executed actions corresponded both in terms of general action (e.g. grasping) and in terms of the way in which that action was executed (e.g. precision grip). We conclude by proposing that mirror neurons form a system for matching observation and execution of motor actions. We discuss the possible role of this system in action recognition and, given the proposed homology between F5 and human Brocca's region, we posit that a matching system, similar to that of mirror neurons exists in humans and could be involved in recognition of actions as well as phonetic gestures.
A wirelessly controlled implantable LED system for deep brain optogenetic stimulation

In recent years optogenetics has rapidly become an essential technique in neuroscience. Its temporal and spatial specificity, combined with efficacy in manipulating neuronal activity, are especially useful in studying the behavior of awake behaving animals. Conventional optogenetics, however, requires the use of lasers and optic fibers, which can place considerable restrictions on behavior. Here we combined a wirelessly controlled interface and small implantable light-emitting diode (LED) that allows flexible and precise placement of light source to illuminate any brain area. We tested this wireless LED system in vivo, in transgenic mice expressing channelrhodopsin-2 in striatonigral neurons expressing D1-like dopamine receptors. In all mice tested, we were able to elicit movements reliably. The frequency of twitches induced by high power stimulation is proportional to the frequency of stimulation. At lower power, contraversive turning was observed. Moreover, the implanted LED remains effective over 50 days after surgery, demonstrating the long-term stability of the light source. Our results show that the wireless LED system can be used to manipulate neural activity chronically in behaving mice without impeding natural movements.
Probabilistic Backpropagation for Scalable Learning of Bayesian Neural Networks

Large multilayer neural networks trained with backpropagation have recently achieved state-ofthe-art results in a wide range of problems. However, using backprop for neural net learning still has some disadvantages, e.g., having to tune a large number of hyperparameters to the data, lack of calibrated probabilistic predictions, and a tendency to overfit the training data. In principle, the Bayesian approach to learning neural networks does not have these problems. However, existing Bayesian techniques lack scalability to large dataset and network sizes. In this work we present a novel scalable method for learning Bayesian neural networks, called probabilistic backpropagation (PBP). Similar to classical backpropagation, PBP works by computing a forward propagation of probabilities through the network and then doing a backward computation of gradients. A series of experiments on ten real-world datasets show that PBP is significantly faster than other techniques, while offering competitive predictive abilities. Our experiments also show that PBP provides accurate estimates of the posterior variance on the network weights.
Wrong, but useful: regional species distribution models may not be improved by range‐wide data under biased sampling

Species distribution modeling (SDM) is an essential method in ecology and conservation. SDMs are often calibrated within one country's borders, typically along a limited environmental gradient with biased and incomplete data, making the quality of these models questionable. In this study, we evaluated how adequate are national presence-only data for calibrating regional SDMs. We trained SDMs for Egyptian bat species at two different scales: only within Egypt and at a species-specific global extent. We used two modeling algorithms: Maxent and elastic net, both under the point-process modeling framework. For each modeling algorithm, we measured the congruence of the predictions of global and regional models for Egypt, assuming that the lower the congruence, the lower the appropriateness of the Egyptian dataset to describe the species' niche. We inspected the effect of incorporating predictions from global models as additional predictor ("prior") to regional models, and quantified the improvement in terms of AUC and the congruence between regional models run with and without priors. Moreover, we analyzed predictive performance improvements after correction for sampling bias at both scales. On average, predictions from global and regional models in Egypt only weakly concur. Collectively, the use of priors did not lead to much improvement: similar AUC and high congruence between regional models calibrated with and without priors. Correction for sampling bias led to higher model performance, whatever prior used, making the use of priors less pronounced. Under biased and incomplete sampling, the use of global bats data did not improve regional model performance. Without enough bias-free regional data, we cannot objectively identify the actual improvement of regional models after incorporating information from the global niche. However, we still believe in great potential for global model predictions to guide future surveys and improve regional sampling in data-poor regions.
Ensembles of nested dichotomies for multi-class problems

Nested dichotomies are a standard statistical technique for tackling certain polytomous classification problems with logistic regression. They can be represented as binary trees that recursively split a multi-class classification task into a system of dichotomies and provide a statistically sound way of applying two-class learning algorithms to multi-class problems (assuming these algorithms generate class probability estimates). However, there are usually many candidate trees for a given problem and in the standard approach the choice of a particular tree is based on domain knowledge that may not be available in practice. An alternative is to treat every system of nested dichotomies as equally likely and to form an ensemble classifier based on this assumption. We show that this approach produces more accurate classifications than applying C4.5 and logistic regression directly to multi-class problems. Our results also show that ensembles of nested dichotomies produce more accurate classifiers than pairwise classification if both techniques are used with C4.5, and comparable results for logistic regression. Compared to error-correcting output codes, they are preferable if logistic regression is used, and comparable in the case of C4.5. An additional benefit is that they generate class probability estimates. Consequently they appear to be a good general-purpose method for applying binary classifiers to multi-class problems.
Accelerated Attributed Network Embedding

Network embedding is to learn low-dimensional vector representations for nodes in a network. It has shown to be effective in a variety of tasks such as node classification and link prediction. While embedding algorithms on pure networks have been intensively studied, in many real-world applications, nodes are often accompanied with a rich set of attributes or features, aka attributed networks. It has been observed that network topological structure and node attributes are often strongly correlated with each other. Thus modeling and incorporating node attribute proximity into network embedding could be potentially helpful, though non-trivial, in learning better vector representations. Meanwhile, real-world networks often contain a large number of nodes and features, which put demands on the scalability of embedding algorithms. To bridge the gap, in this paper, we propose an accelerated attributed network embedding algorithm AANE, which enables the joint learning process to be done in a distributed manner by decomposing the complex modeling and optimization into many sub-problems. Experimental results on several real-world datasets demonstrate the effectiveness and efficiency of the proposed algorithm.
Context-encoding Variational Autoencoder for Unsupervised Anomaly Detection

Unsupervised learning can leverage large-scale data sources without the need for annotations. In this context, deep learning-based auto encoders have shown great potential in detecting anomalies in medical images. However, state-of-the-art anomaly scores are still based on the reconstruction error, which lacks in two essential parts: it ignores the model-internal representation employed for reconstruction, and it lacks formal assertions and comparability between samples. We address these shortcomings by proposing the Context-encoding Variational Autoencoder (ceVAE) which combines reconstructionwith density-based anomaly scoring. This improves the sampleas well as pixel-wise results. In our experiments on the BraTS-2017 and ISLES-2015 segmentation benchmarks the ceVAE achieves unsupervised ROC-AUCs of 0.95 and 0.89, respectively, thus outperforming state-of-the-art methods by a considerable margin.
Automated testing of refactoring engines

Refactorings are behavior-preserving program transformations that improve the design of a program. Refactoring engines are tools that automate the application of refactorings: first the user chooses a refactoring to apply, then the engine checks if the transformation is safe, and if so, transforms the program. Refactoring engines are a key component of modern IDEs, and programmers rely on them to perform refactorings. A bug in the refactoring engine can have severe consequences as it can erroneously change large bodies of source code.
 We present a technique for automated testing of refactoring engines. Test inputs for refactoring engines are programs. The core of our technique is a framework for iterative generation of structurally complex test inputs. We instantiate the framework to generate abstract syntax trees that represent Java programs. We also create several kinds of oracles to automatically check that the refactoring engine transformed the generated program correctly. We have applied our technique to testing Eclipse and NetBeans, two popular open-source IDEs for Java, and we have exposed 21 new bugs in Eclipse and 24 new bugs in NetBeans.
BFS and Coloring-Based Parallel Algorithms for Strongly Connected Components and Related Problems

Finding the strongly connected components (SCCs) of a directed graph is a fundamental graph-theoretic problem. Tarjan's algorithm is an efficient serial algorithm to find SCCs, but relies on the hard-to-parallelize depth-first search (DFS). We observe that implementations of several parallel SCC detection algorithms show poor parallel performance on modern multicore platforms and large-scale networks. This paper introduces the Multistep method, a new approach that avoids work inefficiencies seen in prior SCC approaches. It does not rely on DFS, but instead uses a combination of breadth-first search (BFS) and a parallel graph coloring routine. We show that the Multistep method scales well on several real-world graphs, with performance fairly independent of topological properties such as the size of the largest SCC and the total number of SCCs. On a 16-core Intel Xeon platform, our algorithm achieves a 20X speedup over the serial approach on a 2 billion edge graph, fully decomposing it in under two seconds. For our collection of test networks, we observe that the Multistep method is 1.92X faster (mean speedup) than the state-of-the-art Hong et al. SCC method. In addition, we modify the Multistep method to find connected and weakly connected components, as well as introduce a novel algorithm for determining articulation vertices of biconnected components. These approaches all utilize the same underlying BFS and coloring routines.
metaSEM: an R package for meta-analysis using structural equation modeling

The metaSEM package provides functions to conduct univariate, multivariate, and three-level meta-analyses using a structural equation modeling (SEM) approach via the OpenMx package in the R statistical platform. It also implements the two-stage SEM approach to conducting fixed- and random-effects meta-analytic SEM on correlation or covariance matrices. This paper briefly outlines the theories and their implementations. It provides a summary on how meta-analyses can be formulated as structural equation models. The paper closes with a conclusion on several relevant topics to this SEM-based meta-analysis. Several examples are used to illustrate the procedures in the supplementary material.
Embodiment enables the spinal engine in quadruped robot locomotion

The biological hypothesis of spinal engine states that locomotion is mainly achieved by the spine, while the legs may serve as assistance. Inspired by this hypothesis, a compliant, multiple degree-of-freedom, biologically-inspired spine has been embedded into a quadruped robot, named Kitty, which has no actuation on the legs. In this paper, we demonstrate how versatile behaviors (bounding, trotting, and turning) can be generated exclusively by the spine's movements through dynamical interaction between the controller, the body, and the environment, known as embodiment. Moreover, we introduce information theoretic approach to quantitatively study the spine internal dynamics and its effect on the bounding gait based on three spinal morphologies. These three morphologies differ in the position of virtual spinal joint where the spine is easier to get bent. The experimental results reveal that locomotion can be enhanced by using the spine featuring a rear virtual spinal joint, which offers more freedom for the rear legs to move forward. In addition, the information theoretic analysis shows that, according to the morphological differences of the spine, the information structure changes. The relationship between the observed behavior of the robot and the corresponding information structure is discussed in detail.
Face recognition with one training image per person

At present there are many methods that could deal well with frontal view face recognition. However, most of them cannot work well when there is only one training image per person. In this paper, an extension of the eigenface technique, i.e. (PC)A, is proposed. (PC)A combines the original face image with its horizontal and vertical projections and then performs principal component analysis on the enriched version of the image. It requires less computational cost than the standard eigenface technique and experimental results show that on a gray-level frontal view face database where each person has only one training image, (PC)A achieves 3%-5% higher accuracy than the standard eigenface technique through using 10%-15% fewer eigenfaces.
Data Fusion by Matrix Factorization

For most problems in science and engineering we can obtain data sets that describe the observed system from various perspectives and record the behavior of its individual components. Heterogeneous data sets can be collectively mined by data fusion. Fusion can focus on a specific target relation and exploit directly associated data together with contextual data and data about system's constraints. In the paper we describe a data fusion approach with penalized matrix tri-factorization (DFMF) that simultaneously factorizes data matrices to reveal hidden associations. The approach can directly consider any data that can be expressed in a matrix, including those from feature-based representations, ontologies, associations and networks. We demonstrate the utility of DFMF for gene function prediction task with eleven different data sources and for prediction of pharmacologic actions by fusing six data sources. Our data fusion algorithm compares favorably to alternative data integration approaches and achieves higher accuracy than can be obtained from any single data source alone.
Discovering Available Drinks Through Natural , Robot-Led , Human-Robot Interaction Between a Waiter and a Bartender

This research focuses on natural, robot-led, human-robot interaction that enables a robot to discover what drinks a barman can prepare through continuous application of speech recognition, understanding and generation. Speech was recognised using Google Cloud’s speech to text API, understood by matching either the object or main verb of a sentence against a list of key words and, finally, generated using templates with variable parts. The difficulty lies in the large quantity of key words, as they are based on the properties of the ordered drinks. The results show that having the aforementioned interaction works well to some extent, i.e. the naturalness of the interaction was ranked 5.5 on average. Furthermore, the obtained precision when identifying the unavailable drinks was 0.625 and the obtained recall was 1, resulting in an F1 measure of 0.769.
Chapter 7 Towards Automatically-Tuned Deep Neural Networks

Recent advances in AutoML have led to automated tools that can compete with machine learning experts on supervised learning tasks. In this work, we present two versions of Auto-Net, which provide automatically-tuned deep neural networks without any human intervention. The first version, Auto-Net 1.0, builds upon ideas from the competition-winning system Auto-sklearn by using the Bayesian Optimization method SMAC and uses Theano as the underlying deep learning (DL) framework. The more recent Auto-Net 2.0 builds upon a recent combination of Bayesian Optimization and HyperBand, called BOHB, and uses PyTorch as DL framework. To the best of our knowledge, Auto-Net 1.0 was the first automatically-tuned neural network to win competition datasets against human experts (as part of the first AutoML challenge). Further empirical results show that ensembling Auto-Net 1.0 with Auto-sklearn can perform better than either approach alone, and that Auto-Net 2.0 can perform better yet.
Extensibility, Safety and Performance in the SPIN Operating System

This paper describes the motivation architecture and performance of SPIN an extensible operating system SPIN provides an extension infrastructure together with a core set of extensible services that allow applica tions to safely change the operating system s interface and implementation Extensions allow an application to specialize the underlying operating system in order to achieve a particular level of performance and function ality SPIN uses language and link time mechanisms to inexpensively export ne grained interfaces to operat ing system services Extensions are written in a type safe language and are dynamically linked into the op erating system kernel This approach o ers extensions rapid access to system services while protecting the op erating system code executing within the kernel address space SPIN and its extensions are written in Modula and run on DEC Alpha workstations