nils-herrmann/clean_scirepeval huggingface dataset:
Comparative assessment of methods for aligning multiple genome sequences

Multiple sequence alignment is a difficult computational problem. There have been compelling pleas for methods to assess whole-genome multiple sequence alignments and compare the alignments produced by different tools. We assess the four ENCODE alignments, each of which aligns 28 vertebrates on 554 Mbp of total input sequence. We measure the level of agreement among the alignments and compare their coverage and accuracy. We find a disturbing lack of agreement among the alignments not only in species distant from human, but even in mouse, a well-studied model organism. Overall, the assessment shows that Pecan produces the most accurate or nearly most accurate alignment in all species and genomic location categories, while still providing coverage comparable to or better than that of the other alignments in the placental mammals. Our assessment reveals that constructing accurate whole-genome multiple sequence alignments remains a significant challenge, particularly for noncoding regions and distantly related species.
Centrality based Document Ranking

In this paper, we address the problem of ranking clinical documents using centrality based approach. We model the documents to be ranked as nodes in a graph and place edges between documents based on their similarity. Given a query, we compute similarity of the query with respect to every document in the graph. Based on these similarity values, documents are ranked for a given query. Initially, Lucene is used to retrieve top fifty documents that are relevant to the query and then our proposed approach is applied on these retrieved documents to rerank them. Experimental results show that our approach did not perform well as the documents retrieved by Lucene are not among the top 50 documents in the Gold Standard.
Multi-GCN: Graph Convolutional Networks for Multi-View Networks, with Applications to Global Poverty

With the rapid expansion of mobile phone networks in developing countries, large-scale graph machine learning has gained sudden relevance in the study of global poverty. Recent applications range from humanitarian response and poverty estimation to urban planning and epidemic containment. Yet the vast majority of computational tools and algorithms used in these applications do not account for the multi-view nature of social networks: people are related in myriad ways, but most graph learning models treat relations as binary. In this paper, we develop a graph-based convolutional network for learning on multi-view networks. We show that this method outperforms state-of-the-art semi-supervised learning algorithms on three different prediction tasks using mobile phone datasets from three different developing countries. We also show that, while designed specifically for use in poverty research, the algorithm also outperforms existing benchmarks on a broader set of learning tasks on multi-view networks, including node labelling in citation networks.
Steel Plates Faults Diagnosis with Data Mining Models

Over the last two decades, Fault Diagnosis (FD) ha s a major importance to enhance the quality of manufacturing a d to lessen the cost of product testing. Actually , quick and correct FD system helps to keep away from product quality problems and facilitates precautionary maintenance. FD may be considered as a pattern recognition problem. It has been gaining more and more attention to develop methods f r improving the accuracy and efficiency of pattern recognition. Many computational tools and a lgorithms that have been recently developed could be used.  This study evaluates the performances of three of the popular and effective data mining models to diagnose seven commonly occurring faults of the steel plate namely; Pastry, Z_Scratch, K_Scatch, Stains, Dirtiness, Bumps and O ther_Faults. The models include C5.0 decision tree (C5.0 DT) with boosting, Multi Perception Neur al Network (MLPNN) with pruning and Logistic Regression (LR) with step forward. The steel plates fault dataset investigated in this study is taken from the University of California at Irvine (UCI) m achine learning repository.  Given a training set of such patterns, the individual model learned how to differentiate a new case in the domain. The diagnosis performances of the proposed mo els are presented using statistical accuracy, specificity and sensitivity. The diagnostic accurac y of the C5.0 decision tree with boosting algorithm has achieved a remarkable performance with 97.25 an d 98.09% accuracy on training and test subset. C5.0 has outperformed the other two models.  Experimental results showed that data mining algorithms in general and decision trees in particular have the great impact of on the problem of steel plates fault diagnosis.
Landmark Free Face Attribute Prediction

Face attribute prediction in the wild is important for many facial analysis applications, yet it is very challenging due to ubiquitous face variations. In this paper, we address face attribute prediction in the wild by proposing a novel method, lAndmark Free Face AttrIbute pRediction (AFFAIR). Unlike traditional face attribute prediction methods that require facial landmark detection and face alignment, AFFAIR uses an end-to-end learning pipeline to jointly learn a hierarchy of spatial transformations that optimize facial attribute prediction with no reliance on landmark annotations or pre-trained landmark detectors. AFFAIR achieves this through simultaneously: 1) learning a global transformation which effectively alleviates negative effect of global face variation for the following attribute prediction tailored for each face; 2) locating the most relevant facial part for attribute prediction; and 3) aggregating the global and local features for robust attribute prediction. Within AFFAIR, a new competitive learning strategy is developed that effectively enhances global transformation learning for better attribute prediction. We show that with zero information about landmarks, AFFAIR achieves the state-of-the-art performance on three face attribute prediction benchmarks, which simultaneously learns the face-level transformation and attribute-level localization within a unified framework.
Synthesizing evidence in software engineering research

Synthesizing the evidence from a set of studies that spans many countries and years, and that incorporates a wide variety of research methods and theoretical perspectives, is probably the single most challenging task of performing a systematic review. In this paper, we perform a tertiary review to assess the types and methods of research synthesis in systematic reviews in software engineering. Almost half of the 31 studies included in our review did not contain any synthesis; of the ones that did, two thirds performed a narrative or a thematic synthesis. The results show that, despite the focus on systematic reviews, there is, currently, limited attention to research synthesis in software engineering. This needs to change and a repertoire of synthesis methods needs to be an integral part of systematic reviews to increase their significance and utility for research and practice.
Efficient Clustering-Based Outlier Detection Algorithm for Dynamic Data Stream

Anomaly detection is currently an important and active research problem in many fields and involved in numerous applications. Most of the existing methods are based on distance measure. But in case of data stream these methods are not very efficient as computational point of view. Most of the exiting work on outlier detection in data stream declare a point as an outlier/inlier as soon as it arrive due to limited memory resources as compared to the huge data stream, to declare an outlier as it arrive often can lead us to a wrong decision, because of dynamic nature of the incoming data. In this paper we introduced a clustering based approach, which divide the stream in chunks and cluster each chunk using k-mean in fixed number of clusters. Instead of keeping only the summary information, which often used in case of clustering data stream, we keep the candidate outliers and mean value of every cluster for the next fixed number of steam chunks, to make sure that the detected candidate outliers are the real outliers. By employing the mean value of the clusters of previous chunk with mean values of the current chunk of stream, we decide better outlierness for data stream objects. Several experiments on different dataset confirm that our technique can find better outliers with low computational cost than the other exiting distance based approaches of outlier detection in data stream.
Efficient parallel translating embedding for knowledge graphs

Knowledge graph embedding aims to embed entities and relations of knowledge graphs into low-dimensional vector spaces. Translating embedding methods regard relations as the translation from head entities to tail entities, which achieve the state-of-the-art results among knowledge graph embedding methods. However, a major limitation of these methods is the time consuming training process, which may take several days or even weeks for large knowledge graphs, and result in great difficulty in practical applications. In this paper, we propose an efficient parallel framework for translating embedding methods, called ParTrans-X, which enables the methods to be paralleled without locks by utilizing the distinguished structures of knowledge graphs. Experiments on two datasets with three typical translating embedding methods, i.e., TransE , TransH , and a more efficient variant TransE- AdaGrad [11] validate that ParTrans-X can speed up the training process by more than an order of magnitude.
How to practice person‐centred care: A conceptual framework

Globally, health-care systems and organizations are looking to improve health system performance through the implementation of a person-centred care (PCC) model. While numerous conceptual frameworks for PCC exist, a gap remains in practical guidance on PCC implementation.



Based on a narrative review of the PCC literature, a generic conceptual framework was developed in collaboration with a patient partner, which synthesizes evidence, recommendations and best practice from existing frameworks and implementation case studies. The Donabedian model for health-care improvement was used to classify PCC domains into the categories of "Structure," "Process" and "Outcome" for health-care quality improvement.



The framework emphasizes the structural domain, which relates to the health-care system or context in which care is delivered, providing the foundation for PCC, and influencing the processes and outcomes of care. Structural domains identified include: the creation of a PCC culture across the continuum of care; co-designing educational programs, as well as health promotion and prevention programs with patients; providing a supportive and accommodating environment; and developing and integrating structures to support health information technology and to measure and monitor PCC performance. Process domains describe the importance of cultivating communication and respectful and compassionate care; engaging patients in managing their care; and integration of care. Outcome domains identified include: access to care and Patient-Reported Outcomes.



This conceptual framework provides a step-wise roadmap to guide health-care systems and organizations in the provision PCC across various health-care sectors.
Deep Autoencoding Gaussian Mixture Model for Unsupervised Anomaly Detection

Unsupervised anomaly detection on multior high-dimensional data is of great importance in both fundamental machine learning research and industrial applications, for which density estimation lies at the core. Although previous approaches based on dimensionality reduction followed by density estimation have made fruitful progress, they mainly suffer from decoupled model learning with inconsistent optimization goals and incapability of preserving essential information in the low-dimensional space. In this paper, we present a Deep Autoencoding Gaussian Mixture Model (DAGMM) for unsupervised anomaly detection. Our model utilizes a deep autoencoder to generate a low-dimensional representation and reconstruction error for each input data point, which is further fed into a Gaussian Mixture Model (GMM). Instead of using decoupled two-stage training and the standard Expectation-Maximization (EM) algorithm, DAGMM jointly optimizes the parameters of the deep autoencoder and the mixture model simultaneously in an end-to-end fashion, leveraging a separate estimation network to facilitate the parameter learning of the mixture model. The joint optimization, which well balances autoencoding reconstruction, density estimation of latent representation, and regularization, helps the autoencoder escape from less attractive local optima and further reduce reconstruction errors, avoiding the need of pre-training. Experimental results on several public benchmark datasets show that, DAGMM significantly outperforms state-of-the-art anomaly detection techniques, and achieves up to 14% improvement based on the standard F1 score.
Common Consensus : a web-based game for collecting commonsense goals

In our research on Commonsense reasoning, we have found that an especially important kind of knowledge is knowledge about human goals. Especially when applying Commonsense reasoning to interface agents, we need to recognize goals from user actions (plan recognition), and generate sequences of actions that implement goals (planning). We also often need to answer more general questions about the situations in which goals occur, such as when and where a particular goal might be likely, or how long it is likely to take to achieve. In past work on Commonsense knowledge acquisition, users have been directly asked for such information. Recently, however, another approach has emerged—to entice users into playing games where supplying the knowledge is the means to scoring well in the game, thus motivating the players. This approach has been pioneered by Luis von Ahn and his colleagues, who refer to it as Human Computation. Common Consensus is a fun, self-sustaining web-based game, that both collects and validates Commonsense knowledge about everyday goals. It is based on the structure of the TV game show Family Feud1. A small user study showed that users find the game fun, knowledge quality is very good, and the rate of knowledge collection is rapid.  H.3.3 [INFORMATION STORAGE AND RETRIEVAL]: Information Search and Retrieval; I.2.6 [ARTIFICIAL INTELLIGENCE]: Learning
Visual attention measures for multi-screen TV

We introduce a set of nine measures to characterize viewers' visual attention patterns for multi-screen TV. We apply our measures during an experiment involving nine screen layouts with two, three, and four TV screens, for which we report new findings on visual attention. For example, we found that viewers need an average discovery time up to 4.5 seconds to visually fixate four screens, and their perceptions of how long they watched each screen are substantially accurate, i.e., we report Pearson correlations up to .892 with measured eye tracking data. We hope our set of new measures (and the companion toolkit to compute them automatically) will benefit the community as a first step toward understanding visual attention for emerging multi-screen TV applications.
HMM-Based Word Alignment in Statistical Translation

In this paper, we describe a new model for word alignment in statistical translation and present experimental results. The idea of the model is to make the alignment probabilities dependent on the differences in the alignment positions rather than on the absolute positions. To achieve this goal, the approach uses a first-order Hidden Markov model (HMM) for the word alignment problem as they are used successfully in speech recognition for the time alignment problem. The difference to the time alignment HMM is that there is no monotony constraint for the possible word orderings. We describe the details of the model and test the model on several bilingual corpora.
Exploring the factors affecting MOOC retention: A survey study

Massive Open Online Courses (MOOCs) hold the potential to open up educational opportunities to a global audience. However, evidence suggests that only a small proportion of MOOC participants go on to complete their courses and relatively little is understood about the MOOC design and implementation factors that influence retention. This paper reports a survey study of 379 participants enrolled at university in Cairo who were encouraged to take a MOOC of their own choice as part of their development. 122 participants (32.2%) went onto to complete an entire course. There were no significant differences in completion rates by gender, level of study (undergraduate or postgraduate) or MOOC platform. A post-MOOC survey of students' perceptions found that MOOC Course Content was a significant predictor of MOOC retention, with the relationship mediated by the effect of content on the Perceived Effectiveness of the course. Interaction with the instructor of the MOOC was also found to be significant predictor of MOOC retention. Overall these constructs explained 79% of the variance in MOOC retention.
LETOR : Benchmark Dataset for Research on Learning to Rank for Information Retrieval

This paper is concerned with learning to rank for information retrieval (IR). Ranking is the central problem for information retrieval, and employing machine learning techniques to learn the ranking function is viewed as a promising approach to IR. Unfortunately, there was no benchmark dataset that could be used in comparison of existing learning algorithms and in evaluation of newly proposed algorithms, which stood in the way of the related research. To deal with the problem, we have constructed a benchmark dataset referred to as LETOR and distributed it to the research communities. Specifically we have derived the LETOR data from the existing data sets widely used in IR, namely, OHSUMED and TREC data. The two collections contain queries, the contents of the retrieved documents, and human judgments on the relevance of the documents with respect to the queries. We have extracted features from the datasets, including both conventional features, such as term frequency, inverse document frequency, BM25, and language models for IR, and features proposed recently at SIGIR, such as HostRank, feature propagation, and topical PageRank. We have then packaged LETOR with the extracted features, queries, and relevance judgments. We have also provided the results of several state-ofthe-arts learning to rank algorithms on the data. This paper describes in details about LETOR.
A Novel LTPS-TFT Pixel Circuit Compensating for TFT Threshold-Voltage Shift and OLED Degradation for AMOLED

This letter presents a novel pixel circuit that uses low-temperature polycrystalline-silicon thin-film transistors (LTPS-TFTs) composed of one driving and four switching TFTs for active-matrix organic light-emitting diodes (AMOLEDs) with a voltage-source method. The proposed circuit effectively enables threshold-voltage-shift correction of the drive TFT and compensates for degradation of the OLED using a feedback structure
Dynamic Social-Aware Peer Selection Scheme for Cooperative Device-to-Device Communications

Device-to-device (D2D) communication is a promising technology to improve spectrum efficiency, energy efficiency, and transmission delay due to proximity of user equipments (UEs). With cooperative D2D communications, a UE needs to select an optimal peer to act as a relay to forward data to the base station (BS). Therefore, it is essential to take into account the social relationships among UEs during peer selection so as to enhance data privacy. In this paper, we investigate a dynamic social-aware peer selection problem by formulating it as a dynamic optimization problem and proposing the drift-plus-penalty ratio algorithm to solve it. Simulation results show that the proposed peer selection scheme outperforms other existing schemes while keeping the handover frequency lower than others.
Data mining with Temporal Abstractions: learning rules from time series

A large volume of research in temporal data mining is focusing on discovering temporal rules from time-stamped data. The majority of the methods proposed so far have been mainly devoted to the mining of temporal rules which describe relationships between data sequences or instantaneous events and do not consider the presence of complex temporal patterns into the dataset. Such complex patterns, such as trends or up and down behaviors, are often very interesting for the users. In this paper we propose a new kind of temporal association rule and the related extraction algorithm; the learned rules involve complex temporal patterns in both their antecedent and consequent. Within our proposed approach, the user defines a set of complex patterns of interest that constitute the basis for the construction of the temporal rule; such complex patterns are represented and retrieved in the data through the formalism of knowledge-based Temporal Abstractions. An Apriori-like algorithm looks then for meaningful temporal relationships (in particular, precedence temporal relationships) among the complex patterns of interest. The paper presents the results obtained by the rule extraction algorithm on a simulated dataset and on two different datasets related to biomedical applications: the first one concerns the analysis of time series coming from the monitoring of different clinical variables during hemodialysis sessions, while the other one deals with the biological problem of inferring relationships between genes from DNA microarray data.
Market-Oriented Cloud Computing and the Cloudbus Toolkit

Cloud computing has penetrated the Information Technology industry deep enough to influence major companies to adopt it into their mainstream business. A strong thrust on the use of virtualization technology to realize Infrastructure-as-a-Service (IaaS) has led enterprises to leverage subscription-oriented computing capabilities of public Clouds for hosting their application services. In parallel, research in academia has been investigating transversal aspects such as security, software frameworks, quality of service, and standardization. We believe that the complete realization of the Cloud computing vision will lead to the introduction of a virtual market where Cloud brokers, on behalf of end users, are in charge of selecting and composing the services advertised by different Cloud vendors. In order to make this happen, existing solutions and technologies have to be redesigned and extended from a market-oriented perspective and integrated together, giving rise to what we term Market-Oriented Cloud Computing. In this paper, we will assess the current status of Cloud computing by providing a reference model, discuss the challenges that researchers and IT practitioners are facing and will encounter in the near future, and present the approach for solving them from the perspective of the Cloudbus toolkit, which comprises of a set of technologies geared towards the realization of Market Oriented Cloud Computing vision. We provide experimental results demonstrating market-oriented resource provisioning and brokering within a Cloud and across multiple distributed resources. We also include an application illustrating the hosting of ECG analysis as SaaS on Amazon IaaS (EC2 and S3) services.