nils-herrmann/clean_scirepeval huggingface dataset:
DeepSkeleton: Learning Multi-Task Scale-Associated Deep Side Outputs for Object Skeleton Extraction in Natural Images

Object skeletons are useful for object representation and object detection. They are complementary to the object contour, and provide extra information, such as how object scale (thickness) varies among object parts. But object skeleton extraction from natural images is very challenging, because it requires the extractor to be able to capture both local and non-local image context in order to determine the scale of each skeleton pixel. In this paper, we present a novel fully convolutional network with multiple scale-associated side outputs to address this problem. By observing the relationship between the receptive field sizes of the different layers in the network and the skeleton scales they can capture, we introduce two scale-associated side outputs to each stage of the network. The network is trained by multi-task learning, where one task is skeleton localization to classify whether a pixel is a skeleton pixel or not, and the other is skeleton scale prediction to regress the scale of each skeleton pixel. Supervision is imposed at different stages by guiding the scale-associated side outputs toward the ground-truth skeletons at the appropriate scales. The responses of the multiple scale-associated side outputs are then fused in a scale-specific way to detect skeleton pixels using multiple scales effectively. Our method achieves promising results on two skeleton extraction datasets, and significantly outperforms other competitors. In addition, the usefulness of the obtained skeletons and scales (thickness) are verified on two object detection applications: foreground object segmentation and object proposal detection.
Fabric defect classification using wavelet frames and minimum classification error training

This paper proposes a new method for fabric defect classification by incorporating the design of a wavelet frames based feature extractor with the design of a Euclidean distance based classifier. Channel variances at the outputs of the wavelet frame decomposition are used to characterize each nonoverlapping window of the fabric image. A feature extractor using linear transformation matrix is further employed to extract the classification-oriented features. With a Euclidean distance based classifier, each nonoverlapping window of the fabric image is then assigned to its corresponding category. Minimization of the classification error is achieved by incorporating the design of the feature extractor with the design of the classifier based on minimum classification error (MCE) training method. The proposed method has been evaluated on the classification of 329 defect samples containing nine classes of fabric defects, and 328 nondefect samples, where 93.1% classification accuracy has been achieved.
Hidden Technical Debt in Machine Learning Systems

Machine learning offers a fantastically powerful toolkit for building useful complex prediction systems quickly. This paper argues it is dangerous to think of these quick wins as coming for free. Using the software engineering framework of technical debt, we find it is common to incur massive ongoing maintenance costs in real-world ML systems. We explore several ML-specific risk factors to account for in system design. These include boundary erosion, entanglement, hidden feedback loops, undeclared consumers, data dependencies, configuration issues, changes in the external world, and a variety of system-level anti-patterns.
Characterizing and enhancing global memory data coalescing on GPUs

Effective parallel programming for GPUs requires careful attention to several factors, including ensuring coalesced access of data from global memory. There is a need for tools that can provide feedback to users about statements in a GPU kernel where non-coalesced data access occurs, and assistance in fixing the problem. In this paper, we address both these needs. We develop a two-stage framework where dynamic analysis is first used to detect and characterize uncoalesced accesses in arbitrary PTX programs. Transformations to optimize global memory access by introducing coalesced access are then implemented, using feedback from the dynamic analysis or using a model-driven approach. Experimental results demonstrate the use of the tools on a number of benchmarks from the Rodinia and Polybench suites.
A Measurement Study of a Large-Scale P2P IPTV System

An emerging Internet application, IPTV, has the potential to flood Internet access and backbone ISPs with massive amounts of new traffic. Although many architectures are possible for IPTV video distribution, several mesh-pull P2P architectures have been successfully deployed on the Internet. In order to gain insights into mesh-pull P2P IPTV systems and the traffic loads they place on ISPs, we have undertaken an in-depth measurement study of one of the most popular IPTV systems, namely, PPLive. We have developed a dedicated PPLive crawler, which enables us to study the global characteristics of the mesh-pull PPLive system. We have also collected extensive packet traces for various different measurement scenarios, including both campus access networks and residential access networks. The measurement results obtained through these platforms bring important insights into P2P IPTV systems. Specifically, our results show the following. 1) P2P IPTV users have the similar viewing behaviors as regular TV users. 2) During its session, a peer exchanges video data dynamically with a large number of peers. 3) A small set of super peers act as video proxy and contribute significantly to video data uploading. 4) Users in the measured P2P IPTV system still suffer from long start-up delays and playback lags, ranging from several seconds to a couple of minutes. Insights obtained in this study will be valuable for the development and deployment of future P2P IPTV systems.
Detecting and Characterizing Mental Health Related Self-Disclosure in Social Media

Self-disclosure is an important element facilitating improved psychological wellbeing in individuals with mental illness. As social media is increasingly adopted in health related discourse, we examine how these new platforms might be allowing honest and candid expression of thoughts, experiences and beliefs. Specifically, we seek to detect levels of self-disclosure manifested in posts shared on different mental health forums on Reddit. We develop a classifier for the purpose based on content features. The classifier is able to characterize a Reddit post to be of high, low, or no self-disclosure with 78% accuracy. Applying this classifier to general mental health discourse on Reddit, we find that bulk of such discourse is characterized by high self-disclosure, and that the community responds distinctively to posts that disclose less or more. We conclude with the potential of harnessing our proposed self-disclosure detection algorithm in psychological therapy via social media. We also discuss design considerations for improved community moderation and support in these vulnerable self-disclosing communities.
Multi-objective de novo drug design with conditional graph generative model

Recently, deep generative models have revealed itself as a promising way of performing de novo molecule design. However, previous research has focused mainly on generating SMILES strings instead of molecular graphs. Although available, current graph generative models are are often too general and computationally expensive. In this work, a new de novo molecular design framework is proposed based on a type of sequential graph generators that do not use atom level recurrent units. Compared with previous graph generative models, the proposed method is much more tuned for molecule generation and has been scaled up to cover significantly larger molecules in the ChEMBL database. It is shown that the graph-based model outperforms SMILES based models in a variety of metrics, especially in the rate of valid outputs. For the application of drug design tasks, conditional graph generative model is employed. This method offers highe flexibility and is suitable for generation based on multiple objectives. The results have demonstrated that this approach can be effectively applied to solve several drug design problems, including the generation of compounds containing a given scaffold, compounds with specific drug-likeness and synthetic accessibility requirements, as well as dual inhibitors against JNK3 and GSK-3β.
Toward an episodic context account of retrieval-based learning: dissociating retrieval practice and elaboration.

We tested the predictions of 2 explanations for retrieval-based learning; while the elaborative retrieval hypothesis assumes that the retrieval of studied information promotes the generation of semantically related information, which aids in later retrieval (Carpenter, 2009), the episodic context account proposed by Karpicke, Lehman, and Aue (in press) assumes that retrieval alters the representation of episodic context and improves one's ability to guide memory search on future tests. Subjects studied multiple word lists and either recalled each list (retrieval practice), did a math task (control), or generated associates for each word (elaboration) after each list. After studying the last list, all subjects recalled the list and, after a 5-min delay, recalled all lists. Analyses of correct recall, intrusions, response times, and temporal clustering dissociate retrieval practice from elaboration, supporting the episodic context account.
APATE: A novel approach for automated credit card transaction fraud detection using network-based extensions

In the last decade, the ease of online payment has opened up many new opportunities for e-commerce, lowering the geographical boundaries for retail. While e-commerce is still gaining popularity, it is also the playground of fraudsters who try to misuse the transparency of online purchases and the transfer of credit card records. This paper proposes APATE, a novel approach to detect fraudulent credit card ∗NOTICE: this is the author’s version of a work that was accepted for publication in Decision Support Systems in May 8, 2015, published online as a self-archive copy after the 24 month embargo period. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Please cite this paper as follows: Van Vlasselaer, V., Bravo, C., Caelen, O., Eliassi-Rad, T., Akoglu, L., Snoeck, M., Baesens, B. (2015).  A novel approach for automated credit card transaction fraud detection using network-based extensions. Decision Support Systems, 75, 38-48.
Ten Simple Rules for Taking Advantage of Git and GitHub

1 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom, 2 Computational Proteomics Unit, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom, 3 Applied Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany, 4 Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany, 5 Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America, 6 Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany, 7 Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom, 8 National Center for Supercomputing Applications and Graduate School of Library and Information Science, University of Illinois, Urbana, Illinois, United States of America, 9 MIT Laboratory for Computational Physiology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, 10 Centre for Interdisciplinary Research in Computational Algebra, University of St Andrews, St Andrews, United Kingdom, 11 Department of Molecular Biology and Biochemistry, Markey Cancer Center, Resource Center for Stable IsotopeResolved Metabolomics, University of Kentucky, Lexington, Kentucky, United States of America, 12 The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
Slash(dot) and burn: distributed moderation in a large online conversation space

Can a system of distributed moderation quickly and consistently separate high and low quality comments in an online conversation? Analysis of the site Slashdot.org suggests that the answer is a qualified yes, but that important challenges remain for designers of such systems. Thousands of users act as moderators. Final scores for comments are reasonably dispersed and the community generally agrees that moderations are fair. On the other hand, much of a conversation can pass before the best and worst comments are identified. Of those moderations that were judged unfair, only about half were subsequently counterbalanced by a moderation in the other direction. And comments with low scores, not at top-level, or posted late in a conversation were more likely to be overlooked by moderators.
An approach for QoS-aware service composition based on genetic algorithms

Web services are rapidly changing the landscape of software engineering. One of the most interesting challenges introduced by web services is represented by Quality Of Service (QoS)--aware composition and late--binding. This allows to bind, at run--time, a service--oriented system with a set of services that, among those providing the required features, meet some non--functional constraints, and optimize criteria such as the overall cost or response time. In other words, QoS--aware composition can be modeled as an optimization problem.We propose to adopt Genetic Algorithms to this aim. Genetic Algorithms, while being slower than integer programming, represent a more scalable choice, and are more suitable to handle generic QoS attributes. The paper describes our approach and its applicability, advantages and weaknesses, discussing results of some numerical simulations.
An Internet-Wide View into DNS Lookup Patterns

This paper analyzes the DNS lookup patterns from a large authoritative top-level domain server and characterizes how the lookup patterns for unscrupulous domains may differ from those for legitimate domains. We examine domains for phishing attacks and spam and malware related domains, and see how these lookup patterns vary in terms of both their temporal and spatial characteristics. We find that malicious domains tend to exhibit more variance in the networks that look up these domains, and we also find that these domains become popular considerably more quickly after their initial registration time. We also note that miscreant domains exhibit distinct clusters, in terms to the networks that look up these domains. The distinct spatial and temporal characteristics of these domains, and their tendency to exhibit similar lookup behavior, suggests that it may be possible to ultimately develop more effective blacklisting techniques based on these differing lookup patterns.
A Polynomial Time Approximation Scheme for Minimum Routing Cost Spanning Trees

Given an undirected graph with nonnegative costs on the edges, the routing cost of any of its spanning trees is the sum over all pairs of vertices of the cost of the path between the pair in the tree. Finding a spanning tree of minimum routing cost is NP-hard, even when the costs obey the triangle inequality. We show that the general case is in fact reducible to the metric case and present a polynomial-time approximation scheme valid for both versions of the problem. In particulaf-, we show how to build a spanning tree of an n-vertex weighted graph with routing cost within (1 + E) from the minimum in time O(noct)). Besides the obvious connection to network design, trees with small routing cost also find application in the construction of good multiple sequence alignments in computational biology. The communication cost spanning tree problem is a Eeneralization of the minimum ro&ing c&t tree problem wi;ere the routinK costs of different pairs are weiahted bv different requirement amounts. W6 observe tha; a randomized O(log2 n)-approximation for this problem follows directly from a recent result of Bartal, where n is the number of nodes in a metric graph. This also yields the same approximation for the generalized sum-of-pairs alignment problem in computational biology.
Engineering Human Cooperation : Does Involuntary Neural Activation Increase Public Goods Contributions?

In a laboratory experiment, we use a public goods game to examine the hypothesis that human subjects use an involuntary eye-detector mechanism for evaluating the level of privacy. Half of our subjects are "watched" by images of a robot presented on their computer screen. The robot-named Kismet and invented at MIT-is constructed from objects that are obviously not human with the exception of its eyes. In our experiment, Kismet produces a significant difference in behavior that is not consistent with existing economic models of preferences, either self- or other-regarding. Subjects who are "watched" by Kismet contribute 29% more to the public good than do subjects in the same setting without Kismet.
Video Captioning and Retrieval Models with Semantic Attention

We present the approaches for the four video-tolanguage tasks of LSMDC 2016, including movie description, fill-in-the-blank, multiple-choice test, and movie retrieval. Our key idea is to adopt the semantic attention mechanism; we first build a set of attribute words that are consistently discovered on video frames, and then selectively fuse them with input words for more semantic representation and with output words for more accurate prediction. We show that our implementation of semantic attention indeed improves the performance of multiple video-tolanguage tasks. Specifically, the presented approaches participated in all the four tasks of the LSMDC 2016, and have won three of them, including fill-in-the-blank, multiplechoice test, and movie retrieval.
The Marginal Value of Adaptive Gradient Methods in Machine Learning

Adaptive optimization methods, which perform local optimization with a metric constructed from the history of iterates, are becoming increasingly popular for training deep neural networks. Examples include AdaGrad, RMSProp, and Adam. We show that for simple overparameterized problems, adaptive methods often find drastically different solutions than gradient descent (GD) or stochastic gradient descent (SGD). We construct an illustrative binary classification problem where the data is linearly separable, GD and SGD achieve zero test error, and AdaGrad, Adam, and RMSProp attain test errors arbitrarily close to half. We additionally study the empirical generalization capability of adaptive methods on several state-of-the-art deep learning models. We observe that the solutions found by adaptive methods generalize worse (often significantly worse) than SGD, even when these solutions have better training performance. These results suggest that practitioners should reconsider the use of adaptive methods to train neural networks.
Incorporation of Application Layer Protocol Syntax into Anomaly Detection

The syntax of application layer protocols carries valuable information for network intrusion detection. Hence, the majority of modern IDS perform some form of protocol analysis to refine their signatures with application layer context. Protocol analysis, however, has been mainly used for misuse detection, which limits its application for the detection of unknown and novel attacks. In this contribution we address the issue of incorporating application layer context into anomaly-based intrusion detection. We extend a payload-based anomaly detection method by incorporating structural information obtained from a protocol analyzer. The basis for our extension is computation of similarity between attributed tokens derived from a protocol grammar. The enhanced anomaly detection method is evaluated in experiments on detection of web attacks, yielding an improvement of detection accuracy of 49%. While byte-level anomaly detection is sufficient for detection of buffer overflow attacks, identification of recent attacks such as SQL and PHP code injection strongly depends on the availability of application layer context.
Convolutional Neural Network With Data Augmentation for SAR Target Recognition

Many methods have been proposed to improve the performance of synthetic aperture radar (SAR) target recognition but seldom consider the issues in real-world recognition systems, such as the invariance under target translation, the invariance under speckle variation in different observations, and the tolerance of pose missing in training data. In this letter, we investigate the capability of a deep convolutional neural network (CNN) combined with three types of data augmentation operations in SAR target recognition. Experimental results demonstrate the effectiveness and efficiency of the proposed method. The best performance is obtained by using the CNN trained by all types of augmentation operations, showing that it is a practical approach for target recognition in challenging conditions of target translation, random speckle noise, and missing pose.
ACE: automated CTF estimation.

We present a completely automated algorithm for estimating the parameters of the contrast transfer function (CTF) of a transmission electron microscope. The primary contribution of this paper is the determination of the astigmatism prior to the estimation of the CTF parameters. The CTF parameter estimation is then reduced to a 1D problem using elliptical averaging. We have also implemented an automated method to calculate lower and upper cutoff frequencies to eliminate regions of the power spectrum which perturb the estimation of the CTF parameters. The algorithm comprises three optimization subproblems, two of which are proven to be convex. Results of the CTF estimation method are presented for images of carbon support films as well as for images of single particles embedded in ice and suspended over holes in the support film. A MATLAB implementation of the algorithm, called ACE, is freely available.
Pavement pothole detection and severity measurement using laser imaging

Over the years, Automated Image Analysis Systems (AIAS) have been developed for pavement surface analysis and management. The cameras used by most of the AIAS are based on Charge-Coupled Device (CCD) image sensors where a visible ray is projected. However, the quality of the images captured by the CCD cameras was limited by the inconsistent illumination and shadows caused by sunlight. To enhance the CCD image quality, a high-power artificial lighting system has been used, which requires a complicated lighting system and a significant power source. In this paper, we will introduce an efficient and more economical approach for pavement distress inspection by using laser imaging. After the pavement images are captured, regions corresponding to potholes are represented by a matrix of square tiles and the estimated shape of the pothole is determined. The vertical, horizontal distress measures, the total number of distress tiles and the depth index information are calculated providing input to a three-layer feed-forward neural network for pothole severity and crack type classification. The proposed analysis algorithm is capable of enhancing the pavement image, extracting the pothole from background and analyzing its severity. To validate the system, actual pavement pictures were taken from pavements both in highway and local roads. The experimental results demonstrated that the proposed model works well for pothole and crack detection.