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"doi": "10.1109/ITME53901.2021.00101",
"title": "Interpretability Analysis of Academic Achievement Prediction Based on Machine Learning",
"normalizedTitle": "Interpretability Analysis of Academic Achievement Prediction Based on Machine Learning",
"abstract": "In recent years, with the development of artificial intelligence and information technology, we are gradually stepping into the era of big data, in which education-related data has developed sufficiently in terms of quantity and content. To be able to use machine learning techniques to assist educators to help improve the current quality of education and teaching, more and more researchers have started to data-mine educational data. In this paper, various algorithms of machine learning are applied to the field of education to process the data of students' teaching performance and then model it using various algorithms of machine learning to predict the students' performance and provide some suggestions to the teachers to improve the students' performance. The main contributions of this paper are as follows: Firstly, this paper carries out necessary preprocessing operations on the original data to remove some dirty data or missing data. Then, a variety of machine learning algorithms are used to model students' academic performance. By comparing the prediction accuracy, recall rate, and F1 score of the model, the Gradient Boosting Decision Tree Classifier is finally obtained as the optimal model. We then integrated the three best machine learning models as the base models and proposed a new Stacking learning method with better results. Finally, this paper analyzes the interpretability of the Gradient Boosting Decision Tree Classifier, evaluates the importance of different characteristics, and finally concludes that “Visited resources”, “Raised hand”, “Student Absence Days”, and “Viewing announcements” are the most important factors affecting students' performance. This model has an advanced effect and good interpretability.",
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"content": "In recent years, with the development of artificial intelligence and information technology, we are gradually stepping into the era of big data, in which education-related data has developed sufficiently in terms of quantity and content. To be able to use machine learning techniques to assist educators to help improve the current quality of education and teaching, more and more researchers have started to data-mine educational data. In this paper, various algorithms of machine learning are applied to the field of education to process the data of students' teaching performance and then model it using various algorithms of machine learning to predict the students' performance and provide some suggestions to the teachers to improve the students' performance. The main contributions of this paper are as follows: Firstly, this paper carries out necessary preprocessing operations on the original data to remove some dirty data or missing data. Then, a variety of machine learning algorithms are used to model students' academic performance. By comparing the prediction accuracy, recall rate, and F1 score of the model, the Gradient Boosting Decision Tree Classifier is finally obtained as the optimal model. We then integrated the three best machine learning models as the base models and proposed a new Stacking learning method with better results. Finally, this paper analyzes the interpretability of the Gradient Boosting Decision Tree Classifier, evaluates the importance of different characteristics, and finally concludes that “Visited resources”, “Raised hand”, “Student Absence Days”, and “Viewing announcements” are the most important factors affecting students' performance. This model has an advanced effect and good interpretability.",
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"affiliation": "Shandong Normal University,School of Information Science and Engineering,Jinan,China",
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"affiliation": "Shandong Normal University,School of Information Science and Engineering,Jinan,China",
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"title": "2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS)",
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"title": "Interpretability in HealthCare A Comparative Study of Local Machine Learning Interpretability Techniques",
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"abstract": "Although complex machine learning models (e.g., Random Forest, Neural Networks) are commonly outperforming the traditional simple interpretable models (e.g., Linear Regression, Decision Tree), in the healthcare domain, clinicians find it hard to understand and trust these complex models due to the lack of intuition and explanation of their predictions. With the new General Data Protection Regulation (GDPR), the importance for plausibility and verifiability of the predictions made by machine learning models has become essential. To tackle this challenge, recently, several machine learning interpretability techniques have been developed and introduced. In general, the main aim of these interpretability techniques is to shed light and provide insights into the predictions process of the machine learning models and explain how the model predictions have resulted. However, in practice, assessing the quality of the explanations provided by the various interpretability techniques is still questionable. In this paper, we present a comprehensive experimental evaluation of three recent and popular local model agnostic interpretability techniques, namely, LIME, SHAP and Anchors on different types of real-world healthcare data. Our experimental evaluation covers different aspects for its comparison including identity, stability, separability, similarity, execution time and bias detection. The results of our experiments show that LIME achieves the lowest performance for the identity metric and the highest performance for the separability metric across all datasets included in this study. On average, SHAP has the smallest average time to output explanation across all datasets included in this study. For detecting the bias, SHAP enables the participants to better detect the bias.",
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"content": "Although complex machine learning models (e.g., Random Forest, Neural Networks) are commonly outperforming the traditional simple interpretable models (e.g., Linear Regression, Decision Tree), in the healthcare domain, clinicians find it hard to understand and trust these complex models due to the lack of intuition and explanation of their predictions. With the new General Data Protection Regulation (GDPR), the importance for plausibility and verifiability of the predictions made by machine learning models has become essential. To tackle this challenge, recently, several machine learning interpretability techniques have been developed and introduced. In general, the main aim of these interpretability techniques is to shed light and provide insights into the predictions process of the machine learning models and explain how the model predictions have resulted. However, in practice, assessing the quality of the explanations provided by the various interpretability techniques is still questionable. In this paper, we present a comprehensive experimental evaluation of three recent and popular local model agnostic interpretability techniques, namely, LIME, SHAP and Anchors on different types of real-world healthcare data. Our experimental evaluation covers different aspects for its comparison including identity, stability, separability, similarity, execution time and bias detection. The results of our experiments show that LIME achieves the lowest performance for the identity metric and the highest performance for the separability metric across all datasets included in this study. On average, SHAP has the smallest average time to output explanation across all datasets included in this study. For detecting the bias, SHAP enables the participants to better detect the bias.",
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"normalizedAbstract": "Although complex machine learning models (e.g., Random Forest, Neural Networks) are commonly outperforming the traditional simple interpretable models (e.g., Linear Regression, Decision Tree), in the healthcare domain, clinicians find it hard to understand and trust these complex models due to the lack of intuition and explanation of their predictions. With the new General Data Protection Regulation (GDPR), the importance for plausibility and verifiability of the predictions made by machine learning models has become essential. To tackle this challenge, recently, several machine learning interpretability techniques have been developed and introduced. In general, the main aim of these interpretability techniques is to shed light and provide insights into the predictions process of the machine learning models and explain how the model predictions have resulted. However, in practice, assessing the quality of the explanations provided by the various interpretability techniques is still questionable. In this paper, we present a comprehensive experimental evaluation of three recent and popular local model agnostic interpretability techniques, namely, LIME, SHAP and Anchors on different types of real-world healthcare data. Our experimental evaluation covers different aspects for its comparison including identity, stability, separability, similarity, execution time and bias detection. The results of our experiments show that LIME achieves the lowest performance for the identity metric and the highest performance for the separability metric across all datasets included in this study. On average, SHAP has the smallest average time to output explanation across all datasets included in this study. For detecting the bias, SHAP enables the participants to better detect the bias.",
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"affiliation": "University of Tartu",
"fullName": "Radwa El Shawi",
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"affiliation": "Tartu University",
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"title": "Research on the Innovation of China's Pension Insurance Transfer and Succession Model——Based on Big Data Technology",
"normalizedTitle": "Research on the Innovation of China's Pension Insurance Transfer and Succession Model——Based on Big Data Technology",
"abstract": "In the process of rapid economic development, the state must ensure the rationality and scientific nature of the relevant guarantee system, so as to promote stable economic development. However, there are some problems in the current transfer and continuation model of China's pension insurance, which will affect the flow of labor to a certain extent. The transfer and continuation of pension insurance will cause migrant workers to give up corresponding insurance rights and affect the vigorous development of China's labor market. Therefore, we must study and analyze the transfer and continuation model of China's pension insurance. The application of big data technology has a certain significance in the innovation research work of pension insurance transfer and continuation model. Big data technology can not only provide comprehensive data information for the pension insurance transfer and continuation model, but also can effectively improve the pension insurance transfer and continuation model. This requires us to research and analyze the problems of pension insurance transfer and continuation models, and build a new intelligent pension insurance model based on big data. Only in this way can it be ensured that the pension insurance transfer and continuation model meets the mobility needs of the Chinese labor market and promotes the stable development of the Chinese economy.",
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"content": "In the process of rapid economic development, the state must ensure the rationality and scientific nature of the relevant guarantee system, so as to promote stable economic development. However, there are some problems in the current transfer and continuation model of China's pension insurance, which will affect the flow of labor to a certain extent. The transfer and continuation of pension insurance will cause migrant workers to give up corresponding insurance rights and affect the vigorous development of China's labor market. Therefore, we must study and analyze the transfer and continuation model of China's pension insurance. The application of big data technology has a certain significance in the innovation research work of pension insurance transfer and continuation model. Big data technology can not only provide comprehensive data information for the pension insurance transfer and continuation model, but also can effectively improve the pension insurance transfer and continuation model. This requires us to research and analyze the problems of pension insurance transfer and continuation models, and build a new intelligent pension insurance model based on big data. Only in this way can it be ensured that the pension insurance transfer and continuation model meets the mobility needs of the Chinese labor market and promotes the stable development of the Chinese economy.",
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"normalizedAbstract": "In the process of rapid economic development, the state must ensure the rationality and scientific nature of the relevant guarantee system, so as to promote stable economic development. However, there are some problems in the current transfer and continuation model of China's pension insurance, which will affect the flow of labor to a certain extent. The transfer and continuation of pension insurance will cause migrant workers to give up corresponding insurance rights and affect the vigorous development of China's labor market. Therefore, we must study and analyze the transfer and continuation model of China's pension insurance. The application of big data technology has a certain significance in the innovation research work of pension insurance transfer and continuation model. Big data technology can not only provide comprehensive data information for the pension insurance transfer and continuation model, but also can effectively improve the pension insurance transfer and continuation model. This requires us to research and analyze the problems of pension insurance transfer and continuation models, and build a new intelligent pension insurance model based on big data. Only in this way can it be ensured that the pension insurance transfer and continuation model meets the mobility needs of the Chinese labor market and promotes the stable development of the Chinese economy.",
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"abstract": "With the continuous progress of computer computing performance, network transmission and other information technology, machine learning methods are more widely used in various industries. In this paper, we study the caravan insurance recommendation algorithm based on machine learning methods for the insurance product recommendation business problem. The article analyses data exploration, data pre-processing, building classification models and balancing data sets, focusing on the taking, distribution and visualisation of the various types of feature fields of the data to show the distribution of variables. Based on the construction of a preliminary logistic regression model, this paper performs a balancing dataset operation to address the problem of dataset imbalance. The results of the model tests show that: user characteristics social class and rental house characteristics have a significant negative effect on the purchase of mobile caravan insurance; private insurance, public equipment and the number of fire insurance policies taken out have a significant positive effect on the purchase of mobile caravan insurance.",
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"abstract": "It is worthwhile to incorporate human knowledge with conventional machine learning approaches for big data analytics. Focusing on big video data understanding, this paper presents a formal scenario recognition framework where knowledge-based logic representation and reasoning is combined with data-based learning approach to enhance scenario recognition capabilities. This is achieved via multi-layered (hierarchical) processing. This approach constructs the hierarchical representation structure based on the semantic understanding of considered scenario, and transforms the structure into logic formulas. After applying conventional computer vision methods for low-level events classification, we apply logic based uncertainty reasoning to determine scene content. Experimental results on a benchmark dataset are provided to show the rationality of the proposed approach.",
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"abstract": "Automatic line-art colorization is a demanding research field owing to its expensive and labor-intensive workload. Learning-based approaches have lately emerged to improve the quality of colorization. To handle the lack of paired data in line art and color images, sketch extraction has been widely adopted. This study primarily focuses on the resizing process applied within the sketch extraction procedure, which is essential for normalizing input sketches of various sizes to the target size of the colorization model. We first analyze the inherent risk in a conventional resizing strategy, i.e., early-resizing, which places the resizing step before the line detection process to ensure the practicality. Although the strategy is extensively used, it involves an often overlooked risk of significantly degrading the generalization of the colorization model. Thus, we propose a late-resizing strategy in which resizing is applied after the line detection step. The proposed late-resizing strategy has three advantages: prevention of a quality degradation in the color image, augmentation for downsizing artifacts, and alleviation of look-ahead bias. In conclusion, we present both quantitative and qualitative evaluations on representative learning-based line-art colorization methods, which verify the effectiveness of the proposed method in the generalization of the colorization model.",
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"abstract": "Flat filling is a critical step in digital artistic content creation with the objective of filling line arts with flat colors. We present a deep learning framework for user-guided line art flat filling that can compute the \"influence areas\" of the user color scribbles, i.e., the areas where the user scribbles should propagate and influence. This framework explicitly controls such scribble influence areas for artists to manipulate the colors of image details and avoid color leakage/contamination between scribbles, and simultaneously, leverages data-driven color generation to facilitate content creation. This framework is based on a Split Filling Mechanism (SFM), which first splits the user scribbles into individual groups and then independently processes the colors and influence areas of each group with a Convolutional Neural Network (CNN). Learned from more than a million illustrations, the framework can estimate the scribble influence areas in a content-aware manner, and can smartly generate visually pleasing colors to assist the daily works of artists. We show that our proposed framework is easy to use, allowing even amateurs to obtain professional-quality results on a wide variety of line arts.",
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"abstract": "Obfuscation, code transformations that make the code unintelligible, is still an issue for web malware analysts and is still a weapon of choice for attackers. Worse, some researchers have arbitrarily decided to consider obfuscated contents as malicious although it has been proven wrong. Yet, we can assume than some web attack kits only feature a fraction of existing obfuscating transformations which may make it easy to detect malicious scripting contents. However, because of the undecidability on obfuscated contents, we propose to survey, classify and design deobfuscation methods for each obfuscating transformation. In this paper, we apply abstract syntax tree (AST) based methods to characterize obfuscating transformations found in malicious JavaScript samples. We are able to classify similar obfuscated codes based on AST fingerprints regardless of the original attack code. We are also able to quickly detect these obfuscating transformations by matching these in an analyzed sample's AST using a pushdown automaton (PDA). The PDA accepts a set of sub trees representing obfuscating transformations previously learned. Such quick and lightweight sub tree matching algorithm has the potential to detect obfuscated pieces of code in a script, to be later extracted for deobfuscation.",
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"title": "Extracting the shape and roughness of specular lobe objects using four light photometric stereo",
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"abstract": "A noncontact method of measuring surface shape and surface roughness for part inspection is proposed. The method, called four-light photometric stereo, uses four lights that sequentially illuminate the object under inspection, and a video camera that takes images of the object. Conceptually, the problem has three parts: shape extraction, pixel segmentation, and roughness extraction. The shape information is produced directly by three-light and four-light photometric stereo methods. After shape information is obtained, statistical segmentation techniques can be applied to determine which pixels are specular and which are nonspecular. Then the specular pixels and shape information can be used, in conjunction with a simplified Torrance-Sparrow reflectance model, to determine the surface roughness. The method has successfully been applied to a number of synthetic and real objects.<>",
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"content": "A noncontact method of measuring surface shape and surface roughness for part inspection is proposed. The method, called four-light photometric stereo, uses four lights that sequentially illuminate the object under inspection, and a video camera that takes images of the object. Conceptually, the problem has three parts: shape extraction, pixel segmentation, and roughness extraction. The shape information is produced directly by three-light and four-light photometric stereo methods. After shape information is obtained, statistical segmentation techniques can be applied to determine which pixels are specular and which are nonspecular. Then the specular pixels and shape information can be used, in conjunction with a simplified Torrance-Sparrow reflectance model, to determine the surface roughness. The method has successfully been applied to a number of synthetic and real objects.<>",
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"abstract": "This paper presents a new algorithm for constructing tangent plane continuous (G 1 ) surfaces with piecewise polynomials over triangular meshes. The input mesh can be of arbitrary topological type, that is, any number of faces can meet at a mesh vertex. The mesh is first refined to one solely with quadrilateral cells. Rectangular B?zier patches are then assigned to each of the cells and control points are determined so that G 1 continuity across the patch boundaries is maintained. Since all the patches are rectangular, the resulting surface can be rendered efficiently by current commercial graphic hardware/software. In addition, by exploiting the fact that all the faces of the original mesh are triangular, the degree of each patch is optimized to three while more general method dealing with arbitrary irregular meshes requires biquartic patches. Several surface examples generated from real 3D data are shown.",
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"content": "This paper presents a new algorithm for constructing tangent plane continuous (G 1 ) surfaces with piecewise polynomials over triangular meshes. The input mesh can be of arbitrary topological type, that is, any number of faces can meet at a mesh vertex. The mesh is first refined to one solely with quadrilateral cells. Rectangular B?zier patches are then assigned to each of the cells and control points are determined so that G 1 continuity across the patch boundaries is maintained. Since all the patches are rectangular, the resulting surface can be rendered efficiently by current commercial graphic hardware/software. In addition, by exploiting the fact that all the faces of the original mesh are triangular, the degree of each patch is optimized to three while more general method dealing with arbitrary irregular meshes requires biquartic patches. Several surface examples generated from real 3D data are shown.",
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"abstract": "In this paper we propose a new mesh reconstruction algorithm that produces a displaced subdivision mesh directly from unorganized points. The displaced subdivision surface is a new mesh representation that defines a detailed mesh with a displacement map over a smooth domain surface. This mesh representation has several benefits - compact mesh size, piecewise regular connectivity - to overcome limitations of irregular mesh produced by ordinary mesh reconstruction scheme, but the original displaced subdivision surface generation algorithm needs an explicit polygonal mesh to be converted. Our approach is producing displaced subdivision surface directly from input points during the mesh reconstruction process. The main ideas of our algorithm are building initial coarse control mesh by the shrink-wrapping like projection and sampling fine surface detail from unorganized points along the each limit vertex normal without any connectivity information of given points. We employ an existing subdivision surface fitting scheme to generate a parametric domain surface, and suggest a surface detail sampling scheme that determines a valid sampling triangle which can be made with combinations of input points. We show several reconstruction examples and applications to show the validity of suggested sampling technique and benefits of the result like multiresolution modeling.",
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"content": "In this paper we propose a new mesh reconstruction algorithm that produces a displaced subdivision mesh directly from unorganized points. The displaced subdivision surface is a new mesh representation that defines a detailed mesh with a displacement map over a smooth domain surface. This mesh representation has several benefits - compact mesh size, piecewise regular connectivity - to overcome limitations of irregular mesh produced by ordinary mesh reconstruction scheme, but the original displaced subdivision surface generation algorithm needs an explicit polygonal mesh to be converted. Our approach is producing displaced subdivision surface directly from input points during the mesh reconstruction process. The main ideas of our algorithm are building initial coarse control mesh by the shrink-wrapping like projection and sampling fine surface detail from unorganized points along the each limit vertex normal without any connectivity information of given points. We employ an existing subdivision surface fitting scheme to generate a parametric domain surface, and suggest a surface detail sampling scheme that determines a valid sampling triangle which can be made with combinations of input points. We show several reconstruction examples and applications to show the validity of suggested sampling technique and benefits of the result like multiresolution modeling.",
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"affiliation": "Korea University",
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"title": "Automatic Detection of Characteristic Viscosity Points in Mineralogical Samples",
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"abstract": "Hot stage microscopy (HSM) is a suitable technique for studying the behavior of mineralogical samples (such as basalt, rocks and glasses) viscosity in relation to temperature. HSM researches observe and analyze images of samples recorded during heating. This paper presents the development of a customized software, which uses digital image processing techniques to automatically detect characteristic viscosity points (CVP) based on a series of images that depict the evolution of the sample as it melts over time. This tool was developed to help determine the temperatures corresponding to CVP together with the HSM technique.",
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"content": "Hot stage microscopy (HSM) is a suitable technique for studying the behavior of mineralogical samples (such as basalt, rocks and glasses) viscosity in relation to temperature. HSM researches observe and analyze images of samples recorded during heating. This paper presents the development of a customized software, which uses digital image processing techniques to automatically detect characteristic viscosity points (CVP) based on a series of images that depict the evolution of the sample as it melts over time. This tool was developed to help determine the temperatures corresponding to CVP together with the HSM technique.",
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"abstract": "Polygon mesh is among the most common data structures used for representing objects in computer graphics. Unfortunately, a polygon mesh does not capture high-level structures, unlike a hierarchical model. In general, high-level abstractions are useful for managing data in applications. In this paper, we present a method for decomposing an object represented in polygon meshes into components by means of critical points. The method consists of steps to define the root vertex of the object, define a function on the polygon meshes, compute the geodesic tree and critical points, decide the decomposition order, and extract components using backwards flooding. We have implemented the method. The preliminary results show that it works effectively and efficiently. The decomposition results can be useful for applications such as 3D model retrieval and morphing.",
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"content": "Polygon mesh is among the most common data structures used for representing objects in computer graphics. Unfortunately, a polygon mesh does not capture high-level structures, unlike a hierarchical model. In general, high-level abstractions are useful for managing data in applications. In this paper, we present a method for decomposing an object represented in polygon meshes into components by means of critical points. The method consists of steps to define the root vertex of the object, define a function on the polygon meshes, compute the geodesic tree and critical points, decide the decomposition order, and extract components using backwards flooding. We have implemented the method. The preliminary results show that it works effectively and efficiently. The decomposition results can be useful for applications such as 3D model retrieval and morphing.",
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"abstract": "Abstract: Markov Random Field is a very known model for the generation of textures. However, the estimation of its parameter results quite difficult in many cases. In this article a new algorithm for synthesis of textures is proposed, based on mage pyramids and self-organizing maps. This procedure avoids the explicit computation of its parameters. Preliminary results support the appropriateness of this new approach.",
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"abstract": "Sample based texture synthesis allows the generation of arbitrarily sized textures based on a small sample image. One main drawback of the technique is that a new pixel or patch is selected only considering local information in the generated texture. Thus structural error can't assure to be avoided for structural textures. To accelerate texture synthesis process and to avoid structural mismatch in the output picture, we present in this paper a structural pattern analysis (SPA) algorithm and a texture synthesis method using the algorithm. The pattern analysis tool also quantizes the texture randomness in macro scope view. It can be used in other applications such as automatic texture classification and quality evaluation of synthesized texture. We illustrate our result with some examples.",
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"abstract": "In recent years, a lot of 2D textures have been synthesized from input 2D textures. However, the quality problems still exist for many textures. Further improvements are required to extract more reliable texture features. In this paper, we present a texture synthesis approach using cooperative color and grey-level features. For color feature extraction, we extract appearance vectors to replace RGB color values. For grey-level feature extraction, we extract the statistical features including entropy, contrast, and correlation based on the grey level co-occurrence probabilities (GLCPs). Moreover, we introduce cooperative color and GLCP features for neighborhood matching in the synthesis process. We assign different weights for color and grey-level features according to the characteristics of the input texture. The results show that the proposed approach performs well in terms of the synthesis quality.",
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"abstract": "We describe our approach to the analysis of 2017 VAST Challenge Mini-Challenge 2 data. The challenge deals with readings from air sampler stations. To answer the main question, the provenance of the chemicals measured at the sampler stations, we extend the provided data set by aggregated spatio-temporal provenance data. This data is generated from the provided meteorological data and locations map by using it as input for a particle tracer which calculates the provenance of the particles arriving from the emitters (factories) at the collectors (the locations of sampler stations). We use ComVis [3], a coordinated multiple views (CMV) system, to analyze the whole data set (the provided and generated data) by applying a sensor centric data model.",
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"abstract": "In this paper, we computationally predicted the interactions between HIV-1 and human proteins, based on the hypothesis that proteins with similar interface architecture share similar interaction partners. Evolution – aware protein structural alignment method UniAlign was used to calculate the similarity between two protein interface architectures. Using experimentally verified HIV-1, human protein-protein interactions data, we first selected 12 features, including geometric similarity, conversion similarity etc.; then trained a support vector machine (SVM) with Gaussian kernel for the binary classification problem: whether a given protein pairs ‘interact’ or ‘no interact’. We used the trained and tuned SVM classifier to discover potential novel HIV-1 interacting partners for human proteins. Many predicted interactions had significant literature support, and we modeled the novel 3D interacting complex for HIV-1 envelope gp120 and gp41 proteins. We provided the first structural evidence for those interactions.",
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"abstract": "This paper presents an approach for prediction of protein functions based on protein-protein interaction networks. For the purpose of prediction, we not only consider the interactions of functionunknown proteins with function-known proteins but also the interactions of function-unknown proteins with function-unknown proteins. Prediction is performed in the context of the entire network. This is a min-cut approach because we try to assign function-unknown proteins to different functional groups in such a way so that the number of intergroup interactions becomes the minimum in the whole network. Also, we show some evaluation results by applying the proposed method to yeast Saccharomyces cerevisiae protein-protein interaction network. However, this is a general method and can be applied to other organisms alike.",
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"title": "Essential protein identification based on essential protein-protein interaction prediction by integrated edge weights",
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"abstract": "Essential proteins are crucial to cellular survival and development. Traditionally, essential proteins are identified by knock-out experiments, which are expensive and often fatal to the target organisms. Regarding this, an important approach to essential protein identification is through computational prediction. In this research, we present a novel computational method, Integrated Edge Weights (IEW), to innovatively predict proteins' essentiality based on essential protein-protein interactions. The experimental results on all three organisms: Saccharomyces cere-visiae (Yeast), Escherichia coli (E. coli), and Caenorhabditis ele-gans (C. elegans) show that IEW achieves better performance than the state-of-the-art methods in terms of precision-recall. Furthermore, we have demonstrated that the highly-ranked protein-protein interactions predicted by our approach tend to be biologically significant in Yeast, E. coli, and C. elegans proteinprotein interaction (PPI) networks.",
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"content": "Essential proteins are crucial to cellular survival and development. Traditionally, essential proteins are identified by knock-out experiments, which are expensive and often fatal to the target organisms. Regarding this, an important approach to essential protein identification is through computational prediction. In this research, we present a novel computational method, Integrated Edge Weights (IEW), to innovatively predict proteins' essentiality based on essential protein-protein interactions. The experimental results on all three organisms: Saccharomyces cere-visiae (Yeast), Escherichia coli (E. coli), and Caenorhabditis ele-gans (C. elegans) show that IEW achieves better performance than the state-of-the-art methods in terms of precision-recall. Furthermore, we have demonstrated that the highly-ranked protein-protein interactions predicted by our approach tend to be biologically significant in Yeast, E. coli, and C. elegans proteinprotein interaction (PPI) networks.",
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"affiliation": "Key Laboratory of Symbolic Computation and Knowledge Engineering, College of Computer Science and Technology, Jilin University, Changchun, China",
"fullName": "Yuexu Jiang",
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"affiliation": "Key Laboratory of Symbolic Computation and Knowledge Engineering, College of Computer Science and Technology, Jilin University, Changchun, China",
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"affiliation": "Key Laboratory of Symbolic Computation and Knowledge Engineering, College of Computer Science and Technology, Jilin University, Changchun, China",
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"affiliation": "Key Laboratory of Symbolic Computation and Knowledge Engineering, College of Computer Science and Technology, Jilin University, Changchun, China",
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"affiliation": "Department of Information Engineering and Computer Science, University of Trento, Povo, Italy",
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"abstract": "Recently, scientists start to examine the dynamics of biological networks from a control theory perspective. Based on the determination of minimum dominating sets (MDSets), this paper investigated the properties associated with MDSet proteins in the context of the analysis of protein interaction networks specific to the yeast cell cycle. Statistically significant differences between MDSet and non-MDSet proteins were observed in terms of topological features, Gene Ontology-driven semantic similarities, and the number of protein domains associated with each protein. However, unlike previous studies, MDSet proteins were found to be enriched with essential genes. Furthermore, we constructed and analyzed a PPI network specific to the human cell cycle and highlighted that the distinction between MDSet and non-MDSet proteins is far more complex than that observed in yeast. The system used to determine a minimum dominating set in a protein interaction network was implemented as a user-friendly Java-based plugin for Cytoscape.",
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"abstract": "Proteins interact with each other to regulate their functionality and localization. The accumulated protein interaction evidences are represented by protein interaction network using a graph abstraction. Topological properties of protein interaction networks have been explored to characterize proteins and predict undiscovered interactions. Meanwhile, many researchers have tried to explain how protein interaction network is formed through evolutionary process. While one group of researchers have made efforts to simulate current protein interaction starting from hypothetical infant state of protein interaction networks through suggested evolutionary models, another group of researchers have made efforts to estimate the phylogenetic age of proteins from evolutionary relationship. Recently, these efforts gave rise to the database of phylogenetic age of proteins and this allows many researchers to estimate phylogenetic age of proteins of their interest easily. As seen by their terms, the evolutionary model of protein interaction networks and phylogenetic age of proteins are closely related, thus topological properties of protein interactions, which is important in studies of the evolutionary models, can be linked to the phylogenetic age of proteins. In this paper, we construct a weighted human protein interaction network from a human protein interaction network, which is provided by BioGRID database. The weight of an edge is defined as the number of triangles which contains this edge in the protein interaction network and we call this weight as the triangle score. From the weighted protein interaction network, we extract proteins that are incident to an edge that has a high triangle score. We obtain phylogenetic age of proteins and measure various statistical values to observe correlation between phylogenetic age and the triangle score. As a result, we show that the proteins, that participate in interactions with high triangle score, are old in terms of phylogenetic age. Also we show that for interactions within a same phylogenetic age category tend to have higher triangle scores than the interactions with only one of its participant protein contained in the given age category.",
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"content": "Proteins interact with each other to regulate their functionality and localization. The accumulated protein interaction evidences are represented by protein interaction network using a graph abstraction. Topological properties of protein interaction networks have been explored to characterize proteins and predict undiscovered interactions. Meanwhile, many researchers have tried to explain how protein interaction network is formed through evolutionary process. While one group of researchers have made efforts to simulate current protein interaction starting from hypothetical infant state of protein interaction networks through suggested evolutionary models, another group of researchers have made efforts to estimate the phylogenetic age of proteins from evolutionary relationship. Recently, these efforts gave rise to the database of phylogenetic age of proteins and this allows many researchers to estimate phylogenetic age of proteins of their interest easily. As seen by their terms, the evolutionary model of protein interaction networks and phylogenetic age of proteins are closely related, thus topological properties of protein interactions, which is important in studies of the evolutionary models, can be linked to the phylogenetic age of proteins. In this paper, we construct a weighted human protein interaction network from a human protein interaction network, which is provided by BioGRID database. The weight of an edge is defined as the number of triangles which contains this edge in the protein interaction network and we call this weight as the triangle score. From the weighted protein interaction network, we extract proteins that are incident to an edge that has a high triangle score. We obtain phylogenetic age of proteins and measure various statistical values to observe correlation between phylogenetic age and the triangle score. As a result, we show that the proteins, that participate in interactions with high triangle score, are old in terms of phylogenetic age. Also we show that for interactions within a same phylogenetic age category tend to have higher triangle scores than the interactions with only one of its participant protein contained in the given age category.",
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"normalizedAbstract": "Proteins interact with each other to regulate their functionality and localization. The accumulated protein interaction evidences are represented by protein interaction network using a graph abstraction. Topological properties of protein interaction networks have been explored to characterize proteins and predict undiscovered interactions. Meanwhile, many researchers have tried to explain how protein interaction network is formed through evolutionary process. While one group of researchers have made efforts to simulate current protein interaction starting from hypothetical infant state of protein interaction networks through suggested evolutionary models, another group of researchers have made efforts to estimate the phylogenetic age of proteins from evolutionary relationship. Recently, these efforts gave rise to the database of phylogenetic age of proteins and this allows many researchers to estimate phylogenetic age of proteins of their interest easily. As seen by their terms, the evolutionary model of protein interaction networks and phylogenetic age of proteins are closely related, thus topological properties of protein interactions, which is important in studies of the evolutionary models, can be linked to the phylogenetic age of proteins. In this paper, we construct a weighted human protein interaction network from a human protein interaction network, which is provided by BioGRID database. The weight of an edge is defined as the number of triangles which contains this edge in the protein interaction network and we call this weight as the triangle score. From the weighted protein interaction network, we extract proteins that are incident to an edge that has a high triangle score. We obtain phylogenetic age of proteins and measure various statistical values to observe correlation between phylogenetic age and the triangle score. As a result, we show that the proteins, that participate in interactions with high triangle score, are old in terms of phylogenetic age. Also we show that for interactions within a same phylogenetic age category tend to have higher triangle scores than the interactions with only one of its participant protein contained in the given age category.",
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"affiliation": "Dpt of Mathematics Education, Seoul National University, Seoul, South Korea",
"fullName": "Yun Joo Yoo",
"givenName": "Yun Joo",
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"abstract": "Understanding how pathogen's proteins interact with its host's proteins is the key concept for understanding pathogen's infection mechanism, which can lead to the discovery of improved therapeutics for treating infectious diseases. Several studies suggest that proteins from various pathogens tend to interact with human proteins involved in the same biological pathway. This implies that pathogens are inclined to target host's proteins with similar function. In addition, conservation between a protein's function and its local topological structure in a protein-protein interaction network (PIN) has been previously characterized. This leads to the hypothesis that pathogens target the host's proteins with a similar local topological structure in a PIN. In this work, this hypothesis is examined by adding a graphlet degree vector of a protein in the human PIN as a feature in the prediction model and using that model to predict the protein-protein interaction between human and four pathogens. The results show that this graphlet degree vector increases the performance significantly for all pathogens. This suggests that the intraspecies protein-protein interactions should be taken into consideration when developing prediction methods for host-pathogen protein interaction. The results also support the hypothesis that there exists a relationship between a protein's function and the local topology of the PIN.",
"abstracts": [
{
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"content": "Understanding how pathogen's proteins interact with its host's proteins is the key concept for understanding pathogen's infection mechanism, which can lead to the discovery of improved therapeutics for treating infectious diseases. Several studies suggest that proteins from various pathogens tend to interact with human proteins involved in the same biological pathway. This implies that pathogens are inclined to target host's proteins with similar function. In addition, conservation between a protein's function and its local topological structure in a protein-protein interaction network (PIN) has been previously characterized. This leads to the hypothesis that pathogens target the host's proteins with a similar local topological structure in a PIN. In this work, this hypothesis is examined by adding a graphlet degree vector of a protein in the human PIN as a feature in the prediction model and using that model to predict the protein-protein interaction between human and four pathogens. The results show that this graphlet degree vector increases the performance significantly for all pathogens. This suggests that the intraspecies protein-protein interactions should be taken into consideration when developing prediction methods for host-pathogen protein interaction. The results also support the hypothesis that there exists a relationship between a protein's function and the local topology of the PIN.",
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"normalizedAbstract": "Understanding how pathogen's proteins interact with its host's proteins is the key concept for understanding pathogen's infection mechanism, which can lead to the discovery of improved therapeutics for treating infectious diseases. Several studies suggest that proteins from various pathogens tend to interact with human proteins involved in the same biological pathway. This implies that pathogens are inclined to target host's proteins with similar function. In addition, conservation between a protein's function and its local topological structure in a protein-protein interaction network (PIN) has been previously characterized. This leads to the hypothesis that pathogens target the host's proteins with a similar local topological structure in a PIN. In this work, this hypothesis is examined by adding a graphlet degree vector of a protein in the human PIN as a feature in the prediction model and using that model to predict the protein-protein interaction between human and four pathogens. The results show that this graphlet degree vector increases the performance significantly for all pathogens. This suggests that the intraspecies protein-protein interactions should be taken into consideration when developing prediction methods for host-pathogen protein interaction. The results also support the hypothesis that there exists a relationship between a protein's function and the local topology of the PIN.",
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"Pins",
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"Host Pathogen Interactions",
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"abstract": "Accurate prediction of essential proteins by using computational methods can effectively reduce the cost of wet-lab experiments. Existing computational methods usually rely on constructed protein-protein interaction (PPI) networks with different kinds of biological data. However, high-quality PPI networks and other biological data are not available for all proteins. Thus, it is very necessary and valuable to develop accurate methods for fast and effective prediction of essential proteins by using only protein sequences. We propose EPGBDT, a machine learning ensemble model, to improve the performance of essential protein prediction by using only protein sequences. EP-GBDT has an ensemble structure that combines multiple Gradient Boosting Decision Tree (GBDT) base classifiers. In addition, to reduce the effects of imbalanced dataset, EP-GBDT uses a sampling technique. The results show that EP-GBDT outperforms state-of-the-art sequence-based methods and network-based centrality measures. The source code and datasets can be downloaded from https://github.com/CSUBioGroup/EP-GBDT.",
"abstracts": [
{
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"content": "Accurate prediction of essential proteins by using computational methods can effectively reduce the cost of wet-lab experiments. Existing computational methods usually rely on constructed protein-protein interaction (PPI) networks with different kinds of biological data. However, high-quality PPI networks and other biological data are not available for all proteins. Thus, it is very necessary and valuable to develop accurate methods for fast and effective prediction of essential proteins by using only protein sequences. We propose EPGBDT, a machine learning ensemble model, to improve the performance of essential protein prediction by using only protein sequences. EP-GBDT has an ensemble structure that combines multiple Gradient Boosting Decision Tree (GBDT) base classifiers. In addition, to reduce the effects of imbalanced dataset, EP-GBDT uses a sampling technique. The results show that EP-GBDT outperforms state-of-the-art sequence-based methods and network-based centrality measures. The source code and datasets can be downloaded from https://github.com/CSUBioGroup/EP-GBDT.",
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"authors": [
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"affiliation": "Central South University,Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering,Changsha,Hunan,China,410083",
"fullName": "Min Zeng",
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"affiliation": "Central South University,Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering,Changsha,Hunan,China,410083",
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"affiliation": "Central South University,Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering,Changsha,Hunan,China,410083",
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"content": "Antibiotic resistance genes (ARGs) are responsible for an increasing number of bacterial infections worldwide. ARGs are challenging to track within bacterial genomes as they are often subject to horizontal gene transfer via mobile genetic elements (MGEs). Complex protein-protein networks can reveal proteins contributing to the spread and persistence. Here, we developed a pipeline that facilitates this process by analyzing features of a Protein-Protein Interaction Network (PPIN). This pipeline uses a random forest model to distinguish ARGs from non-ARGs and explores associations between ARGs and proteins with which they functionally interact. We tested the approach using the PPINs of Escherichia coli and Acinetobacter baumannii, two deadly organisms known to carry ARGs harbored by MGEs, and achieved a macro average accuracy of 85% in ARG identification. The approach also revealed that ARGs are disproportionately associated with MGEs and the neighbors (genes connected with only one edge to the ARGs) are likely to be less mobile.",
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